From c4579a75025401d0cd0bcc91ec38e1e4467c810b Mon Sep 17 00:00:00 2001 From: julient31 Date: Wed, 30 Sep 2020 11:43:01 -0600 Subject: [PATCH 001/100] First commit - added spin/kk style files - modified few necessary files - compiles, but SegFault when running --- src/KOKKOS/Install.sh | 2 + src/KOKKOS/atom_kokkos.cpp | 6 + src/KOKKOS/atom_kokkos.h | 5 + src/KOKKOS/atom_vec_spin_kokkos.cpp | 1308 +++++++++++++++++++++++++++ src/KOKKOS/atom_vec_spin_kokkos.h | 132 +++ src/KOKKOS/kokkos_type.h | 59 ++ src/atom_masks.h | 6 + 7 files changed, 1518 insertions(+) create mode 100644 src/KOKKOS/atom_vec_spin_kokkos.cpp create mode 100644 src/KOKKOS/atom_vec_spin_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index 03508578ae..4c5c9d7e1d 100755 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -63,6 +63,8 @@ action atom_vec_bond_kokkos.cpp atom_vec_bond.cpp action atom_vec_bond_kokkos.h atom_vec_bond.h action atom_vec_charge_kokkos.cpp action atom_vec_charge_kokkos.h +action atom_vec_spin_kokkos.cpp +action atom_vec_spin_kokkos.h action atom_vec_dpd_kokkos.cpp atom_vec_dpd.cpp action atom_vec_dpd_kokkos.h atom_vec_dpd.h action atom_vec_full_kokkos.cpp atom_vec_full.cpp diff --git a/src/KOKKOS/atom_kokkos.cpp b/src/KOKKOS/atom_kokkos.cpp index a587494d09..b85b063190 100644 --- a/src/KOKKOS/atom_kokkos.cpp +++ b/src/KOKKOS/atom_kokkos.cpp @@ -76,6 +76,12 @@ AtomKokkos::~AtomKokkos() memoryKK->destroy_kokkos(k_improper_atom3, improper_atom3); memoryKK->destroy_kokkos(k_improper_atom4, improper_atom4); + // SPIN package + + memoryKK->destroy_kokkos(k_sp, sp); + memoryKK->destroy_kokkos(k_fm, fm); + memoryKK->destroy_kokkos(k_fm_long, fm_long); + // USER-DPD package memoryKK->destroy_kokkos(k_uCond,uCond); memoryKK->destroy_kokkos(k_uMech,uMech); diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 6eebbad661..e2c666fea5 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -54,6 +54,11 @@ class AtomKokkos : public Atom { DAT::tdual_float_2d k_dvector; + // SPIN package + + DAT::tdual_sp_array k_sp; + DAT::tdual_fm_array k_fm; + DAT::tdual_fm_long_array k_fm_long; // USER-DPD package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp new file mode 100644 index 0000000000..c5c2ffb5be --- /dev/null +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -0,0 +1,1308 @@ +/* ---------------------------------------------------------------------- + + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. + +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing authors: Julien Tranchida (SNL) + Aidan Thompson (SNL) + + Please cite the related publication: + Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018). + Massively parallel symplectic algorithm for coupled magnetic spin dynamics + and molecular dynamics. Journal of Computational Physics. +------------------------------------------------------------------------- */ + +#include "atom_vec_spin_kokkos.h" + +#include "atom_kokkos.h" +#include "atom_masks.h" +#include "comm_kokkos.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "memory_kokkos.h" +#include "modify.h" + +using namespace LAMMPS_NS; + +#define DELTA 10 + +/* ---------------------------------------------------------------------- */ + +AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) +{ + molecular = 0; + mass_type = 1; + forceclearflag = 1; + + comm_x_only = comm_f_only = 0; + size_forward = 7; + size_reverse = 9; + size_border = 10; + size_velocity = 3; + size_data_atom = 9; + size_data_vel = 4; + xcol_data = 4; + + atom->sp_flag = 1; + + k_count = DAT::tdual_int_1d("atom::k_count",1); + atomKK = (AtomKokkos *) atom; + commKK = (CommKokkos *) comm; +} + +/* ---------------------------------------------------------------------- + grow atom arrays + n = 0 grows arrays by a chunk + n > 0 allocates arrays to size n +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::grow(int n) +{ + int step = MAX(DELTA,nmax*0.01); + if (n == 0) nmax += step; + else nmax = n; + atomKK->nmax = nmax; + if (nmax < 0 || nmax > MAXSMALLINT) + error->one(FLERR,"Per-processor system is too big"); + + atomKK->sync(Device,ALL_MASK); + atomKK->modified(Device,ALL_MASK); + + memoryKK->grow_kokkos(atomKK->k_tag,atomKK->tag,nmax,"atom:tag"); + memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type"); + memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask"); + memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image"); + + // allocating mech. quantities + + memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,"atom:x"); + memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,"atom:v"); + memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,"atom:f"); + + // allocating mag. quantities + + memoryKK->grow_kokkos(atomKK->k_sp,atomKK->sp,nmax,"atom:sp"); + memoryKK->grow_kokkos(atomKK->k_fm,atomKK->fm,nmax,"atom:fm"); + memoryKK->grow_kokkos(atomKK->k_fm_long,atomKK->fm_long,nmax,"atom:fm_long"); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); +} + +/* ---------------------------------------------------------------------- + reset local array ptrs +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::grow_reset() +{ + tag = atomKK->tag; + d_tag = atomKK->k_tag.d_view; + h_tag = atomKK->k_tag.h_view; + + type = atomKK->type; + d_type = atomKK->k_type.d_view; + h_type = atomKK->k_type.h_view; + mask = atomKK->mask; + d_mask = atomKK->k_mask.d_view; + h_mask = atomKK->k_mask.h_view; + image = atomKK->image; + d_image = atomKK->k_image.d_view; + h_image = atomKK->k_image.h_view; + + x = atomKK->x; + d_x = atomKK->k_x.d_view; + h_x = atomKK->k_x.h_view; + v = atomKK->v; + d_v = atomKK->k_v.d_view; + h_v = atomKK->k_v.h_view; + f = atomKK->f; + d_f = atomKK->k_f.d_view; + h_f = atomKK->k_f.h_view; + + sp = atomKK->sp; + d_sp = atomKK->k_sp.d_view; + h_sp = atomKK->k_sp.h_view; + fm = atomKK->fm; + d_fm = atomKK->k_fm.d_view; + h_fm = atomKK->k_fm.h_view; + fm_long = atomKK->fm_long; + d_fm_long = atomKK->k_fm_long.d_view; + h_fm_long = atomKK->k_fm_long.h_view; +} + +/* ---------------------------------------------------------------------- + copy atom I info to atom J +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::copy(int i, int j, int delflag) +{ + h_tag[j] = h_tag[i]; + h_type[j] = h_type[i]; + mask[j] = mask[i]; + h_image[j] = h_image[i]; + h_x(j,0) = h_x(i,0); + h_x(j,1) = h_x(i,1); + h_x(j,2) = h_x(i,2); + h_v(j,0) = h_v(i,0); + h_v(j,1) = h_v(i,1); + h_v(j,2) = h_v(i,2); + + h_sp(j,0) = h_sp(i,0); + h_sp(j,1) = h_sp(i,1); + h_sp(j,2) = h_sp(i,2); + h_sp(j,3) = h_sp(i,3); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag); +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackComm { + typedef DeviceType device_type; + + typename ArrayTypes::t_x_array_randomread _x; + typename ArrayTypes::t_sp_array_randomread _sp; + typename ArrayTypes::t_xfloat_2d_um _buf; + typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; + X_FLOAT _pbc[6]; + + AtomVecSpinKokkos_PackComm( + const typename DAT::tdual_x_array &x, + const typename DAT::tdual_sp_array &sp, + const typename DAT::tdual_xfloat_2d &buf, + const typename DAT::tdual_int_2d &list, + const int & iswap, + const X_FLOAT &xprd, const X_FLOAT &yprd, const X_FLOAT &zprd, + const X_FLOAT &xy, const X_FLOAT &xz, const X_FLOAT &yz, const int* const pbc): + _x(x.view()),_sp(sp.view()), + _list(list.view()),_iswap(iswap), + _xprd(xprd),_yprd(yprd),_zprd(zprd), + _xy(xy),_xz(xz),_yz(yz) { + const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; + // const size_t elements = 3; + const size_t elements = 7; + buffer_view(_buf,buf,maxsend,elements); + _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; + _pbc[3] = pbc[3]; _pbc[4] = pbc[4]; _pbc[5] = pbc[5]; + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } else { + if (TRICLINIC == 0) { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } else { + _buf(i,0) = _x(j,0) + _pbc[0]*_xprd + _pbc[5]*_xy + _pbc[4]*_xz; + _buf(i,1) = _x(j,1) + _pbc[1]*_yprd + _pbc[3]*_yz; + _buf(i,2) = _x(j,2) + _pbc[2]*_zprd; + _buf(i,3) = _sp(j,0); + _buf(i,4) = _sp(j,1); + _buf(i,5) = _sp(j,2); + _buf(i,6) = _sp(j,3); + } + } + } +}; + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackBorder { + typedef DeviceType device_type; + + typename ArrayTypes::t_xfloat_2d _buf; + const typename ArrayTypes::t_int_2d_const _list; + const int _iswap; + const typename ArrayTypes::t_x_array_randomread _x; + const typename ArrayTypes::t_tagint_1d _tag; + const typename ArrayTypes::t_int_1d _type; + const typename ArrayTypes::t_int_1d _mask; + const typename ArrayTypes::t_sp_array_randomread _sp; + X_FLOAT _dx,_dy,_dz; + + AtomVecSpinKokkos_PackBorder( + const typename ArrayTypes::t_xfloat_2d &buf, + const typename ArrayTypes::t_int_2d_const &list, + const int & iswap, + const typename ArrayTypes::t_x_array &x, + const typename ArrayTypes::t_tagint_1d &tag, + const typename ArrayTypes::t_int_1d &type, + const typename ArrayTypes::t_int_1d &mask, + const typename ArrayTypes::t_sp_array &sp, + const X_FLOAT &dx, const X_FLOAT &dy, const X_FLOAT &dz): + _buf(buf),_list(list),_iswap(iswap), + _x(x),_tag(tag),_type(type),_mask(mask),_sp(sp), + _dx(dx),_dy(dy),_dz(dz) {} + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + const int j = _list(_iswap,i); + if (PBC_FLAG == 0) { + _buf(i,0) = _x(j,0); + _buf(i,1) = _x(j,1); + _buf(i,2) = _x(j,2); + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; + _buf(i,6) = _sp(j,0); + _buf(i,7) = _sp(j,1); + _buf(i,8) = _sp(j,2); + _buf(i,9) = _sp(j,3); + } else { + _buf(i,0) = _x(j,0) + _dx; + _buf(i,1) = _x(j,1) + _dy; + _buf(i,2) = _x(j,2) + _dz; + _buf(i,3) = d_ubuf(_tag(j)).d; + _buf(i,4) = d_ubuf(_type(j)).d; + _buf(i,5) = d_ubuf(_mask(j)).d; + _buf(i,6) = _sp(j,0); + _buf(i,7) = _sp(j,1); + _buf(i,8) = _sp(j,2); + _buf(i,9) = _sp(j,3); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space) +{ + X_FLOAT dx,dy,dz; + + if (pbc_flag != 0) { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if(space==Host) { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask,h_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask,d_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } + + } else { + dx = dy = dz = 0; + if(space==Host) { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,h_x,h_tag,h_type,h_mask,h_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } else { + AtomVecSpinKokkos_PackBorder f( + buf.view(), k_sendlist.view(), + iswap,d_x,d_tag,d_type,d_mask,d_sp,dx,dy,dz); + Kokkos::parallel_for(n,f); + } + } + return n*size_border; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_vel(int n, int *list, double *buf, + int pbc_flag, int *pbc) +{ + int i,j,m; + double dx,dy,dz,dvx,dvy,dvz; + + m = 0; + if (pbc_flag == 0) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0); + buf[m++] = h_x(j,1); + buf[m++] = h_x(j,2); + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } else { + if (domain->triclinic == 0) { + dx = pbc[0]*domain->xprd; + dy = pbc[1]*domain->yprd; + dz = pbc[2]*domain->zprd; + } else { + dx = pbc[0]; + dy = pbc[1]; + dz = pbc[2]; + } + if (!deform_vremap) { + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } else { + dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; + dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3]; + dvz = pbc[2]*h_rate[2]; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_x(j,0) + dx; + buf[m++] = h_x(j,1) + dy; + buf[m++] = h_x(j,2) + dz; + buf[m++] = ubuf(h_tag(j)).d; + buf[m++] = ubuf(h_type(j)).d; + buf[m++] = ubuf(h_mask(j)).d; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + if (mask[i] & deform_groupbit) { + buf[m++] = h_v(j,0) + dvx; + buf[m++] = h_v(j,1) + dvy; + buf[m++] = h_v(j,2) + dvz; + } else { + buf[m++] = h_v(j,0); + buf[m++] = h_v(j,1); + buf[m++] = h_v(j,2); + } + } + } + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); + + return m; +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_border_hybrid(int n, int *list, double *buf) +{ + int i,j,m; + + m = 0; + for (i = 0; i < n; i++) { + j = list[i]; + buf[m++] = h_sp(j,0); + buf[m++] = h_sp(j,1); + buf[m++] = h_sp(j,2); + buf[m++] = h_sp(j,3); + } + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_UnpackBorder { + typedef DeviceType device_type; + + const typename ArrayTypes::t_xfloat_2d_const _buf; + typename ArrayTypes::t_x_array _x; + typename ArrayTypes::t_tagint_1d _tag; + typename ArrayTypes::t_int_1d _type; + typename ArrayTypes::t_int_1d _mask; + typename ArrayTypes::t_sp_array _sp; + int _first; + + + AtomVecSpinKokkos_UnpackBorder( + const typename ArrayTypes::t_xfloat_2d_const &buf, + typename ArrayTypes::t_x_array &x, + typename ArrayTypes::t_tagint_1d &tag, + typename ArrayTypes::t_int_1d &type, + typename ArrayTypes::t_int_1d &mask, + typename ArrayTypes::t_sp_array &sp, + const int& first): + _buf(buf),_x(x),_tag(tag),_type(type),_mask(mask),_sp(sp),_first(first){ + }; + + KOKKOS_INLINE_FUNCTION + void operator() (const int& i) const { + _x(i+_first,0) = _buf(i,0); + _x(i+_first,1) = _buf(i,1); + _x(i+_first,2) = _buf(i,2); + _tag(i+_first) = (tagint) d_ubuf(_buf(i,3)).i; + _type(i+_first) = (int) d_ubuf(_buf(i,4)).i; + _mask(i+_first) = (int) d_ubuf(_buf(i,5)).i; + _sp(i+_first,0) = _buf(i,6); + _sp(i+_first,1) = _buf(i,7); + _sp(i+_first,2) = _buf(i,8); + _sp(i+_first,3) = _buf(i,9); + } +}; + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border_kokkos(const int &n, const int &first, + const DAT::tdual_xfloat_2d &buf,ExecutionSpace space) { + if (first+n >= nmax) { + grow(first+n+100); + } + if(space==Host) { + struct AtomVecSpinKokkos_UnpackBorder + f(buf.view(),h_x,h_tag,h_type,h_mask,h_sp,first); + Kokkos::parallel_for(n,f); + } else { + struct AtomVecSpinKokkos_UnpackBorder + f(buf.view(),d_x,d_tag,d_type,d_mask,d_sp,first); + Kokkos::parallel_for(n,f); + } + atomKK->modified(space,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + + for (i = first; i < last; i++) { + if (i == nmax) { + grow(0); + } + atomKK->modified(Host,X_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag(i) = (tagint) ubuf(buf[m++]).i; + h_type(i) = (int) ubuf(buf[m++]).i; + h_mask(i) = (int) ubuf(buf[m++]).i; + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::unpack_border_vel(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) { + if (i == nmax) grow(0); + atomKK->modified(Host,X_MASK|V_MASK|TAG_MASK|TYPE_MASK|MASK_MASK|SP_MASK); + h_x(i,0) = buf[m++]; + h_x(i,1) = buf[m++]; + h_x(i,2) = buf[m++]; + h_tag(i) = (tagint) ubuf(buf[m++]).i; + h_type(i) = (int) ubuf(buf[m++]).i; + h_mask(i) = (int) ubuf(buf[m++]).i; + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + h_v(i,0) = buf[m++]; + h_v(i,1) = buf[m++]; + h_v(i,2) = buf[m++]; + } + + if (atom->nextra_border) + for (int iextra = 0; iextra < atom->nextra_border; iextra++) + m += modify->fix[atom->extra_border[iextra]]-> + unpack_border(n,first,&buf[m]); +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_border_hybrid(int n, int first, double *buf) +{ + int i,m,last; + + m = 0; + last = first + n; + for (i = first; i < last; i++) + h_sp(i,0) = buf[m++]; + h_sp(i,1) = buf[m++]; + h_sp(i,2) = buf[m++]; + h_sp(i,3) = buf[m++]; + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_PackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array_randomread _x; + typename AT::t_v_array_randomread _v; + typename AT::t_tagint_1d_randomread _tag; + typename AT::t_int_1d_randomread _type; + typename AT::t_int_1d_randomread _mask; + typename AT::t_imageint_1d_randomread _image; + typename AT::t_sp_array_randomread _sp; + typename AT::t_x_array _xw; + typename AT::t_v_array _vw; + typename AT::t_tagint_1d _tagw; + typename AT::t_int_1d _typew; + typename AT::t_int_1d _maskw; + typename AT::t_imageint_1d _imagew; + typename AT::t_sp_array _spw; + + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d_const _sendlist; + typename AT::t_int_1d_const _copylist; + int _nlocal,_dim; + X_FLOAT _lo,_hi; + + AtomVecSpinKokkos_PackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d sendlist, + typename AT::tdual_int_1d copylist,int nlocal, int dim, + X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _sp(atom->k_sp.view()), + _xw(atom->k_x.view()), + _vw(atom->k_v.view()), + _tagw(atom->k_tag.view()), + _typew(atom->k_type.view()), + _maskw(atom->k_mask.view()), + _imagew(atom->k_image.view()), + _spw(atom->k_sp.view()), + _sendlist(sendlist.template view()), + _copylist(copylist.template view()), + _nlocal(nlocal),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 15; + const int maxsendlist = (buf.template view().extent(0)* + buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &mysend) const { + const int i = _sendlist(mysend); + _buf(mysend,0) = 15; + _buf(mysend,1) = _x(i,0); + _buf(mysend,2) = _x(i,1); + _buf(mysend,3) = _x(i,2); + _buf(mysend,4) = _v(i,0); + _buf(mysend,5) = _v(i,1); + _buf(mysend,6) = _v(i,2); + _buf(mysend,7) = d_ubuf(_tag[i]).d; + _buf(mysend,8) = d_ubuf(_type[i]).d; + _buf(mysend,9) = d_ubuf(_mask[i]).d; + _buf(mysend,10) = d_ubuf(_image[i]).d; + _buf(mysend,11) = _sp(i,0); + _buf(mysend,12) = _sp(i,1); + _buf(mysend,13) = _sp(i,2); + _buf(mysend,14) = _sp(i,3); + const int j = _copylist(mysend); + + if(j>-1) { + _xw(i,0) = _x(j,0); + _xw(i,1) = _x(j,1); + _xw(i,2) = _x(j,2); + _vw(i,0) = _v(j,0); + _vw(i,1) = _v(j,1); + _vw(i,2) = _v(j,2); + _tagw(i) = _tag(j); + _typew(i) = _type(j); + _maskw(i) = _mask(j); + _imagew(i) = _image(j); + _spw(i,0) = _sp(j,0); + _spw(i,1) = _sp(j,1); + _spw(i,2) = _sp(j,2); + _spw(i,3) = _sp(j,3); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space,int dim, + X_FLOAT lo,X_FLOAT hi ) +{ + if(nsend > (int) (k_buf.view().extent(0)*k_buf.view().extent(1))/15) { + int newsize = nsend*15/k_buf.view().extent(1)+1; + k_buf.resize(newsize,k_buf.view().extent(1)); + } + if(space == Host) { + AtomVecSpinKokkos_PackExchangeFunctor + f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + return nsend*15; + } else { + AtomVecSpinKokkos_PackExchangeFunctor + f(atomKK,k_buf,k_sendlist,k_copylist,atom->nlocal,dim,lo,hi); + Kokkos::parallel_for(nsend,f); + return nsend*15; + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_exchange(int i, double *buf) +{ + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + buf[m++] = ubuf(h_tag(i)).d; + buf[m++] = ubuf(h_type(i)).d; + buf[m++] = ubuf(h_mask(i)).d; + buf[m++] = ubuf(h_image(i)).d; + buf[m++] = h_sp(i,0); + buf[m++] = h_sp(i,1); + buf[m++] = h_sp(i,2); + buf[m++] = h_sp(i,3); + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- */ + +template +struct AtomVecSpinKokkos_UnpackExchangeFunctor { + typedef DeviceType device_type; + typedef ArrayTypes AT; + typename AT::t_x_array _x; + typename AT::t_v_array _v; + typename AT::t_tagint_1d _tag; + typename AT::t_int_1d _type; + typename AT::t_int_1d _mask; + typename AT::t_imageint_1d _image; + typename AT::t_sp_array _sp; + typename AT::t_xfloat_2d_um _buf; + typename AT::t_int_1d _nlocal; + int _dim; + X_FLOAT _lo,_hi; + + AtomVecSpinKokkos_UnpackExchangeFunctor( + const AtomKokkos* atom, + const typename AT::tdual_xfloat_2d buf, + typename AT::tdual_int_1d nlocal, + int dim, X_FLOAT lo, X_FLOAT hi): + _x(atom->k_x.view()), + _v(atom->k_v.view()), + _tag(atom->k_tag.view()), + _type(atom->k_type.view()), + _mask(atom->k_mask.view()), + _image(atom->k_image.view()), + _sp(atom->k_sp.view()), + _nlocal(nlocal.template view()),_dim(dim), + _lo(lo),_hi(hi){ + const size_t elements = 15; + const int maxsendlist = (buf.template view().extent(0)*buf.template view().extent(1))/elements; + + buffer_view(_buf,buf,maxsendlist,elements); + } + + KOKKOS_INLINE_FUNCTION + void operator() (const int &myrecv) const { + X_FLOAT x = _buf(myrecv,_dim+1); + if (x >= _lo && x < _hi) { + int i = Kokkos::atomic_fetch_add(&_nlocal(0),1); + _x(i,0) = _buf(myrecv,1); + _x(i,1) = _buf(myrecv,2); + _x(i,2) = _buf(myrecv,3); + _v(i,0) = _buf(myrecv,4); + _v(i,1) = _buf(myrecv,5); + _v(i,2) = _buf(myrecv,6); + _tag[i] = (tagint) d_ubuf(_buf(myrecv,7)).i; + _type[i] = (int) d_ubuf(_buf(myrecv,8)).i; + _mask[i] = (int) d_ubuf(_buf(myrecv,9)).i; + _image[i] = (imageint) d_ubuf(_buf(myrecv,10)).i; + _sp(i,0) = _buf(myrecv,11); + _sp(i,1) = _buf(myrecv,12); + _sp(i,2) = _buf(myrecv,13); + _sp(i,3) = _buf(myrecv,14); + } + } +}; + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf,int nrecv, + int nlocal,int dim,X_FLOAT lo,X_FLOAT hi, + ExecutionSpace space) { + if(space == Host) { + k_count.h_view(0) = nlocal; + AtomVecSpinKokkos_UnpackExchangeFunctor f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/15,f); + return k_count.h_view(0); + } else { + k_count.h_view(0) = nlocal; + k_count.modify(); + k_count.sync(); + AtomVecSpinKokkos_UnpackExchangeFunctor + f(atomKK,k_buf,k_count,dim,lo,hi); + Kokkos::parallel_for(nrecv/15,f); + k_count.modify(); + k_count.sync(); + + return k_count.h_view(0); + } +} + +/* ---------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_exchange(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; + h_type(nlocal) = (int) ubuf(buf[m++]).i; + h_mask(nlocal) = (int) ubuf(buf[m++]).i; + h_image(nlocal) = (imageint) ubuf(buf[m++]).i; + h_sp(nlocal,0) = buf[m++]; + h_sp(nlocal,1) = buf[m++]; + h_sp(nlocal,2) = buf[m++]; + h_sp(nlocal,3) = buf[m++]; + + if (atom->nextra_grow) + for (int iextra = 0; iextra < atom->nextra_grow; iextra++) + m += modify->fix[atom->extra_grow[iextra]]-> + unpack_exchange(nlocal,&buf[m]); + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + size of restart data for all atoms owned by this proc + include extra data stored by fixes +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::size_restart() +{ + int i; + + int nlocal = atom->nlocal; + int n = 15 * nlocal; + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + for (i = 0; i < nlocal; i++) + n += modify->fix[atom->extra_restart[iextra]]->size_restart(i); + + return n; +} + +/* ---------------------------------------------------------------------- + pack atom I's data for restart file including extra quantities + xyz must be 1st 3 values, so that read_restart can test on them + molecular types may be negative, but write as positive +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_restart(int i, double *buf) +{ + atomKK->sync(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + buf[m++] = h_x(i,0); + buf[m++] = h_x(i,1); + buf[m++] = h_x(i,2); + buf[m++] = ubuf(h_tag(i)).d; + buf[m++] = ubuf(h_type(i)).d; + buf[m++] = ubuf(h_mask(i)).d; + buf[m++] = ubuf(h_image(i)).d; + buf[m++] = h_v(i,0); + buf[m++] = h_v(i,1); + buf[m++] = h_v(i,2); + + buf[m++] = h_sp(i,0); + buf[m++] = h_sp(i,1); + buf[m++] = h_sp(i,2); + buf[m++] = h_sp(i,3); + + if (atom->nextra_restart) + for (int iextra = 0; iextra < atom->nextra_restart; iextra++) + m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]); + + buf[0] = m; + return m; +} + +/* ---------------------------------------------------------------------- + unpack data for one atom from restart file including extra quantities +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::unpack_restart(double *buf) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + grow(0); + if (atom->nextra_store) + memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra"); + } + + atomKK->modified(Host,X_MASK | V_MASK | TAG_MASK | TYPE_MASK | + MASK_MASK | IMAGE_MASK | SP_MASK); + + int m = 1; + h_x(nlocal,0) = buf[m++]; + h_x(nlocal,1) = buf[m++]; + h_x(nlocal,2) = buf[m++]; + h_tag(nlocal) = (tagint) ubuf(buf[m++]).i; + h_type(nlocal) = (int) ubuf(buf[m++]).i; + h_mask(nlocal) = (int) ubuf(buf[m++]).i; + h_image(nlocal) = (imageint) ubuf(buf[m++]).i; + h_v(nlocal,0) = buf[m++]; + h_v(nlocal,1) = buf[m++]; + h_v(nlocal,2) = buf[m++]; + + h_sp(nlocal,0) = buf[m++]; + h_sp(nlocal,1) = buf[m++]; + h_sp(nlocal,2) = buf[m++]; + h_sp(nlocal,3) = buf[m++]; + + double **extra = atom->extra; + if (atom->nextra_store) { + int size = static_cast (buf[0]) - m; + for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++]; + } + + atom->nlocal++; + return m; +} + +/* ---------------------------------------------------------------------- + create one atom of itype at coord + set other values to defaults +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::create_atom(int itype, double *coord) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) { + atomKK->modified(Host,ALL_MASK); + grow(0); + } + atomKK->sync(Host,ALL_MASK); + atomKK->modified(Host,ALL_MASK); + + tag[nlocal] = 0; + type[nlocal] = itype; + h_x(nlocal,0) = coord[0]; + h_x(nlocal,1) = coord[1]; + h_x(nlocal,2) = coord[2]; + h_mask[nlocal] = 1; + h_image[nlocal] = ((imageint) IMGMAX << IMG2BITS) | + ((imageint) IMGMAX << IMGBITS) | IMGMAX; + h_v(nlocal,0) = 0.0; + h_v(nlocal,1) = 0.0; + h_v(nlocal,2) = 0.0; + + h_sp(nlocal,0) = 0.0; + h_sp(nlocal,1) = 0.0; + h_sp(nlocal,2) = 0.0; + h_sp(nlocal,3) = 0.0; + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack one line from Atoms section of data file + initialize other atom quantities +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::data_atom(double *coord, imageint imagetmp, + char **values) +{ + int nlocal = atom->nlocal; + if (nlocal == nmax) grow(0); + + h_tag[nlocal] = utils::inumeric(FLERR,values[0],true,lmp); + h_type[nlocal] = utils::inumeric(FLERR,values[1],true,lmp); + if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) + error->one(FLERR,"Invalid atom type in Atoms section of data file"); + + h_sp(nlocal,3) = utils::numeric(FLERR,values[2],true,lmp); + h_sp(nlocal,0) = utils::numeric(FLERR,values[6],true,lmp); + h_sp(nlocal,1) = utils::numeric(FLERR,values[7],true,lmp); + h_sp(nlocal,2) = utils::numeric(FLERR,values[8],true,lmp); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + h_sp(nlocal,0) *= inorm; + h_sp(nlocal,1) *= inorm; + h_sp(nlocal,2) *= inorm; + + h_x(nlocal,0) = coord[0]; + h_x(nlocal,1) = coord[1]; + h_x(nlocal,2) = coord[2]; + + h_image[nlocal] = imagetmp; + + h_mask[nlocal] = 1; + h_v(nlocal,0) = 0.0; + h_v(nlocal,1) = 0.0; + h_v(nlocal,2) = 0.0; + + atomKK->modified(Host,ALL_MASK); + + atom->nlocal++; +} + +/* ---------------------------------------------------------------------- + unpack hybrid quantities from one line in Atoms section of data file + initialize other atom quantities for this sub-style +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::data_atom_hybrid(int nlocal, char **values) +{ + h_sp(nlocal,3) = utils::numeric(FLERR,values[0],true,lmp); + h_sp(nlocal,0) = utils::numeric(FLERR,values[1],true,lmp); + h_sp(nlocal,1) = utils::numeric(FLERR,values[2],true,lmp); + h_sp(nlocal,2) = utils::numeric(FLERR,values[3],true,lmp); + double inorm = 1.0/sqrt(sp[nlocal][0]*sp[nlocal][0] + + sp[nlocal][1]*sp[nlocal][1] + + sp[nlocal][2]*sp[nlocal][2]); + sp[nlocal][0] *= inorm; + sp[nlocal][1] *= inorm; + sp[nlocal][2] *= inorm; + + return 4; +} + +/* ---------------------------------------------------------------------- + pack atom info for data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::pack_data(double **buf) +{ + int nlocal = atom->nlocal; + for (int i = 0; i < nlocal; i++) { + buf[i][0] = h_tag[i]; + buf[i][1] = h_type[i]; + buf[i][2] = h_sp(i,0); + buf[i][3] = h_x(i,0); + buf[i][4] = h_x(i,1); + buf[i][5] = h_x(i,2); + buf[i][2] = h_sp(i,1); + buf[i][2] = h_sp(i,2); + buf[i][2] = h_sp(i,3); + buf[i][6] = (h_image[i] & IMGMASK) - IMGMAX; + buf[i][7] = (h_image[i] >> IMGBITS & IMGMASK) - IMGMAX; + buf[i][8] = (h_image[i] >> IMG2BITS) - IMGMAX; + } +} + +/* ---------------------------------------------------------------------- + pack hybrid atom info for data file +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::pack_data_hybrid(int i, double *buf) +{ + buf[0] = h_sp(i,3); + buf[1] = h_sp(i,0); + buf[2] = h_sp(i,1); + buf[3] = h_sp(i,2); + return 4; +} + +/* ---------------------------------------------------------------------- + write atom info to data file including 3 image flags +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::write_data(FILE *fp, int n, double **buf) +{ + for (int i = 0; i < n; i++) + fprintf(fp,"%d %d %-1.16e %-1.16e %-1.16e %-1.16e %d %d %d\n", + (int) buf[i][0],(int) buf[i][1],buf[i][2],buf[i][3],buf[i][4], + buf[i][5],(int) buf[i][6],(int) buf[i][7],(int) buf[i][8]); +} + +/* ---------------------------------------------------------------------- + write hybrid atom info to data file +------------------------------------------------------------------------- */ + +int AtomVecSpinKokkos::write_data_hybrid(FILE *fp, double *buf) +{ + fprintf(fp," %-1.16e %-1.16e %-1.16e %-1.16e",buf[0],buf[1],buf[2],buf[3]); + return 4; +} + +/* ---------------------------------------------------------------------- + return # of bytes of allocated memory +------------------------------------------------------------------------- */ + +double AtomVecSpinKokkos::memory_usage() +{ + bigint bytes = 0; + + if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax); + if (atom->memcheck("type")) bytes += memory->usage(type,nmax); + if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax); + if (atom->memcheck("image")) bytes += memory->usage(image,nmax); + if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3); + if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3); + if (atom->memcheck("f")) bytes += memory->usage(f,nmax*commKK->nthreads,3); + + if (atom->memcheck("sp")) bytes += memory->usage(sp,nmax,4); + if (atom->memcheck("fm")) bytes += memory->usage(fm,nmax*comm->nthreads,3); + if (atom->memcheck("fm_long")) bytes += memory->usage(fm_long,nmax*comm->nthreads,3); + + return bytes; +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::sync(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & SP_MASK) atomKK->k_sp.sync(); + if (mask & FM_MASK) atomKK->k_fm.sync(); + if (mask & FML_MASK) atomKK->k_fm_long.sync(); + } else { + if (mask & X_MASK) atomKK->k_x.sync(); + if (mask & V_MASK) atomKK->k_v.sync(); + if (mask & F_MASK) atomKK->k_f.sync(); + if (mask & TAG_MASK) atomKK->k_tag.sync(); + if (mask & TYPE_MASK) atomKK->k_type.sync(); + if (mask & MASK_MASK) atomKK->k_mask.sync(); + if (mask & IMAGE_MASK) atomKK->k_image.sync(); + if (mask & SP_MASK) atomKK->k_sp.sync(); + if (mask & FM_MASK) atomKK->k_fm.sync(); + if (mask & FML_MASK) atomKK->k_fm_long.sync(); + } +} + +/* ---------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::modified(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & SP_MASK) atomKK->k_sp.modify(); + if (mask & FM_MASK) atomKK->k_fm.modify(); + if (mask & FML_MASK) atomKK->k_fm_long.modify(); + } else { + if (mask & X_MASK) atomKK->k_x.modify(); + if (mask & V_MASK) atomKK->k_v.modify(); + if (mask & F_MASK) atomKK->k_f.modify(); + if (mask & TAG_MASK) atomKK->k_tag.modify(); + if (mask & TYPE_MASK) atomKK->k_type.modify(); + if (mask & MASK_MASK) atomKK->k_mask.modify(); + if (mask & IMAGE_MASK) atomKK->k_image.modify(); + if (mask & SP_MASK) atomKK->k_sp.modify(); + if (mask & FM_MASK) atomKK->k_fm.modify(); + if (mask & FML_MASK) atomKK->k_fm_long.modify(); + } +} + +void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned int mask) +{ + if (space == Device) { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_sp,space); + if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_fm,space); + if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + perform_async_copy(atomKK->k_fm_long,space); + } else { + if ((mask & X_MASK) && atomKK->k_x.need_sync()) + perform_async_copy(atomKK->k_x,space); + if ((mask & V_MASK) && atomKK->k_v.need_sync()) + perform_async_copy(atomKK->k_v,space); + if ((mask & F_MASK) && atomKK->k_f.need_sync()) + perform_async_copy(atomKK->k_f,space); + if ((mask & TAG_MASK) && atomKK->k_tag.need_sync()) + perform_async_copy(atomKK->k_tag,space); + if ((mask & TYPE_MASK) && atomKK->k_type.need_sync()) + perform_async_copy(atomKK->k_type,space); + if ((mask & MASK_MASK) && atomKK->k_mask.need_sync()) + perform_async_copy(atomKK->k_mask,space); + if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) + perform_async_copy(atomKK->k_image,space); + if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + perform_async_copy(atomKK->k_sp,space); + if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) + perform_async_copy(atomKK->k_fm,space); + if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + perform_async_copy(atomKK->k_fm_long,space); + } +} + +/* ---------------------------------------------------------------------- + clear all forces (mech and mag) +------------------------------------------------------------------------- */ + +void AtomVecSpinKokkos::force_clear(int /*n*/, size_t nbytes) +{ + memset(&atom->f[0][0],0,3*nbytes); + memset(&atom->fm[0][0],0,3*nbytes); + memset(&atom->fm_long[0][0],0,3*nbytes); +} diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h new file mode 100644 index 0000000000..a9f7077a24 --- /dev/null +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -0,0 +1,132 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifdef ATOM_CLASS + +AtomStyle(spin/kk,AtomVecSpinKokkos) +AtomStyle(spin/kk/device,AtomVecSpinKokkos) +AtomStyle(spin/kk/host,AtomVecSpinKokkos) + +#else + +#ifndef LMP_ATOM_VEC_SPIN_KOKKOS_H +#define LMP_ATOM_VEC_SPIN_KOKKOS_H + +#include "atom_vec_kokkos.h" +#include "kokkos_type.h" + +namespace LAMMPS_NS { + +class AtomVecSpinKokkos : public AtomVecKokkos { + public: + AtomVecSpinKokkos(class LAMMPS *); + void grow(int); + void copy(int, int, int); + int pack_border(int, int *, double *, int, int *); + int pack_border_vel(int, int *, double *, int, int *); + int pack_border_hybrid(int, int *, double *); + void unpack_border(int, int, double *); + void unpack_border_vel(int, int, double *); + int unpack_border_hybrid(int, int, double *); + int pack_exchange(int, double *); + int unpack_exchange(double *); + int size_restart(); + int pack_restart(int, double *); + int unpack_restart(double *); + void create_atom(int, double *); + void data_atom(double *, imageint, char **); + int data_atom_hybrid(int, char **); + void pack_data(double **); + int pack_data_hybrid(int, double *); + void write_data(FILE *, int, double **); + int write_data_hybrid(FILE *, double *); + double memory_usage(); + + // clear magnetic and mechanic forces + + void force_clear(int, size_t); + + void grow_reset(); + // input lists to be checked + int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, + DAT::tdual_xfloat_2d buf,int iswap, + int pbc_flag, int *pbc, ExecutionSpace space); + void unpack_border_kokkos(const int &n, const int &nfirst, + const DAT::tdual_xfloat_2d &buf, + ExecutionSpace space); + int pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &buf, + DAT::tdual_int_1d k_sendlist, + DAT::tdual_int_1d k_copylist, + ExecutionSpace space, int dim, + X_FLOAT lo, X_FLOAT hi); + int unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv, + int nlocal, int dim, X_FLOAT lo, X_FLOAT hi, + ExecutionSpace space); + + void sync(ExecutionSpace space, unsigned int mask); + void modified(ExecutionSpace space, unsigned int mask); + void sync_overlapping_device(ExecutionSpace space, unsigned int mask); + + protected: + tagint *tag; + int *type,*mask; + imageint *image; + double **x,**v,**f; // lattice quantities + + // spin quantities + double **sp; // sp[i][0-2] direction of the spin i + // sp[i][3] atomic magnetic moment of the spin i + double **fm; // fm[i][0-2] direction of magnetic precession + double **fm_long; // storage of long-range spin prec. components + + DAT::t_tagint_1d d_tag; + HAT::t_tagint_1d h_tag; + + DAT::t_int_1d d_type, d_mask; + HAT::t_int_1d h_type, h_mask; + + DAT::t_imageint_1d d_image; + HAT::t_imageint_1d h_image; + + DAT::t_x_array d_x; + DAT::t_v_array d_v; + DAT::t_f_array d_f; + + DAT::t_sp_array d_sp; + DAT::t_fm_array d_fm; + DAT::t_fm_long_array d_fm_long; + + HAT::t_sp_array h_sp; + HAT::t_fm_array h_fm; + HAT::t_fm_long_array h_fm_long; + + DAT::tdual_int_1d k_count; +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Per-processor system is too big + +The number of owned atoms plus ghost atoms on a single +processor must fit in 32-bit integer. + +E: Invalid atom type in Atoms section of data file + +Atom types must range from 1 to specified # of types. + +*/ diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index 5930a9e207..b6992602d0 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -758,6 +758,38 @@ typedef tdual_virial_array::t_dev_um t_virial_array_um; typedef tdual_virial_array::t_dev_const_um t_virial_array_const_um; typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; +// Spin Types + +//3d SP_FLOAT array n*4 +#ifdef LMP_KOKKOS_NO_LEGACY +typedef Kokkos::DualView tdual_sp_array; +#else +typedef Kokkos::DualView tdual_sp_array; +#endif +typedef tdual_sp_array::t_dev t_sp_array; +typedef tdual_sp_array::t_dev_const t_sp_array_const; +typedef tdual_sp_array::t_dev_um t_sp_array_um; +typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; +typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; + +//3d FM_FLOAT array n*3 + +typedef Kokkos::DualView tdual_fm_array; +typedef tdual_fm_array::t_dev t_fm_array; +typedef tdual_fm_array::t_dev_const t_fm_array_const; +typedef tdual_fm_array::t_dev_um t_fm_array_um; +typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; +typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; + +//3d FML_FLOAT array n*3 + +typedef Kokkos::DualView tdual_fm_long_array; +typedef tdual_fm_long_array::t_dev t_fm_long_array; +typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; +typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; +typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; +typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; + //Energy Types //1d E_FLOAT array n @@ -994,6 +1026,33 @@ typedef tdual_virial_array::t_host_um t_virial_array_um; typedef tdual_virial_array::t_host_const_um t_virial_array_const_um; typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; +// Spin types + +//2d X_FLOAT array n*3 +typedef Kokkos::DualView tdual_sp_array; +typedef tdual_sp_array::t_host t_sp_array; +typedef tdual_sp_array::t_host_const t_sp_array_const; +typedef tdual_sp_array::t_host_um t_sp_array_um; +typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; +typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; + +//2d F_FLOAT array n*3 +typedef Kokkos::DualView tdual_fm_array; +//typedef Kokkos::DualView tdual_f_array; +typedef tdual_fm_array::t_host t_fm_array; +typedef tdual_fm_array::t_host_const t_fm_array_const; +typedef tdual_fm_array::t_host_um t_fm_array_um; +typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; +typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; + +//2d F_FLOAT array n*3 +typedef Kokkos::DualView tdual_fm_long_array; +//typedef Kokkos::DualView tdual_f_array; +typedef tdual_fm_long_array::t_host t_fm_long_array; +typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; +typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; +typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; +typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; //Energy Types diff --git a/src/atom_masks.h b/src/atom_masks.h index 8e29448488..daad323835 100644 --- a/src/atom_masks.h +++ b/src/atom_masks.h @@ -42,6 +42,12 @@ #define ENERGY_MASK 0x00010000 #define VIRIAL_MASK 0x00020000 +// SPIN + +#define SP_MASK 0x00000001 +#define FM_MASK 0x00000002 +#define FML_MASK 0x00000004 + // DPD #define DPDRHO_MASK 0x00040000 From aa1a87687bbaec39252f26afe77dc54931857b04 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 8 Oct 2020 07:32:36 -0600 Subject: [PATCH 002/100] Fix minor issues --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 15 +++++++++------ src/KOKKOS/atom_vec_spin_kokkos.h | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-) diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index c5c2ffb5be..188748d655 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -97,6 +97,9 @@ void AtomVecSpinKokkos::grow(int n) memoryKK->grow_kokkos(atomKK->k_fm,atomKK->fm,nmax,"atom:fm"); memoryKK->grow_kokkos(atomKK->k_fm_long,atomKK->fm_long,nmax,"atom:fm_long"); + grow_pointers(); + atomKK->sync(Host,ALL_MASK); + if (atom->nextra_grow) for (int iextra = 0; iextra < atom->nextra_grow; iextra++) modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax); @@ -106,7 +109,7 @@ void AtomVecSpinKokkos::grow(int n) reset local array ptrs ------------------------------------------------------------------------- */ -void AtomVecSpinKokkos::grow_reset() +void AtomVecSpinKokkos::grow_pointers() { tag = atomKK->tag; d_tag = atomKK->k_tag.d_view; @@ -121,7 +124,7 @@ void AtomVecSpinKokkos::grow_reset() image = atomKK->image; d_image = atomKK->k_image.d_view; h_image = atomKK->k_image.h_view; - + x = atomKK->x; d_x = atomKK->k_x.d_view; h_x = atomKK->k_x.h_view; @@ -389,7 +392,7 @@ int AtomVecSpinKokkos::pack_border(int n, int *list, double *buf, buf[m++] = h_sp(j,3); } } - + if (atom->nextra_border) for (int iextra = 0; iextra < atom->nextra_border; iextra++) m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); @@ -478,7 +481,7 @@ int AtomVecSpinKokkos::pack_border_vel(int n, int *list, double *buf, } } } - + if (atom->nextra_border) for (int iextra = 0; iextra < atom->nextra_border; iextra++) m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]); @@ -1026,8 +1029,8 @@ void AtomVecSpinKokkos::create_atom(int itype, double *coord) atomKK->sync(Host,ALL_MASK); atomKK->modified(Host,ALL_MASK); - tag[nlocal] = 0; - type[nlocal] = itype; + h_tag[nlocal] = 0; + h_type[nlocal] = itype; h_x(nlocal,0) = coord[0]; h_x(nlocal,1) = coord[1]; h_x(nlocal,2) = coord[2]; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index a9f7077a24..5dca7b4e13 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -56,7 +56,7 @@ class AtomVecSpinKokkos : public AtomVecKokkos { void force_clear(int, size_t); - void grow_reset(); + void grow_pointers(); // input lists to be checked int pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist, DAT::tdual_xfloat_2d buf,int iswap, From e8ebce1b5281ca0d4e8651918c64f24d940d7ec0 Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Thu, 8 Oct 2020 08:21:55 -0600 Subject: [PATCH 003/100] Fix GPU compile error --- src/KOKKOS/kokkos_type.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index b6992602d0..041a6d4771 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -1028,8 +1028,8 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types -//2d X_FLOAT array n*3 -typedef Kokkos::DualView tdual_sp_array; +//2d X_FLOAT array n*4 +typedef Kokkos::DualView tdual_sp_array; typedef tdual_sp_array::t_host t_sp_array; typedef tdual_sp_array::t_host_const t_sp_array_const; typedef tdual_sp_array::t_host_um t_sp_array_um; From c85498e98baf752c05ec5f2a8ea7ecaaba9535eb Mon Sep 17 00:00:00 2001 From: julient31 Date: Fri, 9 Oct 2020 09:47:47 -0600 Subject: [PATCH 004/100] started to add spin/kk to the doc modified validaion tests for kokkos compatibility --- doc/src/atom_style.rst | 2 +- .../llg_exchange.py | 2 +- .../run-test-exchange.sh | 5 +++-- .../test-spin-precession.in | 12 ++++++++-- .../validation_damped_exchange/two_spins.data | 22 ------------------- .../validation_nve/in.spin.iron-nve | 7 +++++- .../validation_nve/run-test-nve.sh | 5 +++-- 7 files changed, 24 insertions(+), 31 deletions(-) delete mode 100644 examples/SPIN/test_problems/validation_damped_exchange/two_spins.data diff --git a/doc/src/atom_style.rst b/doc/src/atom_style.rst index 4957901676..a59f8d31e0 100644 --- a/doc/src/atom_style.rst +++ b/doc/src/atom_style.rst @@ -27,7 +27,7 @@ Syntax template-ID = ID of molecule template specified in a separate :doc:`molecule ` command *hybrid* args = list of one or more sub-styles, each with their args -* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* +* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk* Examples """""""" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 49eecb5b44..dd1c543bb3 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -65,6 +65,6 @@ for t in range (0,N): # calc. average magnetization Sm = (S1+S2)*0.5 # calc. energy - en = -2.0*J0*(np.dot(S1,S2)) + en = -J0*(np.dot(S1,S2)) # print res. in ps for comparison with LAMMPS print(t*dt/1000.0,Sm[0],Sm[1],Sm[2],en) diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index 599730fe7b..ce8a6c3dbf 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -4,8 +4,9 @@ rm res_*.dat # compute Lammps -./../../../../src/lmp_serial \ - -in test-spin-precession.in +../../../../src/lmp_serial -in test-spin-precession.in +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 0ca49364d2..6eea93224e 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -2,10 +2,18 @@ units metal atom_style spin -atom_modify map array +# atom_style spin/kk boundary f f f -read_data two_spins.data +atom_modify map array +lattice sc 3.0 +region box block 0 2 0 1 0 1 +create_box 1 box +create_atoms 1 box + +mass 1 55.845 +set atom 1 spin 2.0 1.0 0.0 0.0 +set atom 2 spin 2.0 0.0 1.0 0.0 pair_style spin/exchange 3.1 pair_coeff * * exchange 3.1 11.254 0.0 1.0 diff --git a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data b/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data deleted file mode 100644 index 013f813751..0000000000 --- a/examples/SPIN/test_problems/validation_damped_exchange/two_spins.data +++ /dev/null @@ -1,22 +0,0 @@ -LAMMPS data file via write_data, version 19 Sep 2019, timestep = 0 - -2 atoms -1 atom types - -0.0 6.0 xlo xhi -0.0 3.0 ylo yhi -0.0 3.0 zlo zhi - -Masses - -1 1 - -Atoms # spin - -1 1 2.0 0.0 0.0 0.0 1.0 0.0 0.0 0 0 0 -2 1 2.0 3.0 0.0 0.0 0.0 1.0 0.0 0 0 0 - -Velocities - -1 0.0 0.0 0.0 -2 0.0 0.0 0.0 diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index f00fb1ec12..a29d0158cf 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p @@ -46,4 +47,8 @@ variable tmag equal c_out_mag[6] thermo_style custom step time v_tmag temp v_emag ke pe etotal thermo 200 -run 100000 +compute outsp all property/atom spx spy spz sp fmx fmy fmz +dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] + +# run 100000 +run 10000 diff --git a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh index 441e7cf46d..a8eb179b7f 100755 --- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh +++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh @@ -4,8 +4,9 @@ rm res_*.dat # compute Lammps -./../../../../src/lmp_serial \ - -in in.spin.iron-nve +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.iron-nve +../../../../src/lmp_serial -in in.spin.iron-nve in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" From 606b33ea03e824ef9061c5d2f7aa87d0df793c8e Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:05:37 -0600 Subject: [PATCH 005/100] Added fix_charge_regulation source code and documentation. --- doc/src/fix_charge_regulation.rst | 184 +++ examples/USER/misc/charge_regulation/README | 7 + .../misc/charge_regulation/data_acid.chreg | 235 +++ .../misc/charge_regulation/data_polymer.chreg | 264 ++++ .../USER/misc/charge_regulation/in_acid.chreg | 40 + .../misc/charge_regulation/in_polymer.chreg | 35 + .../misc/charge_regulation/log_acid.lammps | 163 ++ .../misc/charge_regulation/log_polymer.lammps | 181 +++ src/USER-MISC/README | 1 + src/USER-MISC/fix_charge_regulation.cpp | 1335 +++++++++++++++++ src/USER-MISC/fix_charge_regulation.h | 117 ++ 11 files changed, 2562 insertions(+) create mode 100644 doc/src/fix_charge_regulation.rst create mode 100644 examples/USER/misc/charge_regulation/README create mode 100644 examples/USER/misc/charge_regulation/data_acid.chreg create mode 100644 examples/USER/misc/charge_regulation/data_polymer.chreg create mode 100644 examples/USER/misc/charge_regulation/in_acid.chreg create mode 100644 examples/USER/misc/charge_regulation/in_polymer.chreg create mode 100644 examples/USER/misc/charge_regulation/log_acid.lammps create mode 100644 examples/USER/misc/charge_regulation/log_polymer.lammps create mode 100644 src/USER-MISC/fix_charge_regulation.cpp create mode 100644 src/USER-MISC/fix_charge_regulation.h diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst new file mode 100644 index 0000000000..585761e8a9 --- /dev/null +++ b/doc/src/fix_charge_regulation.rst @@ -0,0 +1,184 @@ + +.. Yuan documentation master file, created by + sphinx-quickstart on Sat Jan 30 14:06:22 2021. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + tc387: Multiple text additions/changes, Feb 2 2021 +.. index:: fix fix_charge_regulation + +fix_charge_regulation command +============================= +Syntax +"""""" + +.. parsed-literal:: + + fix ID group-ID charge_regulation cation_type anion_type keyword value(s) + +* ID, group-ID are documented in fix command +* charge_regulation = style name of this fix command +* cation_type = atom type of free cations +* anion_type = atom type of free anions + +* zero or more keyword/value pairs may be appended + + .. parsed-literal:: + + keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* + *pH* value = pH of the solution + *pKa* value = acid dissociation constant + *pKb* value = base dissociation constant + *pIp* value = chemical potential of free cations + *pIm* value = chemical potential of free anions + *pKs* value = solution self-dissociation constant + *acid_type* = atom type of acid groups + *base_type* = atom type of base groups + *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) + *temp* value = temperature + *tempfixid* value = fix ID of temperature thermostat + *nevery* value = invoke this fix every nevery steps + *nmc* value = number of charge regulation MC moves to attempt every nevery steps + *xrd* value = cutoff distance for acid/base reaction + *seed* value = random # seed (positive integer) + *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0") + *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups. + *onlysalt* values = flag charge_cation charge_anion. + flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion) + charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes) + *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) + +Examples +"""""""" +.. code-block:: LAMMPS + + fix chareg all charge_regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + + fix chareg all charge_regulation 1 2 pIp 3 pIm 3 tempfixid fT tag yes onlysalt yes 2 -1 + +Description +""""""""""" +This fix performs Monte Carlo (MC) sampling of charge regulation and exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` and :ref:`(Curk2) `. +The implemented method is largely analogous to the grand-reaction ensemble method in :ref:`(Landsgesell) `. +The implementation is parallelized, compatible with existing LAMMPS functionalities, and applicable to any system utilizing discreet, ionizable groups or surface sites. + + +Specifically, the fix implements the following three types of MC moves, which discretely change the charge state of individual particles and insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{X}^-`, +and :math:`\emptyset \rightleftharpoons Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. +In the former two types of reactions, Monte Carlo moves alter the charge value of specific atoms (:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a counterion to preserve the charge neutrality of the system, modeling the dissociation/association process. +The last type of reaction performs grand canonical MC exchange of ion pairs with a (fictitious) reservoir. + +In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, +whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. + +Here we provide several practical examples for modeling charge regulation effects in solvated systems. +An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file + +.. code-block:: LAMMPS + + fix acid_reaction all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 + +where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. +However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. + +A more efficient way is to allow salt ions to +participate in ionization reactions, which can be easily achieved via + +.. code-block:: LAMMPS + + fix acid_reaction all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 + +where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. + + + Similarly, we could have simultanously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) + +.. code-block:: LAMMPS + + fix base_reaction all charge_regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 + +where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. +If neither the acid or the base type is specified, for example, + +.. code-block:: LAMMPS + + fix salt_reaction all charge_regulation 4 5 pIp 2.0 pIm 2.0 + +the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. + + +The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. + +Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: + +.. code-block:: LAMMPS + + compute dtemp all temp + compute_modify dtemp dynamic yes + fix fT all langevin 1.0 1.0 1.0 123 + fix_modify fT temp dtemp + +The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. +Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length +must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.72nm). For example, in the dilute ideal solution limit, the concentration of free ions +will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. + +The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. + +The *xrd* keyword can be used to restrict the inserted/deleted counterions to a specific radial distance from an acid or base particle that is currently participating in a reaction. This can be used to simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / 2, where *L* is the smallest box dimension, the radial restriction is automatically turned off and free ion can be inserted or deleted anywhere in the simulation box. + +If the *tag yes* is used, every inserted atom gets a unique tag ID, otherwise, the tag of every inserted atom is set to 0. *tag yes* might cause an integer overflow in very long simulations since the tags are unique to every particle and thus increase with every successful particle insertion. + +The *pmcmoves* keyword sets the relative probability of attempting the three types of MC moves (reactions): acid charging, base charging, and ion pair exchange. +The fix only attempts to perform particle charging MC moves if *acid_type* or *base_type* is defined. Otherwise fix only performs free ion insertion/deletion. For example, if *acid_type* is not defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, the vector would be normalized to [0,0.5,0.5]. + +The *only_salt* option can be used to perform multivalent grand-canonical ion-exchange moves. If *only_salt yes* is used, no charge exchange is performed, only ion insertion/deletion (*pmcmoves* is set to [0,0,1]), but ions can be multivalent. In the example above, an MC move would consist of three ion insertion/deletion to preserve the charge neutrality of the system. + +The *group* keyword can be used to add inserted particles to a specific group-ID. All inserted particles are automatically added to group *all*. + + +Output +"""""" +This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global cumulative quantities: + +* 1 = cumulative MC attempts +* 2 = cumulative MC successes +* 3 = current # of neutral acid atoms +* 4 = current # of -1 charged acid atoms +* 5 = current # of neutral base atoms +* 6 = current # of +1 charged acid atoms +* 7 = current # of free cations +* 8 = current # of free anions + + +Restrictions +"""""""""""" +This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. +See the :doc:`Build package ` doc page for more info. + +The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. + +Note: Region restrictions are not yet implemented. + +Related commands +"""""""""""""""" + +:doc:`fix gcmc `, +:doc:`fix atom/swap ` + +Default +""""""" +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = -1; base_type = -1; lunit_nm = 0.72; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 2345; tag = no; onlysalt = no, pmcmoves = 0.33 0.33 0.33, group-ID = all + +---------- + +.. _Curk1: + +**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021). + +.. _Curk2: + +**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021) + +.. _Landsgesell: + +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, “Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning,” Macromolecules 53, 3007–3020 (2020). diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README new file mode 100644 index 0000000000..e0be86d7e4 --- /dev/null +++ b/examples/USER/misc/charge_regulation/README @@ -0,0 +1,7 @@ +This directory has two input scripts that illustrates how to use fix charge_regulation in LAMMPS to perform coarse-grained molecular dynamics (MD) simulations with incorporation of charge regulation effects. The charge regulation is implemented via Monte Carlo (MC) sampling following the reaction ensemble MC approach, producing a MC/MD hybrid tool for modeling charge regulation in solvated systems. + +The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. + +The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion +Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. + diff --git a/examples/USER/misc/charge_regulation/data_acid.chreg b/examples/USER/misc/charge_regulation/data_acid.chreg new file mode 100644 index 0000000000..edc7082ad0 --- /dev/null +++ b/examples/USER/misc/charge_regulation/data_acid.chreg @@ -0,0 +1,235 @@ +LAMMPS data file generated by get_input.py + +219 atoms +3 atom types +-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi +-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi +-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi + +Masses + +1 1 +2 1 +3 1 + +Atoms + +1 1 0 2.5983275747497636 -8.368052973860795 20.001288664343484 +2 1 -1 -18.182868728594865 -8.079792367885453 8.253737231981816 +3 1 -1 -17.437350808966414 8.120411567445771 10.747650340639332 +4 1 -1 6.502476583291578 -23.497326620756837 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6.272776670877239 10.035821052072265 22.22030412319301 +216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553 +217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468 +218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285 +219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/data_polymer.chreg b/examples/USER/misc/charge_regulation/data_polymer.chreg new file mode 100644 index 0000000000..2c5bd3e1ed --- /dev/null +++ b/examples/USER/misc/charge_regulation/data_polymer.chreg @@ -0,0 +1,264 @@ +##A Weak PE Chain of N=80 + +160 atoms +79 bonds + +5 atom types +1 bond types + +-50 50 xlo xhi +-50 50 ylo yhi +-50 50 zlo zhi + +Masses + +1 1.0 +2 1.0 +3 1.0 +4 1.0 +5 1.0 + +Atoms +# atom_id molecule_id atom_type charge x y z +1 1 1 -1 0 0 -48.37753795169063 +2 1 1 -1 0 0 -47.255075903381254 +3 1 1 -1 0 0 -46.13261385507188 +4 1 1 -1 0 0 -45.01015180676251 +5 1 1 -1 0 0 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-21.128139356809783 + +Bonds + # bond_id bond_type atom1_id atom2_id +1 1 1 2 +2 1 2 3 +3 1 3 4 +4 1 4 5 +5 1 5 6 +6 1 6 7 +7 1 7 8 +8 1 8 9 +9 1 9 10 +10 1 10 11 +11 1 11 12 +12 1 12 13 +13 1 13 14 +14 1 14 15 +15 1 15 16 +16 1 16 17 +17 1 17 18 +18 1 18 19 +19 1 19 20 +20 1 20 21 +21 1 21 22 +22 1 22 23 +23 1 23 24 +24 1 24 25 +25 1 25 26 +26 1 26 27 +27 1 27 28 +28 1 28 29 +29 1 29 30 +30 1 30 31 +31 1 31 32 +32 1 32 33 +33 1 33 34 +34 1 34 35 +35 1 35 36 +36 1 36 37 +37 1 37 38 +38 1 38 39 +39 1 39 40 +40 1 40 41 +41 1 41 42 +42 1 42 43 +43 1 43 44 +44 1 44 45 +45 1 45 46 +46 1 46 47 +47 1 47 48 +48 1 48 49 +49 1 49 50 +50 1 50 51 +51 1 51 52 +52 1 52 53 +53 1 53 54 +54 1 54 55 +55 1 55 56 +56 1 56 57 +57 1 57 58 +58 1 58 59 +59 1 59 60 +60 1 60 61 +61 1 61 62 +62 1 62 63 +63 1 63 64 +64 1 64 65 +65 1 65 66 +66 1 66 67 +67 1 67 68 +68 1 68 69 +69 1 69 70 +70 1 70 71 +71 1 71 72 +72 1 72 73 +73 1 73 74 +74 1 74 75 +75 1 75 76 +76 1 76 77 +77 1 77 78 +78 1 78 79 +79 1 79 80 diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in_acid.chreg new file mode 100644 index 0000000000..32beeda732 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in_acid.chreg @@ -0,0 +1,40 @@ +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +dimension 3 +boundary p p p +processors * * * +neighbor 3.0 bin +read_data data_acid.chreg + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * 1.0 1.0 ${cut_lj} # charges +kspace_style ewald 1.0e-3 +dielectric 1.0 +pair_modify shift no + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge_regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 10000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg new file mode 100644 index 0000000000..4dc72a8156 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in_polymer.chreg @@ -0,0 +1,35 @@ +# Charge regulation lammps for a polymer chain +units lj +atom_style full +dimension 3 +boundary p p p +processors * * * +neighbor 3.0 bin +read_data data_polymer.chreg + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift no +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 +fix chareg2 all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 +fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] +timestep 0.005 +run 10000 diff --git a/examples/USER/misc/charge_regulation/log_acid.lammps b/examples/USER/misc/charge_regulation/log_acid.lammps new file mode 100644 index 0000000000..cbc3661eb1 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log_acid.lammps @@ -0,0 +1,163 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.001 seconds +Ewald initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group Fix_CR:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.054228269 1 0 0 1 99 0 0 109 10 + 100 -0.058672881 0.99159291 100 71 16 84 0 0 92 8 + 200 -0.05399313 0.92006523 200 154 26 74 0 0 85 11 + 300 -0.047035343 0.92728143 300 240 22 78 0 0 85 7 + 400 -0.049597809 1.0617937 400 319 16 84 0 0 92 8 + 500 -0.052409835 1.0006148 500 404 12 88 0 0 97 9 + 600 -0.056012172 0.98059344 600 481 15 85 0 0 92 7 + 700 -0.053639989 0.99572709 700 561 16 84 0 0 94 10 + 800 -0.060026132 0.95764632 800 639 22 78 0 0 84 6 + 900 -0.050785422 0.98399084 900 719 28 72 0 0 82 10 + 1000 -0.062294743 0.97200068 1000 797 26 74 0 0 82 8 + 1100 -0.051269402 1.0064376 1100 877 25 75 0 0 84 9 + 1200 -0.077744839 1.0159098 1200 955 23 77 0 0 88 11 + 1300 -0.084889696 1.1230485 1300 1037 20 80 0 0 90 10 + 1400 -0.059361445 0.96735845 1400 1120 18 82 0 0 93 11 + 1500 -0.052926174 0.95579188 1500 1199 24 76 0 0 86 10 + 1600 -0.052376649 0.99376378 1600 1284 22 78 0 0 89 11 + 1700 -0.052480188 0.96085964 1700 1361 27 73 0 0 84 11 + 1800 -0.065884306 0.96747971 1800 1441 21 79 0 0 84 5 + 1900 -0.054315859 0.95873145 1900 1521 23 77 0 0 84 7 + 2000 -0.037161802 0.93562039 2000 1604 27 73 0 0 79 6 + 2100 -0.034977265 0.97177103 2100 1684 26 74 0 0 85 11 + 2200 -0.047434868 0.97897613 2200 1762 17 83 0 0 93 10 + 2300 -0.047392634 0.96570672 2300 1837 18 82 0 0 92 10 + 2400 -0.044879306 0.98620033 2400 1910 19 81 0 0 89 8 + 2500 -0.069690496 1.0690505 2500 1988 16 84 0 0 91 7 + 2600 -0.081588407 0.97711054 2600 2067 17 83 0 0 92 9 + 2700 -0.06341681 1.0386711 2700 2146 20 80 0 0 85 5 + 2800 -0.045290012 1.0402055 2800 2230 18 82 0 0 91 9 + 2900 -0.046875012 1.0609775 2900 2317 24 76 0 0 86 10 + 3000 -0.031258722 0.93861202 3000 2400 24 76 0 0 85 9 + 3100 -0.04673342 0.90800583 3100 2485 25 75 0 0 90 15 + 3200 -0.054354227 0.94493881 3200 2567 16 84 0 0 94 10 + 3300 -0.053647746 0.92321446 3300 2641 17 83 0 0 94 11 + 3400 -0.031751732 0.93735127 3400 2725 22 78 0 0 92 14 + 3500 -0.053806113 0.98798136 3500 2795 28 72 0 0 84 12 + 3600 -0.040751349 0.84291639 3600 2873 28 72 0 0 84 12 + 3700 -0.051747138 1.072448 3700 2951 24 76 0 0 92 16 + 3800 -0.043420594 1.0076309 3800 3030 26 74 0 0 79 5 + 3900 -0.050845848 1.0250023 3900 3103 29 71 0 0 76 5 + 4000 -0.039837847 1.064111 4000 3182 29 71 0 0 83 12 + 4100 -0.045638995 1.1249685 4100 3262 28 72 0 0 81 9 + 4200 -0.047956491 0.92255907 4200 3348 26 74 0 0 87 13 + 4300 -0.054052822 1.006239 4300 3423 19 81 0 0 90 9 + 4400 -0.053148034 1.0028887 4400 3506 24 76 0 0 83 7 + 4500 -0.062132076 1.0317847 4500 3587 23 77 0 0 82 5 + 4600 -0.04616043 0.99066453 4600 3673 28 72 0 0 82 10 + 4700 -0.066990889 1.0242064 4700 3755 18 82 0 0 90 8 + 4800 -0.0564736 0.91765628 4800 3832 22 78 0 0 91 13 + 4900 -0.052301294 0.95348659 4900 3912 28 72 0 0 81 9 + 5000 -0.062630677 1.0336579 5000 3989 18 82 0 0 92 10 + 5100 -0.053645908 1.0314613 5100 4062 20 80 0 0 85 5 + 5200 -0.062189568 1.0504732 5200 4133 23 77 0 0 84 7 + 5300 -0.049092746 1.0310832 5300 4217 24 76 0 0 82 6 + 5400 -0.051859257 0.99600428 5400 4299 27 73 0 0 80 7 + 5500 -0.065540815 0.98012128 5500 4381 19 81 0 0 92 11 + 5600 -0.071018582 0.9252814 5600 4455 23 77 0 0 84 7 + 5700 -0.066954185 1.0325214 5700 4535 26 74 0 0 82 8 + 5800 -0.064847249 1.0313536 5800 4617 21 79 0 0 90 11 + 5900 -0.063173056 0.95455853 5900 4703 18 82 0 0 92 10 + 6000 -0.064807837 0.97182222 6000 4790 21 79 0 0 91 12 + 6100 -0.07067683 0.91775921 6100 4875 16 84 0 0 94 10 + 6200 -0.071400842 1.0162225 6200 4952 17 83 0 0 87 4 + 6300 -0.078479449 1.0106706 6300 5033 21 79 0 0 84 5 + 6400 -0.083167651 1.0246584 6400 5111 18 82 0 0 90 8 + 6500 -0.092611537 1.0766467 6500 5195 20 80 0 0 88 8 + 6600 -0.096710071 1.0246648 6600 5274 15 85 0 0 91 6 + 6700 -0.073399857 0.94939392 6700 5351 17 83 0 0 92 9 + 6800 -0.062479375 0.9393967 6800 5434 18 82 0 0 93 11 + 6900 -0.065391043 0.93475954 6900 5514 22 78 0 0 89 11 + 7000 -0.045655499 0.98688239 7000 5601 21 79 0 0 90 11 + 7100 -0.061186309 1.0309063 7100 5684 22 78 0 0 87 9 + 7200 -0.074737514 1.0516593 7200 5769 25 75 0 0 80 5 + 7300 -0.075228979 1.0167704 7300 5847 21 79 0 0 86 7 + 7400 -0.06660147 1.0947107 7400 5930 25 75 0 0 87 12 + 7500 -0.071915247 1.10542 7500 6009 24 76 0 0 84 8 + 7600 -0.029974303 0.99202697 7600 6095 28 72 0 0 80 8 + 7700 -0.029024004 1.0390995 7700 6182 28 72 0 0 83 11 + 7800 -0.056250746 0.96393961 7800 6260 18 82 0 0 91 9 + 7900 -0.072178944 0.9833919 7900 6339 21 79 0 0 86 7 + 8000 -0.070377248 1.021342 8000 6419 23 77 0 0 88 11 + 8100 -0.07753283 0.96194312 8100 6493 26 74 0 0 86 12 + 8200 -0.075617309 0.9715344 8200 6576 25 75 0 0 89 14 + 8300 -0.077480013 0.99106705 8300 6662 20 80 0 0 91 11 + 8400 -0.079901928 0.89855112 8400 6744 23 77 0 0 91 14 + 8500 -0.069192745 1.0606791 8500 6822 19 81 0 0 91 10 + 8600 -0.058657202 1.1270217 8600 6898 15 85 0 0 95 10 + 8700 -0.044985397 1.0367419 8700 6979 27 73 0 0 84 11 + 8800 -0.064266376 0.91557003 8800 7060 21 79 0 0 89 10 + 8900 -0.068680533 0.95963643 8900 7133 19 81 0 0 88 7 + 9000 -0.051736144 1.0398547 9000 7213 13 87 0 0 94 7 + 9100 -0.058381436 0.98047663 9100 7290 17 83 0 0 89 6 + 9200 -0.05531014 0.92541631 9200 7368 22 78 0 0 85 7 + 9300 -0.04386907 0.9339658 9300 7454 22 78 0 0 89 11 + 9400 -0.052293168 0.94314034 9400 7539 22 78 0 0 86 8 + 9500 -0.050362046 1.0489028 9500 7617 18 82 0 0 90 8 + 9600 -0.054272227 1.0879161 9600 7697 11 89 0 0 96 7 + 9700 -0.042514179 1.0051505 9700 7771 22 78 0 0 84 6 + 9800 -0.045365018 0.95363669 9800 7850 25 75 0 0 77 2 + 9900 -0.064287274 0.91994667 9900 7928 27 73 0 0 81 8 + 10000 -0.05689162 0.99963208 10000 8011 22 78 0 0 84 6 +Loop time of 19.4452 on 1 procs for 10000 steps with 190 atoms + +Performance: 222162.510 tau/day, 514.265 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.68864 | 0.68864 | 0.68864 | 0.0 | 3.54 +Kspace | 6.7893 | 6.7893 | 6.7893 | 0.0 | 34.92 +Neigh | 0.060782 | 0.060782 | 0.060782 | 0.0 | 0.31 +Comm | 0.047035 | 0.047035 | 0.047035 | 0.0 | 0.24 +Output | 0.0027227 | 0.0027227 | 0.0027227 | 0.0 | 0.01 +Modify | 11.838 | 11.838 | 11.838 | 0.0 | 60.88 +Other | | 0.01878 | | | 0.10 + +Nlocal: 190.000 ave 190 max 190 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 592.000 ave 592 max 592 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2194.00 ave 2194 max 2194 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2194 +Ave neighs/atom = 11.547368 +Neighbor list builds = 10287 +Dangerous builds = 0 +Total wall time: 0:00:19 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/log_polymer.lammps b/examples/USER/misc/charge_regulation/log_polymer.lammps new file mode 100644 index 0000000000..87cab63a6c --- /dev/null +++ b/examples/USER/misc/charge_regulation/log_polymer.lammps @@ -0,0 +1,181 @@ +LAMMPS (24 Dec 2020) +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.000 seconds + read_data CPU = 0.004 seconds +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision KISS FFT + 3d grid and FFT values/proc = 2197 512 +0 atoms in group Fix_CR:exclusion_group:chareg1 +0 atoms in group Fix_CR:exclusion_group:chareg2 +0 atoms in group Fix_CR:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Setting up Verlet run ... + Unit style : lj + Current step : 0 + Time step : 0.005 +Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.49903297 1 0 80 80 0 0 0 + 100 0.63380666 0.87307225 8 72 77 6 1 0 + 200 0.5865464 1.0048645 16 64 81 16 0 1 + 300 0.55802913 1.0499142 19 61 91 29 0 1 + 400 0.44734087 1.0838048 24 56 98 41 0 1 + 500 0.47010775 1.005226 23 57 106 48 0 1 + 600 0.3452105 0.97814306 28 52 109 56 0 1 + 700 0.29208955 0.99766419 32 48 115 67 0 0 + 800 0.27821915 1.0091641 31 49 128 80 1 0 + 900 0.28943788 0.93619239 26 54 145 91 0 0 + 1000 0.22963142 1.0162138 27 53 150 97 0 0 + 1100 0.24238916 0.99146577 31 49 149 100 0 0 + 1200 0.17029095 1.0406453 38 42 144 102 0 0 + 1300 0.15830969 0.94661447 34 46 155 109 0 0 + 1400 0.16698712 1.0116563 35 45 159 114 0 0 + 1500 0.15432936 0.95600941 36 44 162 118 0 0 + 1600 0.16973501 0.98326602 31 49 171 122 0 0 + 1700 0.19725116 0.9915273 33 47 175 128 0 0 + 1800 0.15278999 1.0304873 29 51 193 142 0 0 + 1900 0.17418479 0.99490216 30 50 194 144 0 0 + 2000 0.14238391 0.9638301 32 48 189 141 0 0 + 2100 0.13054378 0.97164976 32 48 192 144 0 0 + 2200 0.092083069 1.0112059 40 40 191 151 0 0 + 2300 0.085175091 1.0070667 39 41 200 159 0 0 + 2400 0.083367076 0.9934796 35 45 208 163 0 0 + 2500 0.11494744 0.97650855 31 49 220 172 1 0 + 2600 0.10796032 0.97047046 34 46 221 175 0 0 + 2700 0.11080141 0.93570013 36 44 223 179 0 0 + 2800 0.096699277 0.97702627 35 45 223 178 0 0 + 2900 0.079403783 1.0870961 32 48 229 181 0 0 + 3000 0.08288836 1.0642515 35 45 231 186 0 0 + 3100 0.094000833 1.0241111 38 42 229 187 0 0 + 3200 0.10011052 1.043594 34 46 235 189 0 0 + 3300 0.096782103 0.99549134 34 46 234 188 0 0 + 3400 0.057703946 1.00292 34 46 236 190 0 0 + 3500 0.074345642 0.95064523 36 44 234 190 0 0 + 3600 0.085872341 0.9759514 35 45 238 192 0 1 + 3700 0.086427565 0.99843063 35 45 240 194 0 1 + 3800 0.076091357 0.98516844 32 48 252 203 0 1 + 3900 0.047187813 1.0063336 37 43 247 204 0 0 + 4000 0.068269223 1.0390369 35 45 248 203 0 0 + 4100 0.074209582 0.99912762 36 44 249 205 0 0 + 4200 0.087016078 1.050265 36 44 246 202 0 0 + 4300 0.081325479 1.0417103 35 45 245 200 0 0 + 4400 0.047345973 0.96517298 39 41 243 202 0 0 + 4500 0.041856955 0.94569673 38 42 245 203 0 0 + 4600 0.049588267 0.99046371 42 38 249 211 0 0 + 4700 0.043079897 1.0098538 43 37 245 208 0 0 + 4800 0.049122913 1.0229995 41 39 247 208 0 0 + 4900 0.059151797 1.0236679 36 44 249 205 0 0 + 5000 0.053806841 1.0308397 42 38 243 205 0 0 + 5100 0.053623833 1.0638841 39 41 246 205 0 0 + 5200 0.086215806 1.0027613 37 43 243 200 0 0 + 5300 0.031422797 1.0338154 38 42 245 203 0 0 + 5400 0.051341116 0.92205149 34 46 246 200 0 0 + 5500 0.039292708 0.97530704 32 48 251 203 0 0 + 5600 0.035215415 1.023123 33 47 246 199 0 0 + 5700 0.054553598 0.95833063 30 50 253 203 0 0 + 5800 0.035699456 1.0721613 37 43 248 205 0 0 + 5900 0.062426908 1.0612245 38 42 252 210 0 0 + 6000 0.056362902 1.0002968 36 44 248 204 0 0 + 6100 0.061550208 0.97270904 38 42 245 203 0 0 + 6200 0.051825485 0.98187623 36 44 253 209 0 0 + 6300 0.052137885 0.98906723 36 44 253 210 1 0 + 6400 0.068218075 1.0511584 36 44 256 212 0 0 + 6500 0.080167413 0.97270144 36 44 252 208 0 0 + 6600 0.052169204 1.0160108 41 39 249 210 0 0 + 6700 0.057313326 0.98033894 38 42 251 209 0 0 + 6800 0.073008094 0.96239565 35 45 256 211 0 0 + 6900 0.060159599 1.0063892 37 43 264 221 0 0 + 7000 0.061738744 1.0031443 39 41 259 218 0 0 + 7100 0.043263424 1.0425248 44 36 255 219 0 0 + 7200 0.052179167 0.99512151 39 41 261 220 0 0 + 7300 0.053258707 1.0171204 43 37 256 219 0 0 + 7400 0.026037532 0.93786837 45 35 259 224 0 0 + 7500 0.029731213 1.0172281 46 34 250 216 0 0 + 7600 0.023118288 0.95628439 42 38 262 224 0 0 + 7700 0.037021854 0.99991854 42 38 263 225 0 0 + 7800 0.050404736 1.0130826 40 40 260 220 0 0 + 7900 0.035658921 0.95772506 40 40 259 219 0 0 + 8000 0.034426806 1.0028052 40 40 254 214 0 0 + 8100 0.041427611 1.0347682 40 40 256 216 0 0 + 8200 0.05986843 0.9804614 38 42 262 220 0 0 + 8300 0.041419023 1.0613186 37 43 264 221 0 0 + 8400 0.065701758 1.0511531 40 40 256 216 0 0 + 8500 0.091954526 0.97190676 37 43 257 214 0 0 + 8600 0.056982532 1.017813 35 45 252 207 0 0 + 8700 0.075615111 1.0148527 29 51 263 212 0 0 + 8800 0.066070082 1.0259454 33 47 260 213 0 0 + 8900 0.055054194 1.0183535 37 43 247 204 0 0 + 9000 0.063070816 1.0266115 39 41 244 203 0 0 + 9100 0.10174156 0.99457684 34 46 246 200 0 0 + 9200 0.071667261 1.033159 33 47 249 202 0 0 + 9300 0.05520096 0.99821492 38 42 243 201 0 0 + 9400 0.050355422 0.99148522 37 43 243 200 0 0 + 9500 0.062314961 1.0042937 36 44 252 208 0 0 + 9600 0.061148899 1.0052132 37 43 254 211 0 0 + 9700 0.078695273 1.0175164 37 43 252 209 0 0 + 9800 0.067487202 1.0110138 35 45 258 213 0 0 + 9900 0.070340779 0.99640142 31 49 263 214 0 0 + 10000 0.037252172 0.99863894 32 48 259 211 0 0 +Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms + +Performance: 187484.206 tau/day, 433.991 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04 +Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11 +Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56 +Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89 +Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32 +Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02 +Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91 +Other | | 0.03479 | | | 0.15 + +Nlocal: 550.000 ave 550 max 550 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1023.00 ave 1023 max 1023 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 9644.00 ave 9644 max 9644 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 9644 +Ave neighs/atom = 17.534545 +Ave special neighs/atom = 0.85090909 +Neighbor list builds = 7576 +Dangerous builds = 0 +Total wall time: 0:00:23 \ No newline at end of file diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 314fe6146e..ef25a0c116 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,6 +53,7 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 +fix charge_regulation, Tine Curk and Jiaxing Yuan, tcurk5@gmail.com, 02 Feb 2021 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp new file mode 100644 index 0000000000..3bb9de1b27 --- /dev/null +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -0,0 +1,1335 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) +------------------------------------------------------------------------- */ +#include "fix_charge_regulation.h" +#include +#include +#include +#include "atom.h" +#include "atom_vec.h" +#include "molecule.h" +#include "update.h" +#include "modify.h" +#include "fix.h" +#include "comm.h" +#include "compute.h" +#include "group.h" +#include "domain.h" +#include "region.h" +#include "random_park.h" +#include "force.h" +#include "pair.h" +#include "bond.h" +#include "angle.h" +#include "dihedral.h" +#include "improper.h" +#include "kspace.h" +#include "math_extra.h" +#include "math_const.h" +#include "memory.h" +#include "error.h" +#include "neighbor.h" + +using namespace LAMMPS_NS; +using namespace FixConst; +using namespace MathConst; + +// large energy value used to signal overlap +#define MAXENERGYSIGNAL 1.0e100 +#define MAXENERGYTEST 1.0e50 +#define small 0.0000001 +#define PI 3.1415926 + +/* ---------------------------------------------------------------------- */ +Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + ngroups(0), groupstrings(NULL), + random_equal(NULL), random_unequal(NULL), + idftemp(NULL), ptype_ID(NULL) { + + // Region restrictions not yet implemented .. + + vector_flag = 1; + size_vector = 8; + global_freq = 1; + extvector = 0; + restart_global = 1; + time_depend = 1; + cr_nmax = 0; + overlap_flag = 0; + energy_stored = 0; + + // necessary to specify the free ion types + cation_type = utils::inumeric(FLERR, arg[3], false, lmp); + anion_type = utils::inumeric(FLERR, arg[4], false, lmp); + + // set defaults and read optional arguments + options(narg - 5, &arg[5]); + + if (nevery <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (nmc < 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (seed <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (cation_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (anion_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) + error->all(FLERR, + "Illegal fix charge_regulation command, multivalent cation/anion charges are allowed, " + "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); + + if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) + error->all(FLERR, "Illegal fix charge_regulation command"); + if (acid_type < 0) pmcmoves[0] = 0; + if (base_type < 0) pmcmoves[1] = 0; + // normalize + double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; + if (psum <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + pmcmoves[0] /= psum; + pmcmoves[1] /= psum; + pmcmoves[2] /= psum; + + force_reneighbor = 1; + next_reneighbor = update->ntimestep + 1; + random_equal = new RanPark(lmp, seed); + random_unequal = new RanPark(lmp, seed); + nacid_attempts = 0; + nacid_successes = 0; + nbase_attempts = 0; + nbase_successes = 0; + nsalt_attempts = 0; + nsalt_successes = 0; +} + +Fix_charge_regulation::~Fix_charge_regulation() { + + memory->destroy(ptype_ID); + + delete random_equal; + delete random_unequal; + + if (group) { + int igroupall = group->find("all"); + neighbor->exclusion_group_group_delete(exclusion_group, igroupall); + } +} + +int Fix_charge_regulation::setmask() { + int mask = 0; + mask |= PRE_EXCHANGE; + return mask; +} + +void Fix_charge_regulation::init() { + + triclinic = domain->triclinic; + + char *id_pe = (char *) "thermo_pe"; + int ipe = modify->find_compute(id_pe); + c_pe = modify->compute[ipe]; + + if (atom->molecule_flag) { + + int flag = 0; + for (int i = 0; i < atom->nlocal; i++) + if (atom->type[i] == cation_type || atom->type[i] == anion_type) + if (atom->molecule[i]) flag = 1; + int flagall = flag; + + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); + if (flagall && comm->me == 0) + error->all(FLERR, "Fix charge regulation cannot exchange individual atoms (ions) belonging to a molecule"); + } + + if (domain->dimension == 2) + error->all(FLERR, "Cannot use fix charge regulation in a 2d simulation"); + + // create a new group for interaction exclusions + // used for attempted atom deletions + // skip if already exists from previous init() + + if (!exclusion_group_bit) { + char **group_arg = new char *[4]; + + // create unique group name for atoms to be excluded + int len = strlen(id) + 30; + group_arg[0] = new char[len]; + sprintf(group_arg[0], "Fix_CR:exclusion_group:%s", id); + group_arg[1] = (char *) "subtract"; + group_arg[2] = (char *) "all"; + group_arg[3] = (char *) "all"; + group->assign(4, group_arg); + exclusion_group = group->find(group_arg[0]); + if (exclusion_group == -1) + error->all(FLERR, "Could not find fix CR exclusion group ID"); + exclusion_group_bit = group->bitmask[exclusion_group]; + + // neighbor list exclusion setup + // turn off interactions between group all and the exclusion group + + int narg = 4; + char **arg = new char *[narg];; + arg[0] = (char *) "exclude"; + arg[1] = (char *) "group"; + arg[2] = group_arg[0]; + arg[3] = (char *) "all"; + neighbor->modify_params(narg, arg); + delete[] group_arg[0]; + delete[] group_arg; + delete[] arg; + } + + // check that no deletable atoms are in atom->firstgroup + // deleting such an atom would not leave firstgroup atoms first + + if (atom->firstgroup >= 0) { + int *mask = atom->mask; + int firstgroupbit = group->bitmask[atom->firstgroup]; + + int flag = 0; + for (int i = 0; i < atom->nlocal; i++) + if ((mask[i] == groupbit) && (mask[i] && firstgroupbit)) flag = 1; + + int flagall; + MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); + + if (flagall) + error->all(FLERR, "Cannot do Fix charge regulation on atoms in atom_modify first group"); + } + + // construct group bitmask for all new atoms + // aggregated over all group keywords + + groupbitall = 1 | groupbit; + + for (int igroup = 0; igroup < ngroups; igroup++) { + int jgroup = group->find(groupstrings[igroup]); + if (jgroup == -1) + error->all(FLERR, "Could not find specified fix charge regulation group ID"); + groupbitall |= group->bitmask[jgroup]; + } +} + +void Fix_charge_regulation::pre_exchange() { + + if (next_reneighbor != update->ntimestep) return; + xlo = domain->boxlo[0]; + xhi = domain->boxhi[0]; + ylo = domain->boxlo[1]; + yhi = domain->boxhi[1]; + zlo = domain->boxlo[2]; + zhi = domain->boxhi[2]; + + if (triclinic) { + sublo = domain->sublo_lamda; + subhi = domain->subhi_lamda; + } else { + sublo = domain->sublo; + subhi = domain->subhi; + } + volume = domain->xprd * domain->yprd * domain->zprd; + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + energy_stored = energy_full(); + if (energy_stored > MAXENERGYTEST) + error->warning(FLERR, "Energy of old configuration in fix charge_regulation is > MAXENERGYTEST."); + + if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || + (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || + (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { + error->warning(FLERR, + "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + reaction_distance = 0; + } + // volume in units of (N_A * mol / liter) + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * pow(llength_unit_in_nm, 3) * 0.602214; + if (reaction_distance < small) { + vlocal_xrd = volume_rx; + } else { + vlocal_xrd = 4.0 * PI * pow(reaction_distance, 3) / 3.0 * pow(llength_unit_in_nm, 3) * 0.602214; + } + beta = 1.0 / (force->boltz * *target_temperature_tcp); + + // reinitialize counters + nacid_neutral = particle_number(acid_type, 0); + nacid_charged = particle_number(acid_type, -1); + nbase_neutral = particle_number(base_type, 0); + nbase_charged = particle_number(base_type, 1); + ncation = particle_number(cation_type, salt_charge[0]); + nanion = particle_number(anion_type, salt_charge[1]); + + + // Attempt exchanges + if (!only_salt_flag) { + + // Do charge regulation + for (int i = 0; i < nmc; i++) { + double rand_number = random_equal->uniform(); + if (rand_number < pmcmoves[0] / 2) { + forward_acid(); + nacid_attempts++; + } else if (rand_number < pmcmoves[0]) { + backward_acid(); + nacid_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1] / 2) { + forward_base(); + nbase_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1]) { + backward_base(); + nbase_attempts++; + } else if (rand_number < pmcmoves[0] + pmcmoves[1] + pmcmoves[2] / 2) { + forward_ions(); + nsalt_attempts++; + } else { + backward_ions(); + nsalt_attempts++; + } + } + } else { + // do only ion insertion, multivalent cation/anions are implemented + if (salt_charge[0] >= -salt_charge[1]) { + salt_charge_ratio = -salt_charge[0] / salt_charge[1]; + } else { + salt_charge_ratio = -salt_charge[1] / salt_charge[0]; + } + for (int i = 0; i < nmc; i++) { + double rand_number = random_equal->uniform(); + if (rand_number < 0.5) { + forward_ions_multival(); + nsalt_attempts++; + } else { + backward_ions_multival(); + nsalt_attempts++; + } + } + } + + // assign unique tags to newly inserted ions + if (add_tags_flag && atom->tag_enable) assign_tags(); + + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + next_reneighbor = update->ntimestep + nevery; +} + +void Fix_charge_regulation::forward_acid() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m2 = -1; + + m1 = get_random_particle(acid_type, 0, 0, dummyp); + if (npart_xrd != nacid_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nacid_neutral > 0) { + if (m1 >= 0) { + atom->q[m1] = -1; // assign negative charge to acid + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + npart_xrd2 = ncation; + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + npart_xrd2 = particle_number_xrd(cation_type, 1, reaction_distance, pos_all); + } + m2 = insert_particle(cation_type, 1, reaction_distance, pos_all); + factor = nacid_neutral * vlocal_xrd * pow(10, -pKa) + * (1 + pow(10, pH - pI_plus)) / ((1 + nacid_charged) * (1 + npart_xrd2)); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nacid_successes += 1; + ncation++; + nacid_charged++; + nacid_neutral--; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (m1 >= 0) { + atom->q[m1] = 0; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } + } +} + +void Fix_charge_regulation::backward_acid() { + + double energy_before = energy_stored; + double factor; + int mask_tmp; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(acid_type, -1, 0, dummyp); + if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nacid_charged > 0) { + if (m1 >= 0) { + atom->q[m1] = 0; + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + } + m2 = get_random_particle(cation_type, 1, reaction_distance, pos_all); + // note: npart_xrd changes everytime get_random_particle is called. + + if (npart_xrd > 0) { + if (m2 >= 0) { + atom->q[m2] = 0; + mask_tmp = atom->mask[m2]; // remember group bits. + atom->mask[m2] = exclusion_group_bit; + } + factor = (1 + nacid_neutral) * vlocal_xrd * pow(10, -pKa) + * (1 + pow(10, pH - pI_plus)) / (nacid_charged * npart_xrd); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + nacid_successes += 1; + atom->natoms--; + energy_stored = energy_after; + nacid_charged--; + nacid_neutral++; + ncation--; + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + energy_stored = energy_before; + if (m1 >= 0) { + atom->q[m1] = -1; + } + if (m2 >= 0) { + atom->q[m2] = 1; + atom->mask[m2] = mask_tmp; + } + } + } else { + if (m1 >= 0) { + atom->q[m1] = -1; + } + } + } +} + +void Fix_charge_regulation::forward_base() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(base_type, 0, 0, dummyp); + if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nbase_neutral > 0) { + if (m1 >= 0) { + atom->q[m1] = 1; // assign negative charge to acid + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + npart_xrd2 = nanion; + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + npart_xrd2 = particle_number_xrd(anion_type, -1, reaction_distance, pos_all); + } + factor = nbase_neutral * vlocal_xrd * pow(10, -pKb) + * (1 + pow(10, pKs - pH - pI_minus)) / + ((1 + nbase_charged) * (1 + npart_xrd2)); + m2 = insert_particle(anion_type, -1, reaction_distance, pos_all); + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nbase_successes += 1; + nbase_charged++; + nbase_neutral--; + nanion++; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (m1 >= 0) { + atom->q[m1] = 0; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } + } +} + +void Fix_charge_regulation::backward_base() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + int mask_tmp; + double pos[3]; + pos[0] = 0; + pos[1] = 0; + pos[2] = 0; // acid/base particle position + double pos_all[3]; + int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + + m1 = get_random_particle(base_type, 1, 0, dummyp); + if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + + if (nbase_charged > 0) { + if (m1 >= 0) { + atom->q[m1] = 0; + pos[0] = atom->x[m1][0]; + pos[1] = atom->x[m1][1]; + pos[2] = atom->x[m1][2]; + } + if (reaction_distance >= small) { + pos_all[0] = pos[0]; + pos_all[1] = pos[1]; + pos_all[2] = pos[2]; + MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); + } + m2 = get_random_particle(anion_type, -1, reaction_distance, pos_all); + + if (npart_xrd > 0) { + if (m2 >= 0) { + atom->q[m2] = 0; + mask_tmp = atom->mask[m2]; // remember group bits. + atom->mask[m2] = exclusion_group_bit; + } + factor = (1 + nbase_neutral) * vlocal_xrd * pow(10, -pKb) + * (1 + pow(10, pKs - pH - pI_minus)) / (nbase_charged * npart_xrd); + + double energy_after = energy_full(); + + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + nbase_successes += 1; + atom->natoms--; + energy_stored = energy_after; + nbase_charged--; + nbase_neutral++; + nanion--; + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + energy_stored = energy_before; + if (m1 >= 0) { + atom->q[m1] = 1; + } + if (m2 >= 0) { + atom->q[m2] = -1; + atom->mask[m2] = mask_tmp; + } + } + } else { + if (m1 >= 0) { + atom->q[m1] = 1; + } + } + } +} + +void Fix_charge_regulation::forward_ions() { + + double energy_before = energy_stored; + double factor; + double *dummyp; + int m1 = -1, m2 = -1; + factor = volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) + * (pow(10, -pKs + pH) + pow(10, -pI_minus)) / + ((1 + ncation) * (1 + nanion)); + + m1 = insert_particle(cation_type, +1, 0, dummyp); + m2 = insert_particle(anion_type, -1, 0, dummyp); + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + ncation++; + nanion++; + } else { + energy_stored = energy_before; + atom->natoms--; + if (m1 >= 0) { + atom->nlocal--; + } + atom->natoms--; + if (m2 >= 0) { + atom->nlocal--; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } +} + + +void Fix_charge_regulation::backward_ions() { + + double energy_before = energy_stored; + double factor; + int mask1_tmp, mask2_tmp; + double *dummyp; // dummy pointer + int m1 = -1, m2 = -1; + + m1 = get_random_particle(cation_type, +1, 0, dummyp); + if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (ncation > 0) { + m2 = get_random_particle(anion_type, -1, 0, dummyp); + if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (nanion > 0) { + + // attempt deletion + + if (m1 >= 0) { + atom->q[m1] = 0; + mask1_tmp = atom->mask[m1]; + atom->mask[m1] = exclusion_group_bit; + } + if (m2 >= 0) { + atom->q[m2] = 0; + mask2_tmp = atom->mask[m2]; + atom->mask[m2] = exclusion_group_bit; + } + factor = (volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) * + (pow(10, -pKs + pH) + pow(10, -pI_minus))) / (ncation * nanion); + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + ncation--; + nanion--; + + // ions must be deleted in order, otherwise index m could change upon the first deletion + atom->natoms -= 2; + if (m1 > m2) { + if (m1 >= 0) { + atom->avec->copy(atom->nlocal - 1, m1, 1); + atom->nlocal--; + } + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + } else { + if (m2 >= 0) { + atom->avec->copy(atom->nlocal - 1, m2, 1); + atom->nlocal--; + } + if (m1 >= 0) { + atom->avec->copy(atom->nlocal - 1, m1, 1); + atom->nlocal--; + } + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + + } else { + energy_stored = energy_before; + + // reassign original charge and mask + if (m1 >= 0) { + atom->q[m1] = 1; + atom->mask[m1] = mask1_tmp; + } + if (m2 >= 0) { + atom->q[m2] = -1; + atom->mask[m2] = mask2_tmp; + } + } + } else { + // reassign original charge and mask + if (m1 >= 0) { + atom->q[m1] = 1; + atom->mask[m1] = mask1_tmp; + } + } + } +} + +void Fix_charge_regulation::forward_ions_multival() { + + double energy_before = energy_stored; + double factor = 1; + double *dummyp; + int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted + + if (salt_charge[0] <= -salt_charge[1]) { + // insert one anion and (salt_charge_ratio) cations + + mm[0] = insert_particle(anion_type, salt_charge[1], 0, dummyp); + factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion); + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = insert_particle(cation_type, salt_charge[0], 0, dummyp); + factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation + i); + } + } else { + // insert one cation and (salt_charge_ratio) anions + + mm[0] = insert_particle(cation_type, salt_charge[0], 0, dummyp); + factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation); + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = insert_particle(anion_type, salt_charge[1], 0, dummyp); + factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion + i); + } + } + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + nsalt_successes += 1; + + if (salt_charge[0] <= -salt_charge[1]) { + ncation += salt_charge_ratio; + nanion++; + } else { + nanion += salt_charge_ratio; + ncation++; + } + } else { + energy_stored = energy_before; + + // delete inserted ions + for (int i = 0; i < salt_charge_ratio + 1; i++) { + atom->natoms--; + if (mm[i] >= 0) { + atom->nlocal--; + } + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + } +} + +void Fix_charge_regulation::backward_ions_multival() { + + double energy_before = energy_stored; + double factor = 1; + double *dummyp; // dummy pointer + int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions + double qq[salt_charge_ratio + 1]; // charge array for all deleted ions + int mask_tmp[salt_charge_ratio + 1]; // temporary mask array + + if (salt_charge[0] <= -salt_charge[1]) { + // delete one anion and (salt_charge_ratio) cations + if (ncation < salt_charge_ratio || nanion < 1) return; + + mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); + if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_minus) / (nanion); + if (mm[0] >= 0) { + qq[0] = atom->q[mm[0]]; + atom->q[mm[0]] = 0; + mask_tmp[0] = atom->mask[mm[0]]; + atom->mask[mm[0]] = exclusion_group_bit; + } + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); + if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_plus) / (ncation - i); + if (mm[i + 1] >= 0) { + qq[i + 1] = atom->q[mm[i + 1]]; + atom->q[mm[i + 1]] = 0; + mask_tmp[i + 1] = atom->mask[mm[i + 1]]; + atom->mask[mm[i + 1]] = exclusion_group_bit; + } + } + } else { + // delete one cation and (salt_charge_ratio) anions + + if (nanion < salt_charge_ratio || ncation < 1) return; + mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); + if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + factor *= volume_rx * pow(10, -pI_plus) / (ncation); + if (mm[0] >= 0) { + qq[0] = atom->q[mm[0]]; + atom->q[mm[0]] = 0; + mask_tmp[0] = atom->mask[mm[0]]; + atom->mask[mm[0]] = exclusion_group_bit; + } + for (int i = 0; i < salt_charge_ratio; i++) { + mm[i + 1] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); + if (npart_xrd != nanion - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (mm[i + 1] >= 0) { + qq[i + 1] = atom->q[mm[i + 1]]; + atom->q[mm[i + 1]] = 0; + mask_tmp[i + 1] = atom->mask[mm[i + 1]]; + atom->mask[mm[i + 1]] = exclusion_group_bit; + } + factor *= volume_rx * pow(10, -pI_minus) / (nanion - i); + } + } + + // attempt deletion + + double energy_after = energy_full(); + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < (1.0 / factor) * exp(beta * (energy_before - energy_after))) { + energy_stored = energy_after; + + atom->natoms -= 1 + salt_charge_ratio; + // ions must be deleted in order, otherwise index m could change upon the first deletion + for (int i = 0; i < salt_charge_ratio + 1; i++) { + // get max mm value, poor N^2 scaling, but charge ratio is a small number (2 or 3). + int maxmm = -1, jmaxm = -1; + for (int j = 0; j < salt_charge_ratio + 1; j++) { + if (mm[j] > maxmm) { + maxmm = mm[j]; + jmaxm = j; + } + } + if (maxmm < 0) { + break; // already deleted all particles in this thread + } else { + // delete particle maxmm + atom->avec->copy(atom->nlocal - 1, maxmm, 1); + atom->nlocal--; + mm[jmaxm] = -1; + } + } + + // update indices + nsalt_successes += 1; + if (salt_charge[0] <= -salt_charge[1]) { + ncation -= salt_charge_ratio; + nanion--; + } else { + nanion -= salt_charge_ratio; + ncation--; + } + if (force->kspace) force->kspace->qsum_qsq(); + if (force->pair->tail_flag) force->pair->reinit(); + + } else { + energy_stored = energy_before; + + // reassign original charge and mask + for (int i = 0; i < salt_charge_ratio + 1; i++) { + if (mm[i] >= 0) { + atom->q[mm[i]] = qq[i]; + atom->mask[mm[i]] = mask_tmp[i]; + } + } + } +} + +int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, double *target) { + + // insert a particle of type (ptype) with charge (charge) within distance (rd) of (target) + + double coord[3]; + int m = -1; + if (rd < small) { + coord[0] = xlo + random_equal->uniform() * (xhi - xlo); + coord[1] = ylo + random_equal->uniform() * (yhi - ylo); + coord[2] = zlo + random_equal->uniform() * (zhi - zlo); + } else { + double radius = reaction_distance * random_equal->uniform(); + double theta = random_equal->uniform() * PI; + double phi = random_equal->uniform() * 2 * PI; + coord[0] = target[0] + radius * sin(theta) * cos(phi); + coord[1] = target[1] + radius * sin(theta) * sin(phi); + coord[2] = target[2] + radius * cos(theta); + coord[0] = coord[0] - floor(1.0 * (coord[0] - xlo) / (xhi - xlo)) * (xhi - xlo); + coord[1] = coord[1] - floor(1.0 * (coord[1] - ylo) / (yhi - ylo)) * (yhi - ylo); + coord[2] = coord[2] - floor(1.0 * (coord[2] - zlo) / (zhi - zlo)) * (zhi - zlo); + } + + if (coord[0] >= sublo[0] && coord[0] < subhi[0] && + coord[1] >= sublo[1] && coord[1] < subhi[1] && + coord[2] >= sublo[2] && coord[2] < subhi[2]) { + atom->avec->create_atom(ptype, coord); + m = atom->nlocal - 1; + atom->mask[m] = groupbitall; + + sigma = sqrt(force->boltz * *target_temperature_tcp / atom->mass[ptype] / force->mvv2e); + atom->v[m][0] = random_unequal->gaussian() * sigma; + atom->v[m][1] = random_unequal->gaussian() * sigma; + atom->v[m][2] = random_unequal->gaussian() * sigma; + atom->q[m] = charge; + modify->create_attribute(m); + + } + atom->nghost = 0; + comm->borders(); + atom->natoms++; + return m; +} + +int Fix_charge_regulation::get_random_particle(int ptype, double charge, double rd, double *target) { + + // returns a randomly chosen particle of type (ptype) with charge (charge) + // chosen among particles within distance (rd) of (target) + + int nlocal = atom->nlocal; + + // expand memory, if necessary + if (atom->nmax > cr_nmax) { + memory->sfree(ptype_ID); + cr_nmax = atom->nmax; + ptype_ID = (int *) memory->smalloc(cr_nmax * sizeof(int), + "CR: local_atom_list"); + } + + int count_local, count_global, count_before; + int m = -1; + count_local = 0; + count_global = 0; + count_before = 0; + + if (rd < small) { //reaction_distance < small: No geometry constraint on random particle choice + for (int i = 0; i < nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && + atom->mask[i] != exclusion_group_bit) { + ptype_ID[count_local] = i; + count_local++; + } + } + } else { + double dx, dy, dz, distance_check; + for (int i = 0; i < nlocal; i++) { + dx = fabs(atom->x[i][0] - target[0]); + dx -= static_cast(1.0 * dx / (xhi - xlo) + 0.5) * (xhi - xlo); + dy = fabs(atom->x[i][1] - target[1]); + dy -= static_cast(1.0 * dy / (yhi - ylo) + 0.5) * (yhi - ylo); + dz = fabs(atom->x[i][2] - target[2]); + dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); + distance_check = dx * dx + dy * dy + dz * dz; + if ((distance_check < rd * rd) && atom->type[i] == ptype && + fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + ptype_ID[count_local] = i; + count_local++; + } + } + } + count_global = count_local; + count_before = count_local; + MPI_Allreduce(&count_local, &count_global, 1, MPI_INT, MPI_SUM, world); + MPI_Scan(&count_local, &count_before, 1, MPI_INT, MPI_SUM, world); + count_before -= count_local; + + npart_xrd = count_global; // save the number of particles, for use in MC acceptance ratio + if (count_global > 0) { + const int ID_global = floor(random_equal->uniform() * count_global); + if ((ID_global >= count_before) && (ID_global < (count_before + count_local))) { + const int ID_local = ID_global - count_before; + m = ptype_ID[ID_local]; // local ID of the chosen particle + return m; + } + } + return -1; +} + +double Fix_charge_regulation::energy_full() { + int imolecule; + if (triclinic) domain->x2lamda(atom->nlocal); + domain->pbc(); + comm->exchange(); + atom->nghost = 0; + comm->borders(); + if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); + if (modify->n_pre_neighbor) modify->pre_neighbor(); + neighbor->build(1); + int eflag = 1; + int vflag = 0; + if (overlap_flag) { + int overlaptestall; + int overlaptest = 0; + double delx, dely, delz, rsq; + double **x = atom->x; + tagint *molecule = atom->molecule; + int nall = atom->nlocal + atom->nghost; + for (int i = 0; i < atom->nlocal; i++) { + for (int j = i + 1; j < nall; j++) { + delx = x[i][0] - x[j][0]; + dely = x[i][1] - x[j][1]; + delz = x[i][2] - x[j][2]; + rsq = delx * delx + dely * dely + delz * delz; + if (rsq < overlap_cutoffsq) { + overlaptest = 1; + break; + } + } + if (overlaptest) break; + } + overlaptestall = overlaptest; + MPI_Allreduce(&overlaptest, &overlaptestall, 1, + MPI_INT, MPI_MAX, world); + if (overlaptestall) return MAXENERGYSIGNAL; + } + size_t nbytes = sizeof(double) * (atom->nlocal + atom->nghost); + if (nbytes) memset(&atom->f[0][0], 0, 3 * nbytes); + + if (modify->n_pre_force) modify->pre_force(vflag); + + if (force->pair) force->pair->compute(eflag, vflag); + + if (atom->molecular) { + if (force->bond) force->bond->compute(eflag, vflag); + if (force->angle) force->angle->compute(eflag, vflag); + if (force->dihedral) force->dihedral->compute(eflag, vflag); + if (force->improper) force->improper->compute(eflag, vflag); + } + + if (force->kspace) force->kspace->compute(eflag, vflag); + + if (modify->n_post_force) modify->post_force(vflag); + if (modify->n_end_of_step) modify->end_of_step(); + update->eflag_global = update->ntimestep; + double total_energy = c_pe->compute_scalar(); + return total_energy; +} + +int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { + + int count = 0; + if (rd < small) { + for (int i = 0; i < atom->nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + count++; + } + } else { + double dx, dy, dz, distance_check; + for (int i = 0; i < atom->nlocal; i++) { + dx = fabs(atom->x[i][0] - target[0]); + dx -= static_cast(1.0 * dx / (xhi - xlo) + 0.5) * (xhi - xlo); + dy = fabs(atom->x[i][1] - target[1]); + dy -= static_cast(1.0 * dy / (yhi - ylo) + 0.5) * (yhi - ylo); + dz = fabs(atom->x[i][2] - target[2]); + dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); + distance_check = dx * dx + dy * dy + dz * dz; + if ((distance_check < rd * rd) && atom->type[i] == ptype && + fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + count++; + } + } + } + int count_sum = count; + MPI_Allreduce(&count, &count_sum, 1, MPI_INT, MPI_SUM, world); + return count_sum; +} + +int Fix_charge_regulation::particle_number(int ptype, double charge) { + + int count = 0; + for (int i = 0; i < atom->nlocal; i++) { + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + count = count + 1; + } + int count_sum = count; + MPI_Allreduce(&count, &count_sum, 1, MPI_INT, MPI_SUM, world); + return count_sum; +} + +double Fix_charge_regulation::compute_vector(int n) { + double count_temp = 0; + if (n == 0) { + return nacid_attempts + nbase_attempts + nsalt_attempts; + } else if (n == 1) { + return nacid_successes + nbase_successes + nsalt_successes; + } else if (n == 2) { + return particle_number(acid_type, 0); + } else if (n == 3) { + return particle_number(acid_type, -1); + } else if (n == 4) { + return particle_number(base_type, 0); + } else if (n == 5) { + return particle_number(base_type, 1); + } else if (n == 6) { + return particle_number(cation_type, salt_charge[0]); + } else if (n == 7) { + return particle_number(anion_type, salt_charge[1]); + } + return 0.0; +} + +void Fix_charge_regulation::setThermoTemperaturePointer() { + int ifix = -1; + ifix = modify->find_fix(idftemp); + if (ifix == -1) { + error->all(FLERR, + "Fix charge regulation regulation could not find a temperature fix id provided by tempfixid\n"); + } + Fix *temperature_fix = modify->fix[ifix]; + int dim; + target_temperature_tcp = (double *) temperature_fix->extract("t_target", dim); + +} + +void Fix_charge_regulation::assign_tags() { + // Assign tags to ions with zero tags + if (atom->tag_enable) { + tagint *tag = atom->tag; + tagint maxtag_all = 0; + tagint maxtag = 0; + for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag, tag[i]); + maxtag_all = maxtag; + MPI_Allreduce(&maxtag, &maxtag_all, 1, MPI_LMP_TAGINT, MPI_MAX, world); + if (maxtag_all >= MAXTAGINT) + error->all(FLERR, "New atom IDs exceed maximum allowed ID"); + + tagint notag = 0; + tagint notag_all; + for (int i = 0; i < atom->nlocal; i++) + if (tag[i] == 0 && (atom->type[i] == cation_type || atom->type[i] == anion_type))notag++; + notag_all = notag; + MPI_Allreduce(¬ag, ¬ag_all, 1, MPI_LMP_TAGINT, MPI_SUM, world); + if (notag_all >= MAXTAGINT) + error->all(FLERR, "New atom IDs exceed maximum allowed ID"); + + tagint notag_sum = notag; + MPI_Scan(¬ag, ¬ag_sum, 1, MPI_LMP_TAGINT, MPI_SUM, world); + // itag = 1st new tag that my untagged atoms should use + + tagint itag = maxtag_all + notag_sum - notag + 1; + for (int i = 0; i < atom->nlocal; i++) { + if (tag[i] == 0 && (atom->type[i] == cation_type || atom->type[i] == anion_type)) { + tag[i] = itag++; + } + } + if (atom->map_style) atom->map_init(); + atom->nghost = 0; + comm->borders(); + } +} + +/* ---------------------------------------------------------------------- + parse input options +------------------------------------------------------------------------- */ + +void Fix_charge_regulation::options(int narg, char **arg) { + if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); + + // defaults + + pH = 7.0; + pI_plus = 100; + pI_minus = 100; + acid_type = -1; + base_type = -1; + pKa = 100; + pKb = 100; + pKs = 14.0; + nevery = 100; + nmc = 100; + pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = 0.33; + llength_unit_in_nm= 0.72; + + reservoir_temperature = 1.0; + reaction_distance = 0; + seed = 12345; + target_temperature_tcp = &reservoir_temperature; + add_tags_flag = false; + only_salt_flag = false; + salt_charge[0] = 1; // cation charge + salt_charge[1] = -1; // anion charge + + exclusion_group = 0; + exclusion_group_bit = 0; + ngroups = 0; + int ngroupsmax = 0; + groupstrings = NULL; + + int iarg = 0; + while (iarg < narg) { + + if (strcmp(arg[iarg], "lunit_nm") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + llength_unit_in_nm = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "acid_type") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + acid_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "base_type") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + base_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pH") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pH = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pIp") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pI_plus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pIm") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pI_minus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKa") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKa = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKb") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKb = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + + } else if (strcmp(arg[iarg], "temp") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + reservoir_temperature = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pKs") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pKs = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "tempfixid") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + int n = strlen(arg[iarg + 1]) + 1; + delete[] idftemp; + idftemp = new char[n]; + strcpy(idftemp, arg[iarg + 1]); + setThermoTemperaturePointer(); + iarg += 2; + } else if (strcmp(arg[iarg], "rxd") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + reaction_distance = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || + (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || + (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { + error->warning(FLERR, + "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + reaction_distance = 0; + } + iarg += 2; + } else if (strcmp(arg[iarg], "nevery") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "nmc") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + nmc = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "pmcmoves") == 0) { + if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + pmcmoves[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp); + pmcmoves[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + pmcmoves[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + iarg += 4; + } else if (strcmp(arg[iarg], "seed") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + seed = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); + iarg += 2; + } else if (strcmp(arg[iarg], "tag") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (strcmp(arg[iarg + 1], "yes") == 0) { + add_tags_flag = true; + } else if (strcmp(arg[iarg + 1], "no") == 0) { + add_tags_flag = false; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + iarg += 2; + } else if (strcmp(arg[iarg], "onlysalt") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (strcmp(arg[iarg + 1], "yes") == 0) { + only_salt_flag = true; + // need to specify salt charge + if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); + salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); + if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > small) + error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); + if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > small) + error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); + iarg += 4; + } else if (strcmp(arg[iarg + 1], "no") == 0) { + only_salt_flag = false; + iarg += 2; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + + } else if (strcmp(arg[iarg], "group") == 0) { + if (iarg + 2 > narg) error->all(FLERR, "Illegal fix fix charge regulation command"); + if (ngroups >= ngroupsmax) { + ngroupsmax = ngroups + 1; + groupstrings = (char **) + memory->srealloc(groupstrings, + ngroupsmax * sizeof(char *), + "fix_charge_regulation:groupstrings"); + } + int n = strlen(arg[iarg + 1]) + 1; + groupstrings[ngroups] = new char[n]; + strcpy(groupstrings[ngroups], arg[iarg + 1]); + ngroups++; + iarg += 2; + } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } +} + +/* ---------------------------------------------------------------------- + memory usage of local atom-based arrays +------------------------------------------------------------------------- */ + +double Fix_charge_regulation::memory_usage() { + double bytes = cr_nmax * sizeof(int); + return bytes; +} diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h new file mode 100644 index 0000000000..280a6c0d49 --- /dev/null +++ b/src/USER-MISC/fix_charge_regulation.h @@ -0,0 +1,117 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Tine Curk (curk@northwestern.edu) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(charge_regulation,Fix_charge_regulation) + +#else + +#ifndef LMP_FIX_charge_regulation_H +#define LMP_FIX_charge_regulation_H + +#include "fix.h" + +namespace LAMMPS_NS { + + class Fix_charge_regulation : public Fix { + public: + Fix_charge_regulation(class LAMMPS *, int, char **); + ~Fix_charge_regulation(); + int setmask(); + void init(); + void pre_exchange(); + void forward_acid(); + void backward_acid(); + void forward_base(); + void backward_base(); + void forward_ions(); + void forward_ions_multival(); + void backward_ions(); + void backward_ions_multival(); + int get_random_particle(int, double, double, double *); + int insert_particle(int, double, double, double *); + double energy_full(); + int particle_number(int, double); + int particle_number_xrd(int, double, double, double *); + double compute_vector(int n); + void assign_tags(); + void options(int, char **); + void setThermoTemperaturePointer(); + double memory_usage(); + + private: + int exclusion_group, exclusion_group_bit; + int ngcmc_type, nevery, seed; + int nmc; // mc moves per cycle + double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l + double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials + double pmcmoves[3]; // mc move attempt probability, acid, base, salt; and comulative + double pmcc; // mc move cumulative attempt probability + int npart_xrd; // # of particles (ions) within xrd + int npart_xrd2; // # of particles (ions) within xrd + double vlocal_xrd; // # local volume within xrd + bool only_salt_flag; // true if performing only salt insertion/deletion, no acid/base dissociation. + bool add_tags_flag; // true if each inserted atom gets its unique atom tag + int groupbitall; // group bitmask for inserted atoms + int ngroups; // number of group-ids for inserted atoms + char **groupstrings; // list of group-ids for inserted atoms + // counters + unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes; + int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts + int cr_nmax; // max number of local particles + double reservoir_temperature; + double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume + int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion + int salt_charge_ratio; + double xlo, xhi, ylo, yhi, zlo, zhi; // box size + double energy_stored; // full energy of old/current configuration + int triclinic; // 0 = orthog box, 1 = triclinic + double *sublo, *subhi; // triclinic size + int *ptype_ID; // particle ID array + double overlap_cutoffsq; // square distance cutoff for overlap + int overlap_flag; + int acid_type, cation_type, base_type, anion_type; // reacting atom types + int reaction_distance_flag; + double reaction_distance; // max radial distance for atom insertion + + + class Pair *pair; + class Compute *c_pe; // energy compute pointer + class RanPark *random_equal; // random number generator + class RanPark *random_unequal; // random number generator + char *idftemp; // pointer to the temperature fix + + double *target_temperature_tcp; // current temperature of the thermostat + + }; +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +Self-explanatory. + +*/ From 6d862569ea8ab8f44e68207bd41adfe8a28a5e2b Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:24:55 -0600 Subject: [PATCH 006/100] Updated emails --- src/USER-MISC/fix_charge_regulation.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index 280a6c0d49..f0151390e6 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -12,7 +12,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Tine Curk (curk@northwestern.edu) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) + Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ #ifdef FIX_CLASS From d62ba49f1a431b920cb29e0dce8f23b4a9815f26 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 16:57:00 -0600 Subject: [PATCH 007/100] added minor comments --- src/USER-MISC/fix_charge_regulation.h | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index f0151390e6..e64ea6b63f 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -60,7 +60,7 @@ namespace LAMMPS_NS { int nmc; // mc moves per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials - double pmcmoves[3]; // mc move attempt probability, acid, base, salt; and comulative + double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange double pmcc; // mc move cumulative attempt probability int npart_xrd; // # of particles (ions) within xrd int npart_xrd2; // # of particles (ions) within xrd @@ -70,6 +70,7 @@ namespace LAMMPS_NS { int groupbitall; // group bitmask for inserted atoms int ngroups; // number of group-ids for inserted atoms char **groupstrings; // list of group-ids for inserted atoms + // counters unsigned long int nacid_attempts, nacid_successes, nbase_attempts, nbase_successes, nsalt_attempts, nsalt_successes; int nacid_neutral, nacid_charged, nbase_neutral, nbase_charged, ncation, nanion; // particle type counts @@ -77,7 +78,7 @@ namespace LAMMPS_NS { double reservoir_temperature; double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion - int salt_charge_ratio; + int salt_charge_ratio; // charge ration when using multivalent ion exchange double xlo, xhi, ylo, yhi, zlo, zhi; // box size double energy_stored; // full energy of old/current configuration int triclinic; // 0 = orthog box, 1 = triclinic @@ -86,16 +87,15 @@ namespace LAMMPS_NS { double overlap_cutoffsq; // square distance cutoff for overlap int overlap_flag; int acid_type, cation_type, base_type, anion_type; // reacting atom types - int reaction_distance_flag; - double reaction_distance; // max radial distance for atom insertion + int reaction_distance_flag; // radial reaction restriction flag + double reaction_distance; // max radial distance from acid/base for ion insertion class Pair *pair; - class Compute *c_pe; // energy compute pointer + class Compute *c_pe; // energy compute pointer class RanPark *random_equal; // random number generator class RanPark *random_unequal; // random number generator - char *idftemp; // pointer to the temperature fix - + char *idftemp; // pointer to the temperature fix double *target_temperature_tcp; // current temperature of the thermostat }; From 0bc31fad0922d3f3f76ec5fdd894714112a75826 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 17:03:15 -0600 Subject: [PATCH 008/100] header file minor cleanup --- src/USER-MISC/fix_charge_regulation.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index e64ea6b63f..d698bd6bb7 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -56,8 +56,8 @@ namespace LAMMPS_NS { private: int exclusion_group, exclusion_group_bit; - int ngcmc_type, nevery, seed; - int nmc; // mc moves per cycle + int nevery, seed; // begin MC cycle every nevery MD timesteps, random seed + int nmc; // MC move attempts per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange From 2f5588733bf752bef213e0ea47e6c04cc9516df1 Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 18:47:04 -0600 Subject: [PATCH 009/100] fixed doc Latex error --- doc/src/fix_charge_regulation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index 585761e8a9..d2384fdc13 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -70,7 +70,7 @@ The last type of reaction performs grand canonical MC exchange of ion pairs with In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. -Here we provide several practical examples for modeling charge regulation effects in solvated systems. +Here we provide several practical examples for modeling charge regulation effects in solvated systems. An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file .. code-block:: LAMMPS From 4421843604c090ef8e776ca32bdab2a6da74f33b Mon Sep 17 00:00:00 2001 From: tc387 Date: Fri, 5 Feb 2021 19:00:33 -0600 Subject: [PATCH 010/100] fixed Latex doc error #2 --- doc/src/fix_charge_regulation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index d2384fdc13..a98288eb51 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -106,7 +106,7 @@ If neither the acid or the base type is specified, for example, the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. -The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. +The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: From 60113a6ddf92566d4eee3ba03dc960795f1471c5 Mon Sep 17 00:00:00 2001 From: tc387 Date: Wed, 10 Feb 2021 13:24:30 -0600 Subject: [PATCH 011/100] Applied edits/optimizations suggested by Axel. Further simplifified/fixed MC acceptance equations, few clarifications to documentation. --- doc/src/fix_charge_regulation.rst | 38 ++- examples/USER/misc/charge_regulation/README | 5 +- .../USER/misc/charge_regulation/in_acid.chreg | 7 +- .../misc/charge_regulation/in_polymer.chreg | 12 +- src/USER-MISC/fix_charge_regulation.cpp | 282 ++++++++++-------- src/USER-MISC/fix_charge_regulation.h | 17 +- 6 files changed, 193 insertions(+), 168 deletions(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index a98288eb51..cb9f55c7cd 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -1,22 +1,18 @@ -.. Yuan documentation master file, created by - sphinx-quickstart on Sat Jan 30 14:06:22 2021. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - tc387: Multiple text additions/changes, Feb 2 2021 -.. index:: fix fix_charge_regulation +.. index:: fix charge/regulation -fix_charge_regulation command +fix charge/regulation command ============================= + Syntax """""" .. parsed-literal:: - fix ID group-ID charge_regulation cation_type anion_type keyword value(s) + fix ID group-ID charge/regulation cation_type anion_type keyword value(s) * ID, group-ID are documented in fix command -* charge_regulation = style name of this fix command +* charge/regulation = style name of this fix command * cation_type = atom type of free cations * anion_type = atom type of free anions @@ -51,9 +47,9 @@ Examples """""""" .. code-block:: LAMMPS - fix chareg all charge_regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT - fix chareg all charge_regulation 1 2 pIp 3 pIm 3 tempfixid fT tag yes onlysalt yes 2 -1 + fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 Description """"""""""" @@ -75,7 +71,7 @@ An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\ .. code-block:: LAMMPS - fix acid_reaction all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 + fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. @@ -85,7 +81,7 @@ participate in ionization reactions, which can be easily achieved via .. code-block:: LAMMPS - fix acid_reaction all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 + fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. @@ -94,14 +90,14 @@ where particles of atom type 4 and 5 are the salt cations and anions, both at ch .. code-block:: LAMMPS - fix base_reaction all charge_regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 + fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If neither the acid or the base type is specified, for example, .. code-block:: LAMMPS - fix salt_reaction all charge_regulation 4 5 pIp 2.0 pIm 2.0 + fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0 the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. @@ -119,7 +115,7 @@ Note that LAMMPS implicitly assumes a constant number of particles (degrees of f The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length -must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.72nm). For example, in the dilute ideal solution limit, the concentration of free ions +must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.71nm). For example, in the dilute ideal solution limit, the concentration of free ions will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. @@ -138,14 +134,14 @@ The *group* keyword can be used to add inserted particles to a specific group-ID Output """""" -This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global cumulative quantities: +This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global quantities: * 1 = cumulative MC attempts * 2 = cumulative MC successes * 3 = current # of neutral acid atoms * 4 = current # of -1 charged acid atoms * 5 = current # of neutral base atoms -* 6 = current # of +1 charged acid atoms +* 6 = current # of +1 charged base atoms * 7 = current # of free cations * 8 = current # of free anions @@ -157,6 +153,8 @@ See the :doc:`Build package ` doc page for more info. The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. +All interaction potentials used must be continuous, otherwise the MD integration and the particle exchange MC moves do not correspond to the same equilibrium ensemble. For example, if an lj/cut pair style is used, the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. + Note: Region restrictions are not yet implemented. Related commands @@ -167,7 +165,7 @@ Related commands Default """"""" -pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = -1; base_type = -1; lunit_nm = 0.72; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 2345; tag = no; onlysalt = no, pmcmoves = 0.33 0.33 0.33, group-ID = all +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = [1/3, 1/3, 1/3], group-ID = all ---------- @@ -181,4 +179,4 @@ pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs=14.0; acid_type = .. _Landsgesell: -**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, “Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning,” Macromolecules 53, 3007–3020 (2020). +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007–3020 (2020). diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README index e0be86d7e4..5666d6d025 100644 --- a/examples/USER/misc/charge_regulation/README +++ b/examples/USER/misc/charge_regulation/README @@ -2,6 +2,7 @@ This directory has two input scripts that illustrates how to use fix charge_regu The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. -The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion -Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. +The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and monovalent salt chemical potential pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion +Of a proton [type4] and salt anion [type 3]. +The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in_acid.chreg index 32beeda732..73a40f7389 100644 --- a/examples/USER/misc/charge_regulation/in_acid.chreg +++ b/examples/USER/misc/charge_regulation/in_acid.chreg @@ -24,7 +24,7 @@ pair_style lj/cut/coul/long ${cut_lj} ${cut_long} pair_coeff * * 1.0 1.0 ${cut_lj} # charges kspace_style ewald 1.0e-3 dielectric 1.0 -pair_modify shift no +pair_modify shift yes ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### fix fnve all nve @@ -33,8 +33,9 @@ compute_modify dtemp dynamic yes fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -fix chareg all charge_regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT thermo 100 thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +log log_acid.lammps timestep 0.005 -run 10000 +run 20000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg index 4dc72a8156..e35ba28661 100644 --- a/examples/USER/misc/charge_regulation/in_polymer.chreg +++ b/examples/USER/misc/charge_regulation/in_polymer.chreg @@ -14,7 +14,7 @@ velocity all create 1.0 8008 loop geom pair_style lj/cut/coul/long 1.122462 20 pair_coeff * * 1.0 1.0 1.122462 # charges kspace_style pppm 1.0e-3 -pair_modify shift no +pair_modify shift yes dielectric 1.0 ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### @@ -24,12 +24,14 @@ compute_modify dtemp dynamic yes fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -fix chareg1 all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 -fix chareg2 all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 -fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 thermo 100 # print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] +log log_polymer.lammps + timestep 0.005 -run 10000 +run 20000 diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 3bb9de1b27..c43a509f61 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -15,50 +15,56 @@ Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ #include "fix_charge_regulation.h" -#include -#include -#include + +#include "angle.h" #include "atom.h" #include "atom_vec.h" -#include "molecule.h" -#include "update.h" -#include "modify.h" -#include "fix.h" +#include "bond.h" #include "comm.h" #include "compute.h" -#include "group.h" -#include "domain.h" -#include "region.h" -#include "random_park.h" -#include "force.h" -#include "pair.h" -#include "bond.h" -#include "angle.h" #include "dihedral.h" +#include "domain.h" +#include "error.h" +#include "fix.h" +#include "force.h" +#include "group.h" #include "improper.h" #include "kspace.h" -#include "math_extra.h" #include "math_const.h" +#include "math_extra.h" +#include "math_special.h" #include "memory.h" -#include "error.h" +#include "modify.h" +#include "molecule.h" #include "neighbor.h" +#include "pair.h" +#include "random_park.h" +#include "region.h" +#include "update.h" + +#include +#include + using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; +using namespace MathSpecial; // large energy value used to signal overlap #define MAXENERGYSIGNAL 1.0e100 #define MAXENERGYTEST 1.0e50 -#define small 0.0000001 -#define PI 3.1415926 +#define SMALL 0.0000001 +#define NA_RHO0 0.602214 // Avogadro's constant times reference concentration (N_A * mol / liter) [nm^-3] /* ---------------------------------------------------------------------- */ -Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) : - Fix(lmp, narg, arg), - ngroups(0), groupstrings(NULL), - random_equal(NULL), random_unequal(NULL), - idftemp(NULL), ptype_ID(NULL) { + +FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : + Fix(lmp, narg, arg), + ngroups(0), groupstrings(NULL), + random_equal(NULL), random_unequal(NULL), + idftemp(NULL), ptype_ID(NULL) + { // Region restrictions not yet implemented .. @@ -79,28 +85,28 @@ Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) // set defaults and read optional arguments options(narg - 5, &arg[5]); - if (nevery <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (nmc < 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (seed <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (cation_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (anion_type <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); - if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (nevery <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (nmc < 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (seed <= 0) error->all(FLERR, "Illegal fix charge/regulation command: Seed value (positive integer) must be provided "); + if (cation_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (anion_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); + if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge/regulation command"); if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) error->all(FLERR, - "Illegal fix charge_regulation command, multivalent cation/anion charges are allowed, " + "Illegal fix charge/regulation command, multivalent cation/anion charges are allowed, " "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) - error->all(FLERR, "Illegal fix charge_regulation command"); + error->all(FLERR, "Illegal fix charge/regulation command"); if (acid_type < 0) pmcmoves[0] = 0; if (base_type < 0) pmcmoves[1] = 0; // normalize double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; - if (psum <= 0) error->all(FLERR, "Illegal fix charge_regulation command"); + if (psum <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); pmcmoves[0] /= psum; pmcmoves[1] /= psum; pmcmoves[2] /= psum; @@ -117,7 +123,7 @@ Fix_charge_regulation::Fix_charge_regulation(LAMMPS *lmp, int narg, char **arg) nsalt_successes = 0; } -Fix_charge_regulation::~Fix_charge_regulation() { +FixChargeRegulation::~FixChargeRegulation() { memory->destroy(ptype_ID); @@ -130,18 +136,16 @@ Fix_charge_regulation::~Fix_charge_regulation() { } } -int Fix_charge_regulation::setmask() { +int FixChargeRegulation::setmask() { int mask = 0; mask |= PRE_EXCHANGE; return mask; } -void Fix_charge_regulation::init() { +void FixChargeRegulation::init() { - triclinic = domain->triclinic; - - char *id_pe = (char *) "thermo_pe"; - int ipe = modify->find_compute(id_pe); + triclinic = domain->triclinic; + int ipe = modify->find_compute("thermo_pe"); c_pe = modify->compute[ipe]; if (atom->molecule_flag) { @@ -165,34 +169,27 @@ void Fix_charge_regulation::init() { // skip if already exists from previous init() if (!exclusion_group_bit) { - char **group_arg = new char *[4]; // create unique group name for atoms to be excluded - int len = strlen(id) + 30; - group_arg[0] = new char[len]; - sprintf(group_arg[0], "Fix_CR:exclusion_group:%s", id); - group_arg[1] = (char *) "subtract"; - group_arg[2] = (char *) "all"; - group_arg[3] = (char *) "all"; - group->assign(4, group_arg); - exclusion_group = group->find(group_arg[0]); + + auto group_id = std::string("FixChargeRegulation:CR_exclusion_group:") + id; + group->assign(group_id + " subtract all all"); + exclusion_group = group->find(group_id); if (exclusion_group == -1) - error->all(FLERR, "Could not find fix CR exclusion group ID"); + error->all(FLERR,"Could not find fix charge/regulation exclusion group ID"); exclusion_group_bit = group->bitmask[exclusion_group]; // neighbor list exclusion setup // turn off interactions between group all and the exclusion group int narg = 4; - char **arg = new char *[narg];; + char **arg = new char*[narg];; arg[0] = (char *) "exclude"; arg[1] = (char *) "group"; - arg[2] = group_arg[0]; + arg[2] = (char *) group_id.c_str(); arg[3] = (char *) "all"; - neighbor->modify_params(narg, arg); - delete[] group_arg[0]; - delete[] group_arg; - delete[] arg; + neighbor->modify_params(narg,arg); + delete [] arg; } // check that no deletable atoms are in atom->firstgroup @@ -226,7 +223,7 @@ void Fix_charge_regulation::init() { } } -void Fix_charge_regulation::pre_exchange() { +void FixChargeRegulation::pre_exchange() { if (next_reneighbor != update->ntimestep) return; xlo = domain->boxlo[0]; @@ -263,14 +260,22 @@ void Fix_charge_regulation::pre_exchange() { reaction_distance = 0; } // volume in units of (N_A * mol / liter) - volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * pow(llength_unit_in_nm, 3) * 0.602214; - if (reaction_distance < small) { + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * cube(llength_unit_in_nm) * NA_RHO0; + if (reaction_distance < SMALL) { vlocal_xrd = volume_rx; } else { - vlocal_xrd = 4.0 * PI * pow(reaction_distance, 3) / 3.0 * pow(llength_unit_in_nm, 3) * 0.602214; + vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; } beta = 1.0 / (force->boltz * *target_temperature_tcp); + // pre-compute powers + c10pH = pow(10.0,-pH); // dissociated ion (H+) activity + c10pKa = pow(10.0,-pKa); // acid dissociation constant + c10pKb = pow(10.0,-pKb); // base dissociation constant + c10pOH = pow(10.0,-pKs + pH); // dissociated anion (OH-) activity + c10pI_plus = pow(10.0,-pI_plus); // free cation activity + c10pI_minus = pow(10.0,-pI_minus); // free anion activity + // reinitialize counters nacid_neutral = particle_number(acid_type, 0); nacid_charged = particle_number(acid_type, -1); @@ -337,7 +342,7 @@ void Fix_charge_regulation::pre_exchange() { next_reneighbor = update->ntimestep + nevery; } -void Fix_charge_regulation::forward_acid() { +void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; @@ -360,7 +365,7 @@ void Fix_charge_regulation::forward_acid() { pos[2] = atom->x[m1][2]; } npart_xrd2 = ncation; - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -368,8 +373,8 @@ void Fix_charge_regulation::forward_acid() { npart_xrd2 = particle_number_xrd(cation_type, 1, reaction_distance, pos_all); } m2 = insert_particle(cation_type, 1, reaction_distance, pos_all); - factor = nacid_neutral * vlocal_xrd * pow(10, -pKa) - * (1 + pow(10, pH - pI_plus)) / ((1 + nacid_charged) * (1 + npart_xrd2)); + factor = nacid_neutral * vlocal_xrd * c10pKa * c10pI_plus / + (c10pH * (1 + nacid_charged) * (1 + npart_xrd2)); double energy_after = energy_full(); @@ -395,7 +400,7 @@ void Fix_charge_regulation::forward_acid() { } } -void Fix_charge_regulation::backward_acid() { +void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; @@ -418,7 +423,7 @@ void Fix_charge_regulation::backward_acid() { pos[1] = atom->x[m1][1]; pos[2] = atom->x[m1][2]; } - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -433,8 +438,8 @@ void Fix_charge_regulation::backward_acid() { mask_tmp = atom->mask[m2]; // remember group bits. atom->mask[m2] = exclusion_group_bit; } - factor = (1 + nacid_neutral) * vlocal_xrd * pow(10, -pKa) - * (1 + pow(10, pH - pI_plus)) / (nacid_charged * npart_xrd); + factor = (1 + nacid_neutral) * vlocal_xrd * c10pKa * c10pI_plus / + (c10pH * nacid_charged * npart_xrd); double energy_after = energy_full(); @@ -468,7 +473,7 @@ void Fix_charge_regulation::backward_acid() { } } -void Fix_charge_regulation::forward_base() { +void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; @@ -491,16 +496,15 @@ void Fix_charge_regulation::forward_base() { pos[2] = atom->x[m1][2]; } npart_xrd2 = nanion; - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; MPI_Allreduce(pos, pos_all, 3, MPI_DOUBLE, MPI_SUM, world); npart_xrd2 = particle_number_xrd(anion_type, -1, reaction_distance, pos_all); } - factor = nbase_neutral * vlocal_xrd * pow(10, -pKb) - * (1 + pow(10, pKs - pH - pI_minus)) / - ((1 + nbase_charged) * (1 + npart_xrd2)); + factor = nbase_neutral * vlocal_xrd * c10pKb * c10pI_minus / + (c10pOH * (1 + nbase_charged) * (1 + npart_xrd2)); m2 = insert_particle(anion_type, -1, reaction_distance, pos_all); double energy_after = energy_full(); @@ -526,7 +530,7 @@ void Fix_charge_regulation::forward_base() { } } -void Fix_charge_regulation::backward_base() { +void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; @@ -549,7 +553,7 @@ void Fix_charge_regulation::backward_base() { pos[1] = atom->x[m1][1]; pos[2] = atom->x[m1][2]; } - if (reaction_distance >= small) { + if (reaction_distance >= SMALL) { pos_all[0] = pos[0]; pos_all[1] = pos[1]; pos_all[2] = pos[2]; @@ -563,8 +567,8 @@ void Fix_charge_regulation::backward_base() { mask_tmp = atom->mask[m2]; // remember group bits. atom->mask[m2] = exclusion_group_bit; } - factor = (1 + nbase_neutral) * vlocal_xrd * pow(10, -pKb) - * (1 + pow(10, pKs - pH - pI_minus)) / (nbase_charged * npart_xrd); + factor = (1 + nbase_neutral) * vlocal_xrd * c10pKb * c10pI_minus / + (c10pOH * nbase_charged * npart_xrd); double energy_after = energy_full(); @@ -598,20 +602,20 @@ void Fix_charge_regulation::backward_base() { } } -void Fix_charge_regulation::forward_ions() { +void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; double *dummyp; int m1 = -1, m2 = -1; - factor = volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) - * (pow(10, -pKs + pH) + pow(10, -pI_minus)) / + factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); m1 = insert_particle(cation_type, +1, 0, dummyp); m2 = insert_particle(anion_type, -1, 0, dummyp); double energy_after = energy_full(); - if (energy_after < MAXENERGYTEST && random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { + if (energy_after < MAXENERGYTEST && + random_equal->uniform() < factor * exp(beta * (energy_before - energy_after))) { energy_stored = energy_after; nsalt_successes += 1; ncation++; @@ -632,7 +636,7 @@ void Fix_charge_regulation::forward_ions() { } -void Fix_charge_regulation::backward_ions() { +void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; @@ -659,8 +663,7 @@ void Fix_charge_regulation::backward_ions() { mask2_tmp = atom->mask[m2]; atom->mask[m2] = exclusion_group_bit; } - factor = (volume_rx * volume_rx * (pow(10, -pH) + pow(10, -pI_plus)) * - (pow(10, -pKs + pH) + pow(10, -pI_minus))) / (ncation * nanion); + factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / (ncation * nanion); double energy_after = energy_full(); if (energy_after < MAXENERGYTEST && @@ -717,7 +720,7 @@ void Fix_charge_regulation::backward_ions() { } } -void Fix_charge_regulation::forward_ions_multival() { +void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; @@ -728,19 +731,19 @@ void Fix_charge_regulation::forward_ions_multival() { // insert one anion and (salt_charge_ratio) cations mm[0] = insert_particle(anion_type, salt_charge[1], 0, dummyp); - factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion); + factor *= volume_rx * c10pI_minus / (1 + nanion); for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = insert_particle(cation_type, salt_charge[0], 0, dummyp); - factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation + i); + factor *= volume_rx *c10pI_plus / (1 + ncation + i); } } else { // insert one cation and (salt_charge_ratio) anions mm[0] = insert_particle(cation_type, salt_charge[0], 0, dummyp); - factor *= volume_rx * pow(10, -pI_plus) / (1 + ncation); + factor *= volume_rx * c10pI_plus / (1 + ncation); for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = insert_particle(anion_type, salt_charge[1], 0, dummyp); - factor *= volume_rx * pow(10, -pI_minus) / (1 + nanion + i); + factor *= volume_rx * c10pI_minus / (1 + nanion + i); } } @@ -771,7 +774,7 @@ void Fix_charge_regulation::forward_ions_multival() { } } -void Fix_charge_regulation::backward_ions_multival() { +void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; @@ -786,7 +789,7 @@ void Fix_charge_regulation::backward_ions_multival() { mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_minus) / (nanion); + factor *= volume_rx * c10pI_minus / (nanion); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; atom->q[mm[0]] = 0; @@ -796,7 +799,7 @@ void Fix_charge_regulation::backward_ions_multival() { for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_plus) / (ncation - i); + factor *= volume_rx * c10pI_plus / (ncation - i); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; atom->q[mm[i + 1]] = 0; @@ -810,7 +813,7 @@ void Fix_charge_regulation::backward_ions_multival() { if (nanion < salt_charge_ratio || ncation < 1) return; mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); - factor *= volume_rx * pow(10, -pI_plus) / (ncation); + factor *= volume_rx * c10pI_plus / (ncation); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; atom->q[mm[0]] = 0; @@ -826,7 +829,7 @@ void Fix_charge_regulation::backward_ions_multival() { mask_tmp[i + 1] = atom->mask[mm[i + 1]]; atom->mask[mm[i + 1]] = exclusion_group_bit; } - factor *= volume_rx * pow(10, -pI_minus) / (nanion - i); + factor *= volume_rx * c10pI_minus / (nanion - i); } } @@ -840,7 +843,7 @@ void Fix_charge_regulation::backward_ions_multival() { atom->natoms -= 1 + salt_charge_ratio; // ions must be deleted in order, otherwise index m could change upon the first deletion for (int i = 0; i < salt_charge_ratio + 1; i++) { - // get max mm value, poor N^2 scaling, but charge ratio is a small number (2 or 3). + // get max mm value, poor N^2 scaling, but charge ratio is a SMALL number (2 or 3). int maxmm = -1, jmaxm = -1; for (int j = 0; j < salt_charge_ratio + 1; j++) { if (mm[j] > maxmm) { @@ -883,23 +886,42 @@ void Fix_charge_regulation::backward_ions_multival() { } } -int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::insert_particle(int ptype, double charge, double rd, double *target) { // insert a particle of type (ptype) with charge (charge) within distance (rd) of (target) double coord[3]; int m = -1; - if (rd < small) { + if (rd < SMALL) { coord[0] = xlo + random_equal->uniform() * (xhi - xlo); coord[1] = ylo + random_equal->uniform() * (yhi - ylo); coord[2] = zlo + random_equal->uniform() * (zhi - zlo); } else { - double radius = reaction_distance * random_equal->uniform(); - double theta = random_equal->uniform() * PI; - double phi = random_equal->uniform() * 2 * PI; - coord[0] = target[0] + radius * sin(theta) * cos(phi); - coord[1] = target[1] + radius * sin(theta) * sin(phi); - coord[2] = target[2] + radius * cos(theta); + // get a random point inside a sphere with radius rd + // simple rejection sampling, probably the fastest method + double dxx=1,dyy=1,dzz=1; + while (dxx * dxx + dyy * dyy + dzz * dzz > 1.0) { + dxx = 2 * random_equal->uniform() - 1.0; + dyy = 2 * random_equal->uniform() - 1.0; + dzz = 2 * random_equal->uniform() - 1.0; + } + coord[0] = target[0] + rd * dxx; + coord[1] = target[1] + rd * dyy; + coord[2] = target[2] + rd * dzz; + + // Alternative way, but likely somewhat less efficient + /* + double radius = rd * pow(random_equal->uniform(), THIRD); + double theta = acos(2 * random_equal->uniform() - 1); + double phi = random_equal->uniform() * 2 * MY_PI; + double sinphi = sin(phi); + double cosphi = cos(phi); + double sintheta = sin(theta); + double costheta = cos(theta); + coord[0] = target[0] + radius * sintheta * cosphi; + coord[1] = target[1] + radius * sintheta * sinphi; + coord[2] = target[2] + radius * costheta; + */ coord[0] = coord[0] - floor(1.0 * (coord[0] - xlo) / (xhi - xlo)) * (xhi - xlo); coord[1] = coord[1] - floor(1.0 * (coord[1] - ylo) / (yhi - ylo)) * (yhi - ylo); coord[2] = coord[2] - floor(1.0 * (coord[2] - zlo) / (zhi - zlo)) * (zhi - zlo); @@ -926,7 +948,7 @@ int Fix_charge_regulation::insert_particle(int ptype, double charge, double rd, return m; } -int Fix_charge_regulation::get_random_particle(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::get_random_particle(int ptype, double charge, double rd, double *target) { // returns a randomly chosen particle of type (ptype) with charge (charge) // chosen among particles within distance (rd) of (target) @@ -947,9 +969,9 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double count_global = 0; count_before = 0; - if (rd < small) { //reaction_distance < small: No geometry constraint on random particle choice + if (rd < SMALL) { //reaction_distance < SMALL: No constraint on random particle choice for (int i = 0; i < nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { ptype_ID[count_local] = i; count_local++; @@ -966,7 +988,7 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); distance_check = dx * dx + dy * dy + dz * dz; if ((distance_check < rd * rd) && atom->type[i] == ptype && - fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { ptype_ID[count_local] = i; count_local++; } @@ -990,7 +1012,7 @@ int Fix_charge_regulation::get_random_particle(int ptype, double charge, double return -1; } -double Fix_charge_regulation::energy_full() { +double FixChargeRegulation::energy_full() { int imolecule; if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); @@ -1050,12 +1072,12 @@ double Fix_charge_regulation::energy_full() { return total_energy; } -int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { +int FixChargeRegulation::particle_number_xrd(int ptype, double charge, double rd, double *target) { int count = 0; - if (rd < small) { + if (rd < SMALL) { for (int i = 0; i < atom->nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) count++; } } else { @@ -1069,7 +1091,7 @@ int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double dz -= static_cast(1.0 * dz / (zhi - zlo) + 0.5) * (zhi - zlo); distance_check = dx * dx + dy * dy + dz * dz; if ((distance_check < rd * rd) && atom->type[i] == ptype && - fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) { + fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) { count++; } } @@ -1079,11 +1101,11 @@ int Fix_charge_regulation::particle_number_xrd(int ptype, double charge, double return count_sum; } -int Fix_charge_regulation::particle_number(int ptype, double charge) { +int FixChargeRegulation::particle_number(int ptype, double charge) { int count = 0; for (int i = 0; i < atom->nlocal; i++) { - if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < small && atom->mask[i] != exclusion_group_bit) + if (atom->type[i] == ptype && fabs(atom->q[i] - charge) < SMALL && atom->mask[i] != exclusion_group_bit) count = count + 1; } int count_sum = count; @@ -1091,7 +1113,7 @@ int Fix_charge_regulation::particle_number(int ptype, double charge) { return count_sum; } -double Fix_charge_regulation::compute_vector(int n) { +double FixChargeRegulation::compute_vector(int n) { double count_temp = 0; if (n == 0) { return nacid_attempts + nbase_attempts + nsalt_attempts; @@ -1113,7 +1135,7 @@ double Fix_charge_regulation::compute_vector(int n) { return 0.0; } -void Fix_charge_regulation::setThermoTemperaturePointer() { +void FixChargeRegulation::setThermoTemperaturePointer() { int ifix = -1; ifix = modify->find_fix(idftemp); if (ifix == -1) { @@ -1126,7 +1148,7 @@ void Fix_charge_regulation::setThermoTemperaturePointer() { } -void Fix_charge_regulation::assign_tags() { +void FixChargeRegulation::assign_tags() { // Assign tags to ions with zero tags if (atom->tag_enable) { tagint *tag = atom->tag; @@ -1167,14 +1189,14 @@ void Fix_charge_regulation::assign_tags() { parse input options ------------------------------------------------------------------------- */ -void Fix_charge_regulation::options(int narg, char **arg) { +void FixChargeRegulation::options(int narg, char **arg) { if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); // defaults pH = 7.0; - pI_plus = 100; - pI_minus = 100; + pI_plus = 5; + pI_minus = 5; acid_type = -1; base_type = -1; pKa = 100; @@ -1182,12 +1204,12 @@ void Fix_charge_regulation::options(int narg, char **arg) { pKs = 14.0; nevery = 100; nmc = 100; - pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = 0.33; - llength_unit_in_nm= 0.72; + pmcmoves[0] = pmcmoves[1] = pmcmoves[2] = THIRD; + llength_unit_in_nm= 0.71; // Default set to Bjerrum length in water at 20 degrees C [nm] reservoir_temperature = 1.0; reaction_distance = 0; - seed = 12345; + seed = 0; target_temperature_tcp = &reservoir_temperature; add_tags_flag = false; only_salt_flag = false; @@ -1297,9 +1319,9 @@ void Fix_charge_regulation::options(int narg, char **arg) { if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); - if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > small) + if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > SMALL) error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); - if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > small) + if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > SMALL) error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); iarg += 4; } else if (strcmp(arg[iarg + 1], "no") == 0) { @@ -1329,7 +1351,7 @@ void Fix_charge_regulation::options(int narg, char **arg) { memory usage of local atom-based arrays ------------------------------------------------------------------------- */ -double Fix_charge_regulation::memory_usage() { +double FixChargeRegulation::memory_usage() { double bytes = cr_nmax * sizeof(int); return bytes; } diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/USER-MISC/fix_charge_regulation.h index d698bd6bb7..3afaffddb7 100644 --- a/src/USER-MISC/fix_charge_regulation.h +++ b/src/USER-MISC/fix_charge_regulation.h @@ -17,21 +17,21 @@ #ifdef FIX_CLASS -FixStyle(charge_regulation,Fix_charge_regulation) +FixStyle(charge/regulation,FixChargeRegulation) #else -#ifndef LMP_FIX_charge_regulation_H -#define LMP_FIX_charge_regulation_H +#ifndef LMP_FIX_CHARGE_REGULATION_H +#define LMP_FIX_CHARGE_REGULATION_H #include "fix.h" namespace LAMMPS_NS { - class Fix_charge_regulation : public Fix { + class FixChargeRegulation : public Fix { public: - Fix_charge_regulation(class LAMMPS *, int, char **); - ~Fix_charge_regulation(); + FixChargeRegulation(class LAMMPS *, int, char **); + ~FixChargeRegulation(); int setmask(); void init(); void pre_exchange(); @@ -59,7 +59,8 @@ namespace LAMMPS_NS { int nevery, seed; // begin MC cycle every nevery MD timesteps, random seed int nmc; // MC move attempts per cycle double llength_unit_in_nm ; // LAMMPS unit of length in nm, needed since chemical potentials are in units of mol/l - double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials + double pH, pKa, pKb, pKs, pI_plus, pI_minus; // chemical potentials and equilibrium constant in log10 base + double c10pH, c10pKa, c10pKb, c10pOH, c10pI_plus, c10pI_minus; // 10 raised to chemical potential value, in units of concentration [mol/liter] double pmcmoves[3]; // mc move attempt probability: acid, base, ion pair exchange double pmcc; // mc move cumulative attempt probability int npart_xrd; // # of particles (ions) within xrd @@ -78,7 +79,7 @@ namespace LAMMPS_NS { double reservoir_temperature; double beta, sigma, volume, volume_rx; // inverse temperature, speed, total volume, reacting volume int salt_charge[2]; // charge of salt ions: [0] - cation, [1] - anion - int salt_charge_ratio; // charge ration when using multivalent ion exchange + int salt_charge_ratio; // charge ratio when using multivalent ion exchange double xlo, xhi, ylo, yhi, zlo, zhi; // box size double energy_stored; // full energy of old/current configuration int triclinic; // 0 = orthog box, 1 = triclinic From faa2407aa46805bea4caf9e90c768b5bd187a8ed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:04:19 -0500 Subject: [PATCH 012/100] plug memory leak --- src/USER-MISC/fix_charge_regulation.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index c43a509f61..0a9619096e 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -129,6 +129,7 @@ FixChargeRegulation::~FixChargeRegulation() { delete random_equal; delete random_unequal; + delete idftemp; if (group) { int igroupall = group->find("all"); From 8ee693204a7b7f3fb5071770dae1713b34dd8270 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:05:07 -0500 Subject: [PATCH 013/100] use nullptr instead of NULL to initialize pointers --- src/USER-MISC/fix_charge_regulation.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 0a9619096e..7608849190 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -61,10 +61,10 @@ using namespace MathSpecial; FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), - ngroups(0), groupstrings(NULL), - random_equal(NULL), random_unequal(NULL), - idftemp(NULL), ptype_ID(NULL) - { + ngroups(0), groupstrings(nullptr), ptype_ID(nullptr), + random_equal(nullptr), random_unequal(nullptr), + idftemp(nullptr) +{ // Region restrictions not yet implemented .. @@ -1221,7 +1221,7 @@ void FixChargeRegulation::options(int narg, char **arg) { exclusion_group_bit = 0; ngroups = 0; int ngroupsmax = 0; - groupstrings = NULL; + groupstrings = nullptr; int iarg = 0; while (iarg < narg) { From 9671ba79003171d7d50e8bc3c385c99d78d05774 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:05:28 -0500 Subject: [PATCH 014/100] silence compiler warnings --- src/USER-MISC/fix_charge_regulation.cpp | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 7608849190..8a6530ef2b 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -347,7 +347,7 @@ void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -406,13 +406,13 @@ void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; int mask_tmp; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, -1, 0, dummyp); if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -478,13 +478,13 @@ void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 0, 0, dummyp); if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -535,14 +535,14 @@ void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; int mask_tmp; double pos[3]; pos[0] = 0; pos[1] = 0; pos[2] = 0; // acid/base particle position double pos_all[3]; - int m1 = -1, m1_all = -1, m2 = -1, m2_all = -1; + int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 1, 0, dummyp); if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); @@ -607,7 +607,7 @@ void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; - double *dummyp; + double *dummyp = nullptr; int m1 = -1, m2 = -1; factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); @@ -642,7 +642,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; int mask1_tmp, mask2_tmp; - double *dummyp; // dummy pointer + double *dummyp = nullptr; int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); @@ -1014,7 +1014,6 @@ int FixChargeRegulation::get_random_particle(int ptype, double charge, double rd } double FixChargeRegulation::energy_full() { - int imolecule; if (triclinic) domain->x2lamda(atom->nlocal); domain->pbc(); comm->exchange(); @@ -1030,7 +1029,6 @@ double FixChargeRegulation::energy_full() { int overlaptest = 0; double delx, dely, delz, rsq; double **x = atom->x; - tagint *molecule = atom->molecule; int nall = atom->nlocal + atom->nghost; for (int i = 0; i < atom->nlocal; i++) { for (int j = i + 1; j < nall; j++) { @@ -1115,7 +1113,6 @@ int FixChargeRegulation::particle_number(int ptype, double charge) { } double FixChargeRegulation::compute_vector(int n) { - double count_temp = 0; if (n == 0) { return nacid_attempts + nbase_attempts + nsalt_attempts; } else if (n == 1) { From 676191f3303751c39ce4a36bcb964f7d079d527d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:28:15 -0500 Subject: [PATCH 015/100] various cosmetic changes - print warnings only on MPI rank 0 - use the fix name charge/regulation consistently - use domain->prd_half for half box length instead of computing it - use utils::inumeric() to guarantee integer charge input - LAMMPS coding style adjustments --- src/USER-MISC/fix_charge_regulation.cpp | 194 ++++++++++++++---------- 1 file changed, 114 insertions(+), 80 deletions(-) diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/USER-MISC/fix_charge_regulation.cpp index 8a6530ef2b..5479082158 100644 --- a/src/USER-MISC/fix_charge_regulation.cpp +++ b/src/USER-MISC/fix_charge_regulation.cpp @@ -85,25 +85,27 @@ FixChargeRegulation::FixChargeRegulation(LAMMPS *lmp, int narg, char **arg) : // set defaults and read optional arguments options(narg - 5, &arg[5]); - if (nevery <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (nmc < 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (llength_unit_in_nm < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (*target_temperature_tcp < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (seed <= 0) error->all(FLERR, "Illegal fix charge/regulation command: Seed value (positive integer) must be provided "); - if (cation_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (anion_type <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (reaction_distance < 0.0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (salt_charge[0] <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if (salt_charge[1] >= 0) error->all(FLERR, "Illegal fix charge/regulation command"); - if ((salt_charge[1] % salt_charge[0] != 0) && (salt_charge[0] % salt_charge[1] != 0)) - error->all(FLERR, - "Illegal fix charge/regulation command, multivalent cation/anion charges are allowed, " - "but must be divisible, e.g. (3,-1) is fine, but (3,-2) is not implemented"); + if ((nevery <= 0) || (nmc < 0) || (llength_unit_in_nm < 0.0) + || (*target_temperature_tcp < 0.0) || (cation_type <= 0) + || (anion_type <= 0) || (reaction_distance < 0.0) + || (salt_charge[0] <= 0) || (salt_charge[1] >= 0)) + error->all(FLERR, "Illegal fix charge/regulation command"); + + if (seed <= 0) + error->all(FLERR, "Illegal fix charge/regulation command: " + "Seed value (positive integer) must be provided "); + if ((salt_charge[1] % salt_charge[0] != 0) + && (salt_charge[0] % salt_charge[1] != 0)) + error->all(FLERR,"Illegal fix charge/regulation command, " + "multivalent cation/anion charges are allowed, " + "but must be divisible, e.g. (3,-1) is fine, " + "but (3,-2) is not implemented"); if (pmcmoves[0] < 0 || pmcmoves[1] < 0 || pmcmoves[2] < 0) error->all(FLERR, "Illegal fix charge/regulation command"); if (acid_type < 0) pmcmoves[0] = 0; if (base_type < 0) pmcmoves[1] = 0; + // normalize double psum = pmcmoves[0] + pmcmoves[1] + pmcmoves[2]; if (psum <= 0) error->all(FLERR, "Illegal fix charge/regulation command"); @@ -159,11 +161,12 @@ void FixChargeRegulation::init() { MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); if (flagall && comm->me == 0) - error->all(FLERR, "Fix charge regulation cannot exchange individual atoms (ions) belonging to a molecule"); + error->all(FLERR, "fix charge/regulation cannot exchange " + "individual atoms (ions) belonging to a molecule"); } if (domain->dimension == 2) - error->all(FLERR, "Cannot use fix charge regulation in a 2d simulation"); + error->all(FLERR, "Cannot use fix charge/regulation in a 2d simulation"); // create a new group for interaction exclusions // used for attempted atom deletions @@ -173,11 +176,12 @@ void FixChargeRegulation::init() { // create unique group name for atoms to be excluded - auto group_id = std::string("FixChargeRegulation:CR_exclusion_group:") + id; + auto group_id = fmt::format("FixChargeRegulation:exclusion_group:{}",id); group->assign(group_id + " subtract all all"); exclusion_group = group->find(group_id); if (exclusion_group == -1) - error->all(FLERR,"Could not find fix charge/regulation exclusion group ID"); + error->all(FLERR,"Could not find fix charge/regulation exclusion " + "group ID"); exclusion_group_bit = group->bitmask[exclusion_group]; // neighbor list exclusion setup @@ -208,7 +212,8 @@ void FixChargeRegulation::init() { MPI_Allreduce(&flag, &flagall, 1, MPI_INT, MPI_SUM, world); if (flagall) - error->all(FLERR, "Cannot do Fix charge regulation on atoms in atom_modify first group"); + error->all(FLERR, "Cannot use fix charge/regulation on atoms " + "in atom_modify first group"); } // construct group bitmask for all new atoms @@ -219,7 +224,7 @@ void FixChargeRegulation::init() { for (int igroup = 0; igroup < ngroups; igroup++) { int jgroup = group->find(groupstrings[igroup]); if (jgroup == -1) - error->all(FLERR, "Could not find specified fix charge regulation group ID"); + error->all(FLERR, "Could not find fix charge/regulation group ID"); groupbitall |= group->bitmask[jgroup]; } } @@ -250,22 +255,26 @@ void FixChargeRegulation::pre_exchange() { if (triclinic) domain->lamda2x(atom->nlocal + atom->nghost); energy_stored = energy_full(); - if (energy_stored > MAXENERGYTEST) - error->warning(FLERR, "Energy of old configuration in fix charge_regulation is > MAXENERGYTEST."); + if ((energy_stored > MAXENERGYTEST) && (comm->me == 0)) + error->warning(FLERR, "Energy of old configuration in fix " + "charge/regulation is > MAXENERGYTEST."); - if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || - (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || - (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { - error->warning(FLERR, - "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + if ((reaction_distance > domain->prd_half[0]) || + (reaction_distance > domain->prd_half[1]) || + (reaction_distance > domain->prd_half[2])) { + if (comm->me == 0) + error->warning(FLERR,"reaction distance (rxd) is larger than " + "half the box dimension, resetting default: xrd = 0."); reaction_distance = 0; } // volume in units of (N_A * mol / liter) - volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) * cube(llength_unit_in_nm) * NA_RHO0; + volume_rx = (xhi - xlo) * (yhi - ylo) * (zhi - zlo) + * cube(llength_unit_in_nm) * NA_RHO0; if (reaction_distance < SMALL) { vlocal_xrd = volume_rx; } else { - vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; + vlocal_xrd = 4.0 * MY_PI * cube(reaction_distance) + / 3.0 * cube(llength_unit_in_nm) * NA_RHO0; } beta = 1.0 / (force->boltz * *target_temperature_tcp); @@ -356,7 +365,7 @@ void FixChargeRegulation::forward_acid() { int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, 0, 0, dummyp); - if (npart_xrd != nacid_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nacid_neutral) error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nacid_neutral > 0) { if (m1 >= 0) { @@ -415,7 +424,8 @@ void FixChargeRegulation::backward_acid() { int m1 = -1, m2 = -1; m1 = get_random_particle(acid_type, -1, 0, dummyp); - if (npart_xrd != nacid_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nacid_charged) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nacid_charged > 0) { if (m1 >= 0) { @@ -487,7 +497,8 @@ void FixChargeRegulation::forward_base() { int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 0, 0, dummyp); - if (npart_xrd != nbase_neutral) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nbase_neutral) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nbase_neutral > 0) { if (m1 >= 0) { @@ -545,7 +556,8 @@ void FixChargeRegulation::backward_base() { int m1 = -1, m2 = -1; m1 = get_random_particle(base_type, 1, 0, dummyp); - if (npart_xrd != nbase_charged) error->all(FLERR, "Fix charge regulation acid count inconsistent"); + if (npart_xrd != nbase_charged) + error->all(FLERR, "fix charge/regulation acid count inconsistent"); if (nbase_charged > 0) { if (m1 >= 0) { @@ -646,10 +658,12 @@ void FixChargeRegulation::backward_ions() { int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); - if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (ncation > 0) { m2 = get_random_particle(anion_type, -1, 0, dummyp); - if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (nanion > 0) { // attempt deletion @@ -789,7 +803,8 @@ void FixChargeRegulation::backward_ions_multival() { if (ncation < salt_charge_ratio || nanion < 1) return; mm[0] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); - if (npart_xrd != nanion) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_minus / (nanion); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; @@ -799,7 +814,8 @@ void FixChargeRegulation::backward_ions_multival() { } for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); - if (npart_xrd != ncation - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation - i) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_plus / (ncation - i); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; @@ -813,7 +829,8 @@ void FixChargeRegulation::backward_ions_multival() { if (nanion < salt_charge_ratio || ncation < 1) return; mm[0] = get_random_particle(cation_type, salt_charge[0], 0, dummyp); - if (npart_xrd != ncation) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != ncation) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); factor *= volume_rx * c10pI_plus / (ncation); if (mm[0] >= 0) { qq[0] = atom->q[mm[0]]; @@ -823,7 +840,8 @@ void FixChargeRegulation::backward_ions_multival() { } for (int i = 0; i < salt_charge_ratio; i++) { mm[i + 1] = get_random_particle(anion_type, salt_charge[1], 0, dummyp); - if (npart_xrd != nanion - i) error->all(FLERR, "Fix charge regulation salt count inconsistent"); + if (npart_xrd != nanion - i) + error->all(FLERR, "fix charge/regulation salt count inconsistent"); if (mm[i + 1] >= 0) { qq[i + 1] = atom->q[mm[i + 1]]; atom->q[mm[i + 1]] = 0; @@ -1138,7 +1156,7 @@ void FixChargeRegulation::setThermoTemperaturePointer() { ifix = modify->find_fix(idftemp); if (ifix == -1) { error->all(FLERR, - "Fix charge regulation regulation could not find a temperature fix id provided by tempfixid\n"); + "fix charge/regulation regulation could not find a temperature fix id provided by tempfixid\n"); } Fix *temperature_fix = modify->fix[ifix]; int dim; @@ -1188,7 +1206,7 @@ void FixChargeRegulation::assign_tags() { ------------------------------------------------------------------------- */ void FixChargeRegulation::options(int narg, char **arg) { - if (narg < 0) error->all(FLERR, "Illegal fix charge regulation command"); + if (narg < 0) error->all(FLERR, "Illegal fix charge/regulation command"); // defaults @@ -1224,48 +1242,59 @@ void FixChargeRegulation::options(int narg, char **arg) { while (iarg < narg) { if (strcmp(arg[iarg], "lunit_nm") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); llength_unit_in_nm = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "acid_type") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); acid_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "base_type") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); base_type = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pH") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pH = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pIp") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pI_plus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pIm") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pI_minus = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKa") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKa = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKb") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKb = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "temp") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); reservoir_temperature = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pKs") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pKs = utils::numeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "tempfixid") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); int n = strlen(arg[iarg + 1]) + 1; delete[] idftemp; idftemp = new char[n]; @@ -1273,75 +1302,81 @@ void FixChargeRegulation::options(int narg, char **arg) { setThermoTemperaturePointer(); iarg += 2; } else if (strcmp(arg[iarg], "rxd") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); reaction_distance = utils::numeric(FLERR, arg[iarg + 1], false, lmp); - if ((reaction_distance > fabs(domain->boxhi[0] - domain->boxlo[0]) / 2) || - (reaction_distance > fabs(domain->boxhi[1] - domain->boxlo[1]) / 2) || - (reaction_distance > fabs(domain->boxhi[2] - domain->boxlo[2]) / 2)) { - error->warning(FLERR, - "reaction distance (rxd) is larger than half the box dimension, resetting default: xrd = 0."); + if ((reaction_distance > domain->prd_half[0]) || + (reaction_distance > domain->prd_half[1]) || + (reaction_distance > domain->prd_half[2])) { + if (comm->me == 0) + error->warning(FLERR,"reaction distance (rxd) is larger than half " + "the box dimension, resetting default: xrd = 0."); reaction_distance = 0; } iarg += 2; } else if (strcmp(arg[iarg], "nevery") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); nevery = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "nmc") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); nmc = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "pmcmoves") == 0) { - if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 4 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); pmcmoves[0] = utils::numeric(FLERR, arg[iarg + 1], false, lmp); pmcmoves[1] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); pmcmoves[2] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); iarg += 4; } else if (strcmp(arg[iarg], "seed") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); seed = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); iarg += 2; } else if (strcmp(arg[iarg], "tag") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); if (strcmp(arg[iarg + 1], "yes") == 0) { add_tags_flag = true; } else if (strcmp(arg[iarg + 1], "no") == 0) { add_tags_flag = false; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); iarg += 2; } else if (strcmp(arg[iarg], "onlysalt") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); if (strcmp(arg[iarg + 1], "yes") == 0) { only_salt_flag = true; // need to specify salt charge - if (iarg + 4 > narg) error->all(FLERR, "Illegal fix charge regulation command"); - salt_charge[0] = utils::numeric(FLERR, arg[iarg + 2], false, lmp); - salt_charge[1] = utils::numeric(FLERR, arg[iarg + 3], false, lmp); - if (fabs(salt_charge[0] - utils::inumeric(FLERR, arg[iarg + 2], false, lmp)) > SMALL) - error->all(FLERR, "Illegal fix charge regulation command, cation charge must be an integer"); - if (fabs(salt_charge[1] - utils::inumeric(FLERR, arg[iarg + 3], false, lmp)) > SMALL) - error->all(FLERR, "Illegal fix charge regulation command, anion charge must be an integer"); + if (iarg + 4 > narg) + error->all(FLERR, "Illegal fix charge/regulation command"); + salt_charge[0] = utils::inumeric(FLERR, arg[iarg + 2], false, lmp); + salt_charge[1] = utils::inumeric(FLERR, arg[iarg + 3], false, lmp); iarg += 4; } else if (strcmp(arg[iarg + 1], "no") == 0) { only_salt_flag = false; iarg += 2; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); } else if (strcmp(arg[iarg], "group") == 0) { - if (iarg + 2 > narg) error->all(FLERR, "Illegal fix fix charge regulation command"); + if (iarg + 2 > narg) + error->all(FLERR, "Illegal fix fix charge/regulation command"); if (ngroups >= ngroupsmax) { ngroupsmax = ngroups + 1; groupstrings = (char **) - memory->srealloc(groupstrings, - ngroupsmax * sizeof(char *), - "fix_charge_regulation:groupstrings"); + memory->srealloc(groupstrings, + ngroupsmax * sizeof(char *), + "fix_charge_regulation:groupstrings"); } int n = strlen(arg[iarg + 1]) + 1; groupstrings[ngroups] = new char[n]; strcpy(groupstrings[ngroups], arg[iarg + 1]); ngroups++; iarg += 2; - } else { error->all(FLERR, "Illegal fix charge regulation command"); } + } else error->all(FLERR, "Illegal fix charge/regulation command"); } } @@ -1350,6 +1385,5 @@ void FixChargeRegulation::options(int narg, char **arg) { ------------------------------------------------------------------------- */ double FixChargeRegulation::memory_usage() { - double bytes = cr_nmax * sizeof(int); - return bytes; + return (double)cr_nmax * sizeof(int); } From 6c2abf4739a2ba78dc35d122d0697b826405ab9b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 07:53:19 -0500 Subject: [PATCH 016/100] update fix charge/regulation input example to follow LAMMPS conventions closer --- examples/USER/misc/charge_regulation/README | 38 +++- .../{data_acid.chreg => data.chreg-acid} | 0 ...{data_polymer.chreg => data.chreg-polymer} | 0 .../{in_acid.chreg => in.chreg-acid} | 41 ++--- .../misc/charge_regulation/in.chreg-polymer | 33 ++++ .../misc/charge_regulation/in_polymer.chreg | 37 ---- .../misc/charge_regulation/log_acid.lammps | 163 ------------------ 7 files changed, 84 insertions(+), 228 deletions(-) rename examples/USER/misc/charge_regulation/{data_acid.chreg => data.chreg-acid} (100%) rename examples/USER/misc/charge_regulation/{data_polymer.chreg => data.chreg-polymer} (100%) rename examples/USER/misc/charge_regulation/{in_acid.chreg => in.chreg-acid} (52%) create mode 100644 examples/USER/misc/charge_regulation/in.chreg-polymer delete mode 100644 examples/USER/misc/charge_regulation/in_polymer.chreg delete mode 100644 examples/USER/misc/charge_regulation/log_acid.lammps diff --git a/examples/USER/misc/charge_regulation/README b/examples/USER/misc/charge_regulation/README index 5666d6d025..c704b67dea 100644 --- a/examples/USER/misc/charge_regulation/README +++ b/examples/USER/misc/charge_regulation/README @@ -1,8 +1,36 @@ -This directory has two input scripts that illustrates how to use fix charge_regulation in LAMMPS to perform coarse-grained molecular dynamics (MD) simulations with incorporation of charge regulation effects. The charge regulation is implemented via Monte Carlo (MC) sampling following the reaction ensemble MC approach, producing a MC/MD hybrid tool for modeling charge regulation in solvated systems. +This directory has two input scripts that illustrates how to use fix +charge_regulation in LAMMPS to perform coarse-grained molecular dynamics +(MD) simulations with incorporation of charge regulation effects. The +charge regulation is implemented via Monte Carlo (MC) sampling following +the reaction ensemble MC approach, producing a MC/MD hybrid tool for +modeling charge regulation in solvated systems. -The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`. +The script `in.chreg-acid` sets up a simple weak acid electrolyte +(pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: +acid protonation & de-protonation, and monovalent ion pair insertion and +deletion. Note here we have grouped all free monovalent ions into a +single type, a physically natural choice on the level of coarse-grained +primitive electrolyte models, which increases the calculation +performance but has no effects on thermodynamic observables. The +variables such as pH, pKa, pI, and lb at the top of the input script can +be adjusted to play with various simulation parameters. The cumulative +MC attempted moves and cumulative number of accepted moves, as well as, +current number of neutral and charged acid particles, neutral and +charged base particles (in this example always 0), and the current +number of free cations and anions in the system are printed in the +output. -The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and monovalent salt chemical potential pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion -Of a proton [type4] and salt anion [type 3]. -The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`. +The script `in.chreg-polymer` sets up a weak poly-electrolyte chain of +N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 +and monovalent salt chemical potential pI=3. In this example, we choose +to treat salt ions, protons, and hydroxyl ions separately, which results +in 5 types of MC moves: acid [type 1] protonation & de-protonation (with +protons [type 4] insertion & deletion), acid [type 1] protonation & +de-protonation (with salt cation [type 2] insertion & deletion), water +self-ionization (insertion and deletion of proton [type4] and hydroxyl +ion [type 5] pair), insertion and deletion of monovalent salt pair [type +2 and type 3] , insertion and deletion of a proton [type4] and salt +anion [type 3]. The current number of neutral and charged acid +particles, the current number of free salt cations and anions, and the +current number of protons and hydroxyl ions are printed in the output. diff --git a/examples/USER/misc/charge_regulation/data_acid.chreg b/examples/USER/misc/charge_regulation/data.chreg-acid similarity index 100% rename from examples/USER/misc/charge_regulation/data_acid.chreg rename to examples/USER/misc/charge_regulation/data.chreg-acid diff --git a/examples/USER/misc/charge_regulation/data_polymer.chreg b/examples/USER/misc/charge_regulation/data.chreg-polymer similarity index 100% rename from examples/USER/misc/charge_regulation/data_polymer.chreg rename to examples/USER/misc/charge_regulation/data.chreg-polymer diff --git a/examples/USER/misc/charge_regulation/in_acid.chreg b/examples/USER/misc/charge_regulation/in.chreg-acid similarity index 52% rename from examples/USER/misc/charge_regulation/in_acid.chreg rename to examples/USER/misc/charge_regulation/in.chreg-acid index 73a40f7389..68ef5e1b7c 100644 --- a/examples/USER/misc/charge_regulation/in_acid.chreg +++ b/examples/USER/misc/charge_regulation/in.chreg-acid @@ -1,12 +1,9 @@ # Charge regulation lammps for simple weak electrolyte -units lj -atom_style charge -dimension 3 -boundary p p p -processors * * * -neighbor 3.0 bin -read_data data_acid.chreg +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid variable cut_long equal 12.5 variable nevery equal 100 @@ -16,26 +13,24 @@ variable pKa equal 6.0 variable pIm equal 3.0 variable pIp equal 3.0 -variable cut_lj equal 2^(1.0/6.0) -variable lunit_nm equal 0.72 # in the units of nm -velocity all create 1.0 8008 loop geom +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom -pair_style lj/cut/coul/long ${cut_lj} ${cut_long} -pair_coeff * * 1.0 1.0 ${cut_lj} # charges -kspace_style ewald 1.0e-3 -dielectric 1.0 -pair_modify shift yes +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes ######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### -fix fnve all nve -compute dtemp all temp -compute_modify dtemp dynamic yes -fix fT all langevin 1.0 1.0 1.0 123 +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT -thermo 100 +thermo 100 thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] -log log_acid.lammps -timestep 0.005 -run 20000 +timestep 0.005 +run 2000 diff --git a/examples/USER/misc/charge_regulation/in.chreg-polymer b/examples/USER/misc/charge_regulation/in.chreg-polymer new file mode 100644 index 0000000000..0adab9b5e7 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in.chreg-polymer @@ -0,0 +1,33 @@ +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 diff --git a/examples/USER/misc/charge_regulation/in_polymer.chreg b/examples/USER/misc/charge_regulation/in_polymer.chreg deleted file mode 100644 index e35ba28661..0000000000 --- a/examples/USER/misc/charge_regulation/in_polymer.chreg +++ /dev/null @@ -1,37 +0,0 @@ -# Charge regulation lammps for a polymer chain -units lj -atom_style full -dimension 3 -boundary p p p -processors * * * -neighbor 3.0 bin -read_data data_polymer.chreg - -bond_style harmonic -bond_coeff 1 100 1.122462 # K R0 -velocity all create 1.0 8008 loop geom - -pair_style lj/cut/coul/long 1.122462 20 -pair_coeff * * 1.0 1.0 1.122462 # charges -kspace_style pppm 1.0e-3 -pair_modify shift yes -dielectric 1.0 - -######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### -fix fnve all nve -compute dtemp all temp -compute_modify dtemp dynamic yes -fix fT all langevin 1.0 1.0 1.0 123 -fix_modify fT temp dtemp - -fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 -fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 -fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 - -thermo 100 -# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions -thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] -log log_polymer.lammps - -timestep 0.005 -run 20000 diff --git a/examples/USER/misc/charge_regulation/log_acid.lammps b/examples/USER/misc/charge_regulation/log_acid.lammps deleted file mode 100644 index cbc3661eb1..0000000000 --- a/examples/USER/misc/charge_regulation/log_acid.lammps +++ /dev/null @@ -1,163 +0,0 @@ -LAMMPS (24 Dec 2020) -Reading data file ... - orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 219 atoms - read_data CPU = 0.001 seconds -Ewald initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:339) - G vector (1/distance) = 0.14221027 - estimated absolute RMS force accuracy = 0.0010128126 - estimated relative force accuracy = 0.0010128126 - KSpace vectors: actual max1d max3d = 257 5 665 - kxmax kymax kzmax = 5 5 5 -0 atoms in group Fix_CR:exclusion_group:chareg -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 15.5 - ghost atom cutoff = 15.5 - binsize = 7.75, bins = 7 7 7 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/atomonly/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : lj - Current step : 0 - Time step : 0.005 -Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes -Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] - 0 -0.054228269 1 0 0 1 99 0 0 109 10 - 100 -0.058672881 0.99159291 100 71 16 84 0 0 92 8 - 200 -0.05399313 0.92006523 200 154 26 74 0 0 85 11 - 300 -0.047035343 0.92728143 300 240 22 78 0 0 85 7 - 400 -0.049597809 1.0617937 400 319 16 84 0 0 92 8 - 500 -0.052409835 1.0006148 500 404 12 88 0 0 97 9 - 600 -0.056012172 0.98059344 600 481 15 85 0 0 92 7 - 700 -0.053639989 0.99572709 700 561 16 84 0 0 94 10 - 800 -0.060026132 0.95764632 800 639 22 78 0 0 84 6 - 900 -0.050785422 0.98399084 900 719 28 72 0 0 82 10 - 1000 -0.062294743 0.97200068 1000 797 26 74 0 0 82 8 - 1100 -0.051269402 1.0064376 1100 877 25 75 0 0 84 9 - 1200 -0.077744839 1.0159098 1200 955 23 77 0 0 88 11 - 1300 -0.084889696 1.1230485 1300 1037 20 80 0 0 90 10 - 1400 -0.059361445 0.96735845 1400 1120 18 82 0 0 93 11 - 1500 -0.052926174 0.95579188 1500 1199 24 76 0 0 86 10 - 1600 -0.052376649 0.99376378 1600 1284 22 78 0 0 89 11 - 1700 -0.052480188 0.96085964 1700 1361 27 73 0 0 84 11 - 1800 -0.065884306 0.96747971 1800 1441 21 79 0 0 84 5 - 1900 -0.054315859 0.95873145 1900 1521 23 77 0 0 84 7 - 2000 -0.037161802 0.93562039 2000 1604 27 73 0 0 79 6 - 2100 -0.034977265 0.97177103 2100 1684 26 74 0 0 85 11 - 2200 -0.047434868 0.97897613 2200 1762 17 83 0 0 93 10 - 2300 -0.047392634 0.96570672 2300 1837 18 82 0 0 92 10 - 2400 -0.044879306 0.98620033 2400 1910 19 81 0 0 89 8 - 2500 -0.069690496 1.0690505 2500 1988 16 84 0 0 91 7 - 2600 -0.081588407 0.97711054 2600 2067 17 83 0 0 92 9 - 2700 -0.06341681 1.0386711 2700 2146 20 80 0 0 85 5 - 2800 -0.045290012 1.0402055 2800 2230 18 82 0 0 91 9 - 2900 -0.046875012 1.0609775 2900 2317 24 76 0 0 86 10 - 3000 -0.031258722 0.93861202 3000 2400 24 76 0 0 85 9 - 3100 -0.04673342 0.90800583 3100 2485 25 75 0 0 90 15 - 3200 -0.054354227 0.94493881 3200 2567 16 84 0 0 94 10 - 3300 -0.053647746 0.92321446 3300 2641 17 83 0 0 94 11 - 3400 -0.031751732 0.93735127 3400 2725 22 78 0 0 92 14 - 3500 -0.053806113 0.98798136 3500 2795 28 72 0 0 84 12 - 3600 -0.040751349 0.84291639 3600 2873 28 72 0 0 84 12 - 3700 -0.051747138 1.072448 3700 2951 24 76 0 0 92 16 - 3800 -0.043420594 1.0076309 3800 3030 26 74 0 0 79 5 - 3900 -0.050845848 1.0250023 3900 3103 29 71 0 0 76 5 - 4000 -0.039837847 1.064111 4000 3182 29 71 0 0 83 12 - 4100 -0.045638995 1.1249685 4100 3262 28 72 0 0 81 9 - 4200 -0.047956491 0.92255907 4200 3348 26 74 0 0 87 13 - 4300 -0.054052822 1.006239 4300 3423 19 81 0 0 90 9 - 4400 -0.053148034 1.0028887 4400 3506 24 76 0 0 83 7 - 4500 -0.062132076 1.0317847 4500 3587 23 77 0 0 82 5 - 4600 -0.04616043 0.99066453 4600 3673 28 72 0 0 82 10 - 4700 -0.066990889 1.0242064 4700 3755 18 82 0 0 90 8 - 4800 -0.0564736 0.91765628 4800 3832 22 78 0 0 91 13 - 4900 -0.052301294 0.95348659 4900 3912 28 72 0 0 81 9 - 5000 -0.062630677 1.0336579 5000 3989 18 82 0 0 92 10 - 5100 -0.053645908 1.0314613 5100 4062 20 80 0 0 85 5 - 5200 -0.062189568 1.0504732 5200 4133 23 77 0 0 84 7 - 5300 -0.049092746 1.0310832 5300 4217 24 76 0 0 82 6 - 5400 -0.051859257 0.99600428 5400 4299 27 73 0 0 80 7 - 5500 -0.065540815 0.98012128 5500 4381 19 81 0 0 92 11 - 5600 -0.071018582 0.9252814 5600 4455 23 77 0 0 84 7 - 5700 -0.066954185 1.0325214 5700 4535 26 74 0 0 82 8 - 5800 -0.064847249 1.0313536 5800 4617 21 79 0 0 90 11 - 5900 -0.063173056 0.95455853 5900 4703 18 82 0 0 92 10 - 6000 -0.064807837 0.97182222 6000 4790 21 79 0 0 91 12 - 6100 -0.07067683 0.91775921 6100 4875 16 84 0 0 94 10 - 6200 -0.071400842 1.0162225 6200 4952 17 83 0 0 87 4 - 6300 -0.078479449 1.0106706 6300 5033 21 79 0 0 84 5 - 6400 -0.083167651 1.0246584 6400 5111 18 82 0 0 90 8 - 6500 -0.092611537 1.0766467 6500 5195 20 80 0 0 88 8 - 6600 -0.096710071 1.0246648 6600 5274 15 85 0 0 91 6 - 6700 -0.073399857 0.94939392 6700 5351 17 83 0 0 92 9 - 6800 -0.062479375 0.9393967 6800 5434 18 82 0 0 93 11 - 6900 -0.065391043 0.93475954 6900 5514 22 78 0 0 89 11 - 7000 -0.045655499 0.98688239 7000 5601 21 79 0 0 90 11 - 7100 -0.061186309 1.0309063 7100 5684 22 78 0 0 87 9 - 7200 -0.074737514 1.0516593 7200 5769 25 75 0 0 80 5 - 7300 -0.075228979 1.0167704 7300 5847 21 79 0 0 86 7 - 7400 -0.06660147 1.0947107 7400 5930 25 75 0 0 87 12 - 7500 -0.071915247 1.10542 7500 6009 24 76 0 0 84 8 - 7600 -0.029974303 0.99202697 7600 6095 28 72 0 0 80 8 - 7700 -0.029024004 1.0390995 7700 6182 28 72 0 0 83 11 - 7800 -0.056250746 0.96393961 7800 6260 18 82 0 0 91 9 - 7900 -0.072178944 0.9833919 7900 6339 21 79 0 0 86 7 - 8000 -0.070377248 1.021342 8000 6419 23 77 0 0 88 11 - 8100 -0.07753283 0.96194312 8100 6493 26 74 0 0 86 12 - 8200 -0.075617309 0.9715344 8200 6576 25 75 0 0 89 14 - 8300 -0.077480013 0.99106705 8300 6662 20 80 0 0 91 11 - 8400 -0.079901928 0.89855112 8400 6744 23 77 0 0 91 14 - 8500 -0.069192745 1.0606791 8500 6822 19 81 0 0 91 10 - 8600 -0.058657202 1.1270217 8600 6898 15 85 0 0 95 10 - 8700 -0.044985397 1.0367419 8700 6979 27 73 0 0 84 11 - 8800 -0.064266376 0.91557003 8800 7060 21 79 0 0 89 10 - 8900 -0.068680533 0.95963643 8900 7133 19 81 0 0 88 7 - 9000 -0.051736144 1.0398547 9000 7213 13 87 0 0 94 7 - 9100 -0.058381436 0.98047663 9100 7290 17 83 0 0 89 6 - 9200 -0.05531014 0.92541631 9200 7368 22 78 0 0 85 7 - 9300 -0.04386907 0.9339658 9300 7454 22 78 0 0 89 11 - 9400 -0.052293168 0.94314034 9400 7539 22 78 0 0 86 8 - 9500 -0.050362046 1.0489028 9500 7617 18 82 0 0 90 8 - 9600 -0.054272227 1.0879161 9600 7697 11 89 0 0 96 7 - 9700 -0.042514179 1.0051505 9700 7771 22 78 0 0 84 6 - 9800 -0.045365018 0.95363669 9800 7850 25 75 0 0 77 2 - 9900 -0.064287274 0.91994667 9900 7928 27 73 0 0 81 8 - 10000 -0.05689162 0.99963208 10000 8011 22 78 0 0 84 6 -Loop time of 19.4452 on 1 procs for 10000 steps with 190 atoms - -Performance: 222162.510 tau/day, 514.265 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.68864 | 0.68864 | 0.68864 | 0.0 | 3.54 -Kspace | 6.7893 | 6.7893 | 6.7893 | 0.0 | 34.92 -Neigh | 0.060782 | 0.060782 | 0.060782 | 0.0 | 0.31 -Comm | 0.047035 | 0.047035 | 0.047035 | 0.0 | 0.24 -Output | 0.0027227 | 0.0027227 | 0.0027227 | 0.0 | 0.01 -Modify | 11.838 | 11.838 | 11.838 | 0.0 | 60.88 -Other | | 0.01878 | | | 0.10 - -Nlocal: 190.000 ave 190 max 190 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 592.000 ave 592 max 592 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2194.00 ave 2194 max 2194 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2194 -Ave neighs/atom = 11.547368 -Neighbor list builds = 10287 -Dangerous builds = 0 -Total wall time: 0:00:19 \ No newline at end of file From 7f8e8c635c10f0c99343c0f31565b91ac2de951b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 08:00:59 -0500 Subject: [PATCH 017/100] create new reference log files --- .../log.10Feb21.chreg-acid.g++.1 | 125 ++++++++++++ .../log.10Feb21.chreg-acid.g++.4 | 125 ++++++++++++ .../log.10Feb21.chreg-polymer.g++.1 | 131 +++++++++++++ .../log.10Feb21.chreg-polymer.g++.4 | 131 +++++++++++++ .../misc/charge_regulation/log_polymer.lammps | 181 ------------------ 5 files changed, 512 insertions(+), 181 deletions(-) create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 delete mode 100644 examples/USER/misc/charge_regulation/log_polymer.lammps diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 new file mode 100644 index 0000000000..627281217b --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.1 @@ -0,0 +1,125 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.003 seconds + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 12.5 +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 2000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.049662059 1 0 0 1 99 0 0 109 10 + 100 -0.053672881 0.99159291 100 71 16 84 0 0 92 8 + 200 -0.053383027 0.90935145 200 156 26 74 0 0 85 11 + 300 -0.040471335 0.97937429 300 240 21 79 0 0 87 8 + 400 -0.036188123 1.0837424 400 319 14 86 0 0 92 6 + 500 -0.057294925 1.0507526 500 407 10 90 0 0 98 8 + 600 -0.056009748 1.0669354 600 487 15 85 0 0 92 7 + 700 -0.069686562 0.99202496 700 567 14 86 0 0 96 10 + 800 -0.054695624 1.0592933 800 647 25 75 0 0 82 7 + 900 -0.058693653 0.97870458 900 728 27 73 0 0 83 10 + 1000 -0.062352957 1.0008923 1000 805 24 76 0 0 84 8 + 1100 -0.065011926 0.91691048 1100 886 22 78 0 0 87 9 + 1200 -0.080463686 0.98879304 1200 963 23 77 0 0 88 11 + 1300 -0.062146141 1.0566033 1300 1047 21 79 0 0 88 9 + 1400 -0.046980246 1.0847512 1400 1129 17 83 0 0 94 11 + 1500 -0.042935292 1.0075805 1500 1203 24 76 0 0 86 10 + 1600 -0.056075891 0.94173489 1600 1277 23 77 0 0 90 13 + 1700 -0.042279161 1.1126317 1700 1355 28 72 0 0 82 10 + 1800 -0.036842528 1.0255327 1800 1436 24 76 0 0 83 7 + 1900 -0.038816022 0.93883373 1900 1511 23 77 0 0 86 9 + 2000 -0.047008287 0.98904085 2000 1592 26 74 0 0 81 7 +Loop time of 11.6365 on 1 procs for 2000 steps with 188 atoms + +Performance: 74249.079 tau/day, 171.873 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.24337 | 0.24337 | 0.24337 | 0.0 | 2.09 +Kspace | 4.6009 | 4.6009 | 4.6009 | 0.0 | 39.54 +Neigh | 0.023451 | 0.023451 | 0.023451 | 0.0 | 0.20 +Comm | 0.027729 | 0.027729 | 0.027729 | 0.0 | 0.24 +Output | 0.0007813 | 0.0007813 | 0.0007813 | 0.0 | 0.01 +Modify | 6.7345 | 6.7345 | 6.7345 | 0.0 | 57.87 +Other | | 0.005713 | | | 0.05 + +Nlocal: 188.000 ave 188 max 188 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 597.000 ave 597 max 597 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2196.00 ave 2196 max 2196 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2196 +Ave neighs/atom = 11.680851 +Neighbor list builds = 2059 +Dangerous builds = 0 +Total wall time: 0:00:11 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 new file mode 100644 index 0000000000..465dcbdb4e --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-acid.g++.4 @@ -0,0 +1,125 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for simple weak electrolyte + +units lj +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid +Reading data file ... + orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.003 seconds + +variable cut_long equal 12.5 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0) +variable lunit_nm equal 0.72 # in the units of nm +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 ${cut_long} +pair_style lj/cut/coul/long 1.12246204830937 12.5 +pair_coeff * * 1.0 1.0 +kspace_style ewald 1.0e-3 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.72 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep 0.005 +run 2000 +Ewald initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.14221027 + estimated absolute RMS force accuracy = 0.0010128126 + estimated relative force accuracy = 0.0010128126 + KSpace vectors: actual max1d max3d = 257 5 665 + kxmax kymax kzmax = 5 5 5 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 15.5 + ghost atom cutoff = 15.5 + binsize = 7.75, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 11.89 | 11.89 | 11.89 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -0.049662059 1 0 0 1 99 0 0 109 10 + 100 -0.06196414 1.0156327 100 72 15 85 0 0 93 8 + 200 -0.053901683 0.95128403 200 160 24 76 0 0 87 11 + 300 -0.043852423 0.98035058 300 246 22 78 0 0 85 7 + 400 -0.048370798 1.0909844 400 324 16 84 0 0 91 7 + 500 -0.042546472 1.026849 500 410 13 87 0 0 95 8 + 600 -0.06133022 0.97805065 600 494 14 86 0 0 93 7 + 700 -0.053815853 1.0641005 700 572 17 83 0 0 91 8 + 800 -0.059974814 1.0192348 800 650 23 77 0 0 83 6 + 900 -0.051808132 1.0773288 900 728 25 75 0 0 85 10 + 1000 -0.050390995 1.0236954 1000 804 28 72 0 0 81 9 + 1100 -0.069766444 1.030965 1100 890 25 75 0 0 85 10 + 1200 -0.074580231 1.0490058 1200 963 21 79 0 0 88 9 + 1300 -0.060169443 0.93456607 1300 1043 22 78 0 0 86 8 + 1400 -0.05120764 1.0374062 1400 1127 19 81 0 0 92 11 + 1500 -0.027644416 0.99804782 1500 1204 24 76 0 0 85 9 + 1600 -0.038599195 0.99015524 1600 1283 22 78 0 0 90 12 + 1700 -0.050222686 1.1444379 1700 1365 27 73 0 0 84 11 + 1800 -0.049338003 1.1188048 1800 1449 22 78 0 0 84 6 + 1900 -0.04533154 0.99894341 1900 1527 22 78 0 0 86 8 + 2000 -0.058837311 0.95302017 2000 1608 26 74 0 0 81 7 +Loop time of 3.98119 on 4 procs for 2000 steps with 188 atoms + +Performance: 217020.495 tau/day, 502.362 timesteps/s +96.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.050626 | 0.061127 | 0.071318 | 3.4 | 1.54 +Kspace | 1.1987 | 1.2504 | 1.288 | 3.1 | 31.41 +Neigh | 0.0056982 | 0.0063858 | 0.0069821 | 0.7 | 0.16 +Comm | 0.068302 | 0.11638 | 0.17922 | 12.8 | 2.92 +Output | 0.00055408 | 0.00092399 | 0.0020106 | 0.0 | 0.02 +Modify | 2.5399 | 2.5406 | 2.5417 | 0.0 | 63.81 +Other | | 0.005394 | | | 0.14 + +Nlocal: 47.0000 ave 55 max 42 min +Histogram: 1 0 1 1 0 0 0 0 0 1 +Nghost: 328.250 ave 335 max 317 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 547.000 ave 659 max 466 min +Histogram: 2 0 0 0 0 0 1 0 0 1 + +Total # of neighbors = 2188 +Ave neighs/atom = 11.638298 +Neighbor list builds = 2057 +Dangerous builds = 0 +Total wall time: 0:00:04 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 new file mode 100644 index 0000000000..c386b2bed9 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.1 @@ -0,0 +1,131 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.009 seconds + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision FFTW3 + 3d grid and FFT values/proc = 2197 512 +0 atoms in group FixChargeRegulation:exclusion_group:chareg1 +0 atoms in group FixChargeRegulation:exclusion_group:chareg2 +0 atoms in group FixChargeRegulation:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.50528297 1 0 80 80 0 0 0 + 100 0.61185377 0.95892928 13 67 74 7 0 0 + 200 0.54355177 1.1282424 19 61 76 15 0 0 + 300 0.4519957 1.0764688 20 60 85 26 1 0 + 400 0.41479389 0.99212685 24 56 92 36 0 0 + 500 0.37382446 0.99776674 28 52 98 46 0 0 + 600 0.34785337 1.1115081 28 52 109 57 0 0 + 700 0.34637618 1.0332262 28 52 120 68 0 0 + 800 0.21020932 1.1264036 29 51 125 74 0 0 + 900 0.21246108 1.1168609 30 50 131 81 0 0 + 1000 0.20997475 1.1201478 32 48 132 84 0 0 + 1100 0.1984165 1.0209092 31 49 144 95 0 0 + 1200 0.2061932 0.95880059 35 45 151 106 0 0 + 1300 0.17220376 0.980077 36 44 156 112 0 0 + 1400 0.15671143 0.93535342 37 43 161 118 0 0 + 1500 0.16174665 0.9495928 36 44 168 124 0 0 + 1600 0.11062965 0.94072924 40 40 164 124 0 0 + 1700 0.13002563 0.95010828 38 42 167 125 0 0 + 1800 0.14527814 0.93555342 37 43 172 129 0 0 + 1900 0.17627465 0.96682495 32 48 176 128 0 0 + 2000 0.16497265 0.95226954 33 47 180 133 0 0 +Loop time of 7.45499 on 1 procs for 2000 steps with 393 atoms + +Performance: 115895.577 tau/day, 268.277 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.45607 | 0.45607 | 0.45607 | 0.0 | 6.12 +Bond | 0.0062385 | 0.0062385 | 0.0062385 | 0.0 | 0.08 +Kspace | 2.3257 | 2.3257 | 2.3257 | 0.0 | 31.20 +Neigh | 0.067103 | 0.067103 | 0.067103 | 0.0 | 0.90 +Comm | 0.02577 | 0.02577 | 0.02577 | 0.0 | 0.35 +Output | 0.00087047 | 0.00087047 | 0.00087047 | 0.0 | 0.01 +Modify | 4.5664 | 4.5664 | 4.5664 | 0.0 | 61.25 +Other | | 0.006848 | | | 0.09 + +Nlocal: 393.000 ave 393 max 393 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 749.000 ave 749 max 749 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 5359.00 ave 5359 max 5359 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 5359 +Ave neighs/atom = 13.636132 +Ave special neighs/atom = 1.1908397 +Neighbor list builds = 1489 +Dangerous builds = 0 +Total wall time: 0:00:07 diff --git a/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 new file mode 100644 index 0000000000..c623d3048b --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.10Feb21.chreg-polymer.g++.4 @@ -0,0 +1,131 @@ +LAMMPS (10 Feb 2021) + using 1 OpenMP thread(s) per MPI task +# Charge regulation lammps for a polymer chain +units lj +atom_style full +neighbor 3.0 bin +read_data data.chreg-polymer +Reading data file ... + orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 160 atoms + scanning bonds ... + 1 = max bonds/atom + reading bonds ... + 79 bonds +Finding 1-2 1-3 1-4 neighbors ... + special bond factors lj: 0 0 0 + special bond factors coul: 0 0 0 + 2 = max # of 1-2 neighbors + 2 = max # of 1-3 neighbors + 4 = max # of 1-4 neighbors + 6 = max # of special neighbors + special bonds CPU = 0.001 seconds + read_data CPU = 0.016 seconds + +bond_style harmonic +bond_coeff 1 100 1.122462 # K R0 +velocity all create 1.0 8008 loop geom + +pair_style lj/cut/coul/long 1.122462 20 +pair_coeff * * 1.0 1.0 1.122462 # charges +kspace_style pppm 1.0e-3 +pair_modify shift yes +dielectric 1.0 + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin 1.0 1.0 1.0 123 +fix_modify fT temp dtemp + +fix chareg1 all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40 seed 2345 +fix chareg2 all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40 seed 2345 +fix chareg3 all charge/regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20 seed 2345 + +thermo 100 +# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions +thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + +timestep 0.005 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (src/kspace.cpp:339) + G vector (1/distance) = 0.077106934 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00074388331 + estimated relative force accuracy = 0.00074388331 + using double precision FFTW3 + 3d grid and FFT values/proc = 1053 128 +0 atoms in group FixChargeRegulation:exclusion_group:chareg1 +0 atoms in group FixChargeRegulation:exclusion_group:chareg2 +0 atoms in group FixChargeRegulation:exclusion_group:chareg3 +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 23 + ghost atom cutoff = 23 + binsize = 11.5, bins = 9 9 9 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 6.878 | 6.935 | 6.992 Mbytes +Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] + 0 0.50528297 1 0 80 80 0 0 0 + 100 0.60223729 0.89547569 13 67 75 8 0 0 + 200 0.65253636 0.87662399 18 62 78 16 0 0 + 300 0.51550501 1.0542131 22 58 84 27 1 0 + 400 0.43566766 0.94557633 26 54 90 36 0 0 + 500 0.36269507 1.0386276 31 49 94 45 0 0 + 600 0.32430641 0.99903033 27 53 111 58 0 0 + 700 0.30255299 0.91225991 28 52 121 69 0 0 + 800 0.27189951 0.9747089 28 52 127 75 0 0 + 900 0.25495247 1.0747821 28 52 135 83 0 0 + 1000 0.25950416 0.95256449 32 48 134 86 0 0 + 1100 0.22561248 1.0102255 32 48 147 99 0 0 + 1200 0.1734754 0.99475154 33 47 157 110 0 0 + 1300 0.20081084 0.99873599 36 44 160 116 0 0 + 1400 0.14240417 0.99442152 36 44 164 121 1 0 + 1500 0.15314186 0.94559876 39 41 167 126 0 0 + 1600 0.13574107 1.0484195 43 37 164 127 0 0 + 1700 0.14477789 1.0105172 42 38 166 128 0 0 + 1800 0.13493107 1.0349667 41 39 171 132 0 0 + 1900 0.14849779 0.9994329 33 47 178 131 0 0 + 2000 0.14485171 0.99739608 34 46 183 137 0 0 +Loop time of 3.18871 on 4 procs for 2000 steps with 400 atoms + +Performance: 270955.695 tau/day, 627.212 timesteps/s +94.5% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.086456 | 0.11738 | 0.18562 | 11.8 | 3.68 +Bond | 0.00099182 | 0.0018544 | 0.0030079 | 1.8 | 0.06 +Kspace | 0.77406 | 0.79354 | 0.80895 | 1.5 | 24.89 +Neigh | 0.017894 | 0.017948 | 0.018002 | 0.0 | 0.56 +Comm | 0.029044 | 0.07885 | 0.11432 | 11.3 | 2.47 +Output | 0.00054932 | 0.0009656 | 0.0021319 | 0.0 | 0.03 +Modify | 2.1676 | 2.1706 | 2.1733 | 0.2 | 68.07 +Other | | 0.007591 | | | 0.24 + +Nlocal: 100.000 ave 110 max 89 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Nghost: 415.000 ave 418 max 411 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 1360.75 ave 1872 max 1018 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 5443 +Ave neighs/atom = 13.607500 +Ave special neighs/atom = 1.1700000 +Neighbor list builds = 1492 +Dangerous builds = 0 +Total wall time: 0:00:03 diff --git a/examples/USER/misc/charge_regulation/log_polymer.lammps b/examples/USER/misc/charge_regulation/log_polymer.lammps deleted file mode 100644 index 87cab63a6c..0000000000 --- a/examples/USER/misc/charge_regulation/log_polymer.lammps +++ /dev/null @@ -1,181 +0,0 @@ -LAMMPS (24 Dec 2020) -Reading data file ... - orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 160 atoms - scanning bonds ... - 1 = max bonds/atom - reading bonds ... - 79 bonds -Finding 1-2 1-3 1-4 neighbors ... - special bond factors lj: 0 0 0 - special bond factors coul: 0 0 0 - 2 = max # of 1-2 neighbors - 2 = max # of 1-3 neighbors - 4 = max # of 1-4 neighbors - 6 = max # of special neighbors - special bonds CPU = 0.000 seconds - read_data CPU = 0.004 seconds -PPPM initialization ... - using 12-bit tables for long-range coulomb (../kspace.cpp:339) - G vector (1/distance) = 0.077106934 - grid = 8 8 8 - stencil order = 5 - estimated absolute RMS force accuracy = 0.00074388331 - estimated relative force accuracy = 0.00074388331 - using double precision KISS FFT - 3d grid and FFT values/proc = 2197 512 -0 atoms in group Fix_CR:exclusion_group:chareg1 -0 atoms in group Fix_CR:exclusion_group:chareg2 -0 atoms in group Fix_CR:exclusion_group:chareg3 -WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) -Neighbor list info ... - update every 1 steps, delay 10 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 23 - ghost atom cutoff = 23 - binsize = 11.5, bins = 9 9 9 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/cut/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Setting up Verlet run ... - Unit style : lj - Current step : 0 - Time step : 0.005 -Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes -Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8] - 0 0.49903297 1 0 80 80 0 0 0 - 100 0.63380666 0.87307225 8 72 77 6 1 0 - 200 0.5865464 1.0048645 16 64 81 16 0 1 - 300 0.55802913 1.0499142 19 61 91 29 0 1 - 400 0.44734087 1.0838048 24 56 98 41 0 1 - 500 0.47010775 1.005226 23 57 106 48 0 1 - 600 0.3452105 0.97814306 28 52 109 56 0 1 - 700 0.29208955 0.99766419 32 48 115 67 0 0 - 800 0.27821915 1.0091641 31 49 128 80 1 0 - 900 0.28943788 0.93619239 26 54 145 91 0 0 - 1000 0.22963142 1.0162138 27 53 150 97 0 0 - 1100 0.24238916 0.99146577 31 49 149 100 0 0 - 1200 0.17029095 1.0406453 38 42 144 102 0 0 - 1300 0.15830969 0.94661447 34 46 155 109 0 0 - 1400 0.16698712 1.0116563 35 45 159 114 0 0 - 1500 0.15432936 0.95600941 36 44 162 118 0 0 - 1600 0.16973501 0.98326602 31 49 171 122 0 0 - 1700 0.19725116 0.9915273 33 47 175 128 0 0 - 1800 0.15278999 1.0304873 29 51 193 142 0 0 - 1900 0.17418479 0.99490216 30 50 194 144 0 0 - 2000 0.14238391 0.9638301 32 48 189 141 0 0 - 2100 0.13054378 0.97164976 32 48 192 144 0 0 - 2200 0.092083069 1.0112059 40 40 191 151 0 0 - 2300 0.085175091 1.0070667 39 41 200 159 0 0 - 2400 0.083367076 0.9934796 35 45 208 163 0 0 - 2500 0.11494744 0.97650855 31 49 220 172 1 0 - 2600 0.10796032 0.97047046 34 46 221 175 0 0 - 2700 0.11080141 0.93570013 36 44 223 179 0 0 - 2800 0.096699277 0.97702627 35 45 223 178 0 0 - 2900 0.079403783 1.0870961 32 48 229 181 0 0 - 3000 0.08288836 1.0642515 35 45 231 186 0 0 - 3100 0.094000833 1.0241111 38 42 229 187 0 0 - 3200 0.10011052 1.043594 34 46 235 189 0 0 - 3300 0.096782103 0.99549134 34 46 234 188 0 0 - 3400 0.057703946 1.00292 34 46 236 190 0 0 - 3500 0.074345642 0.95064523 36 44 234 190 0 0 - 3600 0.085872341 0.9759514 35 45 238 192 0 1 - 3700 0.086427565 0.99843063 35 45 240 194 0 1 - 3800 0.076091357 0.98516844 32 48 252 203 0 1 - 3900 0.047187813 1.0063336 37 43 247 204 0 0 - 4000 0.068269223 1.0390369 35 45 248 203 0 0 - 4100 0.074209582 0.99912762 36 44 249 205 0 0 - 4200 0.087016078 1.050265 36 44 246 202 0 0 - 4300 0.081325479 1.0417103 35 45 245 200 0 0 - 4400 0.047345973 0.96517298 39 41 243 202 0 0 - 4500 0.041856955 0.94569673 38 42 245 203 0 0 - 4600 0.049588267 0.99046371 42 38 249 211 0 0 - 4700 0.043079897 1.0098538 43 37 245 208 0 0 - 4800 0.049122913 1.0229995 41 39 247 208 0 0 - 4900 0.059151797 1.0236679 36 44 249 205 0 0 - 5000 0.053806841 1.0308397 42 38 243 205 0 0 - 5100 0.053623833 1.0638841 39 41 246 205 0 0 - 5200 0.086215806 1.0027613 37 43 243 200 0 0 - 5300 0.031422797 1.0338154 38 42 245 203 0 0 - 5400 0.051341116 0.92205149 34 46 246 200 0 0 - 5500 0.039292708 0.97530704 32 48 251 203 0 0 - 5600 0.035215415 1.023123 33 47 246 199 0 0 - 5700 0.054553598 0.95833063 30 50 253 203 0 0 - 5800 0.035699456 1.0721613 37 43 248 205 0 0 - 5900 0.062426908 1.0612245 38 42 252 210 0 0 - 6000 0.056362902 1.0002968 36 44 248 204 0 0 - 6100 0.061550208 0.97270904 38 42 245 203 0 0 - 6200 0.051825485 0.98187623 36 44 253 209 0 0 - 6300 0.052137885 0.98906723 36 44 253 210 1 0 - 6400 0.068218075 1.0511584 36 44 256 212 0 0 - 6500 0.080167413 0.97270144 36 44 252 208 0 0 - 6600 0.052169204 1.0160108 41 39 249 210 0 0 - 6700 0.057313326 0.98033894 38 42 251 209 0 0 - 6800 0.073008094 0.96239565 35 45 256 211 0 0 - 6900 0.060159599 1.0063892 37 43 264 221 0 0 - 7000 0.061738744 1.0031443 39 41 259 218 0 0 - 7100 0.043263424 1.0425248 44 36 255 219 0 0 - 7200 0.052179167 0.99512151 39 41 261 220 0 0 - 7300 0.053258707 1.0171204 43 37 256 219 0 0 - 7400 0.026037532 0.93786837 45 35 259 224 0 0 - 7500 0.029731213 1.0172281 46 34 250 216 0 0 - 7600 0.023118288 0.95628439 42 38 262 224 0 0 - 7700 0.037021854 0.99991854 42 38 263 225 0 0 - 7800 0.050404736 1.0130826 40 40 260 220 0 0 - 7900 0.035658921 0.95772506 40 40 259 219 0 0 - 8000 0.034426806 1.0028052 40 40 254 214 0 0 - 8100 0.041427611 1.0347682 40 40 256 216 0 0 - 8200 0.05986843 0.9804614 38 42 262 220 0 0 - 8300 0.041419023 1.0613186 37 43 264 221 0 0 - 8400 0.065701758 1.0511531 40 40 256 216 0 0 - 8500 0.091954526 0.97190676 37 43 257 214 0 0 - 8600 0.056982532 1.017813 35 45 252 207 0 0 - 8700 0.075615111 1.0148527 29 51 263 212 0 0 - 8800 0.066070082 1.0259454 33 47 260 213 0 0 - 8900 0.055054194 1.0183535 37 43 247 204 0 0 - 9000 0.063070816 1.0266115 39 41 244 203 0 0 - 9100 0.10174156 0.99457684 34 46 246 200 0 0 - 9200 0.071667261 1.033159 33 47 249 202 0 0 - 9300 0.05520096 0.99821492 38 42 243 201 0 0 - 9400 0.050355422 0.99148522 37 43 243 200 0 0 - 9500 0.062314961 1.0042937 36 44 252 208 0 0 - 9600 0.061148899 1.0052132 37 43 254 211 0 0 - 9700 0.078695273 1.0175164 37 43 252 209 0 0 - 9800 0.067487202 1.0110138 35 45 258 213 0 0 - 9900 0.070340779 0.99640142 31 49 263 214 0 0 - 10000 0.037252172 0.99863894 32 48 259 211 0 0 -Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms - -Performance: 187484.206 tau/day, 433.991 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04 -Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11 -Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56 -Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89 -Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32 -Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02 -Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91 -Other | | 0.03479 | | | 0.15 - -Nlocal: 550.000 ave 550 max 550 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1023.00 ave 1023 max 1023 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 9644.00 ave 9644 max 9644 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 9644 -Ave neighs/atom = 17.534545 -Ave special neighs/atom = 0.85090909 -Neighbor list builds = 7576 -Dangerous builds = 0 -Total wall time: 0:00:23 \ No newline at end of file From f705d49d4557014e6af45a45fff89606799ac61e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 11 Feb 2021 09:17:14 -0500 Subject: [PATCH 018/100] reformat docs, correct spelling errors, and update false positives list --- doc/src/fix_charge_regulation.rst | 202 ++++++++++++++------ doc/utils/sphinx-config/false_positives.txt | 28 ++- 2 files changed, 172 insertions(+), 58 deletions(-) diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index cb9f55c7cd..fb63c8d7a5 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -8,21 +8,21 @@ Syntax """""" .. parsed-literal:: - + fix ID group-ID charge/regulation cation_type anion_type keyword value(s) * ID, group-ID are documented in fix command * charge/regulation = style name of this fix command * cation_type = atom type of free cations * anion_type = atom type of free anions - + * zero or more keyword/value pairs may be appended .. parsed-literal:: - - keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* + + keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves* *pH* value = pH of the solution - *pKa* value = acid dissociation constant + *pKa* value = acid dissociation constant *pKb* value = base dissociation constant *pIp* value = chemical potential of free cations *pIm* value = chemical potential of free anions @@ -30,7 +30,7 @@ Syntax *acid_type* = atom type of acid groups *base_type* = atom type of base groups *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers) - *temp* value = temperature + *temp* value = temperature *tempfixid* value = fix ID of temperature thermostat *nevery* value = invoke this fix every nevery steps *nmc* value = number of charge regulation MC moves to attempt every nevery steps @@ -38,124 +38,212 @@ Syntax *seed* value = random # seed (positive integer) *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0") *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups. - *onlysalt* values = flag charge_cation charge_anion. + *onlysalt* values = flag charge_cation charge_anion. flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion) charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes) - *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) + *pmcmoves* values = pmcA pmcB pmcI - MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI) Examples """""""" .. code-block:: LAMMPS - fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT + fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0 Description """"""""""" -This fix performs Monte Carlo (MC) sampling of charge regulation and exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` and :ref:`(Curk2) `. -The implemented method is largely analogous to the grand-reaction ensemble method in :ref:`(Landsgesell) `. -The implementation is parallelized, compatible with existing LAMMPS functionalities, and applicable to any system utilizing discreet, ionizable groups or surface sites. +This fix performs Monte Carlo (MC) sampling of charge regulation and +exchange of ions with a reservoir as discussed in :ref:`(Curk1) ` +and :ref:`(Curk2) `. The implemented method is largely analogous +to the grand-reaction ensemble method in :ref:`(Landsgesell) +`. The implementation is parallelized, compatible with +existing LAMMPS functionalities, and applicable to any system utilizing +discrete, ionizable groups or surface sites. -Specifically, the fix implements the following three types of MC moves, which discretely change the charge state of individual particles and insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{X}^-`, -and :math:`\emptyset \rightleftharpoons Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. -In the former two types of reactions, Monte Carlo moves alter the charge value of specific atoms (:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a counterion to preserve the charge neutrality of the system, modeling the dissociation/association process. -The last type of reaction performs grand canonical MC exchange of ion pairs with a (fictitious) reservoir. +Specifically, the fix implements the following three types of MC moves, +which discretely change the charge state of individual particles and +insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons +\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons +\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons +Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`. In the former two types of +reactions, Monte Carlo moves alter the charge value of specific atoms +(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a +counterion to preserve the charge neutrality of the system, modeling the +dissociation/association process. The last type of reaction performs +grand canonical MC exchange of ion pairs with a (fictitious) reservoir. -In our implementation "acid" refers to particles that can attain charge :math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, -whereas the MC exchange of free ions allows any integer charge values of :math:`{Z^+}` and :math:`{Z^-}`. +In our implementation "acid" refers to particles that can attain charge +:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`, +whereas the MC exchange of free ions allows any integer charge values of +:math:`{Z^+}` and :math:`{Z^-}`. -Here we provide several practical examples for modeling charge regulation effects in solvated systems. -An acid ionization reaction (:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be defined via a single line in the input file +Here we provide several practical examples for modeling charge +regulation effects in solvated systems. An acid ionization reaction +(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be +defined via a single line in the input file .. code-block:: LAMMPS fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0 -where the fix attempts to charge :math:`\mathrm{A}` (discharge :math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and insert (delete) a proton (atom type 2). Besides, the fix implements self-ionization reaction of water :math:`\emptyset \rightleftharpoons \mathrm{H}^++\mathrm{OH}^-`. -However, this approach is highly inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of both protons and hydroxyl ions is low, resulting in a relatively low acceptance rate of MC moves. +where the fix attempts to charge :math:`\mathrm{A}` (discharge +:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and +insert (delete) a proton (atom type 2). Besides, the fix implements +self-ionization reaction of water :math:`\emptyset \rightleftharpoons +\mathrm{H}^++\mathrm{OH}^-`. However, this approach is highly +inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of +both protons and hydroxyl ions is low, resulting in a relatively low +acceptance rate of MC moves. -A more efficient way is to allow salt ions to -participate in ionization reactions, which can be easily achieved via +A more efficient way is to allow salt ions to participate in ionization +reactions, which can be easily achieved via .. code-block:: LAMMPS fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0 -where particles of atom type 4 and 5 are the salt cations and anions, both at chemical potential pI=2.0, see :ref:`(Curk1) ` and :ref:`(Landsgesell) ` for more details. +where particles of atom type 4 and 5 are the salt cations and anions, +both at chemical potential pI=2.0, see :ref:`(Curk1) ` and +:ref:`(Landsgesell) ` for more details. - Similarly, we could have simultanously added a base ionization reaction (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) + Similarly, we could have simultaneously added a base ionization reaction + (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`) .. code-block:: LAMMPS fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0 - -where the fix will attempt to charge :math:`\mathrm{B}` (discharge :math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. -If neither the acid or the base type is specified, for example, + +where the fix will attempt to charge :math:`\mathrm{B}` (discharge +:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and +insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3. If +neither the acid or the base type is specified, for example, .. code-block:: LAMMPS fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0 - -the fix simply inserts or deletes an ion pair of a free cation (atom type 4) and a free anion (atom type 5) as done in a conventional grand-canonical MC simulation. + +the fix simply inserts or deletes an ion pair of a free cation (atom +type 4) and a free anion (atom type 5) as done in a conventional +grand-canonical MC simulation. -The fix is compatible with LAMMPS sub-packages such as *molecule* or *rigid*. That said, the acid and base particles can be part of larger molecules or rigid bodies. Free ions that are inserted to or deleted from the system must be defined as single particles (no bonded interactions allowed) and cannot be part of larger molecules or rigid bodies. If *molecule* package is used, all inserted ions have a molecule ID equal to zero. +The fix is compatible with LAMMPS sub-packages such as *molecule* or +*rigid*. That said, the acid and base particles can be part of larger +molecules or rigid bodies. Free ions that are inserted to or deleted +from the system must be defined as single particles (no bonded +interactions allowed) and cannot be part of larger molecules or rigid +bodies. If *molecule* package is used, all inserted ions have a molecule +ID equal to zero. -Note that LAMMPS implicitly assumes a constant number of particles (degrees of freedom). Since using this fix alters the total number of particles during the simulation, any thermostat used by LAMMPS, such as NVT or Langevin, must use a dynamic calculation of system temperature. This can be achieved by specifying a dynamic temperature compute (e.g. dtemp) and using it with the desired thermostat, e.g. a Langevin thermostat: +Note that LAMMPS implicitly assumes a constant number of particles +(degrees of freedom). Since using this fix alters the total number of +particles during the simulation, any thermostat used by LAMMPS, such as +NVT or Langevin, must use a dynamic calculation of system +temperature. This can be achieved by specifying a dynamic temperature +compute (e.g. dtemp) and using it with the desired thermostat, e.g. a +Langevin thermostat: .. code-block:: LAMMPS compute dtemp all temp - compute_modify dtemp dynamic yes - fix fT all langevin 1.0 1.0 1.0 123 + compute_modify dtemp dynamic yes + fix fT all langevin 1.0 1.0 1.0 123 fix_modify fT temp dtemp -The chemical potential units (e.g. pH) are in the standard log10 representation assuming reference concentration :math:`\rho_0 = \mathrm{mol}/\mathrm{l}`. -Therefore, to perform the internal unit conversion, the length (in nanometers) of the LAMMPS unit length -must be specified via *lunit_nm* (default is set to the Bjerrum length in water at room temprature *lunit_nm* = 0.71nm). For example, in the dilute ideal solution limit, the concentration of free ions -will be :math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. +The chemical potential units (e.g. pH) are in the standard log10 +representation assuming reference concentration :math:`\rho_0 = +\mathrm{mol}/\mathrm{l}`. Therefore, to perform the internal unit +conversion, the length (in nanometers) of the LAMMPS unit length must be +specified via *lunit_nm* (default is set to the Bjerrum length in water +at room temperature *lunit_nm* = 0.71nm). For example, in the dilute +ideal solution limit, the concentration of free ions will be +:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`. -The temperature used in MC acceptance probability is set by *temp*. This temperature should be the same as the temperature set by the molecular dynamics thermostat. For most purposes, it is probably best to use *tempfixid* keyword which dynamically sets the temperature equal to the chosen MD thermostat temperature, in the example above we assumed the thermostat fix-ID is *fT*. The inserted particles attain a random velocity corresponding to the specified temperature. Using *tempfixid* overrides any fixed temperature set by *temp*. +The temperature used in MC acceptance probability is set by *temp*. This +temperature should be the same as the temperature set by the molecular +dynamics thermostat. For most purposes, it is probably best to use +*tempfixid* keyword which dynamically sets the temperature equal to the +chosen MD thermostat temperature, in the example above we assumed the +thermostat fix-ID is *fT*. The inserted particles attain a random +velocity corresponding to the specified temperature. Using *tempfixid* +overrides any fixed temperature set by *temp*. -The *xrd* keyword can be used to restrict the inserted/deleted counterions to a specific radial distance from an acid or base particle that is currently participating in a reaction. This can be used to simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / 2, where *L* is the smallest box dimension, the radial restriction is automatically turned off and free ion can be inserted or deleted anywhere in the simulation box. +The *xrd* keyword can be used to restrict the inserted/deleted +counterions to a specific radial distance from an acid or base particle +that is currently participating in a reaction. This can be used to +simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* / +2, where *L* is the smallest box dimension, the radial restriction is +automatically turned off and free ion can be inserted or deleted +anywhere in the simulation box. -If the *tag yes* is used, every inserted atom gets a unique tag ID, otherwise, the tag of every inserted atom is set to 0. *tag yes* might cause an integer overflow in very long simulations since the tags are unique to every particle and thus increase with every successful particle insertion. +If the *tag yes* is used, every inserted atom gets a unique tag ID, +otherwise, the tag of every inserted atom is set to 0. *tag yes* might +cause an integer overflow in very long simulations since the tags are +unique to every particle and thus increase with every successful +particle insertion. -The *pmcmoves* keyword sets the relative probability of attempting the three types of MC moves (reactions): acid charging, base charging, and ion pair exchange. -The fix only attempts to perform particle charging MC moves if *acid_type* or *base_type* is defined. Otherwise fix only performs free ion insertion/deletion. For example, if *acid_type* is not defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, the vector would be normalized to [0,0.5,0.5]. +The *pmcmoves* keyword sets the relative probability of attempting the +three types of MC moves (reactions): acid charging, base charging, and +ion pair exchange. The fix only attempts to perform particle charging +MC moves if *acid_type* or *base_type* is defined. Otherwise fix only +performs free ion insertion/deletion. For example, if *acid_type* is not +defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is +automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33, +the vector would be normalized to [0,0.5,0.5]. -The *only_salt* option can be used to perform multivalent grand-canonical ion-exchange moves. If *only_salt yes* is used, no charge exchange is performed, only ion insertion/deletion (*pmcmoves* is set to [0,0,1]), but ions can be multivalent. In the example above, an MC move would consist of three ion insertion/deletion to preserve the charge neutrality of the system. +The *only_salt* option can be used to perform multivalent +grand-canonical ion-exchange moves. If *only_salt yes* is used, no +charge exchange is performed, only ion insertion/deletion (*pmcmoves* is +set to [0,0,1]), but ions can be multivalent. In the example above, an +MC move would consist of three ion insertion/deletion to preserve the +charge neutrality of the system. -The *group* keyword can be used to add inserted particles to a specific group-ID. All inserted particles are automatically added to group *all*. +The *group* keyword can be used to add inserted particles to a specific +group-ID. All inserted particles are automatically added to group *all*. Output """""" -This fix computes a global vector of length 8, which can be accessed by various output commands. The vector values are the following global quantities: + +This fix computes a global vector of length 8, which can be accessed by +various output commands. The vector values are the following global +quantities: * 1 = cumulative MC attempts * 2 = cumulative MC successes -* 3 = current # of neutral acid atoms -* 4 = current # of -1 charged acid atoms -* 5 = current # of neutral base atoms -* 6 = current # of +1 charged base atoms -* 7 = current # of free cations +* 3 = current # of neutral acid atoms +* 4 = current # of -1 charged acid atoms +* 5 = current # of neutral base atoms +* 6 = current # of +1 charged base atoms +* 7 = current # of free cations * 8 = current # of free anions Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. -See the :doc:`Build package ` doc page for more info. -The :doc:`atom_style `, used must contain the charge property, for example, the style could be *charge* or *full*. Only usable for 3D simulations. Atoms specified as free ions cannot be part of rigid bodies or molecules and cannot have bonding interactions. The scheme is limited to integer charges, any atoms with non-integer charges will not be considered by the fix. +This fix is part of the USER-MISC package. It is only enabled if LAMMPS +was built with that package. See the :doc:`Build package +` doc page for more info. -All interaction potentials used must be continuous, otherwise the MD integration and the particle exchange MC moves do not correspond to the same equilibrium ensemble. For example, if an lj/cut pair style is used, the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. +The :doc:`atom_style `, used must contain the charge +property, for example, the style could be *charge* or *full*. Only +usable for 3D simulations. Atoms specified as free ions cannot be part +of rigid bodies or molecules and cannot have bonding interactions. The +scheme is limited to integer charges, any atoms with non-integer charges +will not be considered by the fix. -Note: Region restrictions are not yet implemented. +All interaction potentials used must be continuous, otherwise the MD +integration and the particle exchange MC moves do not correspond to the +same equilibrium ensemble. For example, if an lj/cut pair style is used, +the LJ potential must be shifted so that it vanishes at the cutoff. This +can be easily achieved using the :doc:`pair_modify ` +command, i.e., by using: *pair_modify shift yes*. + +Note: Region restrictions are not yet implemented. Related commands """""""""""""""" diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 9937a98850..3a3729eefa 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -260,6 +260,7 @@ bitmask bitrate bitrates Bitzek +Bjerrum Blaise blanchedalmond blocksize @@ -500,6 +501,8 @@ coulgauss coulombic Coulombic Coulombics +counterion +counterions Courant covalent covalently @@ -728,6 +731,7 @@ DRUDE dsf dsmc dt +dtemp dtgrow dtheta dtshrink @@ -876,6 +880,7 @@ equilibrates equilibrating equilibration Equilibria +equilibria equilization equipartitioning Ercolessi @@ -1210,6 +1215,7 @@ hbnewflag hbond hcp heatconduction +Hebbeker Hebenstreit Hecht Heenen @@ -1277,6 +1283,7 @@ hy hydrophobicity hydrostatic hydrostatically +hydroxyl Hynninen Hyoungki hyperdynamics @@ -1367,6 +1374,7 @@ ints inv invariants inversed +ionizable ionocovalent iostreams iparam @@ -1546,6 +1554,7 @@ Koning Kooser Korn Koskinen +Kosovan Koster Kosztin Kp @@ -1591,6 +1600,7 @@ Lamoureux Lanczos Lande Landron +Landsgesell langevin Langevin Langston @@ -1728,10 +1738,13 @@ lpsapi lrt lsfftw ltbbmalloc +Lua lubricateU lucy -Lua Luding +Luijten +lunit +Lunkad Lussetti Lustig lval @@ -2015,6 +2028,7 @@ multiscale multisectioning multithreading Multithreading +multivalent Mundy Murdick Murtola @@ -2060,6 +2074,7 @@ Nanoletters nanomechanics nanometer nanometers +nanoparticle nanoparticles Nanotube nanotube @@ -2167,6 +2182,7 @@ nm Nm Nmax nmax +nmc Nmin nmin Nmols @@ -2299,6 +2315,7 @@ omp OMP onelevel oneway +onlysalt onn ons OO @@ -2380,6 +2397,8 @@ pbc pc pchain Pchain +pcmoves +pmcmoves Pdamp pdb pdf @@ -2424,6 +2443,7 @@ phosphide Phs Physica physik +pI Piaggi picocoulomb picocoulombs @@ -2435,7 +2455,9 @@ pid piecewise Pieniazek Pieter +pIm pimd +pIp Piola Pisarev Pishevar @@ -2450,6 +2472,9 @@ ploop PloS plt plumedfile +pKa +pKb +pKs pmb Pmolrotate Pmoltrans @@ -2768,6 +2793,7 @@ rst rstyle Rubensson Rubia +Rud Rudd Rudra Rudranarayan From 213fc06321270fa11eff0255e1d5bb16190546d4 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 29 Mar 2021 18:05:04 -0400 Subject: [PATCH 019/100] Add GzFileWriter implementation --- src/COMPRESS/dump_atom_gz.cpp | 89 +++++++-------- src/COMPRESS/dump_atom_gz.h | 5 +- src/COMPRESS/dump_atom_zstd.cpp | 6 +- src/COMPRESS/gz_file_writer.cpp | 105 ++++++++++++++++++ src/COMPRESS/gz_file_writer.h | 47 ++++++++ src/COMPRESS/zstd_file_writer.cpp | 8 +- src/COMPRESS/zstd_file_writer.h | 2 +- src/file_writer.h | 2 +- .../formats/test_dump_atom_compressed.cpp | 4 +- 9 files changed, 207 insertions(+), 61 deletions(-) create mode 100644 src/COMPRESS/gz_file_writer.cpp create mode 100644 src/COMPRESS/gz_file_writer.h diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index f252e32064..071af2167d 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -14,6 +14,7 @@ #include "dump_atom_gz.h" #include "domain.h" #include "error.h" +#include "file_writer.h" #include "update.h" @@ -25,10 +26,6 @@ using namespace LAMMPS_NS; DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtom(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump atom/gz only writes compressed files"); } @@ -37,9 +34,6 @@ DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : DumpAtomGZ::~DumpAtomGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } /* ---------------------------------------------------------------------- @@ -91,17 +85,12 @@ void DumpAtomGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +101,34 @@ void DumpAtomGZ::openfile() void DumpAtomGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: ATOMS {}\n", columns); + + writer.write(header.c_str(), header.length()); } } @@ -142,7 +136,7 @@ void DumpAtomGZ::write_header(bigint ndump) void DumpAtomGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -152,11 +146,11 @@ void DumpAtomGZ::write() DumpAtom::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -167,14 +161,15 @@ int DumpAtomGZ::modify_param(int narg, char **arg) { int consumed = DumpAtom::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_atom_gz.h b/src/COMPRESS/dump_atom_gz.h index 0c0b95974f..d540f5300a 100644 --- a/src/COMPRESS/dump_atom_gz.h +++ b/src/COMPRESS/dump_atom_gz.h @@ -21,7 +21,7 @@ DumpStyle(atom/gz,DumpAtomGZ) #define LMP_DUMP_ATOM_GZ_H #include "dump_atom.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpAtomGZ : public DumpAtom { virtual ~DumpAtomGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index 3dde07bbf4..300a4c81cb 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -90,12 +90,8 @@ void DumpAtomZstd::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - if (append_flag) { - error->one(FLERR, "dump/zstd currently doesn't support append"); - } - try { - writer.open(filecurrent); + writer.open(filecurrent, append_flag); } catch (FileWriterException &e) { error->one(FLERR, e.what()); } diff --git a/src/COMPRESS/gz_file_writer.cpp b/src/COMPRESS/gz_file_writer.cpp new file mode 100644 index 0000000000..d24d77b21a --- /dev/null +++ b/src/COMPRESS/gz_file_writer.cpp @@ -0,0 +1,105 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#include "gz_file_writer.h" +#include +#include "fmt/format.h" + +using namespace LAMMPS_NS; + +GzFileWriter::GzFileWriter() : FileWriter(), + compression_level(Z_BEST_COMPRESSION), + gzFp(nullptr) +{ +} + +/* ---------------------------------------------------------------------- */ + +GzFileWriter::~GzFileWriter() +{ + close(); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::open(const std::string &path, bool append) +{ + if (isopen()) return; + + std::string mode; + if (append) { + mode = fmt::format("ab{}", mode, compression_level); + } else { + mode = fmt::format("wb{}", mode, compression_level); + } + + gzFp = gzopen(path.c_str(), mode.c_str()); + + if (gzFp == nullptr) + throw FileWriterException(fmt::format("Could not open file '{}'", path)); +} + +/* ---------------------------------------------------------------------- */ + +size_t GzFileWriter::write(const void * buffer, size_t length) +{ + if (!isopen()) return 0; + + return gzwrite(gzFp, buffer, length); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::flush() +{ + if (!isopen()) return; + + gzflush(gzFp, Z_SYNC_FLUSH); +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::close() +{ + if (!isopen()) return; + + gzclose(gzFp); + gzFp = nullptr; +} + +/* ---------------------------------------------------------------------- */ + +bool GzFileWriter::isopen() const +{ + return gzFp; +} + +/* ---------------------------------------------------------------------- */ + +void GzFileWriter::setCompressionLevel(int level) +{ + if (isopen()) + throw FileWriterException("Compression level can not be changed while file is open"); + + const int min_level = Z_DEFAULT_COMPRESSION; + const int max_level = Z_BEST_COMPRESSION; + + if (level < min_level || level > max_level) + throw FileWriterException(fmt::format("Compression level must in the range of [{}, {}]", min_level, max_level)); + + compression_level = level; +} diff --git a/src/COMPRESS/gz_file_writer.h b/src/COMPRESS/gz_file_writer.h new file mode 100644 index 0000000000..28473b1164 --- /dev/null +++ b/src/COMPRESS/gz_file_writer.h @@ -0,0 +1,47 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing author: Richard Berger (Temple U) +------------------------------------------------------------------------- */ + +#ifndef LMP_GZ_FILE_WRITER_H +#define LMP_GZ_FILE_WRITER_H + +#include "file_writer.h" +#include +#include +#include + +namespace LAMMPS_NS { + +class GzFileWriter : public FileWriter { + int compression_level; + + gzFile gzFp; // file pointer for the compressed output stream +public: + GzFileWriter(); + virtual ~GzFileWriter(); + virtual void open(const std::string &path, bool append = false) override; + virtual void close() override; + virtual void flush() override; + virtual size_t write(const void * buffer, size_t length) override; + virtual bool isopen() const override; + + void setCompressionLevel(int level); +}; + + +} + +#endif diff --git a/src/COMPRESS/zstd_file_writer.cpp b/src/COMPRESS/zstd_file_writer.cpp index f82ade605c..3356fc1ad5 100644 --- a/src/COMPRESS/zstd_file_writer.cpp +++ b/src/COMPRESS/zstd_file_writer.cpp @@ -46,11 +46,15 @@ ZstdFileWriter::~ZstdFileWriter() /* ---------------------------------------------------------------------- */ -void ZstdFileWriter::open(const std::string &path) +void ZstdFileWriter::open(const std::string &path, bool append) { if (isopen()) return; - fp = fopen(path.c_str(), "wb"); + if (append) { + fp = fopen(path.c_str(), "ab"); + } else { + fp = fopen(path.c_str(), "wb"); + } if (!fp) { throw FileWriterException(fmt::format("Could not open file '{}'", path)); diff --git a/src/COMPRESS/zstd_file_writer.h b/src/COMPRESS/zstd_file_writer.h index 30afc86994..a4dbbdff64 100644 --- a/src/COMPRESS/zstd_file_writer.h +++ b/src/COMPRESS/zstd_file_writer.h @@ -38,7 +38,7 @@ class ZstdFileWriter : public FileWriter { public: ZstdFileWriter(); virtual ~ZstdFileWriter(); - virtual void open(const std::string &path) override; + virtual void open(const std::string &path, bool append = false) override; virtual void close() override; virtual void flush() override; virtual size_t write(const void * buffer, size_t length) override; diff --git a/src/file_writer.h b/src/file_writer.h index 8597ab570d..02eef6ad70 100644 --- a/src/file_writer.h +++ b/src/file_writer.h @@ -27,7 +27,7 @@ class FileWriter { public: FileWriter() = default; virtual ~FileWriter() = default; - virtual void open(const std::string &path) = 0; + virtual void open(const std::string &path, bool append = false) = 0; virtual void close() = 0; virtual void flush() = 0; virtual size_t write(const void * buffer, size_t length) = 0; diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index ed591184c3..51ce44fbb4 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -344,7 +344,7 @@ TEST_F(DumpAtomCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt"))); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -357,7 +357,7 @@ TEST_F(DumpAtomCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt"))); if (!verbose) ::testing::internal::GetCapturedStdout(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 39dc3e69ba716d63298cc8aca7e973268a94f8fe Mon Sep 17 00:00:00 2001 From: julient31 Date: Tue, 30 Mar 2021 10:35:25 -0600 Subject: [PATCH 020/100] Commit before pull --- doc/src/Howto_spins.rst | 4 ++-- .../validation_damped_exchange/run-test-exchange.sh | 12 +++++++++--- .../test-spin-precession.in | 8 +++++++- src/SPIN/pair_spin_exchange_biquadratic.cpp | 2 +- 4 files changed, 19 insertions(+), 7 deletions(-) diff --git a/doc/src/Howto_spins.rst b/doc/src/Howto_spins.rst index 0afcc12c91..87e30a5f6f 100644 --- a/doc/src/Howto_spins.rst +++ b/doc/src/Howto_spins.rst @@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances. The command :doc:`fix precession/spin ` allows to apply a constant magnetic torque on all the spins in the system. This -torque can be an external magnetic field (Zeeman interaction), or an -uniaxial magnetic anisotropy. +torque can be an external magnetic field (Zeeman interaction), and an +uniaxial or cubic magnetic anisotropy. A Langevin thermostat can be applied to those magnetic spins using :doc:`fix langevin/spin `. Typically, this thermostat diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index bd878a52de..a714e22fcf 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps -./../../../../src/lmp_serial \ - -in test-spin-precession.in +# test standard Lammps +# ./../../../../src/lmp_serial \ +# -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ + -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 9dfb4a98d6..bea5f53bf4 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -1,16 +1,22 @@ #LAMMPS in.run units metal -atom_style spin +# atom_style spin +atom_style spin/kk atom_modify map array boundary f f f +shell echo "test1" atom_modify map array lattice sc 3.0 region box block 0 2 0 1 0 1 +shell echo "test1" create_box 1 box +shell echo "test1" create_atoms 1 box +shell echo "test1" + mass 1 55.845 set atom 1 spin 2.0 1.0 0.0 0.0 set atom 2 spin 2.0 0.0 1.0 0.0 diff --git a/src/SPIN/pair_spin_exchange_biquadratic.cpp b/src/SPIN/pair_spin_exchange_biquadratic.cpp index 352949e5c3..a00d1cc8b0 100644 --- a/src/SPIN/pair_spin_exchange_biquadratic.cpp +++ b/src/SPIN/pair_spin_exchange_biquadratic.cpp @@ -393,7 +393,7 @@ void PairSpinExchangeBiquadratic::compute_exchange(int i, int j, double rsq, jtype = type[j]; r2j = rsq/J3[itype][jtype]/J3[itype][jtype]; - r2k = rsq/J3[itype][jtype]/J3[itype][jtype]; + r2k = rsq/K3[itype][jtype]/K3[itype][jtype]; Jex = 4.0*J1_mag[itype][jtype]*r2j; Jex *= (1.0-J2[itype][jtype]*r2j); From b34585762b2d87cb8a931b5ef344b9d1f501339d Mon Sep 17 00:00:00 2001 From: snikolo Date: Thu, 1 Apr 2021 01:00:25 -0600 Subject: [PATCH 021/100] updated sectoring function to account for triclinic cells. I didn't see a triclinic cell error warnings in SPIN/* or KOKKOS/atom_vec_spin_kokkos.cpp files. --- src/SPIN/fix_nve_spin.cpp | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index 364994741e..0df63951e4 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -507,13 +507,25 @@ void FixNVESpin::sectoring() { int sec[3]; double sublo[3],subhi[3]; - double* sublotmp = domain->sublo; - double* subhitmp = domain->subhi; - for (int dim = 0 ; dim < 3 ; dim++) { - sublo[dim]=sublotmp[dim]; - subhi[dim]=subhitmp[dim]; + + if (domain->triclinic == 1){ + double* sublotmp = domain->sublo_lamda; + double* subhitmp = domain->subhi_lamda; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]*domain->boxhi[dim]; + subhi[dim]=subhitmp[dim]*domain->boxhi[dim]; + } } + else { + double* sublotmp = domain->sublo; + double* subhitmp = domain->subhi; + for (int dim = 0 ; dim < 3 ; dim++) { + sublo[dim]=sublotmp[dim]; + subhi[dim]=subhitmp[dim]; + } + } + const double rsx = subhi[0] - sublo[0]; const double rsy = subhi[1] - sublo[1]; const double rsz = subhi[2] - sublo[2]; From 4975295e0fa3221a442aa7a459adb91a841f02f1 Mon Sep 17 00:00:00 2001 From: julient31 Date: Thu, 1 Apr 2021 11:45:16 -0600 Subject: [PATCH 022/100] - adding a force/clear equivalent for spins in verlet/kk - setting all validation problems for spin/kk --- .../llg_exchange.py | 2 +- .../run-test-exchange.sh | 8 +++--- .../test-spin-precession.in | 4 +-- .../run-test-prec.sh | 8 +++++- .../test-spin-precession.in | 1 + .../run-test-prec.sh | 7 +++++ .../test-prec-spin.template | 1 + .../validation_nve/in.spin.iron-nve | 4 +-- .../validation_nve/run-test-nve.sh | 8 ++++-- .../validation_nvt/in.spin.nvt_lattice | 1 + .../validation_nvt/in.spin.nvt_spin | 1 + .../validation_nvt/run-test-nvt.sh | 20 ++++++++++++-- src/KOKKOS/atom_vec_spin_kokkos.cpp | 8 +++--- src/KOKKOS/verlet_kokkos.cpp | 27 +++++++++++++++++++ 14 files changed, 82 insertions(+), 18 deletions(-) diff --git a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py index 5b93ac5c2d..a4cba3a940 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py +++ b/examples/SPIN/test_problems/validation_damped_exchange/llg_exchange.py @@ -6,7 +6,7 @@ import matplotlib.pyplot as plt import mpmath as mp hbar=0.658212 # Planck's constant (eV.fs/rad) -# J0=0.05 # per-neighbor exchange interaction (eV) +J0=0.05 # per-neighbor exchange interaction (eV) # exchange interaction parameters J1 = 11.254 # in eV diff --git a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh index a714e22fcf..9d00318473 100755 --- a/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh +++ b/examples/SPIN/test_problems/validation_damped_exchange/run-test-exchange.sh @@ -4,12 +4,12 @@ rm res_*.dat # test standard Lammps -# ./../../../../src/lmp_serial \ -# -in test-spin-precession.in +./../../../../src/lmp_serial \ + -in test-spin-precession.in # test spin/kk with Kokkos Lammps -mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ - -k on -sf kk -in test-spin-precession.in +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in # extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" diff --git a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in index 0615d384ec..c195c046ec 100644 --- a/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_exchange/test-spin-precession.in @@ -1,8 +1,8 @@ #LAMMPS in.run units metal -# atom_style spin -atom_style spin/kk +atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f shell echo "test1" diff --git a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh index 8609179376..e7a943beef 100755 --- a/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_damped_precession/run-test-prec.sh @@ -3,9 +3,15 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps ./../../../../src/lmp_serial \ -in test-spin-precession.in + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in test-spin-precession.in + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in index b8e943e579..56abdded15 100644 --- a/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in +++ b/examples/SPIN/test_problems/validation_damped_precession/test-spin-precession.in @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary f f f diff --git a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh index bcdd337903..ecdbb2c156 100755 --- a/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh +++ b/examples/SPIN/test_problems/validation_langevin_precession/run-test-prec.sh @@ -12,7 +12,14 @@ do temp="$(echo "$tempi+$i*($tempf-$tempi)/$N" | bc -l)" sed s/temperature/${temp}/g test-prec-spin.template > \ test-prec-spin.in + + # test standard Lammps ./../../../../src/lmp_serial -in test-prec-spin.in + + # test spin/kk with Kokkos Lammps + # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ + # -k on -sf kk -in test-prec-spin.in + Hz="$(tail -n 1 average_spin | awk -F " " '{print $3}')" sz="$(tail -n 1 average_spin | awk -F " " '{print $5}')" en="$(tail -n 1 average_spin | awk -F " " '{print $6}')" diff --git a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template index 52f6a105ea..bec7126e69 100644 --- a/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template +++ b/examples/SPIN/test_problems/validation_langevin_precession/test-prec-spin.template @@ -2,6 +2,7 @@ units metal atom_style spin +# atom_style spin/kk atom_modify map array boundary p p p diff --git a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve index a29d0158cf..38c669e166 100644 --- a/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve +++ b/examples/SPIN/test_problems/validation_nve/in.spin.iron-nve @@ -50,5 +50,5 @@ thermo 200 compute outsp all property/atom spx spy spz sp fmx fmy fmz dump 1 all custom 10 dump_iron.lammpstrj type x y z c_outsp[1] c_outsp[2] c_outsp[3] -# run 100000 -run 10000 +run 100000 +# run 1 diff --git a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh index a349fb91f7..04d3d60847 100755 --- a/examples/SPIN/test_problems/validation_nve/run-test-nve.sh +++ b/examples/SPIN/test_problems/validation_nve/run-test-nve.sh @@ -3,10 +3,14 @@ # clean old res rm res_*.dat -# compute Lammps +# test standard Lammps +../../../../src/lmp_serial -in in.spin.iron-nve + +# test spin/kk with Kokkos Lammps # mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ # -k on -sf kk -in in.spin.iron-nve -../../../../src/lmp_serial -in in.spin.iron-nve + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice index 2375c0ff8d..cc7bcfa68d 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_lattice @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p diff --git a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin index 6b65df7109..7e8152f481 100644 --- a/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin +++ b/examples/SPIN/test_problems/validation_nvt/in.spin.nvt_spin @@ -3,6 +3,7 @@ clear units metal atom_style spin +# atom_style spin/kk dimension 3 boundary p p p diff --git a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh index d3abbbe1a5..1372e1bd2c 100755 --- a/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh +++ b/examples/SPIN/test_problems/validation_nvt/run-test-nvt.sh @@ -3,16 +3,32 @@ # clean old res rm res_*.dat -# compute NVT Spin -> Lattice +### compute NVT Spin -> Lattice + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_spin + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_spin + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" en="$(echo "$en-$in" | bc -l)" tail -n +$in log.lammps | head -n $en > res_nvt_spin.dat -# compute NVT Lattice -> Spin +### compute NVT Lattice -> Spin + +# test standard Lammps ./../../../../src/lmp_serial -in in.spin.nvt_lattice + +# test spin/kk with Kokkos Lammps +# mpirun -np 1 ../../../../src/lmp_kokkos_mpi_only \ +# -k on -sf kk -in in.spin.nvt_lattice + +# extract data from Lammps run in="$(grep -n Step log.lammps | awk -F ':' '{print $1}')" en="$(grep -n Loop log.lammps | awk -F ':' '{print $1}')" in="$(echo "$in+1" | bc -l)" diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 188748d655..e513ff2ffa 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -1303,9 +1303,9 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i clear all forces (mech and mag) ------------------------------------------------------------------------- */ -void AtomVecSpinKokkos::force_clear(int /*n*/, size_t nbytes) +void AtomVecSpinKokkos::force_clear(int n, size_t nbytes) { - memset(&atom->f[0][0],0,3*nbytes); - memset(&atom->fm[0][0],0,3*nbytes); - memset(&atom->fm_long[0][0],0,3*nbytes); + memset(&f[n][0],0,3*nbytes); + memset(&fm[n][0],0,3*nbytes); + memset(&fm_long[n][0],0,3*nbytes); } diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 3aa7a3575a..27f4646366 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -594,6 +594,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(nall, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(nall, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } // neighbor includegroup flag is set // clear force only on initial nfirst particles @@ -607,6 +616,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(atomKK->nfirst, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(atomKK->nfirst, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } if (force->newton) { auto range = Kokkos::RangePolicy(atomKK->nlocal, atomKK->nlocal + atomKK->nghost); @@ -617,6 +635,15 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } + + // reset SPIN forces + + if (extraflag) { + Kokkos::parallel_for(range, Zero::t_fm_array>(atomKK->k_fm.view())); + atomKK->modified(Device,FM_MASK); + Kokkos::parallel_for(range, Zero::t_fm_array>(atomKK->k_fm_long.view())); + atomKK->modified(Device,FML_MASK); + } } } } From 6a99f5b5c54e0385aa314afd1e7f1c3d187196ce Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Tue, 6 Apr 2021 17:24:54 +0200 Subject: [PATCH 023/100] WIP: - no auto-download of user-pace src yet - lib/pace/*.cpp,*.h are provided explicitly yet. - implement CMake integration in USER-PACE.cmake and in CMakeLists.txt --- cmake/CMakeLists.txt | 6 +- cmake/Modules/Packages/USER-PACE.cmake | 14 + lib/pace/Install.py | 1 + lib/pace/LICENSE | 674 ++++++++ lib/pace/README | 0 lib/pace/TODO | 30 + lib/pace/ace_abstract_basis.cpp | 184 +++ lib/pace/ace_abstract_basis.h | 169 ++ lib/pace/ace_array2dlm.h | 579 +++++++ lib/pace/ace_arraynd.h | 1949 ++++++++++++++++++++++++ lib/pace/ace_c_basis.cpp | 980 ++++++++++++ lib/pace/ace_c_basis.h | 155 ++ lib/pace/ace_c_basisfunction.h | 251 +++ lib/pace/ace_complex.h | 266 ++++ lib/pace/ace_contigous_array.h | 249 +++ lib/pace/ace_evaluator.cpp | 660 ++++++++ lib/pace/ace_evaluator.h | 230 +++ lib/pace/ace_flatten_basis.cpp | 130 ++ lib/pace/ace_flatten_basis.h | 135 ++ lib/pace/ace_radial.cpp | 566 +++++++ lib/pace/ace_radial.h | 324 ++++ lib/pace/ace_recursive.cpp | 1340 ++++++++++++++++ lib/pace/ace_recursive.h | 247 +++ lib/pace/ace_spherical_cart.cpp | 221 +++ lib/pace/ace_spherical_cart.h | 134 ++ lib/pace/ace_timing.h | 126 ++ lib/pace/ace_types.h | 45 + lib/pace/ace_version.h | 39 + lib/pace/ships_radial.cpp | 388 +++++ lib/pace/ships_radial.h | 158 ++ src/Makefile | 4 +- src/USER-PACE/Install.sh | 68 + src/USER-PACE/LICENSE | 674 ++++++++ src/USER-PACE/pair_pace.cpp | 458 ++++++ src/USER-PACE/pair_pace.h | 97 ++ 35 files changed, 11546 insertions(+), 5 deletions(-) create mode 100644 cmake/Modules/Packages/USER-PACE.cmake create mode 100644 lib/pace/Install.py create mode 100644 lib/pace/LICENSE create mode 100644 lib/pace/README create mode 100644 lib/pace/TODO create mode 100644 lib/pace/ace_abstract_basis.cpp create mode 100644 lib/pace/ace_abstract_basis.h create mode 100644 lib/pace/ace_array2dlm.h create mode 100644 lib/pace/ace_arraynd.h create mode 100644 lib/pace/ace_c_basis.cpp create mode 100644 lib/pace/ace_c_basis.h create mode 100644 lib/pace/ace_c_basisfunction.h create mode 100644 lib/pace/ace_complex.h create mode 100644 lib/pace/ace_contigous_array.h create mode 100644 lib/pace/ace_evaluator.cpp create mode 100644 lib/pace/ace_evaluator.h create mode 100644 lib/pace/ace_flatten_basis.cpp create mode 100644 lib/pace/ace_flatten_basis.h create mode 100644 lib/pace/ace_radial.cpp create mode 100644 lib/pace/ace_radial.h create mode 100644 lib/pace/ace_recursive.cpp create mode 100644 lib/pace/ace_recursive.h create mode 100644 lib/pace/ace_spherical_cart.cpp create mode 100644 lib/pace/ace_spherical_cart.h create mode 100644 lib/pace/ace_timing.h create mode 100644 lib/pace/ace_types.h create mode 100644 lib/pace/ace_version.h create mode 100644 lib/pace/ships_radial.cpp create mode 100644 lib/pace/ships_radial.h create mode 100644 src/USER-PACE/Install.sh create mode 100644 src/USER-PACE/LICENSE create mode 100644 src/USER-PACE/pair_pace.cpp create mode 100644 src/USER-PACE/pair_pace.h diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index 21d965ebba..4bd5ea8fec 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -119,7 +119,7 @@ set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH - USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF) + USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE) set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP) @@ -382,9 +382,9 @@ else() endif() foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM - USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS) + USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE) if(PKG_${PKG_WITH_INCL}) - include(Packages/${PKG_WITH_INCL}) + include(Packages/${PKG_WITH_INCL}) endif() endforeach() diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake new file mode 100644 index 0000000000..c9e8e1bcfe --- /dev/null +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -0,0 +1,14 @@ +set(PACE_EVALUATOR_PATH ${LAMMPS_LIB_SOURCE_DIR}/pace) +message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") +set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) + +FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) +set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) + + +##### aceevaluator ##### +add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) +target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_compile_options(aceevaluator PRIVATE -O2) +set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +target_link_libraries(lammps PRIVATE aceevaluator) \ No newline at end of file diff --git a/lib/pace/Install.py b/lib/pace/Install.py new file mode 100644 index 0000000000..f87f5c14cb --- /dev/null +++ b/lib/pace/Install.py @@ -0,0 +1 @@ +# TODO \ No newline at end of file diff --git a/lib/pace/LICENSE b/lib/pace/LICENSE new file mode 100644 index 0000000000..f288702d2f --- /dev/null +++ b/lib/pace/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/lib/pace/README b/lib/pace/README new file mode 100644 index 0000000000..e69de29bb2 diff --git a/lib/pace/TODO b/lib/pace/TODO new file mode 100644 index 0000000000..8021916923 --- /dev/null +++ b/lib/pace/TODO @@ -0,0 +1,30 @@ +[TODO/DONE] pair_pace.cpp and pair_pace.h will have to go into src/USER-PACE and thus also need to conform to our requirements. + +[TODO] also src/USER-PACE would need to have an Install.sh file that integrates the settings from the lib folder into the conventional build process. +[TODO] there would have to be a lib/pace folder for building/interfacing to the library. + +[TODO] how you organize your repo is up to you. a better way to describe what you would have to do is to point you to examples. +which of the examples is relevant depends on what build system you are using for your "PACE" external package. + +If you are using CMake to build it, you can look at the KIM package +If you are using autoconf/automake, you can look at the USER-PLUMED package +If you are using neither (just a plain Makefile), you can look at the VORONOI or QUIP package +The following additional modifications are needed: + +[TODO] lib/pace: needs one or more Makefile.lammps, a README and an Install.py file +[TODO] src/Makefile: needs support for the USER-PACE package and compiling via lib-pace. Also the package needs to be added to the PACKEXT and PACKLIB variables + +[DONE] cmake/Modules/Packages/USER-PACE.cmake needs to be added +[DONE] cmake/CMakeLists.txt needs to include it in case the package is enabled. + +[TODO] doc/src/Build_extra.rst needs to include the build instructions for CMake and traditional make +[TODO] doc/src/Package_user.rst and doc/src/Package_details.rst needs to contain relevant information and links + + +Because of the different build systems, there are different steps required, but each of the examples I've pointed out are tested and used regularly and thus should be working sufficiently well. +Mind you the QUIP package is set up in such a way, that no automatic download is possible and a manual download and compilation is required. So that is the least preferred and least convenient option. + +We are happy to provide more details, but that requires that you first have something that already is following either of the suggested variants, so that we don't have to discuss in all generality. + +I would also suggest to close this pull request here, leave all files in place, but then start a new branch from the current master and then move the few things over you need to retain, +add the build environment files and then start working on getting it to do what it should. \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.cpp b/lib/pace/ace_abstract_basis.cpp new file mode 100644 index 0000000000..3d8afafdaf --- /dev/null +++ b/lib/pace/ace_abstract_basis.cpp @@ -0,0 +1,184 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Lysogorskiy Yury on 28.04.2020. + +#include "ace_abstract_basis.h" + +////embedding function +////case nemb = 1 only implementation +////F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) +//// !! no prefactor wpre +void Fexp(DOUBLE_TYPE x, DOUBLE_TYPE m, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { + DOUBLE_TYPE w = 1.e6; + DOUBLE_TYPE eps = 1e-10; + + DOUBLE_TYPE lambda = pow(1.0 / w, m - 1.0); + if (abs(x) > eps) { + DOUBLE_TYPE g; + DOUBLE_TYPE a = abs(x); + DOUBLE_TYPE am = pow(a, m); + DOUBLE_TYPE w3x3 = pow(w * a, 3); + DOUBLE_TYPE sign_factor = (signbit(x) ? -1 : 1); + if (w3x3 > 30.0) + g = 0.0; + else + g = exp(-w3x3); + + DOUBLE_TYPE omg = 1.0 - g; + F = sign_factor * (omg * am + lambda * g * a); + DOUBLE_TYPE dg = -3.0 * w * w * w * a * a * g; + DF = m * pow(a, m - 1.0) * omg - am * dg + lambda * dg * a + lambda * g; + } else { + F = lambda * x; + DF = lambda; + } +} + + +//Scaled-shifted embedding function +//F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) +// !! no prefactor wpre +void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { + DOUBLE_TYPE eps = 1e-10; + DOUBLE_TYPE a, xoff, yoff, nx, exprho; + + if (abs(mexp - 1.0) < eps) { + F = rho; + DF = 1; + } else { + a = abs(rho); + exprho = exp(-a); + nx = 1. / mexp; + xoff = pow(nx, (nx / (1.0 - nx))) * exprho; + yoff = pow(nx, (1 / (1.0 - nx))) * exprho; + DOUBLE_TYPE sign_factor = (signbit(rho) ? -1 : 1); + F = sign_factor * (pow(xoff + a, mexp) - yoff); + DF = yoff + mexp * (-xoff + 1.0) * pow(xoff + a, mexp - 1.); + } +} + +void ACEAbstractBasisSet::inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, + DOUBLE_TYPE &fcut, DOUBLE_TYPE &dfcut) { + + DOUBLE_TYPE rho_low = rho_cut - drho_cut; + if (rho_core >= rho_cut) { + fcut = 0; + dfcut = 0; + } else if (rho_core <= rho_low) { + fcut = 1; + dfcut = 0; + } else { + fcut = 0.5 * (1 + cos(M_PI * (rho_core - rho_low) / drho_cut)); + dfcut = -0.5 * sin(M_PI * (rho_core - rho_low) / drho_cut) * M_PI / drho_cut; + } +} + +void ACEAbstractBasisSet::FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, + Array1D &derivatives, DENSITY_TYPE ndensity) { + DOUBLE_TYPE F, DF = 0, wpre, mexp; + for (int p = 0; p < ndensity; p++) { + wpre = FS_parameters.at(p * ndensity + 0); + mexp = FS_parameters.at(p * ndensity + 1); + if (this->npoti == "FinnisSinclair") + Fexp(rhos(p), mexp, F, DF); + else if (this->npoti == "FinnisSinclairShiftedScaled") + FexpShiftedScaled(rhos(p), mexp, F, DF); + value += F * wpre; // * weight (wpre) + derivatives(p) = DF * wpre;// * weight (wpre) + } +} + +void ACEAbstractBasisSet::_clean() { + + delete[] elements_name; + elements_name = nullptr; + delete radial_functions; + radial_functions = nullptr; +} + +ACEAbstractBasisSet::ACEAbstractBasisSet(const ACEAbstractBasisSet &other) { + ACEAbstractBasisSet::_copy_scalar_memory(other); + ACEAbstractBasisSet::_copy_dynamic_memory(other); +} + +ACEAbstractBasisSet &ACEAbstractBasisSet::operator=(const ACEAbstractBasisSet &other) { + if (this != &other) { + // deallocate old memory + ACEAbstractBasisSet::_clean(); + //copy scalar values + ACEAbstractBasisSet::_copy_scalar_memory(other); + //copy dynamic memory + ACEAbstractBasisSet::_copy_dynamic_memory(other); + } + return *this; +} + +ACEAbstractBasisSet::~ACEAbstractBasisSet() { + ACEAbstractBasisSet::_clean(); +} + +void ACEAbstractBasisSet::_copy_scalar_memory(const ACEAbstractBasisSet &src) { + deltaSplineBins = src.deltaSplineBins; + FS_parameters = src.FS_parameters; + npoti = src.npoti; + + nelements = src.nelements; + rankmax = src.rankmax; + ndensitymax = src.ndensitymax; + nradbase = src.nradbase; + lmax = src.lmax; + nradmax = src.nradmax; + cutoffmax = src.cutoffmax; + + spherical_harmonics = src.spherical_harmonics; + + rho_core_cutoffs = src.rho_core_cutoffs; + drho_core_cutoffs = src.drho_core_cutoffs; + + + E0vals = src.E0vals; +} + +void ACEAbstractBasisSet::_copy_dynamic_memory(const ACEAbstractBasisSet &src) {//allocate new memory + if (src.elements_name == nullptr) + throw runtime_error("Could not copy ACEAbstractBasisSet::elements_name - array not initialized"); + elements_name = new string[nelements]; + //copy + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + elements_name[mu] = src.elements_name[mu]; + } + radial_functions = src.radial_functions->clone(); +} + +SPECIES_TYPE ACEAbstractBasisSet::get_species_index_by_name(const string &elemname) { + for (SPECIES_TYPE t = 0; t < nelements; t++) { + if (this->elements_name[t] == elemname) + return t; + } + return -1; +} \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.h b/lib/pace/ace_abstract_basis.h new file mode 100644 index 0000000000..165ea9496f --- /dev/null +++ b/lib/pace/ace_abstract_basis.h @@ -0,0 +1,169 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Lysogorskiy Yury on 28.04.2020. + +#ifndef ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H +#define ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H + +#include +#include + +#include "ace_c_basisfunction.h" +#include "ace_contigous_array.h" +#include "ace_radial.h" +#include "ace_spherical_cart.h" +#include "ace_types.h" + +using namespace std; + +/** + * Abstract basis set class + */ +class ACEAbstractBasisSet { +public: + SPECIES_TYPE nelements = 0; ///< number of elements in basis set + RANK_TYPE rankmax = 0; ///< maximum value of rank + DENSITY_TYPE ndensitymax = 0; ///< maximum number of densities \f$ \rho^{(p)} \f$ + NS_TYPE nradbase = 0; ///< maximum number of radial \f$\textbf{basis}\f$ function \f$ g_{k}(r) \f$ + LS_TYPE lmax = 0; ///< \f$ l_\textrm{max} \f$ - maximum value of orbital moment \f$ l \f$ + NS_TYPE nradmax = 0; ///< maximum number \f$ n \f$ of radial function \f$ R_{nl}(r) \f$ + DOUBLE_TYPE cutoffmax = 0; ///< maximum value of cutoff distance among all species in basis set + DOUBLE_TYPE deltaSplineBins = 0; ///< Spline interpolation density + + string npoti = "FinnisSinclair"; ///< FS and embedding function combination + + string *elements_name = nullptr; ///< Array of elements name for mapping from index (0..nelements-1) to element symbol (string) + + AbstractRadialBasis *radial_functions = nullptr; ///< object to work with radial functions + ACECartesianSphericalHarmonics spherical_harmonics; ///< object to work with spherical harmonics in Cartesian representation + + + Array1D rho_core_cutoffs; ///< energy-based inner cut-off + Array1D drho_core_cutoffs; ///< decay of energy-based inner cut-off + + vector FS_parameters; ///< parameters for cluster functional, see Eq.(3) in implementation notes or Eq.(53) in PRB 99, 014104 (2019) + + // E0 values + Array1D E0vals; + + /** + * Default empty constructor + */ + ACEAbstractBasisSet() = default; + + // copy constructor, operator= and destructor (see. Rule of Three) + + /** + * Copy constructor (see. Rule of Three) + * @param other + */ + ACEAbstractBasisSet(const ACEAbstractBasisSet &other); + + /** + * operator= (see. Rule of Three) + * @param other + * @return + */ + ACEAbstractBasisSet &operator=(const ACEAbstractBasisSet &other); + + /** + * virtual destructor (see. Rule of Three) + */ + virtual ~ACEAbstractBasisSet(); + + /** + * Computing cluster functional \f$ F(\rho_i^{(1)}, \dots, \rho_i^{(P)}) \f$ + * and its derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ + * @param rhos array with densities \f$ \rho^{(p)} \f$ + * @param value (out) return value of cluster functional + * @param derivatives (out) array of derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ + * @param ndensity number \f$ P \f$ of densities to use + */ + void FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, Array1D &derivatives, + DENSITY_TYPE ndensity); + + /** + * Computing hard core pairwise repulsive potential \f$ f_{cut}(\rho_i^{(\textrm{core})})\f$ and its derivative, + * see Eq.(29) of implementation notes + * @param rho_core value of \f$ \rho_i^{(\textrm{core})} \f$ + * @param rho_cut \f$ \rho_{cut}^{\mu_i} \f$ value + * @param drho_cut \f$ \Delta_{cut}^{\mu_i} \f$ value + * @param fcut (out) return inner cutoff function + * @param dfcut (out) return derivative of inner cutoff function + */ + static void inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, DOUBLE_TYPE &fcut, + DOUBLE_TYPE &dfcut); + + + /** + * Virtual method to save potential to file + * @param filename file name + */ + virtual void save(const string &filename) = 0; + + /** + * Virtual method to load potential from file + * @param filename file name + */ + virtual void load(const string filename) = 0; + + /** + * Get the species index by its element name + * @param elemname element name + * @return species index + */ + SPECIES_TYPE get_species_index_by_name(const string &elemname); + + + // routines for copying and cleaning dynamic memory of the class (see. Rule of Three) + + /** + * Routine for clean the dynamically allocated memory\n + * IMPORTANT! It must be idempotent for safety. + */ + virtual void _clean(); + + /** + * Copy dynamic memory from src. Must be override and extended in derived classes! + * @param src source object to copy from + */ + virtual void _copy_dynamic_memory(const ACEAbstractBasisSet &src); + + /** + * Copy scalar values from src. Must be override and extended in derived classes! + * @param src source object to copy from + */ + virtual void _copy_scalar_memory(const ACEAbstractBasisSet &src); +}; + +void Fexp(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); + +void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); + +#endif //ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H diff --git a/lib/pace/ace_array2dlm.h b/lib/pace/ace_array2dlm.h new file mode 100644 index 0000000000..2b38602bc7 --- /dev/null +++ b/lib/pace/ace_array2dlm.h @@ -0,0 +1,579 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 11.01.20. + + +#ifndef ACE_ARRAY2DLM_H +#define ACE_ARRAY2DLM_H + +#include +#include + +#include "ace_arraynd.h" +#include "ace_contigous_array.h" +#include "ace_types.h" + +using namespace std; + +/** + * Contiguous array to organize values by \f$ (l,m) \f$ indiced (orbital moment and its projection). + * Only \f$ l_\textrm{max}\f$ should be provided, \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array2DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + + bool is_proxy = false; ///< flag to show, if object is owning the memory or just represent it (proxying)dimensions + +public: + /** + * Default empty constructor + */ + Array2DLM() = default; + + /** + * Parametrized constructor + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array2DLM(LS_TYPE lmax, string array_name = "Array2DLM") { + init(lmax, array_name); + } + + + /** + * Constructor to create slices-proxy array, i.e. to provide access to the memory, but not to own it. + * @param lmax maximum value of \f$ l \f$ + * @param data_ptr pointer to original data + * @param array_name name of the array + */ + Array2DLM(LS_TYPE lmax, T *data_ptr, string array_name = "Array2DLM") { + this->lmax = lmax; + this->size = (lmax + 1) * (lmax + 1); + this->data = data_ptr; + this->array_name = array_name; + is_proxy = true; + }; + + /** + * Destructor + */ + ~Array2DLM() { + if (!is_proxy) { + if (data != nullptr) delete[] data; + } + data = nullptr; + } + + /** + * Initialize array, allocate memory + * @param lmax maximum value of l + * @param array_name name of the array + */ + void init(LS_TYPE lmax, string array_name = "Array2DLM") { + if (is_proxy) { + char s[1024]; + sprintf(s, "Could not re-initialize proxy-array %s\n", this->array_name.c_str()); + throw logic_error(s); + } + this->lmax = lmax; + this->array_name = array_name; + //for m = -l .. l + if (size != (lmax + 1) * (lmax + 1)) { + size = (lmax + 1) * (lmax + 1); + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0.0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + } + +#ifdef MULTIARRAY_INDICES_CHECK +/** + * Check if indices (l,m) are within array + */ + void check_indices(LS_TYPE l, MS_TYPE m) const { + + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + size_t ii = l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (l,m) for reading + * @param l + * @param m + * @return array value + */ + inline const T &operator()(LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(l, m); +#endif + //l^2 + l + m + return data[l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (l,m) for writing + * @param l + * @param m + * @return array value + */ + inline T &operator()(LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(l, m); +#endif + //l^2 + l + m + return data[l * (l + 1) + m]; + } + + /** + * Convert array to STL vector> container + * @return vector> container + */ + vector> to_vector() const { + vector> res; + res.resize(lmax + 1); + + for (int i = 0; i < lmax + 1; i++) { + res[i].resize(i + 1); + for (int j = 0; j < i + 1; j++) { + res[i][j] = operator()(i, j); + } + } + return res; + } +}; + +/** + * Contiguous array to organize values by \f$ (i_0, l , m) \f$ indices. + * Only \f$ d_{0}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array3DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + + + size_t dim[1] = {0}; ///< linear dimension \f$ d_{0} \f$ + + size_t s[1] = {0}; ///< strides for linear dimensions + + Array1D *> _proxy_slices; ///< slices representation +public: + /** + * Default empty constructor + */ + Array3DLM() = default; + + /** + * Parametrized constructor + * @param array_name name of the array + */ + Array3DLM(string array_name) { + this->array_name = array_name; + }; + + /** + * Parametrized constructor + * @param d0 maximum value of \f$ i_0 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array3DLM(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { + init(d0, lmax, array_name); + } + + /** + * Initialize array and its slices + * @param d0 maximum value of \f$ i_0 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + void init(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { + this->array_name = array_name; + this->lmax = lmax; + dim[0] = d0; + s[0] = lmax * lmax; + if (size != s[0] * dim[0]) { + size = s[0] * dim[0]; + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + + _proxy_slices.set_array_name(array_name + "_proxy"); + //arrange proxy-slices + _clear_proxies(); + _proxy_slices.resize(dim[0]); + for (size_t i0 = 0; i0 < dim[0]; ++i0) { + _proxy_slices(i0) = new Array2DLM(this->lmax, &this->data[i0 * s[0]], + array_name + "_slice"); + } + } + + /** + * Release pointers to slices + */ + void _clear_proxies() { + for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) { + delete _proxy_slices(i0); + _proxy_slices(i0) = nullptr; + } + } + + /** + * Destructor, clear proxies + */ + ~Array3DLM() { + _clear_proxies(); + } + + /** + * Resize array to new dimensions + * @param d0 + * @param lmax + */ + void resize(size_t d0, LS_TYPE lmax) { + _clear_proxies(); + init(d0, lmax, this->array_name); + } + + /** + * Get array dimensions + * @param d dimension index + * @return dimension along axis 'd' + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + /** + * Check if indices (i0, l,m) are within array + */ + void check_indices(size_t i0, LS_TYPE l, MS_TYPE m) const { + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + + if ((i0 < 0) | (i0 >= dim[0])) { + fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + exit(EXIT_FAILURE); + } + + size_t ii = i0 * s[0] + l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (i0,l,m) for reading + * @param i0 + * @param l + * @param m + * @return array value + */ + inline const T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, l, m); +#endif + return data[i0 * s[0] + l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (i0,l,m) for writing + * @param i0 + * @param l + * @param m + * @return array value + */ + inline T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, l, m); +#endif + return data[i0 * s[0] + l * (l + 1) + m]; + } + + /** + * Return proxy Array2DLM pointing to i0, l=0, m=0 to read + * @param i0 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline const Array2DLM &operator()(size_t i0) const { + return *_proxy_slices(i0); + } + + /** + * Return proxy Array2DLM pointing to i0, l=0, m=0 to write + * @param i0 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline Array2DLM &operator()(size_t i0) { + return *_proxy_slices(i0); + } +}; + + +/** + * Contiguous array to organize values by \f$ (i_0, i_1, l , m) \f$ indices. + * Only \f$ d_{0}, d_{1}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ + * for \f$ l = 0, \dots, l_\textrm{max}\f$ + * @tparam T type of values to store + */ +template +class Array4DLM : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + + LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ + size_t dim[2] = {0, 0}; ///< linear dimension \f$ d_{0}, d_{1} \f$ + size_t s[2] = {0, 0}; ///< strides for linear dimensions + + Array2D *> _proxy_slices; ///< slices representation +public: + /** + * Default empty constructor + */ + Array4DLM() = default; + + /** + * Parametrized constructor + * @param array_name name of the array + */ + Array4DLM(string array_name) { + this->array_name = array_name; + }; + + /** + * Parametrized constructor + * @param d0 maximum value of \f$ i_0 \f$ + * @param d1 maximum value of \f$ i_1 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + explicit Array4DLM(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { + init(d0, d1, lmax, array_name); + } + + /** + * Initialize array, reallocate memory and its slices + * @param d0 maximum value of \f$ i_0 \f$ + * @param d1 maximum value of \f$ i_1 \f$ + * @param lmax maximum value of \f$ l \f$ + * @param array_name name of the array + */ + void init(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { + this->array_name = array_name; + this->lmax = lmax; + dim[1] = d1; + dim[0] = d0; + s[1] = lmax * lmax; + s[0] = s[1] * dim[1]; + if (size != s[0] * dim[0]) { + size = s[0] * dim[0]; + if (data) delete[] data; + data = new T[size]{}; + memset(data, 0, size * sizeof(T)); + } else { + memset(data, 0, size * sizeof(T)); + } + + _proxy_slices.set_array_name(array_name + "_proxy"); + //release old memory if there is any + _clear_proxies(); + //arrange proxy-slices + _proxy_slices.resize(dim[0], dim[1]); + for (size_t i0 = 0; i0 < dim[0]; ++i0) + for (size_t i1 = 0; i1 < dim[1]; ++i1) { + _proxy_slices(i0, i1) = new Array2DLM(this->lmax, &this->data[i0 * s[0] + i1 * s[1]], + array_name + "_slice"); + } + } + + /** + * Release pointers to slices + */ + void _clear_proxies() { + + for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) + for (size_t i1 = 0; i1 < _proxy_slices.get_dim(1); ++i1) { + delete _proxy_slices(i0, i1); + _proxy_slices(i0, i1) = nullptr; + } + } + + /** + * Destructor, clear proxies + */ + ~Array4DLM() { + _clear_proxies(); + } + + /** + * Deallocate memory, reallocate with the new dimensions + * @param d0 + * @param lmax + */ + void resize(size_t d0, size_t d1, LS_TYPE lmax) { + _clear_proxies(); + init(d0, d1, lmax, this->array_name); + } + + /** + * Get array dimensions + * @param d dimension index + * @return dimension along axis 'd' + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + /** + * Check if indices (i0, l,m) are within array + */ + void check_indices(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { + if ((l < 0) | (l > lmax)) { + fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); + exit(EXIT_FAILURE); + } + + if ((m < -l) | (m > l)) { + fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); + exit(EXIT_FAILURE); + } + + if ((i0 < 0) | (i0 >= dim[0])) { + fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + exit(EXIT_FAILURE); + } + + + if ((i1 < 0) | (i1 >= dim[1])) { + fprintf(stderr, "%s: index i1 = %ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + exit(EXIT_FAILURE); + } + + size_t ii = i0 * s[0] + i1 * s[1] + l * (l + 1) + m; + if (ii >= size) { + fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); + exit(EXIT_FAILURE); + } + } +#endif + + /** + * Accessing the array value by index (i0,l,m) for reading + * @param i0 + * @param i1 + * @param l + * @param m + * @return array value + */ + inline const T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, l, m); +#endif + return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; + } + + /** + * Accessing the array value by index (i0,l,m) for writing + * @param i0 + * @param i1 + * @param l + * @param m + * @return array value + */ + inline T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, l, m); +#endif + return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; + } + + /** + * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to read + * @param i0 + * @param i1 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline const Array2DLM &operator()(size_t i0, size_t i1) const { + return *_proxy_slices(i0, i1); + } + + /** + * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to write + * @param i0 + * @param i1 + * @return proxy Array2DLM pointing to i0, l=0, m=0 + */ + inline Array2DLM &operator()(size_t i0, size_t i1) { + return *_proxy_slices(i0, i1); + } +}; + +#endif //ACE_ARRAY2DLM_H \ No newline at end of file diff --git a/lib/pace/ace_arraynd.h b/lib/pace/ace_arraynd.h new file mode 100644 index 0000000000..1044b5654e --- /dev/null +++ b/lib/pace/ace_arraynd.h @@ -0,0 +1,1949 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +//automatically generate source code + +#ifndef ACE_MULTIARRAY_H +#define ACE_MULTIARRAY_H + +#include +#include +#include + +#include "ace_contigous_array.h" + +using namespace std; + + +/** + * Multidimensional (1 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array1D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[1] = {0}; ///< dimensions + size_t s[1] = {0}; ///< strides + int ndim = 1; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array1D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array1D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array1D(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { + init(d0, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0) { + + dim[0] = d0; + + s[0] = 1; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0) { + init(d0, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0) { + //check data size consistency + size_t new_size = d0; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0); +#endif + + return data[i0]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0); +#endif + + return data[i0]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array1D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector to_vector() const { + vector res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0] = operator()(i0); + + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector &vec) { + size_t d0 = 0; + d0 = vec.size(); + + + init(d0, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + operator()(i0) = vec.at(i0); + + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array1D(const vector &vec, const string &array_name = "Array1D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array1D &operator=(const vector &vec) { + this->set_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (2 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array2D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[2] = {0}; ///< dimensions + size_t s[2] = {0}; ///< strides + int ndim = 2; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array2D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array2D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array2D(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { + init(d0, d1, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1) { + + dim[0] = d0; + dim[1] = d1; + + s[1] = 1; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1) { + init(d0, d1, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1) { + //check data size consistency + size_t new_size = d0 * d1; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1); +#endif + + return data[i0 * s[0] + i1]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1); +#endif + + return data[i0 * s[0] + i1]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array2D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector> to_vector() const { + vector> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1] = operator()(i0, i1); + + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector> &vec) { + size_t d0 = 0; + size_t d1 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + + + } + + init(d0, d1, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + operator()(i0, i1) = vec.at(i0).at(i1); + + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array2D(const vector> &vec, const string &array_name = "Array2D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array2D &operator=(const vector> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array2D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (3 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array3D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[3] = {0}; ///< dimensions + size_t s[3] = {0}; ///< strides + int ndim = 3; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array3D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array3D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array3D(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { + init(d0, d1, d2, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + + s[2] = 1; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2) { + init(d0, d1, d2, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2) { + //check data size consistency + size_t new_size = d0 * d1 * d2; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array3D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>> to_vector() const { + vector>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2] = operator()(i0, i1, i2); + + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + + + } + } + + init(d0, d1, d2, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + operator()(i0, i1, i2) = vec.at(i0).at(i1).at(i2); + + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array3D(const vector>> &vec, const string &array_name = "Array3D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array3D &operator=(const vector>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array3D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (4 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array4D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[4] = {0}; ///< dimensions + size_t s[4] = {0}; ///< strides + int ndim = 4; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array4D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array4D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array4D(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { + init(d0, d1, d2, d3, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + + s[3] = 1; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3) { + init(d0, d1, d2, d3, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array4D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>> to_vector() const { + vector>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3] = operator()(i0, i1, i2, i3); + + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + + + } + } + } + + init(d0, d1, d2, d3, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + operator()(i0, i1, i2, i3) = vec.at(i0).at(i1).at(i2).at(i3); + + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array4D(const vector>>> &vec, const string &array_name = "Array4D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array4D &operator=(const vector>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array4D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (5 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array5D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[5] = {0}; ///< dimensions + size_t s[5] = {0}; ///< strides + int ndim = 5; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array5D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array5D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array5D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", + T *new_data = nullptr) { + init(d0, d1, d2, d3, d4, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + dim[4] = d4; + + s[4] = 1; + s[3] = s[4] * dim[4]; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", + T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3, d4); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + init(d0, d1, d2, d3, d4, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3 * d4; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3, d4); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + if ((i4 < 0) | (i4 >= dim[4])) { + char buf[1024]; + sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array5D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>>> to_vector() const { + vector>>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3].resize(dim[4]); + + + for (int i4 = 0; i4 < dim[4]; i4++) { + res[i0][i1][i2][i3][i4] = operator()(i0, i1, i2, i3, i4); + + } + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + size_t d4 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + if (d3 > 0) { + d4 = vec.at(0).at(0).at(0).at(0).size(); + + + } + } + } + } + + init(d0, d1, d2, d3, d4, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) + throw std::invalid_argument("Vector size is not constant at dimension 4"); + + for (int i4 = 0; i4 < dim[4]; i4++) { + operator()(i0, i1, i2, i3, i4) = vec.at(i0).at(i1).at(i2).at(i3).at(i4); + + } + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array5D(const vector>>>> &vec, const string &array_name = "Array5D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array5D &operator=(const vector>>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array5D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +/** + * Multidimensional (6 - dimensional) array of type T with contiguous memory layout. + * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @tparam T data type + */ +template +class Array6D : public ContiguousArrayND { + using ContiguousArrayND::array_name; + using ContiguousArrayND::data; + using ContiguousArrayND::size; + using ContiguousArrayND::is_proxy_; + + size_t dim[6] = {0}; ///< dimensions + size_t s[6] = {0}; ///< strides + int ndim = 6; ///< number of dimensions +public: + + /** + * Default empty constructor + */ + Array6D() = default; + + /** + * Parametrized constructor with array name + * @param array_name name of array (for error logging) + */ + Array6D(const string &array_name) { this->array_name = array_name; } + + /** + * Parametrized constructor + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + Array6D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", + T *new_data = nullptr) { + init(d0, d1, d2, d3, d4, d5, array_name, new_data); + } + + /** + * Setup the dimensions and strides of array + * @param d0,... array sizes for different dimensions + */ + void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + + dim[0] = d0; + dim[1] = d1; + dim[2] = d2; + dim[3] = d3; + dim[4] = d4; + dim[5] = d5; + + s[5] = 1; + s[4] = s[5] * dim[5]; + s[3] = s[4] * dim[4]; + s[2] = s[3] * dim[3]; + s[1] = s[2] * dim[2]; + s[0] = s[1] * dim[1]; + + size = s[0] * dim[0]; + }; + + /** + * Initialize array storage, dimensions and strides + * @param d0,... array sizes for different dimensions + * @param array_name string name of the array + */ + void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", + T *new_data = nullptr) { + this->array_name = array_name; + + size_t old_size = size; + set_dimensions(d0, d1, d2, d3, d4, d5); + + bool new_is_proxy = (new_data != nullptr); + + if (new_is_proxy) { + if (!is_proxy_) delete[] data; + data = new_data; + } else { + if (size != old_size) { + T *old_data = data; //preserve the pointer to the old data + data = new T[size]; // allocate new data + if (old_data != nullptr) { // + size_t min_size = old_size < size ? old_size : size; + memcpy(data, old_data, min_size * sizeof(T)); + if (!is_proxy_) delete[] old_data; + } + //memset(data, 0, size * sizeof(T)); + } else { + //memset(data, 0, size * sizeof(T)); + } + } + + is_proxy_ = new_is_proxy; + } + + /** + * Resize array + * @param d0,... array sizes for different dimensions + */ + void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + init(d0, d1, d2, d3, d4, d5, this->array_name); + } + + /** + * Reshape array without reset the data + * @param d0,... array sizes for different dimensions + */ + void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { + //check data size consistency + size_t new_size = d0 * d1 * d2 * d3 * d4 * d5; + if (new_size != size) + throw invalid_argument("Couldn't reshape array when the size is not conserved"); + set_dimensions(d0, d1, d2, d3, d4, d5); + } + + /** + * Get array size in dimension "d" + * @param d dimension index + */ + size_t get_dim(int d) const { + return dim[d]; + } + +#ifdef MULTIARRAY_INDICES_CHECK + + /** + * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { + + if ((i0 < 0) | (i0 >= dim[0])) { + char buf[1024]; + sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); + throw std::out_of_range(buf); + } + + if ((i1 < 0) | (i1 >= dim[1])) { + char buf[1024]; + sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); + throw std::out_of_range(buf); + } + + if ((i2 < 0) | (i2 >= dim[2])) { + char buf[1024]; + sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); + throw std::out_of_range(buf); + } + + if ((i3 < 0) | (i3 >= dim[3])) { + char buf[1024]; + sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); + throw std::out_of_range(buf); + } + + if ((i4 < 0) | (i4 >= dim[4])) { + char buf[1024]; + sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); + throw std::out_of_range(buf); + } + + if ((i5 < 0) | (i5 >= dim[5])) { + char buf[1024]; + sprintf(buf, "%s: index i5=%ld out of range (0, %ld)\n", array_name.c_str(), i5, dim[5] - 1); + throw std::out_of_range(buf); + } + + } + +#endif + + /** + * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4, i5); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; + + } + + /** + * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will + * be performed before accessing memory. By default this is turned off. + * @param i0,... indices + */ + inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) { +#ifdef MULTIARRAY_INDICES_CHECK + check_indices(i0, i1, i2, i3, i4, i5); +#endif + + return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; + + } + + /** + * Array comparison operator + * @param other + */ + bool operator==(const Array6D &other) const { + //compare dimensions + for (int d = 0; d < ndim; d++) { + if (this->dim[d] != other.dim[d]) + return false; + } + return ContiguousArrayND::operator==(other); + } + + /** + * Convert to nested vector> container + * @return vector container + */ + vector>>>>> to_vector() const { + vector>>>>> res; + + res.resize(dim[0]); + + for (int i0 = 0; i0 < dim[0]; i0++) { + res[i0].resize(dim[1]); + + + for (int i1 = 0; i1 < dim[1]; i1++) { + res[i0][i1].resize(dim[2]); + + + for (int i2 = 0; i2 < dim[2]; i2++) { + res[i0][i1][i2].resize(dim[3]); + + + for (int i3 = 0; i3 < dim[3]; i3++) { + res[i0][i1][i2][i3].resize(dim[4]); + + + for (int i4 = 0; i4 < dim[4]; i4++) { + res[i0][i1][i2][i3][i4].resize(dim[5]); + + + for (int i5 = 0; i5 < dim[5]; i5++) { + res[i0][i1][i2][i3][i4][i5] = operator()(i0, i1, i2, i3, i4, i5); + + } + } + } + } + } + } + + + return res; + } // end to_vector() + + + /** + * Set values to vector> container + * @param vec container + */ + void set_vector(const vector>>>>> &vec) { + size_t d0 = 0; + size_t d1 = 0; + size_t d2 = 0; + size_t d3 = 0; + size_t d4 = 0; + size_t d5 = 0; + d0 = vec.size(); + + if (d0 > 0) { + d1 = vec.at(0).size(); + if (d1 > 0) { + d2 = vec.at(0).at(0).size(); + if (d2 > 0) { + d3 = vec.at(0).at(0).at(0).size(); + if (d3 > 0) { + d4 = vec.at(0).at(0).at(0).at(0).size(); + if (d4 > 0) { + d5 = vec.at(0).at(0).at(0).at(0).at(0).size(); + + + } + } + } + } + } + + init(d0, d1, d2, d3, d4, d5, array_name); + for (int i0 = 0; i0 < dim[0]; i0++) { + if (vec.at(i0).size() != d1) + throw std::invalid_argument("Vector size is not constant at dimension 1"); + + for (int i1 = 0; i1 < dim[1]; i1++) { + if (vec.at(i0).at(i1).size() != d2) + throw std::invalid_argument("Vector size is not constant at dimension 2"); + + for (int i2 = 0; i2 < dim[2]; i2++) { + if (vec.at(i0).at(i1).at(i2).size() != d3) + throw std::invalid_argument("Vector size is not constant at dimension 3"); + + for (int i3 = 0; i3 < dim[3]; i3++) { + if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) + throw std::invalid_argument("Vector size is not constant at dimension 4"); + + for (int i4 = 0; i4 < dim[4]; i4++) { + if (vec.at(i0).at(i1).at(i2).at(i3).at(i4).size() != d5) + throw std::invalid_argument("Vector size is not constant at dimension 5"); + + for (int i5 = 0; i5 < dim[5]; i5++) { + operator()(i0, i1, i2, i3, i4, i5) = vec.at(i0).at(i1).at(i2).at(i3).at(i4).at(i5); + + } + } + } + } + } + } + + } + + /** + * Parametrized constructor from vector> container + * @param vec container + * @param array_name array name + */ + Array6D(const vector>>>>> &vec, const string &array_name = "Array6D") { + this->set_vector(vec); + this->array_name = array_name; + } + + /** + * operator= to vector> container + * @param vec container + */ + Array6D &operator=(const vector>>>>> &vec) { + this->set_vector(vec); + return *this; + } + + + /** + * operator= to flatten vector container + * @param vec container + */ + Array6D &operator=(const vector &vec) { + this->set_flatten_vector(vec); + return *this; + } + + + vector get_shape() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = dim[d]; + return sh; + } + + vector get_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d]; + return sh; + } + + vector get_memory_strides() const { + vector sh(ndim); + for (int d = 0; d < ndim; d++) + sh[d] = s[d] * sizeof(T); + return sh; + } +}; + + +#endif //ACE_MULTIARRAY_H diff --git a/lib/pace/ace_c_basis.cpp b/lib/pace/ace_c_basis.cpp new file mode 100644 index 0000000000..d1c55700b7 --- /dev/null +++ b/lib/pace/ace_c_basis.cpp @@ -0,0 +1,980 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 1.04.20. + +#include "ace_c_basis.h" +#include "ships_radial.h" + +using namespace std; + +ACECTildeBasisSet::ACECTildeBasisSet(string filename) { + load(filename); +} + +ACECTildeBasisSet::ACECTildeBasisSet(const ACECTildeBasisSet &other) { + ACECTildeBasisSet::_copy_scalar_memory(other); + ACECTildeBasisSet::_copy_dynamic_memory(other); + pack_flatten_basis(); +} + + +ACECTildeBasisSet &ACECTildeBasisSet::operator=(const ACECTildeBasisSet &other) { + if (this != &other) { + _clean(); + _copy_scalar_memory(other); + _copy_dynamic_memory(other); + pack_flatten_basis(); + } + return *this; +} + + +ACECTildeBasisSet::~ACECTildeBasisSet() { + ACECTildeBasisSet::_clean(); +} + +void ACECTildeBasisSet::_clean() { + // call parent method + ACEFlattenBasisSet::_clean(); + _clean_contiguous_arrays(); + _clean_basis_arrays(); +} + +void ACECTildeBasisSet::_copy_scalar_memory(const ACECTildeBasisSet &src) { + ACEFlattenBasisSet::_copy_scalar_memory(src); + num_ctilde_max = src.num_ctilde_max; +} + +void ACECTildeBasisSet::_copy_dynamic_memory(const ACECTildeBasisSet &src) {//allocate new memory + ACEFlattenBasisSet::_copy_dynamic_memory(src); + + if (src.basis_rank1 == nullptr) + throw runtime_error("Could not copy ACECTildeBasisSet::basis_rank1 - array not initialized"); + if (src.basis == nullptr) throw runtime_error("Could not copy ACECTildeBasisSet::basis - array not initialized"); + + + basis_rank1 = new ACECTildeBasisFunction *[src.nelements]; + basis = new ACECTildeBasisFunction *[src.nelements]; + + //copy basis arrays + for (SPECIES_TYPE mu = 0; mu < src.nelements; ++mu) { + basis_rank1[mu] = new ACECTildeBasisFunction[src.total_basis_size_rank1[mu]]; + + for (size_t i = 0; i < src.total_basis_size_rank1[mu]; i++) { + basis_rank1[mu][i] = src.basis_rank1[mu][i]; + } + + + basis[mu] = new ACECTildeBasisFunction[src.total_basis_size[mu]]; + for (size_t i = 0; i < src.total_basis_size[mu]; i++) { + basis[mu][i] = src.basis[mu][i]; + } + } + //DON"T COPY CONTIGUOUS ARRAY, REBUILD THEM +} + +void ACECTildeBasisSet::_clean_contiguous_arrays() { + ACEFlattenBasisSet::_clean_contiguous_arrays(); + + delete[] full_c_tildes_rank1; + full_c_tildes_rank1 = nullptr; + + delete[] full_c_tildes; + full_c_tildes = nullptr; +} + +//re-pack the constituent dynamic arrays of all basis functions in contiguous arrays +void ACECTildeBasisSet::pack_flatten_basis() { + compute_array_sizes(basis_rank1, basis); + + //1. clean contiguous arrays + _clean_contiguous_arrays(); + //2. allocate contiguous arrays + delete[] full_ns_rank1; + full_ns_rank1 = new NS_TYPE[rank_array_total_size_rank1]; + delete[] full_ls_rank1; + full_ls_rank1 = new NS_TYPE[rank_array_total_size_rank1]; + delete[] full_mus_rank1; + full_mus_rank1 = new SPECIES_TYPE[rank_array_total_size_rank1]; + delete[] full_ms_rank1; + full_ms_rank1 = new MS_TYPE[rank_array_total_size_rank1]; + + delete[] full_c_tildes_rank1; + full_c_tildes_rank1 = new DOUBLE_TYPE[coeff_array_total_size_rank1]; + + + delete[] full_ns; + full_ns = new NS_TYPE[rank_array_total_size]; + delete[] full_ls; + full_ls = new LS_TYPE[rank_array_total_size]; + delete[] full_mus; + full_mus = new SPECIES_TYPE[rank_array_total_size]; + delete[] full_ms; + full_ms = new MS_TYPE[ms_array_total_size]; + + delete[] full_c_tildes; + full_c_tildes = new DOUBLE_TYPE[coeff_array_total_size]; + + + //3. copy the values from private C_tilde_B_basis_function arrays to new contigous space + //4. clean private memory + //5. reassign private array pointers + + //r = 0, rank = 1 + size_t rank_array_ind_rank1 = 0; + size_t coeff_array_ind_rank1 = 0; + size_t ms_array_ind_rank1 = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + for (int func_ind_r1 = 0; func_ind_r1 < total_basis_size_rank1[mu]; ++func_ind_r1) { + ACECTildeBasisFunction &func = basis_rank1[mu][func_ind_r1]; + + //copy values ns from c_tilde_basis_function private memory to contigous memory part + full_ns_rank1[rank_array_ind_rank1] = func.ns[0]; + + //copy values ls from c_tilde_basis_function private memory to contigous memory part + full_ls_rank1[rank_array_ind_rank1] = func.ls[0]; + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + full_mus_rank1[rank_array_ind_rank1] = func.mus[0]; + + //copy values ctildes from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_c_tildes_rank1[coeff_array_ind_rank1], func.ctildes, + func.ndensity * sizeof(DOUBLE_TYPE)); + + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ms_rank1[ms_array_ind_rank1], func.ms_combs, + func.num_ms_combs * + func.rank * sizeof(MS_TYPE)); + + //release memory of each ACECTildeBasisFunction if it is not proxy + func._clean(); + + func.mus = &full_mus_rank1[rank_array_ind_rank1]; + func.ns = &full_ns_rank1[rank_array_ind_rank1]; + func.ls = &full_ls_rank1[rank_array_ind_rank1]; + func.ms_combs = &full_ms_rank1[ms_array_ind_rank1]; + func.ctildes = &full_c_tildes_rank1[coeff_array_ind_rank1]; + func.is_proxy = true; + + rank_array_ind_rank1 += func.rank; + ms_array_ind_rank1 += func.rank * + func.num_ms_combs; + coeff_array_ind_rank1 += func.num_ms_combs * func.ndensity; + + } + } + + + //rank>1, r>0 + size_t rank_array_ind = 0; + size_t coeff_array_ind = 0; + size_t ms_array_ind = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + ACECTildeBasisFunction &func = basis[mu][func_ind]; + + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_mus[rank_array_ind], func.mus, + func.rank * sizeof(SPECIES_TYPE)); + + //copy values ns from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ns[rank_array_ind], func.ns, + func.rank * sizeof(NS_TYPE)); + //copy values ls from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ls[rank_array_ind], func.ls, + func.rank * sizeof(LS_TYPE)); + //copy values mus from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_ms[ms_array_ind], func.ms_combs, + func.num_ms_combs * + func.rank * sizeof(MS_TYPE)); + + //copy values ctildes from c_tilde_basis_function private memory to contigous memory part + memcpy(&full_c_tildes[coeff_array_ind], func.ctildes, + func.num_ms_combs * func.ndensity * sizeof(DOUBLE_TYPE)); + + + //release memory of each ACECTildeBasisFunction if it is not proxy + func._clean(); + + func.ns = &full_ns[rank_array_ind]; + func.ls = &full_ls[rank_array_ind]; + func.mus = &full_mus[rank_array_ind]; + func.ctildes = &full_c_tildes[coeff_array_ind]; + func.ms_combs = &full_ms[ms_array_ind]; + func.is_proxy = true; + + rank_array_ind += func.rank; + ms_array_ind += func.rank * + func.num_ms_combs; + coeff_array_ind += func.num_ms_combs * func.ndensity; + } + } +} + +void fwrite_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { + RANK_TYPE r; + fprintf(fptr, "ctilde_basis_func: "); + fprintf(fptr, "rank=%d ndens=%d mu0=%d ", func.rank, func.ndensity, func.mu0); + + fprintf(fptr, "mu=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.mus[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "n=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ns[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "l=("); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ls[r]); + fprintf(fptr, ")\n"); + + fprintf(fptr, "num_ms=%d\n", func.num_ms_combs); + + for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { + fprintf(fptr, "<"); + for (r = 0; r < func.rank; ++r) + fprintf(fptr, " %d ", func.ms_combs[m_ind * func.rank + r]); + fprintf(fptr, ">: "); + for (DENSITY_TYPE p = 0; p < func.ndensity; p++) + fprintf(fptr, " %.18f ", func.ctildes[m_ind * func.ndensity + p]); + fprintf(fptr, "\n"); + } + +} + +void ACECTildeBasisSet::save(const string &filename) { + FILE *fptr; + fptr = fopen(filename.c_str(), "w"); + + fprintf(fptr, "nelements=%d\n", nelements); + + //elements mapping + fprintf(fptr, "elements:"); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) + fprintf(fptr, " %s", elements_name[mu].c_str()); + fprintf(fptr, "\n\n"); + + fprintf(fptr, "lmax=%d\n\n", lmax); + + fprintf(fptr, "embedding-function: %s\n", npoti.c_str()); + + fprintf(fptr, "%ld FS parameters: ", FS_parameters.size()); + for (int i = 0; i < FS_parameters.size(); ++i) { + fprintf(fptr, " %f", FS_parameters.at(i)); + } + fprintf(fptr, "\n"); + + //hard-core energy cutoff repulsion + fprintf(fptr, "core energy-cutoff parameters: "); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + fprintf(fptr, "%.18f %.18f\n", rho_core_cutoffs(mu_i), drho_core_cutoffs(mu_i)); + + // save E0 values + fprintf(fptr, "E0:"); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + fprintf(fptr, " %.18f", E0vals(mu_i)); + fprintf(fptr, "\n"); + + + fprintf(fptr, "\n"); + + + fprintf(fptr, "radbasename=%s\n", radial_functions->radbasename.c_str()); + fprintf(fptr, "nradbase=%d\n", nradbase); + fprintf(fptr, "nradmax=%d\n", nradmax); + + + fprintf(fptr, "cutoffmax=%f\n", cutoffmax); + + fprintf(fptr, "deltaSplineBins=%f\n", deltaSplineBins); + + //hard-core repulsion + fprintf(fptr, "core repulsion parameters: "); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, "%.18f %.18f\n", radial_functions->prehc(mu_i, mu_j), radial_functions->lambdahc(mu_j, mu_j)); + + + + + + //TODO: radial functions + //radparameter + fprintf(fptr, "radparameter="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->lambda(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "cutoff="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->cut(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "dcut="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + fprintf(fptr, " %.18f", radial_functions->dcut(mu_i, mu_j)); + fprintf(fptr, "\n"); + + fprintf(fptr, "crad="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + for (NS_TYPE k = 0; k < nradbase; k++) { + for (NS_TYPE n = 0; n < nradmax; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fprintf(fptr, " %.18f", radial_functions->crad(mu_i, mu_j, n, l, k)); + } + fprintf(fptr, "\n"); + } + } + } + + fprintf(fptr, "\n"); + + fprintf(fptr, "rankmax=%d\n", rankmax); + fprintf(fptr, "ndensitymax=%d\n", ndensitymax); + fprintf(fptr, "\n"); + + //num_c_tilde_max + fprintf(fptr, "num_c_tilde_max=%d\n", num_ctilde_max); + fprintf(fptr, "num_ms_combinations_max=%d\n", num_ms_combinations_max); + + + //write total_basis_size and total_basis_size_rank1 + fprintf(fptr, "total_basis_size_rank1: "); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + fprintf(fptr, "%d ", total_basis_size_rank1[mu]); + } + fprintf(fptr, "\n"); + + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) + fwrite_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); + + fprintf(fptr, "total_basis_size: "); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + fprintf(fptr, "%d ", total_basis_size[mu]); + } + fprintf(fptr, "\n"); + + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) + fwrite_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); + + + fclose(fptr); +} + +void fread_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { + RANK_TYPE r; + int res; + char buf[3][128]; + + res = fscanf(fptr, " ctilde_basis_func: "); + + res = fscanf(fptr, "rank=%s ndens=%s mu0=%s ", buf[0], buf[1], buf[2]); + if (res != 3) + throw invalid_argument("Could not read C-tilde basis function"); + + func.rank = (RANK_TYPE) stol(buf[0]); + func.ndensity = (DENSITY_TYPE) stol(buf[1]); + func.mu0 = (SPECIES_TYPE) stol(buf[2]); + + func.mus = new SPECIES_TYPE[func.rank]; + func.ns = new NS_TYPE[func.rank]; + func.ls = new LS_TYPE[func.rank]; + + res = fscanf(fptr, " mu=("); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.mus[r] = (SPECIES_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); // ")" + + res = fscanf(fptr, " n=("); // "n=" + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + + func.ns[r] = (NS_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); + + res = fscanf(fptr, " l=("); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ls[r] = (NS_TYPE) stol(buf[0]); + } + res = fscanf(fptr, " )"); + + res = fscanf(fptr, " num_ms=%s\n", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + + func.num_ms_combs = (SHORT_INT_TYPE) stoi(buf[0]); + + func.ms_combs = new MS_TYPE[func.rank * func.num_ms_combs]; + func.ctildes = new DOUBLE_TYPE[func.ndensity * func.num_ms_combs]; + + for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { + res = fscanf(fptr, " <"); + for (r = 0; r < func.rank; ++r) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ms_combs[m_ind * func.rank + r] = stoi(buf[0]); + } + res = fscanf(fptr, " >:"); + for (DENSITY_TYPE p = 0; p < func.ndensity; p++) { + res = fscanf(fptr, "%s", buf[0]); + if (res != 1) + throw invalid_argument("Could not read C-tilde basis function"); + func.ctildes[m_ind * func.ndensity + p] = stod(buf[0]); + } + } +} + +string +format_error_message(const char *buffer, const string &filename, const string &var_name, const string &expected) { + string err_message = "File '" + filename + "': couldn't read '" + var_name + "'"; + if (buffer) + err_message = err_message + ", read:'" + buffer + "'"; + if (!expected.empty()) + err_message = err_message + ". Expected format: '" + expected + "'"; + return err_message; +} + +void throw_error(const string &filename, const string &var_name, const string expected = "") { + throw invalid_argument(format_error_message(nullptr, filename, var_name, expected)); +} + +DOUBLE_TYPE stod_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stod(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +int stoi_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stoi(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +long int stol_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { + try { + return stol(buffer); + } catch (invalid_argument &exc) { + throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); + } +} + +void ACECTildeBasisSet::load(const string filename) { + int res; + char buffer[1024], buffer2[1024]; + string radbasename = "ChebExpCos"; + + FILE *fptr; + fptr = fopen(filename.c_str(), "r"); + if (fptr == NULL) + throw invalid_argument("Could not open file " + filename); + + //read number of elements + res = fscanf(fptr, " nelements="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nelements", "nelements=[number]"); + nelements = stoi_err(buffer, filename, "nelements", "nelements=[number]"); + + //elements mapping + elements_name = new string[nelements]; + res = fscanf(fptr, " elements:"); + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "elements", "elements: Ele1 Ele2 ..."); + elements_name[mu] = buffer; + } + + // load angular basis - only need spherical harmonics parameter + res = fscanf(fptr, " lmax=%s\n", buffer); + if (res != 1) + throw_error(filename, "lmax", "lmax=[number]"); + lmax = stoi_err(buffer, filename, "lmax", "lmax=[number]"); + spherical_harmonics.init(lmax); + + + // reading "embedding-function:" + bool is_embedding_function_specified = false; + res = fscanf(fptr, " embedding-function: %s", buffer); + if (res == 0) { + //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); + this->npoti = "FinnisSinclair"; // default values + //printf("Warning! No embedding-function is specified, embedding-function: FinnisSinclair would be assumed\n"); + is_embedding_function_specified = false; + } else { + this->npoti = buffer; + is_embedding_function_specified = true; + } + int parameters_size; + res = fscanf(fptr, "%s FS parameters:", buffer); + if (res != 1) + throw_error(filename, "FS parameters size", "[number] FS parameters: par1 par2 ..."); + parameters_size = stoi_err(buffer, filename, "FS parameters size", "[number] FS parameters"); + FS_parameters.resize(parameters_size); + for (int i = 0; i < FS_parameters.size(); ++i) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); + FS_parameters[i] = stod_err(buffer, filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); + } + + if (!is_embedding_function_specified) { + // assuming non-linear potential, and embedding function type is important + for (int j = 1; j < parameters_size; j += 2) + if (FS_parameters[j] != 1.0) { //if not ensure linearity of embedding function parameters + printf("ERROR! Your potential is non-linear\n"); + printf("Please specify 'embedding-function: FinnisSinclair' or 'embedding-function: FinnisSinclairShiftedScaled' before 'FS parameters size' line\n"); + throw_error(filename, "embedding-function", "FinnisSinclair or FinnisSinclairShiftedScaled"); + } + printf("Notice! No embedding-function is specified, but potential has linear embedding, default embedding-function: FinnisSinclair would be assumed\n"); + } + + //hard-core energy cutoff repulsion + res = fscanf(fptr, " core energy-cutoff parameters:"); + if (res != 0) + throw_error(filename, "core energy-cutoff parameters", "core energy-cutoff parameters: [par1] [par2]"); + + rho_core_cutoffs.init(nelements, "rho_core_cutoffs"); + drho_core_cutoffs.init(nelements, "drho_core_cutoffs"); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) { + res = fscanf(fptr, "%s %s", buffer, buffer2); + if (res != 2) + throw_error(filename, "core energy-cutoff parameters", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + rho_core_cutoffs(mu_i) = stod_err(buffer, filename, "rho core cutoff", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + drho_core_cutoffs(mu_i) = stod_err(buffer2, filename, "drho_core_cutoff", + "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); + } + + // atom energy shift E0 (energy of isolated atom) + E0vals.init(nelements); + + // reading "E0:" + res = fscanf(fptr, " E0: %s", buffer); + if (res == 0) { + //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); + E0vals.fill(0.0); + } else { + double E0 = atof(buffer); + E0vals(0) = E0; + + for (SPECIES_TYPE mu_i = 1; mu_i < nelements; ++mu_i) { + res = fscanf(fptr, " %lf", &E0); + if (res != 1) + throw_error(filename, "E0", " couldn't read one of the E0 values"); + E0vals(mu_i) = E0; + } + res = fscanf(fptr, "\n"); + if (res != 0) + printf("file %s : format seems broken near E0; trying to continue...\n", filename.c_str()); + } + + // check which radial basis we need to load + res = fscanf(fptr, " radbasename=%s\n", buffer); + if (res != 1) { + throw_error(filename, "radbasename", "rabbasename=ChebExpCos|ChebPow|ACE.jl.Basic"); + } else { + radbasename = buffer; + } + +// printf("radbasename = `%s`\n", radbasename.c_str()); + if (radbasename == "ChebExpCos" | radbasename == "ChebPow") { + _load_radial_ACERadial(fptr, filename, radbasename); + } else if (radbasename == "ACE.jl.Basic") { + _load_radial_SHIPsBasic(fptr, filename, radbasename); + } else { + throw invalid_argument( + ("File '" + filename + "': I don't know how to read radbasename = " + radbasename).c_str()); + } + + res = fscanf(fptr, " rankmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "rankmax", "rankmax=[number]"); + rankmax = stoi_err(buffer, filename, "rankmax", "rankmax=[number]"); + + res = fscanf(fptr, " ndensitymax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "ndensitymax", "ndensitymax=[number]"); + ndensitymax = stoi_err(buffer, filename, "ndensitymax", "ndensitymax=[number]"); + + // read the list of correlations to be put into the basis + //num_c_tilde_max + res = fscanf(fptr, " num_c_tilde_max="); + res = fscanf(fptr, "%s\n", buffer); + if (res != 1) + throw_error(filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); + num_ctilde_max = stol_err(buffer, filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); + + res = fscanf(fptr, " num_ms_combinations_max="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); +// throw invalid_argument(("File '" + filename + "': couldn't read num_ms_combinations_max").c_str()); + num_ms_combinations_max = stol_err(buffer, filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); + + //read total_basis_size_rank1 + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + basis_rank1 = new ACECTildeBasisFunction *[nelements]; + res = fscanf(fptr, " total_basis_size_rank1: "); + + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "total_basis_size_rank1", "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); +// throw invalid_argument(("File '" + filename + "': couldn't read total_basis_size_rank1").c_str()); + total_basis_size_rank1[mu] = stoi_err(buffer, filename, "total_basis_size_rank1", + "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); + basis_rank1[mu] = new ACECTildeBasisFunction[total_basis_size_rank1[mu]]; + } + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) { + fread_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); + } + + //read total_basis_size + res = fscanf(fptr, " total_basis_size: "); + total_basis_size = new SHORT_INT_TYPE[nelements]; + basis = new ACECTildeBasisFunction *[nelements]; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "total_basis_size", "total_basis_size: [size_ele1] [size_ele2] ..."); + total_basis_size[mu] = stoi_err(buffer, filename, "total_basis_size", + "total_basis_size: [size_ele1] [size_ele2] ..."); + basis[mu] = new ACECTildeBasisFunction[total_basis_size[mu]]; + } + for (SPECIES_TYPE mu = 0; mu < nelements; mu++) + for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + fread_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); + } + + fclose(fptr); + +// radial_functions->radbasename = radbasename; + radial_functions->setuplookupRadspline(); + pack_flatten_basis(); +} + +void ACECTildeBasisSet::compute_array_sizes(ACECTildeBasisFunction **basis_rank1, ACECTildeBasisFunction **basis) { + //compute arrays sizes + rank_array_total_size_rank1 = 0; + //ms_array_total_size_rank1 = rank_array_total_size_rank1; + coeff_array_total_size_rank1 = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + if (total_basis_size_rank1[mu] > 0) { + rank_array_total_size_rank1 += total_basis_size_rank1[mu]; + + ACEAbstractBasisFunction &func = basis_rank1[mu][0];//TODO: get total density instead of density from first function + coeff_array_total_size_rank1 += total_basis_size_rank1[mu] * func.ndensity; + } + } + + rank_array_total_size = 0; + coeff_array_total_size = 0; + + ms_array_total_size = 0; + max_dB_array_size = 0; + + + max_B_array_size = 0; + + size_t cur_ms_size = 0; + size_t cur_ms_rank_size = 0; + + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + + cur_ms_size = 0; + cur_ms_rank_size = 0; + for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { + auto &func = basis[mu][func_ind]; + rank_array_total_size += func.rank; + ms_array_total_size += func.rank * func.num_ms_combs; + coeff_array_total_size += func.ndensity * func.num_ms_combs; + + cur_ms_size += func.num_ms_combs; + cur_ms_rank_size += func.rank * func.num_ms_combs; + } + + if (cur_ms_size > max_B_array_size) + max_B_array_size = cur_ms_size; + + if (cur_ms_rank_size > max_dB_array_size) + max_dB_array_size = cur_ms_rank_size; + } +} + +void ACECTildeBasisSet::_clean_basis_arrays() { + if (basis_rank1 != nullptr) + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + delete[] basis_rank1[mu]; + basis_rank1[mu] = nullptr; + } + + if (basis != nullptr) + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + delete[] basis[mu]; + basis[mu] = nullptr; + } + delete[] basis; + basis = nullptr; + + delete[] basis_rank1; + basis_rank1 = nullptr; +} + +//pack into 1D array with all basis functions +void ACECTildeBasisSet::flatten_basis(C_tilde_full_basis_vector2d &mu0_ctilde_basis_vector) { + + _clean_basis_arrays(); + basis_rank1 = new ACECTildeBasisFunction *[nelements]; + basis = new ACECTildeBasisFunction *[nelements]; + + delete[] total_basis_size_rank1; + delete[] total_basis_size; + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + total_basis_size = new SHORT_INT_TYPE[nelements]; + + + size_t tot_size_rank1 = 0; + size_t tot_size = 0; + + for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { + tot_size = 0; + tot_size_rank1 = 0; + + for (auto &func: mu0_ctilde_basis_vector[mu]) { + if (func.rank == 1) tot_size_rank1 += 1; + else tot_size += 1; + } + + total_basis_size_rank1[mu] = tot_size_rank1; + basis_rank1[mu] = new ACECTildeBasisFunction[tot_size_rank1]; + + total_basis_size[mu] = tot_size; + basis[mu] = new ACECTildeBasisFunction[tot_size]; + } + + + for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { + size_t ind_rank1 = 0; + size_t ind = 0; + + for (auto &func: mu0_ctilde_basis_vector[mu]) { + if (func.rank == 1) { //r=0, rank=1 + basis_rank1[mu][ind_rank1] = func; + ind_rank1 += 1; + } else { //r>0, rank>1 + basis[mu][ind] = func; + ind += 1; + } + } + + } +} + + +void ACECTildeBasisSet::_load_radial_ACERadial(FILE *fptr, + const string filename, + const string radbasename) { + int res; + char buffer[1024], buffer2[1024]; + + res = fscanf(fptr, " nradbase="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nradbase", "nradbase=[number]"); +// throw invalid_argument(("File '" + filename + "': couldn't read nradbase").c_str()); + nradbase = stoi_err(buffer, filename, "nradbase", "nradbase=[number]"); + + res = fscanf(fptr, " nradmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "nradmax", "nradmax=[number]"); + nradmax = stoi_err(buffer, filename, "nradmax", "nradmax=[number]"); + + res = fscanf(fptr, " cutoffmax="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "cutoffmax", "cutoffmax=[number]"); + cutoffmax = stod_err(buffer, filename, "cutoffmax", "cutoffmax=[number]"); + + + res = fscanf(fptr, " deltaSplineBins="); + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); +// throw invalid_argument(("File '" + filename + "': couldn't read ntot").c_str()); + deltaSplineBins = stod_err(buffer, filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); + + + if (radial_functions == nullptr) + radial_functions = new ACERadialFunctions(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + else + radial_functions->init(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + + + //hard-core repulsion + res = fscanf(fptr, " core repulsion parameters:"); + if (res != 0) + throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); +// throw invalid_argument(("File '" + filename + "': couldn't read core repulsion parameters").c_str()); + + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s %s", buffer, buffer2); + if (res != 2) + throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); + radial_functions->prehc(mu_i, mu_j) = stod_err(buffer, filename, "core repulsion parameters", + "core repulsion parameters: [prehc lambdahc] ..."); + radial_functions->lambdahc(mu_i, mu_j) = stod_err(buffer2, filename, "core repulsion parameters", + "core repulsion parameters: [prehc lambdahc] ..."); + } + + + + //read radial functions parameter + res = fscanf(fptr, " radparameter="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "radparameter", "radparameter=[param_ele1] [param_ele2]"); + radial_functions->lambda(mu_i, mu_j) = stod_err(buffer, filename, "radparameter", + "radparameter=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " cutoff="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "cutoff", "cutoff=[param_ele1] [param_ele2]"); + radial_functions->cut(mu_i, mu_j) = stod_err(buffer, filename, "cutoff", + "cutoff=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " dcut="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { + res = fscanf(fptr, " %s", buffer); + if (res != 1) + throw_error(filename, "dcut", "dcut=[param_ele1] [param_ele2]"); + radial_functions->dcut(mu_i, mu_j) = stod_err(buffer, filename, "dcut", "dcut=[param_ele1] [param_ele2]"); + } + + + res = fscanf(fptr, " crad="); + for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) + for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) + for (NS_TYPE k = 0; k < nradbase; k++) + for (NS_TYPE n = 0; n < nradmax; n++) + for (LS_TYPE l = 0; l <= lmax; l++) { + res = fscanf(fptr, "%s", buffer); + if (res != 1) + throw_error(filename, "crad", "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); + radial_functions->crad(mu_i, mu_j, n, l, k) = stod_err(buffer, filename, "crad", + "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); + } +} + +void ACECTildeBasisSet::_load_radial_SHIPsBasic(FILE *fptr, + const string filename, + const string radbasename) { + // create a radial basis object, and read it from the file pointer + SHIPsRadialFunctions *ships_radial_functions = new SHIPsRadialFunctions(); + ships_radial_functions->fread(fptr); + + //mimic ships_radial_functions to ACERadialFunctions + ships_radial_functions->nradial = ships_radial_functions->get_maxn(); + ships_radial_functions->nradbase = ships_radial_functions->get_maxn(); + + nradbase = ships_radial_functions->get_maxn(); + nradmax = ships_radial_functions->get_maxn(); + cutoffmax = ships_radial_functions->get_rcut(); + deltaSplineBins = 0.001; + + ships_radial_functions->init(nradbase, lmax, nradmax, + deltaSplineBins, + nelements, + cutoffmax, radbasename); + + + if (radial_functions) delete radial_functions; + radial_functions = ships_radial_functions; + radial_functions->prehc.fill(0); + radial_functions->lambdahc.fill(1); + radial_functions->lambda.fill(0); + + + radial_functions->cut.fill(ships_radial_functions->get_rcut()); + radial_functions->dcut.fill(0); + + radial_functions->crad.fill(0); + +} \ No newline at end of file diff --git a/lib/pace/ace_c_basis.h b/lib/pace/ace_c_basis.h new file mode 100644 index 0000000000..ec6b9e8afc --- /dev/null +++ b/lib/pace/ace_c_basis.h @@ -0,0 +1,155 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 1.04.20. + +#ifndef ACE_C_BASIS_H +#define ACE_C_BASIS_H + +#include "ace_flatten_basis.h" + +typedef vector> C_tilde_full_basis_vector2d; + +/** + * ACE basis set of C-tilde basis functions + */ +class ACECTildeBasisSet : public ACEFlattenBasisSet { +public: + + ACECTildeBasisFunction **basis_rank1 = nullptr; ///< two-dimensional array of first-rank basis function with indices: [species index][func index] + ACECTildeBasisFunction **basis = nullptr; ///< two-dimensional array of higher rank basis function with indices: [species index][func index] + + DOUBLE_TYPE *full_c_tildes_rank1 = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size_rank1 + DOUBLE_TYPE *full_c_tildes = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size + + //TODO: remove? + SHORT_INT_TYPE num_ctilde_max = 0; + + + /** + * Default constructor + */ + ACECTildeBasisSet() = default; + + /** + * Constructor from .ace file + */ + ACECTildeBasisSet(const string filename); + + /** + * Copy constructor (see. Rule of Three) + * @param other + */ + ACECTildeBasisSet(const ACECTildeBasisSet &other); + + /** + * operator= (see. Rule of Three) + * @param other + * @return + */ + ACECTildeBasisSet &operator=(const ACECTildeBasisSet &other); + + /** + * Destructor (see. Rule of Three) + */ + ~ACECTildeBasisSet() override; + + /** + * Cleaning dynamic memory of the class (see. Rule of Three) + */ + void _clean() override; + + /** + * Copying and cleaning dynamic memory of the class (see. Rule of Three) + * @param src + */ + void _copy_dynamic_memory(const ACECTildeBasisSet &src); + + /** + * Copying scalar variables + * @param src + */ + void _copy_scalar_memory(const ACECTildeBasisSet &src); + + /** + * Clean contiguous arrays (full_c_tildes_rank1, full_c_tildes) and those of base class + */ + void _clean_contiguous_arrays() override ; + + /** + * Save potential to .ace file + * @param filename .ace file name + */ + void save(const string &filename) override; + + /** + * Load potential from .ace + * @param filename .ace file name + */ + void load(const string filename) override; + + /** + * Load the ACE type radial basis + */ + void _load_radial_ACERadial(FILE *fptr, + const string filename, + const string radbasename); + + void _load_radial_SHIPsBasic(FILE * fptr, + const string filename, + const string radbasename ); + + /** + * Re-pack the constituent dynamic arrays of all basis functions in contiguous arrays + */ + void pack_flatten_basis() override; + + /** + * Computes flatten array sizes + * @param basis_rank1 two-dimensional array of first-rank ACECTildeBasisFunctions + * @param basis two-dimensional array of higher-rank ACECTildeBasisFunctions + */ + void compute_array_sizes(ACECTildeBasisFunction** basis_rank1, ACECTildeBasisFunction** basis); + + /** + * Clean basis arrays 'basis_rank1' and 'basis' + */ + void _clean_basis_arrays(); + + /** + * Pack two-dimensional vector of ACECTildeBasisFunction into 1D dynami array with all basis functions + * @param mu0_ctilde_basis_vector vector> + */ + void flatten_basis(C_tilde_full_basis_vector2d& mu0_ctilde_basis_vector); + + /** + * Empty stub implementation + */ + void flatten_basis() override{}; +}; + +#endif //ACE_C_BASIS_H diff --git a/lib/pace/ace_c_basisfunction.h b/lib/pace/ace_c_basisfunction.h new file mode 100644 index 0000000000..4e2795590e --- /dev/null +++ b/lib/pace/ace_c_basisfunction.h @@ -0,0 +1,251 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 26.02.20. + +#ifndef ACE_C_BASISFUNCTION_H +#define ACE_C_BASISFUNCTION_H + +#include +#include +#include +#include + +#include "ace_types.h" + +//macros for copying the member-array from "other" object for C-tilde and B-basis +#define basis_mem_copy(other, array, size, type) if(other.array) { \ + if(!is_proxy) delete[] array;\ + array = new type[(size)];\ + is_proxy = false;\ + memcpy(array, other.array, (size) * sizeof(type));\ +} + +/** + * Abstract basis function, that stores general quantities + */ +struct ACEAbstractBasisFunction { + /** + * flattened array of computed combinations of (m1, m2, ..., m_rank) + * which have non-zero general Clebsch-Gordan coefficient: + * \f$ \mathbf{m}_1, \dots, \mathbf{m}_\mathrm{num ms combs}\f$ = + * \f$ (m_1, m_2, \dots, m_{rank})_1, \dots, (m_1, m_2, \dots, m_{rank})_{\mathrm{num ms combs}} \f$, + * size = num_ms_combs * rank, + * effective shape: [num_ms_combs][rank] + */ + MS_TYPE *ms_combs = nullptr; + + /** + * species types of neighbours atoms \f$ \mathbf{\mu} = (\mu_1, \mu_2, \dots, \mu_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + SPECIES_TYPE *mus = nullptr; + + /** + * indices for radial part \f$ \mathbf{n} = (n_1, n_2, \dots, n_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + NS_TYPE *ns = nullptr; + + + /** + * indices for radial part \f$ \mathbf{l} = (l_1, l_2, \dots, l_{rank}) \f$, + * should be lexicographically sorted, + * size = rank, + * effective shape: [rank] + */ + LS_TYPE *ls = nullptr; + + SHORT_INT_TYPE num_ms_combs = 0; ///< number of different ms-combinations + + RANK_TYPE rank = 0; ///< number of atomic base functions "A"s in basis function product B + + DENSITY_TYPE ndensity = 0; ///< number of densities + + SPECIES_TYPE mu0 = 0; ///< species type of central atom + + /** + * whether ms array contains only "non-negative" ms-combinations. + * positive ms-combination is when the first non-zero m is positive (0 1 -1) + * negative ms-combination is when the first non-zero m is negative (0 -1 1) + */ + bool is_half_ms_basis = false; + + /* + * flag, whether object is "owner" (i.e. responsible for memory cleaning) of + * the ms, ns, ls, mus and other dynamically allocated arrases or just a proxy for them + */ + bool is_proxy = false; + + /** + * Copying static and dynamic memory variables from another ACEAbstractBasisFunction. + * Always copy the dynamic memory, even if the source is a proxy object + * @param other + */ + virtual void _copy_from(const ACEAbstractBasisFunction &other) { + rank = other.rank; + ndensity = other.ndensity; + mu0 = other.mu0; + num_ms_combs = other.num_ms_combs; + is_half_ms_basis = other.is_half_ms_basis; + is_proxy = false; + + basis_mem_copy(other, mus, rank, SPECIES_TYPE) + basis_mem_copy(other, ns, rank, NS_TYPE) + basis_mem_copy(other, ls, rank, LS_TYPE) + basis_mem_copy(other, ms_combs, num_ms_combs * rank, MS_TYPE) + } + + /** + * Clean the dynamically allocated memory if object is responsible for it + */ + virtual void _clean() { + //release memory if the structure is not proxy + if (!is_proxy) { + delete[] mus; + delete[] ns; + delete[] ls; + delete[] ms_combs; + } + + mus = nullptr; + ns = nullptr; + ls = nullptr; + ms_combs = nullptr; + } + +}; + +/** + * Representation of C-tilde basis function, i.e. the function that is summed up over a group of B-functions + * that differs only by intermediate coupling orbital moment \f$ L \f$ and coefficients. + */ +struct ACECTildeBasisFunction : public ACEAbstractBasisFunction { + + /** + * c_tilde coefficients for all densities, + * size = num_ms_combs*ndensity, + * effective shape [num_ms_combs][ndensity] + */ + DOUBLE_TYPE *ctildes = nullptr; + + /* + * Default constructor + */ + ACECTildeBasisFunction() = default; + + // Because the ACECTildeBasisFunction contains dynamically allocated arrays, the Rule of Three should be + // fulfilled, i.e. copy constructor (copy the dynamic arrays), operator= (release previous arrays and + // copy the new dynamic arrays) and destructor (release all dynamically allocated memory) + + /** + * Copy constructor, to fulfill the Rule of Three. + * Always copy the dynamic memory, even if the source is a proxy object. + */ + ACECTildeBasisFunction(const ACECTildeBasisFunction &other) { + _copy_from(other); + } + + /* + * operator=, to fulfill the Rule of Three. + * Always copy the dynamic memory, even if the source is a proxy object + */ + ACECTildeBasisFunction &operator=(const ACECTildeBasisFunction &other) { + _clean(); + _copy_from(other); + return *this; + } + + /* + * Destructor + */ + ~ACECTildeBasisFunction() { + _clean(); + } + + /** + * Copy from another object, always copy the memory, even if the source is a proxy object + * @param other + */ + void _copy_from(const ACECTildeBasisFunction &other) { + ACEAbstractBasisFunction::_copy_from(other); + is_proxy = false; + basis_mem_copy(other, ctildes, num_ms_combs * ndensity, DOUBLE_TYPE) + } + + /** + * Clean the dynamically allocated memory if object is responsible for it + */ + void _clean() override { + ACEAbstractBasisFunction::_clean(); + //release memory if the structure is not proxy + if (!is_proxy) { + delete[] ctildes; + } + ctildes = nullptr; + } + + /** + * Print the information about basis function to cout, in order to ease the output redirection. + */ + void print() const { + using namespace std; + cout << "ACECTildeBasisFunction: ndensity= " << (int) this->ndensity << ", mu0 = " << (int) this->mu0 << " "; + cout << " mus=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << (int) this->mus[r] << " "; + cout << "), ns=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ns[r] << " "; + cout << "), ls=("; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ls[r] << " "; + + cout << "), " << this->num_ms_combs << " m_s combinations: {" << endl; + + for (int i = 0; i < this->num_ms_combs; i++) { + cout << "\t< "; + for (RANK_TYPE r = 0; r < this->rank; r++) + cout << this->ms_combs[i * this->rank + r] << " "; + cout << " >: c_tilde="; + for (DENSITY_TYPE p = 0; p < this->ndensity; ++p) + cout << " " << this->ctildes[i * this->ndensity + p] << " "; + cout << endl; + } + if (this->is_proxy) + cout << "proxy "; + if (this->is_half_ms_basis) + cout << "half_ms_basis"; + cout << "}" << endl; + } +}; + +#endif //ACE_C_BASISFUNCTION_H diff --git a/lib/pace/ace_complex.h b/lib/pace/ace_complex.h new file mode 100644 index 0000000000..5fdb4b5b93 --- /dev/null +++ b/lib/pace/ace_complex.h @@ -0,0 +1,266 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 26.02.20. + +#ifndef ACE_COMPLEX_H +#define ACE_COMPLEX_H + + +/** +A custom data structure for complex numbers and overloaded operations with them. +*/ +struct ACEComplex { +public: + /** + Double, real part of the complex number + */ + DOUBLE_TYPE real; + /** + Double, imaginary part of the complex number + */ + DOUBLE_TYPE img; + + ACEComplex &operator=(const ACEComplex &rhs) = default; + + ACEComplex &operator=(const DOUBLE_TYPE &rhs) { + this->real = rhs; + this->img = 0.; + return *this; + } + + /** + Overloading of arithmetical operator += ACEComplex + */ + ACEComplex &operator+=(const ACEComplex &rhs) { + this->real += rhs.real; + this->img += rhs.img; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator += DOUBLE_TYPE + */ + ACEComplex &operator+=(const DOUBLE_TYPE &rhs) { + this->real += rhs; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator *= DOUBLE_TYPE + */ + ACEComplex &operator*=(const DOUBLE_TYPE &rhs) { + this->real *= rhs; + this->img *= rhs; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator *= ACEComplex + */ + ACEComplex &operator*=(const ACEComplex &rhs) { + DOUBLE_TYPE old_real = this->real; + this->real = old_real * rhs.real - this->img * rhs.img; + this->img = old_real * rhs.img + this->img * rhs.real; + return *this; // return the result by reference + } + + /** + Overloading of arithmetical operator * ACEComplex + */ + ACEComplex operator*(const ACEComplex &cm2) const { + ACEComplex res{real * cm2.real - img * cm2.img, + real * cm2.img + img * cm2.real}; + return res; + } + + /* + * Return complex conjugated copy of itself + */ + ACEComplex conjugated() const { + ACEComplex res{real, -img}; + return res; + } + + /* + * Complex conjugate itself inplace + */ + void conjugate() { + img = -img; + } + + /* + * Multiplication by ACEComplex and return real-part only + */ + DOUBLE_TYPE real_part_product(const ACEComplex &cm2) const { + return real * cm2.real - img * cm2.img; + } + + /* + * Multiplication by DOUBLE_TYPE and return real-part only + */ + DOUBLE_TYPE real_part_product(const DOUBLE_TYPE &cm2) const { + return real * cm2; + } + + /* + * Overloading of arithmetical operator * by DOUBLE_TYPE + */ + ACEComplex operator*(const DOUBLE_TYPE &cm2) const { + ACEComplex res{real * cm2, + img * cm2}; + return res; + } + + /* + * Overloading of arithmetical operator + ACEComplex + */ + ACEComplex operator+(const ACEComplex &cm2) const { + ACEComplex res{real + cm2.real, + img + cm2.img}; + return res; + } + + /* + * Overloading of arithmetical operator + with DOUBLE_TYPE + */ + ACEComplex operator+(const DOUBLE_TYPE &cm2) const { + ACEComplex res{real + cm2, img}; + return res; + } + + /* + * Overloading of arithmetical operator == ACEComplex + */ + bool operator==(const ACEComplex &c2) const { + return (real == c2.real) && (img == c2.img); + } + + /* + * Overloading of arithmetical operator == DOUBLE_TYPE + */ + bool operator==(const DOUBLE_TYPE &d2) const { + return (real == d2) && (img == 0.); + } + + /* + * Overloading of arithmetical operator != ACEComplex + */ + bool operator!=(const ACEComplex &c2) const { + return (real != c2.real) || (img != c2.img); + } + + /* + * Overloading of arithmetical operator != DOUBLE_TYPE + */ + bool operator!=(const DOUBLE_TYPE &d2) const { + return (real != d2) || (img != 0.); + } + +}; + +/* + * double * complex for commutativity with complex * double + */ +inline ACEComplex operator*(const DOUBLE_TYPE &real, const ACEComplex &cm) { + return cm * real; +} + +/* + * double + complex for commutativity with complex + double + */ +inline ACEComplex operator+(const DOUBLE_TYPE &real, const ACEComplex &cm) { + return cm + real; +} + +/** +A structure to store the derivative of \f$ Y_{lm} \f$ +*/ +struct ACEDYcomponent { +public: + /** + complex, contains the three components of derivative of Ylm, + \f$ \frac{dY_{lm}}{dx}, \frac{dY_{lm}}{dy} and \frac{dY_{lm}}{dz}\f$ + */ + ACEComplex a[3]; + + /* + * Overloading of arithmetical operator*= DOUBLE_TYPE + */ + ACEDYcomponent &operator*=(const DOUBLE_TYPE &rhs) { + this->a[0] *= rhs; + this->a[1] *= rhs; + this->a[2] *= rhs; + return *this; + } + + /* + * Overloading of arithmetical operator * ACEComplex + */ + ACEDYcomponent operator*(const ACEComplex &rhs) const { + ACEDYcomponent res; + res.a[0] = this->a[0] * rhs; + res.a[1] = this->a[1] * rhs; + res.a[2] = this->a[2] * rhs; + return res; + } + + /* + * Overloading of arithmetical operator * DOUBLE_TYPE + */ + ACEDYcomponent operator*(const DOUBLE_TYPE &rhs) const { + ACEDYcomponent res; + res.a[0] = this->a[0] * rhs; + res.a[1] = this->a[1] * rhs; + res.a[2] = this->a[2] * rhs; + return res; + } + + /* + * Return conjugated copy of itself + */ + ACEDYcomponent conjugated() const { + ACEDYcomponent res; + res.a[0] = this->a[0].conjugated(); + res.a[1] = this->a[1].conjugated(); + res.a[2] = this->a[2].conjugated(); + return res; + } + + /* + * Conjugated itself in-place + */ + void conjugate() { + this->a[0].conjugate(); + this->a[1].conjugate(); + this->a[2].conjugate(); + } + +}; + + +#endif //ACE_COMPLEX_H diff --git a/lib/pace/ace_contigous_array.h b/lib/pace/ace_contigous_array.h new file mode 100644 index 0000000000..f008fa203f --- /dev/null +++ b/lib/pace/ace_contigous_array.h @@ -0,0 +1,249 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 11.01.20. +#ifndef ACE_CONTIGUOUSARRAYND_H +#define ACE_CONTIGUOUSARRAYND_H + +#include + +#include "ace_types.h" + +using namespace std; + +/** + * Common predecessor class to represent multidimensional array of type T + * and store it in memory contiguous form + * + * @tparam T data type + */ +template +class ContiguousArrayND { +protected: + T *data = nullptr; ///< pointer to contiguous data + size_t size = 0; ///< total array size + string array_name = "Array"; /// 0) { + data = new T[size]; + for (size_t ind = 0; ind < size; ind++) + data[ind] = other.data[ind]; + } + } else { //is proxy, then copy the pointer + data = other.data; + } + } + + /** + * Overload operator= + * @param other another ContiguousArrayND + * @return itself + */ + + ContiguousArrayND &operator=(const ContiguousArrayND &other) { +#ifdef MULTIARRAY_LIFE_CYCLE + cout< 0) { + + if(data!=nullptr) delete[] data; + data = new T[size]; + + for (size_t ind = 0; ind < size; ind++) + data[ind] = other.data[ind]; + } + } else { //is proxy, then copy the pointer + data = other.data; + } + } + return *this; + } + + + //TODO: make destructor virtual, check the destructors in inherited classes + + /** + * Destructor + */ + ~ContiguousArrayND() { +#ifdef MULTIARRAY_LIFE_CYCLE + cout<array_name = name; + } + + /** + * Get total number of elements in array (its size) + * @return array size + */ + size_t get_size() const { + return size; + } + + /** + * Fill array with value + * @param value value to fill + */ + void fill(T value) { + for (size_t ind = 0; ind < size; ind++) + data[ind] = value; + } + + /** + * Get array data at absolute index ind for reading + * @param ind absolute index + * @return array value + */ + inline const T &get_data(size_t ind) const { +#ifdef MULTIARRAY_INDICES_CHECK + if ((ind < 0) | (ind >= size)) { + printf("%s: get_data ind=%d out of range (0, %d)\n", array_name, ind, size); + exit(EXIT_FAILURE); + } +#endif + return data[ind]; + } + + /** + * Get array data at absolute index ind for writing + * @param ind absolute index + * @return array value + */ + inline T &get_data(size_t ind) { +#ifdef MULTIARRAY_INDICES_CHECK + if ((ind < 0) | (ind >= size)) { + printf("%s: get_data ind=%ld out of range (0, %ld)\n", array_name.c_str(), ind, size); + exit(EXIT_FAILURE); + } +#endif + return data[ind]; + } + + /** + * Get array data pointer + * @return data array pointer + */ + inline T* get_data() const { + return data; + } + + /** + * Overload comparison operator== + * Compare the total size and array values elementwise. + * + * @param other another array + * @return + */ + bool operator==(const ContiguousArrayND &other) const { + if (this->size != other.size) + return false; + + for (size_t i = 0; i < this->size; ++i) + if (this->data[i] != other.data[i]) + return false; + + return true; + } + + + /** + * Convert to flatten vector container + * @return vector container + */ + vector to_flatten_vector() const { + vector res; + + res.resize(size); + size_t vec_ind = 0; + + for (int vec_ind = 0; vec_ind < size; vec_ind++) + res.at(vec_ind) = data[vec_ind]; + + return res; + } // end to_flatten_vector() + + + /** + * Set values from flatten vector container + * @param vec container + */ + void set_flatten_vector(const vector &vec) { + if (vec.size() != size) + throw std::invalid_argument("Flatten vector size is not consistent with expected size"); + for (size_t i = 0; i < size; i++) { + data[i] = vec[i]; + } + } + + bool is_proxy(){ + return is_proxy_; + } + +}; + + +#endif //ACE_CONTIGUOUSARRAYND_H \ No newline at end of file diff --git a/lib/pace/ace_evaluator.cpp b/lib/pace/ace_evaluator.cpp new file mode 100644 index 0000000000..987f4502bf --- /dev/null +++ b/lib/pace/ace_evaluator.cpp @@ -0,0 +1,660 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 31.01.20. + +#include "ace_evaluator.h" + +#include "ace_abstract_basis.h" +#include "ace_types.h" + +void ACEEvaluator::init(ACEAbstractBasisSet *basis_set) { + A.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, "A"); + A_rank1.init(basis_set->nelements, basis_set->nradbase, "A_rank1"); + + rhos.init(basis_set->ndensitymax + 1, "rhos"); // +1 density for core repulsion + dF_drho.init(basis_set->ndensitymax + 1, "dF_drho"); // +1 density for core repulsion +} + +void ACEEvaluator::init_timers() { + loop_over_neighbour_timer.init(); + forces_calc_loop_timer.init(); + forces_calc_neighbour_timer.init(); + energy_calc_timer.init(); + per_atom_calc_timer.init(); + total_time_calc_timer.init(); +} + +//================================================================================================================ + +void ACECTildeEvaluator::set_basis(ACECTildeBasisSet &bas) { + basis_set = &bas; + init(basis_set); +} + +void ACECTildeEvaluator::init(ACECTildeBasisSet *basis_set) { + + ACEEvaluator::init(basis_set); + + + weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, + "weights"); + + weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); + + + DG_cache.init(1, basis_set->nradbase, "DG_cache"); + DG_cache.fill(0); + + R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); + R_cache.fill(0); + + DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); + DR_cache.fill(0); + + Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); + Y_cache.fill({0, 0}); + + DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); + DY_cache.fill({0.}); + + //hard-core repulsion + DCR_cache.init(1, "DCR_cache"); + DCR_cache.fill(0); + dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); + + +} + +void ACECTildeEvaluator::resize_neighbours_cache(int max_jnum) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); + } + if (R_cache.get_dim(0) < max_jnum) { + + //TODO: implement grow + R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + R_cache.fill(0); + + DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + DR_cache.fill(0); + + DG_cache.resize(max_jnum, basis_set->nradbase); + DG_cache.fill(0); + + Y_cache.resize(max_jnum, basis_set->lmax + 1); + Y_cache.fill({0, 0}); + + DY_cache.resize(max_jnum, basis_set->lmax + 1); + DY_cache.fill({0}); + + //hard-core repulsion + DCR_cache.init(max_jnum, "DCR_cache"); + DCR_cache.fill(0); + } +} + + + +// double** r - atomic coordinates of atom I +// int* types - atomic types if atom I +// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; +// Usage: j = jlist_of_i[jj]; +// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; + +void +ACECTildeEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); + } + per_atom_calc_timer.start(); +#ifdef PRINT_MAIN_STEPS + printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); +#endif + DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; + DOUBLE_TYPE r_norm; + DOUBLE_TYPE xn, yn, zn, r_xyz; + DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; + DOUBLE_TYPE *r_hat; + + SPECIES_TYPE mu_j; + RANK_TYPE r, rank, t; + NS_TYPE n; + LS_TYPE l; + MS_TYPE m, m_t; + + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + int j, jj, func_ind, ms_ind; + SHORT_INT_TYPE factor; + + ACEComplex Y{0}, Y_DR{0.}; + ACEComplex B{0.}; + ACEComplex dB{0}; + ACEComplex A_cache[basis_set->rankmax]; + + dB_flatten.fill({0.}); + + ACEDYcomponent grad_phi_nlm{0}, DY{0.}; + + //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme + ACEComplex A_forward_prod[basis_set->rankmax + 1]; + ACEComplex A_backward_prod[basis_set->rankmax + 1]; + + DOUBLE_TYPE inv_r_norm; + DOUBLE_TYPE r_norms[jnum]; + DOUBLE_TYPE inv_r_norms[jnum]; + DOUBLE_TYPE rhats[jnum][3];//normalized vector + SPECIES_TYPE elements[jnum]; + const DOUBLE_TYPE xtmp = x[i][0]; + const DOUBLE_TYPE ytmp = x[i][1]; + const DOUBLE_TYPE ztmp = x[i][2]; + DOUBLE_TYPE f_ji[3]; + + bool is_element_mapping = element_type_mapping.get_size() > 0; + SPECIES_TYPE mu_i; + if (is_element_mapping) + mu_i = element_type_mapping(type[i]); + else + mu_i = type[i]; + + const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + + ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; + DOUBLE_TYPE dF_drho_core; + + //TODO: lmax -> lmaxi (get per-species type) + const LS_TYPE lmaxi = basis_set->lmax; + + //TODO: nradmax -> nradiali (get per-species type) + const NS_TYPE nradiali = basis_set->nradmax; + + //TODO: nradbase -> nradbasei (get per-species type) + const NS_TYPE nradbasei = basis_set->nradbase; + + //TODO: get per-species type number of densities + const DENSITY_TYPE ndensity= basis_set->ndensitymax; + + neighbours_forces.resize(jnum, 3); + neighbours_forces.fill(0); + + //TODO: shift nullifications to place where arrays are used + weights.fill({0}); + weights_rank1.fill(0); + A.fill({0}); + A_rank1.fill(0); + rhos.fill(0); + dF_drho.fill(0); + +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); + basis_projections.init(total_basis_size, ndensity, "c_projections"); +#endif + + //proxy references to spherical harmonics and radial functions arrays + const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; + const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; + + const Array2D &fr = basis_set->radial_functions->fr; + const Array2D &dfr = basis_set->radial_functions->dfr; + + const Array1D &gr = basis_set->radial_functions->gr; + const Array1D &dgr = basis_set->radial_functions->dgr; + + loop_over_neighbour_timer.start(); + + int jj_actual = 0; + SPECIES_TYPE type_j = 0; + int neighbour_index_mapping[jnum]; // jj_actual -> jj + //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); + r_xyz = sqrt(xn * xn + yn * yn + zn * zn); + + if (r_xyz >= current_cutoff) + continue; + + inv_r_norm = 1 / r_xyz; + + r_norms[jj_actual] = r_xyz; + inv_r_norms[jj_actual] = inv_r_norm; + rhats[jj_actual][0] = xn * inv_r_norm; + rhats[jj_actual][1] = yn * inv_r_norm; + rhats[jj_actual][2] = zn * inv_r_norm; + elements[jj_actual] = mu_j; + neighbour_index_mapping[jj_actual] = jj; + jj_actual++; + } + + int jnum_actual = jj_actual; + + //ALGORITHM 1: Atomic base A + for (jj = 0; jj < jnum_actual; ++jj) { + r_norm = r_norms[jj]; + mu_j = elements[jj]; + r_hat = rhats[jj]; + + //proxies + Array2DLM &Y_jj = Y_cache(jj); + Array2DLM &DY_jj = DY_cache(jj); + + + basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); + basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); + //loop for computing A's + //rank = 1 + for (n = 0; n < basis_set->nradbase; n++) { + GR = gr(n); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("-neigh atom %d\n", jj); + printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); + printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); +#endif + DG_cache(jj, n) = dgr(n); + A_rank1(mu_j, n) += GR * Y00; + } + //loop for computing A's + // for rank > 1 + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + R = fr(n, l); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); +#endif + + DR_cache(jj, n, l) = dfr(n, l); + R_cache(jj, n, l) = R; + + for (m = 0; m <= l; m++) { + Y = ylm(l, m); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); +#endif + A_lm(l, m) += R * Y; //accumulation sum over neighbours + Y_jj(l, m) = Y; + DY_jj(l, m) = dylm(l, m); + } + } + } + + //hard-core repulsion + rho_core += basis_set->radial_functions->cr; + DCR_cache(jj) = basis_set->radial_functions->dcr; + + } //end loop over neighbours + + //complex conjugate A's (for NEGATIVE (-m) terms) + // for rank > 1 + for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm + for (m = 1; m <= l; m++) { + factor = m % 2 == 0 ? 1 : -1; + A_lm(l, -m) = A_lm(l, m).conjugated() * factor; + } + } + } + } //now A's are constructed + loop_over_neighbour_timer.stop(); + + // ==================== ENERGY ==================== + + energy_calc_timer.start(); +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.fill(0); + basis_projections.fill(0); +#endif + + //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation + //rank=1 + for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { + ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; +// ndensity = func->ndensity; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = 0\n",(int) ndensity ); + print_C_tilde_B_basis_function(*func); +#endif + double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); + printf(" coeff[0] = %f\n", func->ctildes[0]); +#endif + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + rhos(p) += func->ctildes[p] * A_cur; +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; +#endif + } + } // end loop for rank=1 + + //rank>1 + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + //TODO: check if func->ctildes are zero, then skip +// ndensity = func->ndensity; + rank = func->rank; + r = rank - 1; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = %d\n",(int) ndensity, (int)r ); + print_C_tilde_B_basis_function(*func); +#endif + mus = func->mus; + ns = func->ns; + ls = func->ls; + + //loop over {ms} combinations in sum + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * rank]; // current ms-combination (of length = rank) + + //loop over m, collect B = product of A with given ms + A_forward_prod[0] = 1; + A_backward_prod[r] = 1; + + //fill forward A-product triangle + for (t = 0; t < rank; t++) { + //TODO: optimize ns[t]-1 -> ns[t] during functions construction + A_cache[t] = A(mus[t], ns[t] - 1, ls[t], ms[t]); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A(x=%d, n=%d, l=%d, m=%d)=(%f,%f)\n", mus[t], ns[t], ls[t], ms[t], A_cache[t].real, + A_cache[t].img); +#endif + A_forward_prod[t + 1] = A_forward_prod[t] * A_cache[t]; + } + + B = A_forward_prod[t]; + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("B = (%f, %f)\n", (B).real, (B).img); +#endif + //fill backward A-product triangle + for (t = r; t >= 1; t--) { + A_backward_prod[t - 1] = + A_backward_prod[t] * A_cache[t]; + } + + for (t = 0; t < rank; ++t, ++func_ms_t_ind) { + dB = A_forward_prod[t] * A_backward_prod[t]; //dB - product of all A's except t-th + dB_flatten(func_ms_t_ind) = dB; +#ifdef DEBUG_FORCES_CALCULATIONS + m_t = ms[t]; + printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); +#endif + } + + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //real-part only multiplication + rhos(p) += B.real_part_product(func->ctildes[ms_ind * ndensity + p]); + +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections(func_ind, p)+=B.real_part_product(func->ctildes[ms_ind * ndensity + p]); +#endif + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("rhos(%d) += %f\n", p, B.real_part_product(func->ctildes[ms_ind * ndensity + p])); + printf("Rho[i = %d][p = %d] = %f\n", i , p , rhos(p)); +#endif + } + }//end of loop over {ms} combinations in sum + }// end loop for rank>1 + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("rhos = "); + for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); + drho_cut = basis_set->drho_core_cutoffs(mu_i); + + basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); + basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); + + dF_drho_core = evdwl * dfcut + 1; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + dF_drho(p) *= fcut; + evdwl_cut = evdwl * fcut + rho_core; + + // E0 shift + evdwl_cut += basis_set->E0vals(mu_i); + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dFrhos = "); + for(DENSITY_TYPE p =0; pndensity; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; + } + } + + // rank>1 + func_ms_ind = 0; + func_ms_t_ind = 0;// index for dB + DOUBLE_TYPE theta = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; +// ndensity = func->ndensity; + rank = func->rank; + mus = func->mus; + ns = func->ns; + ls = func->ls; + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * rank]; + theta = 0; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + theta += dF_drho(p) * func->ctildes[ms_ind * ndensity + p]; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("(p=%d) theta += dF_drho[p] * func.ctildes[ms_ind * ndensity + p] = %f * %f = %f\n",p, dF_drho(p), func->ctildes[ms_ind * ndensity + p],dF_drho(p)*func->ctildes[ms_ind * ndensity + p]); + printf("theta=%f\n",theta); +#endif + } + + theta *= 0.5; // 0.5 factor due to possible double counting ??? + for (t = 0; t < rank; ++t, ++func_ms_t_ind) { + m_t = ms[t]; + factor = (m_t % 2 == 0 ? 1 : -1); + dB = dB_flatten(func_ms_t_ind); + weights(mus[t], ns[t] - 1, ls[t], m_t) += theta * dB; //Theta_array(func_ms_ind); + // update -m_t (that could also be positive), because the basis is half_basis + weights(mus[t], ns[t] - 1, ls[t], -m_t) += + theta * (dB).conjugated() * factor;// Theta_array(func_ms_ind); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); + printf("theta = %f\n",theta); + printf("weights(n,l,m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], m_t, (theta * dB * 0.5).real, + (theta * dB * 0.5).img); + printf("weights(n,l,-m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], -m_t, + ( theta * (dB).conjugated() * factor * 0.5).real, + ( theta * (dB).conjugated() * factor * 0.5).img); +#endif + } + } + } + energy_calc_timer.stop(); + +// ==================== FORCES ==================== +#ifdef PRINT_MAIN_STEPS + printf("\nFORCE CALCULATION\n"); + printf("loop over neighbours\n"); +#endif + + forces_calc_loop_timer.start(); +// loop over neighbour atoms for force calculations + for (jj = 0; jj < jnum_actual; ++jj) { + mu_j = elements[jj]; + r_hat = rhats[jj]; + inv_r_norm = inv_r_norms[jj]; + + Array2DLM &Y_cache_jj = Y_cache(jj); + Array2DLM &DY_cache_jj = DY_cache(jj); + +#ifdef PRINT_LOOPS_INDICES + printf("\nneighbour atom #%d\n", jj); + printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); +#endif + + forces_calc_neighbour_timer.start(); + + f_ji[0] = f_ji[1] = f_ji[2] = 0; + +//for rank = 1 + for (n = 0; n < nradbasei; ++n) { + if (weights_rank1(mu_j, n) == 0) + continue; + auto &DG = DG_cache(jj, n); + DGR = DG * Y00; + DGR *= weights_rank1(mu_j, n); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); + printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); + printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); + printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); +#endif + f_ji[0] += DGR * r_hat[0]; + f_ji[1] += DGR * r_hat[1]; + f_ji[2] += DGR * r_hat[2]; + } + +//for rank > 1 + for (n = 0; n < nradiali; n++) { + for (l = 0; l <= lmaxi; l++) { + R_over_r = R_cache(jj, n, l) * inv_r_norm; + DR = DR_cache(jj, n, l); + + // for m>=0 + for (m = 0; m <= l; m++) { + ACEComplex w = weights(mu_j, n, l, m); + if (w == 0) + continue; + //counting for -m cases if m>0 + if (m > 0) w *= 2; + + DY = DY_cache_jj(l, m); + Y_DR = Y_cache_jj(l, m) * DR; + + grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; + grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; + grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, + grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, + grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, + grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); + + printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m,w.real, w.img); + //if (m>0) w*=2; + printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, + w.real_part_product(grad_phi_nlm.a[0]), + w.real_part_product(grad_phi_nlm.a[1]), + w.real_part_product(grad_phi_nlm.a[2]) + ); +#endif +// real-part multiplication only + f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); + f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); + f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); + } + } + } + + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); +#endif + + //hard-core repulsion + DCR = DCR_cache(jj); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("DCR = %f\n",DCR); +#endif + f_ji[0] += dF_drho_core * DCR * r_hat[0]; + f_ji[1] += dF_drho_core * DCR * r_hat[1]; + f_ji[2] += dF_drho_core * DCR * r_hat[2]; +#ifdef PRINT_INTERMEDIATE_VALUES + printf("with core-repulsion\n"); + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); + printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); +#endif + + neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; + neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; + neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; + + forces_calc_neighbour_timer.stop(); + }// end loop over neighbour atoms for forces + + forces_calc_loop_timer.stop(); + + //now, energies and forces are ready + //energies(i) = evdwl + rho_core; + e_atom = evdwl_cut; + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); +#endif + per_atom_calc_timer.stop(); +} \ No newline at end of file diff --git a/lib/pace/ace_evaluator.h b/lib/pace/ace_evaluator.h new file mode 100644 index 0000000000..356ea52563 --- /dev/null +++ b/lib/pace/ace_evaluator.h @@ -0,0 +1,230 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 31.01.20. + +#ifndef ACE_EVALUATOR_H +#define ACE_EVALUATOR_H + +#include "ace_abstract_basis.h" +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_c_basis.h" +#include "ace_complex.h" +#include "ace_timing.h" +#include "ace_types.h" + +/** + * Basic evaluator class, that should accept the basis set and implement the "compute_atom" method using given basis set. + */ +class ACEEvaluator { +protected: + + Array2D A_rank1 = Array2D("A_rank1"); ///< 2D-array for storing A's for rank=1, shape: A(mu_j,n) + Array4DLM A = Array4DLM("A"); ///< 4D array with (l,m) last indices for storing A's for rank>1: A(mu_j, n, l, m) + + Array1D rhos = Array1D("rhos"); ///< densities \f$ \rho^{(p)} \f$(ndensity), p = 0 .. ndensity-1 + Array1D dF_drho = Array1D("dF_drho"); ///< derivatives of cluster functional wrt. densities, index = 0 .. ndensity-1 + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACEAbstractBasisSet *basis_set); + +public: + // set of timers for code profiling + + ACETimer loop_over_neighbour_timer; ///< timer for loop over neighbours when constructing A's for single central atom + ACETimer per_atom_calc_timer; ///< timer for single compute_atom call + + + ACETimer forces_calc_loop_timer; ///< timer for forces calculations for single central atom + ACETimer forces_calc_neighbour_timer; ///< timer for loop over neighbour atoms for force calculations + + ACETimer energy_calc_timer; ///< timer for energy calculation + ACETimer total_time_calc_timer; ///< timer for total calculations of all atoms within given atomic environment system + + /** + * Initialize all timers + */ + void init_timers(); + + /** + * Mapping from external atoms types, i.e. LAMMPS, to internal SPECIES_TYPE, used in basis functions + */ + Array1D element_type_mapping = Array1D("element_type_mapping"); + + + DOUBLE_TYPE e_atom = 0; ///< energy of current atom, including core-repulsion + + /** + * temporary array for the pair forces between current atom_i and its neighbours atom_k + * neighbours_forces(k,3), k = 0..num_of_neighbours(atom_i)-1 + */ + Array2D neighbours_forces = Array2D("neighbours_forces"); + + ACEEvaluator() = default; + + virtual ~ACEEvaluator() = default; + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + virtual void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) = 0; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + virtual void resize_neighbours_cache(int max_jnum) = 0; + +#ifdef EXTRA_C_PROJECTIONS + /** + * 2D array to store projections of basis function for rank = 1, shape: [func_ind][ndensity] + */ + Array2D basis_projections_rank1 = Array2D("basis_projections_rank1"); + + /** + * 2D array to store projections of basis function for rank > 1, shape: [func_ind][ndensity] + */ + Array2D basis_projections = Array2D("basis_projections"); +#endif +}; + +//TODO: split into separate file +/** + * Evaluator for C-tilde basis set, that should accept the basis set and implement the "compute_atom" method using given basis set. + */ +class ACECTildeEvaluator : public ACEEvaluator { + + /** + * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase] + */ + Array2D weights_rank1 = Array2D("weights_rank1"); + + /** + * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] + */ + Array4DLM weights = Array4DLM("weights"); + + /** + * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) + * shape:[max_jnum][nradbase] + */ + Array2D DG_cache = Array2D("DG_cache"); + + + /** + * cache for \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D R_cache = Array3D("R_cache"); + /** + * cache for derivatives of \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D DR_cache = Array3D("DR_cache"); + /** + * cache for \f$ Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM Y_cache = Array3DLM("Y_cache"); + /** + * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM DY_cache = Array3DLM("dY_dense_cache"); + + /** + * cache for derivatives of hard-core repulsion + * shape:[max_jnum] + */ + Array1D DCR_cache = Array1D("DCR_cache"); + + /** + * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], + * shape:[func_ms_r_ind] + */ + Array1D dB_flatten = Array1D("dB_flatten"); + + /** + * pointer to the ACEBasisSet object + */ + ACECTildeBasisSet *basis_set = nullptr; + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACECTildeBasisSet *basis_set); + +public: + + ACECTildeEvaluator() = default; + + explicit ACECTildeEvaluator(ACECTildeBasisSet &bas) { + set_basis(bas); + } + + /** + * set the basis function to the ACE evaluator + * @param bas + */ + void set_basis(ACECTildeBasisSet &bas); + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + void resize_neighbours_cache(int max_jnum) override; +}; + + +#endif //ACE_EVALUATOR_H \ No newline at end of file diff --git a/lib/pace/ace_flatten_basis.cpp b/lib/pace/ace_flatten_basis.cpp new file mode 100644 index 0000000000..541785a202 --- /dev/null +++ b/lib/pace/ace_flatten_basis.cpp @@ -0,0 +1,130 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by yury on 28.04.2020. + +#include "ace_flatten_basis.h" + +ACEFlattenBasisSet::ACEFlattenBasisSet(const ACEFlattenBasisSet &other) { + _copy_scalar_memory(other); + _copy_dynamic_memory(other); +} + +ACEFlattenBasisSet &ACEFlattenBasisSet::operator=(const ACEFlattenBasisSet &other) { + if (this != &other) { + _clean(); + _copy_scalar_memory(other); + _copy_dynamic_memory(other); + } + return *this; +} + + +ACEFlattenBasisSet::~ACEFlattenBasisSet() { + ACEFlattenBasisSet::_clean(); +} + +void ACEFlattenBasisSet::_clean() { + //chained call of base class method + ACEAbstractBasisSet::_clean(); + _clean_contiguous_arrays(); + _clean_basissize_arrays(); + +} + +void ACEFlattenBasisSet::_clean_basissize_arrays() { + delete[] total_basis_size; + total_basis_size = nullptr; + + delete[] total_basis_size_rank1; + total_basis_size_rank1 = nullptr; +} + +void ACEFlattenBasisSet::_clean_contiguous_arrays() { + delete[] full_ns_rank1; + full_ns_rank1 = nullptr; + + delete[] full_ls_rank1; + full_ls_rank1 = nullptr; + + delete[] full_mus_rank1; + full_mus_rank1 = nullptr; + + delete[] full_ms_rank1; + full_ms_rank1 = nullptr; + + ////// + + delete[] full_ns; + full_ns = nullptr; + + delete[] full_ls; + full_ls = nullptr; + + delete[] full_mus; + full_mus = nullptr; + + delete[] full_ms; + full_ms = nullptr; +} + +void ACEFlattenBasisSet::_copy_scalar_memory(const ACEFlattenBasisSet &src) { + ACEAbstractBasisSet::_copy_scalar_memory(src); + + rank_array_total_size_rank1 = src.rank_array_total_size_rank1; + coeff_array_total_size_rank1 = src.coeff_array_total_size_rank1; + rank_array_total_size = src.rank_array_total_size; + ms_array_total_size = src.ms_array_total_size; + coeff_array_total_size = src.coeff_array_total_size; + + max_B_array_size = src.max_B_array_size; + max_dB_array_size = src.max_dB_array_size; + num_ms_combinations_max = src.num_ms_combinations_max; +} + +void ACEFlattenBasisSet::_copy_dynamic_memory(const ACEFlattenBasisSet &src) { //allocate new memory + + ACEAbstractBasisSet::_copy_dynamic_memory(src); + + if (src.total_basis_size_rank1 == nullptr) + throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size_rank1 - array not initialized"); + if (src.total_basis_size == nullptr) + throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size - array not initialized"); + + delete[] total_basis_size_rank1; + total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; + delete[] total_basis_size; + total_basis_size = new SHORT_INT_TYPE[nelements]; + + //copy + for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { + total_basis_size_rank1[mu] = src.total_basis_size_rank1[mu]; + total_basis_size[mu] = src.total_basis_size[mu]; + } +} + diff --git a/lib/pace/ace_flatten_basis.h b/lib/pace/ace_flatten_basis.h new file mode 100644 index 0000000000..e21cbb749a --- /dev/null +++ b/lib/pace/ace_flatten_basis.h @@ -0,0 +1,135 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Lysogroskiy Yury on 28.04.2020. + +#ifndef ACE_EVALUATOR_ACE_FLATTEN_BASIS_H +#define ACE_EVALUATOR_ACE_FLATTEN_BASIS_H + + +#include "ace_abstract_basis.h" +#include "ace_c_basisfunction.h" +#include "ace_radial.h" +#include "ace_spherical_cart.h" +#include "ace_types.h" + +/** + * Basis set with basis function attributes, i.e. \f$ \mathbf{n}, \mathbf{l}, \mathbf{m}\f$, etc. + * packed into contiguous arrays for the cache-friendly memory layout. + */ +class ACEFlattenBasisSet : public ACEAbstractBasisSet { +public: + //arrays and its sizes for rank = 1 basis functions for packed basis + + size_t rank_array_total_size_rank1 = 0; ///< size for full_ns_rank1, full_ls_rank1, full_Xs_rank1 + size_t coeff_array_total_size_rank1 = 0; ///< size for full coefficients array (depends on B or C-Tilde basis) + + NS_TYPE *full_ns_rank1 = nullptr; ///< ns contiguous package [rank_array_total_size_rank1] + LS_TYPE *full_ls_rank1 = nullptr; ///< ls contiguous package [rank_array_total_size_rank1] + SPECIES_TYPE *full_mus_rank1 = nullptr; ///< mus contiguous package [rank_array_total_size_rank1] + MS_TYPE *full_ms_rank1 = nullptr; ///< m_s contiguous package[rank_array_total_size_rank1] + + //arrays and its sizes for rank > 1 basis functions for packed basis + size_t rank_array_total_size = 0; ///< size for full_ns, full_ls, full_Xs + size_t ms_array_total_size = 0; ///< size for full_ms array + size_t coeff_array_total_size = 0;///< size for full coefficients arrays (depends on B- or C- basis) + + NS_TYPE *full_ns = nullptr; ///< ns contiguous package [rank_array_total_size] + LS_TYPE *full_ls = nullptr; ///< ls contiguous package [rank_array_total_size] + SPECIES_TYPE *full_mus = nullptr; ///< mus contiguous package [rank_array_total_size] + MS_TYPE *full_ms = nullptr; ///< //m_s contiguous package [ms_array_total_size] + + /** + * Rearrange basis functions in contiguous memory to optimize cache access + */ + virtual void pack_flatten_basis() = 0; + + virtual void flatten_basis() = 0; + + //1D flat array basis representation: [mu] + SHORT_INT_TYPE *total_basis_size_rank1 = nullptr; ///< per-species type array of total_basis_rank1[mu] sizes + SHORT_INT_TYPE *total_basis_size = nullptr; ///< per-species type array of total_basis[mu] sizes + + size_t max_B_array_size = 0; ///< maximum over elements array size for B[func_ind][ms_ind] + size_t max_dB_array_size = 0; ///< maximum over elements array size for dB[func_ind][ms_ind][r] + + SHORT_INT_TYPE num_ms_combinations_max = 0; ///< maximum number of ms combinations among all basis functions + + /** + * Default constructor + */ + ACEFlattenBasisSet() = default; + + /** + * Copy constructor (see Rule of Three) + * @param other + */ + ACEFlattenBasisSet(const ACEFlattenBasisSet &other); + + /** + * operator= (see Rule of Three) + * @param other + * @return + */ + ACEFlattenBasisSet &operator=(const ACEFlattenBasisSet &other); + + /** + * Destructor (see Rule of Three) + */ + ~ACEFlattenBasisSet() override; + + // routines for copying and cleaning dynamic memory of the class (see Rule of Three) + /** + * Cleaning dynamic memory of the class (see. Rule of Three), + * must be idempotent for safety + */ + void _clean() override; + + /** + * Copying scalar variables + * @param src + */ + void _copy_scalar_memory(const ACEFlattenBasisSet &src); + + /** + * Copying and cleaning dynamic memory of the class (see. Rule of Three) + * @param src + */ + void _copy_dynamic_memory(const ACEFlattenBasisSet &src); + + /** + * Clean contiguous arrays + */ + virtual void _clean_contiguous_arrays(); + + /** + * Release dynamic arrays with basis set sizes + */ + void _clean_basissize_arrays(); +}; + +#endif //ACE_EVALUATOR_ACE_FLATTEN_BASIS_H diff --git a/lib/pace/ace_radial.cpp b/lib/pace/ace_radial.cpp new file mode 100644 index 0000000000..01348a719c --- /dev/null +++ b/lib/pace/ace_radial.cpp @@ -0,0 +1,566 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +#include +#include +#include + +#include "ace_radial.h" + +const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi + +ACERadialFunctions::ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + init(nradb, lmax, nradial, deltaSplineBins, nelements, cutoff, radbasename); +} + +void ACERadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + this->nradbase = nradb; + this->lmax = lmax; + this->nradial = nradial; + this->deltaSplineBins = deltaSplineBins; + this->nelements = nelements; + this->cutoff = cutoff; + this->radbasename = radbasename; + + gr.init(nradbase, "gr"); + dgr.init(nradbase, "dgr"); + d2gr.init(nradbase, "d2gr"); + + + fr.init(nradial, lmax + 1, "fr"); + dfr.init(nradial, lmax + 1, "dfr"); + d2fr.init(nradial, lmax + 1, "d2fr"); + + + cheb.init(nradbase + 1, "cheb"); + dcheb.init(nradbase + 1, "dcheb"); + cheb2.init(nradbase + 1, "cheb2"); + + + splines_gk.init(nelements, nelements, "splines_gk"); + splines_rnl.init(nelements, nelements, "splines_rnl"); + splines_hc.init(nelements, nelements, "splines_hc"); + + lambda.init(nelements, nelements, "lambda"); + lambda.fill(1.); + + cut.init(nelements, nelements, "cut"); + cut.fill(1.); + + dcut.init(nelements, nelements, "dcut"); + dcut.fill(1.); + + crad.init(nelements, nelements, nradial, (lmax + 1), nradbase, "crad"); + crad.fill(0.); + + //hard-core repulsion + prehc.init(nelements, nelements, "prehc"); + prehc.fill(0.); + + lambdahc.init(nelements, nelements, "lambdahc"); + lambdahc.fill(1.); + +} + + +/** +Function that computes Chebyshev polynomials of first and second kind + to setup the radial functions and the derivatives + +@param n, x + +@returns cheb1, dcheb1 +*/ +void ACERadialFunctions::calcCheb(NS_TYPE n, DOUBLE_TYPE x) { + if (n < 0) { + char s[1024]; + sprintf(s, "The order n of the polynomials should be positive %d\n", n); + throw std::invalid_argument(s); + } + DOUBLE_TYPE twox = 2.0 * x; + cheb(0) = 1.; + dcheb(0) = 0.; + cheb2(0) = 1.; + + if (nradbase > 1) { + cheb(1) = x; + cheb2(1) = twox; + } + for (NS_TYPE m = 1; m <= n - 1; m++) { + cheb(m + 1) = twox * cheb(m) - cheb(m - 1); + cheb2(m + 1) = twox * cheb2(m) - cheb2(m - 1); + } + for (NS_TYPE m = 1; m <= n; m++) { + dcheb(m) = m * cheb2(m - 1); + } +#ifdef DEBUG_RADIAL + for ( NS_TYPE m=0; m<=n; m++ ) { + printf(" m %d cheb %f dcheb %f \n", m, cheb(m), dcheb(m)); + } +#endif +} + +/** +Function that computes radial basis. + +@param lam, nradbase, cut, dcut, r + +@returns gr, dgr +*/ +void ACERadialFunctions::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + /*lam is given by the formula (24), that contains cut */ + + if (r < cut) { + if (radbasename == "ChebExpCos") { + chebExpCos(lam, cut, dcut, r); + } else if (radbasename == "ChebPow") { + chebPow(lam, cut, dcut, r); + } else if (radbasename == "ChebLinear") { + chebLinear(lam, cut, dcut, r); + } else { + throw invalid_argument("Unknown radial basis function name: " + radbasename); + } + } else { + gr.fill(0); + dgr.fill(0); + } +} + +/*** + * Radial function: ChebExpCos, cheb exp scaling including cos envelope + * @param lam function parameter + * @param cut cutoff distance + * @param r function input argument + * @return fills in gr and dgr arrays + */ +void +ACERadialFunctions::chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE y2, y1, x, dx; + DOUBLE_TYPE env, denv, fcut, dfcut; + /* scaled distance x and derivative*/ + y1 = exp(-lam * r / cut); + y2 = exp(-lam); + x = 1.0 - 2.0 * ((y1 - y2) / (1 - y2)); + dx = 2 * (lam / cut) * (y1 / (1 - y2)); + /* calculation of Chebyshev polynomials from the recursion */ + calcCheb(nradbase - 1, x); + gr(0) = cheb(0); + dgr(0) = dcheb(0) * dx; + for (NS_TYPE n = 2; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n - 1); + dgr(n - 1) = -0.5 * dcheb(n - 1) * dx; + } + env = 0.5 * (1.0 + cos(M_PI * r / cut)); + denv = -0.5 * sin(M_PI * r / cut) * M_PI / cut; + for (NS_TYPE n = 0; n < nradbase; n++) { + dgr(n) = gr(n) * denv + dgr(n) * env; + gr(n) = gr(n) * env; + } + // for radtype = 3 a smooth cut is already included in the basis function + dx = cut - dcut; + if (r > dx) { + fcut = 0.5 * (1.0 + cos(M_PI * (r - dx) / dcut)); + dfcut = -0.5 * sin(M_PI * (r - dx) / dcut) * M_PI / dcut; + for (NS_TYPE n = 0; n < nradbase; n++) { + dgr(n) = gr(n) * dfcut + dgr(n) * fcut; + gr(n) = gr(n) * fcut; + } + } +} + +/*** +* Radial function: ChebPow, Radial function: ChebPow +* - argument of Chebyshev polynomials +* x = 2.0*( 1.0 - (1.0 - r/rcut)^lam ) - 1.0 +* - radial function +* gr(n) = ( 1.0 - Cheb(n) )/2.0, n = 1,...,nradbase +* - the function fulfills: +* gr(n) = 0 at rcut +* dgr(n) = 0 at rcut for lam >= 1 +* second derivative zero at rcut for lam >= 2 +* -> the radial function does not require a separate cutoff function +* - corresponds to radial basis radtype=5 in Fortran code +* +* @param lam function parameter +* @param cut cutoff distance +* @param r function input argument +* @return fills in gr and dgr arrays +*/ +void +ACERadialFunctions::chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE y, dy, x, dx; + /* scaled distance x and derivative*/ + y = (1.0 - r / cut); + dy = pow(y, (lam - 1.0)); + y = dy * y; + dy = -lam / cut * dy; + + x = 2.0 * (1.0 - y) - 1.0; + dx = -2.0 * dy; + calcCheb(nradbase, x); + for (NS_TYPE n = 1; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n); + dgr(n - 1) = -0.5 * dcheb(n) * dx; + } +} + + +void +ACERadialFunctions::chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { + DOUBLE_TYPE x, dx; + /* scaled distance x and derivative*/ + x = (1.0 - r / cut); + dx = -1 / cut; + calcCheb(nradbase, x); + for (NS_TYPE n = 1; n <= nradbase; n++) { + gr(n - 1) = 0.5 - 0.5 * cheb(n); + dgr(n - 1) = -0.5 * dcheb(n) * dx; + } +} + +/** +Function that computes radial functions. + +@param nradbase, nelements, elei, elej + +@returns fr, dfr +*/ +void ACERadialFunctions::radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej) { + DOUBLE_TYPE frval, dfrval; + for (NS_TYPE n = 0; n < nradial; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + frval = 0.0; + dfrval = 0.0; + for (NS_TYPE k = 0; k < nradbase; k++) { + frval += crad(elei, elej, n, l, k) * gr(k); + dfrval += crad(elei, elej, n, l, k) * dgr(k); + } + fr(n, l) = frval; + dfr(n, l) = dfrval; + } + } +} + + +void ACERadialFunctions::all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r) { + DOUBLE_TYPE lam = lambda(mu_i, mu_j); + DOUBLE_TYPE r_cut = cut(mu_i, mu_j); + DOUBLE_TYPE dr_cut = dcut(mu_i, mu_j); + // set up radial functions + radbase(lam, r_cut, dr_cut, r); //update gr, dgr + radfunc(mu_i, mu_j); // update fr(nr, l), dfr(nr, l) +} + + +void ACERadialFunctions::setuplookupRadspline() { + using namespace std::placeholders; + DOUBLE_TYPE lam, r_cut, dr_cut; + DOUBLE_TYPE cr_c, dcr_c, pre, lamhc; + + // at r = rcut + eps the function and its derivatives is zero + for (SPECIES_TYPE elei = 0; elei < nelements; elei++) { + for (SPECIES_TYPE elej = 0; elej < nelements; elej++) { + + lam = lambda(elei, elej); + r_cut = cut(elei, elej); + dr_cut = dcut(elei, elej); + + splines_gk(elei, elej).setupSplines(gr.get_size(), + std::bind(&ACERadialFunctions::radbase, this, lam, r_cut, dr_cut, + _1),//update gr, dgr + gr.get_data(), + dgr.get_data(), deltaSplineBins, cutoff); + + splines_rnl(elei, elej).setupSplines(fr.get_size(), + std::bind(&ACERadialFunctions::all_radfunc, this, elei, elej, + _1), // update fr(nr, l), dfr(nr, l) + fr.get_data(), + dfr.get_data(), deltaSplineBins, cutoff); + + + pre = prehc(elei, elej); + lamhc = lambdahc(elei, elej); +// radcore(r, pre, lamhc, cutoff, cr_c, dcr_c); + splines_hc(elei, elej).setupSplines(1, + std::bind(&ACERadialFunctions::radcore, _1, pre, lamhc, cutoff, + std::ref(cr_c), std::ref(dcr_c)), + &cr_c, + &dcr_c, deltaSplineBins, cutoff); + } + } + +} + +/** +Function that gets radial function from look-up table using splines. + +@param r, nradbase_c, nradial_c, lmax, mu_i, mu_j + +@returns fr, dfr, gr, dgr, cr, dcr +*/ +void +ACERadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, bool calc_second_derivatives) { + auto &spline_gk = splines_gk(mu_i, mu_j); + auto &spline_rnl = splines_rnl(mu_i, mu_j); + auto &spline_hc = splines_hc(mu_i, mu_j); + + spline_gk.calcSplines(r, calc_second_derivatives); // populate splines_gk.values, splines_gk.derivatives; + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr(nr) = spline_gk.values(nr); + dgr(nr) = spline_gk.derivatives(nr); + if (calc_second_derivatives) + d2gr(nr) = spline_gk.second_derivatives(nr); + } + + spline_rnl.calcSplines(r, calc_second_derivatives); + for (size_t ind = 0; ind < fr.get_size(); ind++) { + fr.get_data(ind) = spline_rnl.values.get_data(ind); + dfr.get_data(ind) = spline_rnl.derivatives.get_data(ind); + if (calc_second_derivatives) + d2fr.get_data(ind) = spline_rnl.second_derivatives.get_data(ind); + } + + spline_hc.calcSplines(r, calc_second_derivatives); + cr = spline_hc.values(0); + dcr = spline_hc.derivatives(0); + if (calc_second_derivatives) + d2cr = spline_hc.second_derivatives(0); +} + + +void +ACERadialFunctions::radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, + DOUBLE_TYPE &dcr) { +/* pseudocode for hard core repulsion +in: + r: distance + pre: prefactor: read from input, depends on pair of atoms mu_i mu_j + lambda: exponent: read from input, depends on pair of atoms mu_i mu_j + cutoff: cutoff distance: read from input, depends on pair of atoms mu_i mu_j +out: +cr: hard core repulsion +dcr: derivative of hard core repulsion + + function + \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f + +*/ + + DOUBLE_TYPE r2, lr2, y, x0, env, denv; + +// repulsion strictly positive and decaying + pre = abs(pre); + lambda = abs(lambda); + + r2 = r * r; + lr2 = lambda * r2; + if (lr2 < 50.0) { + y = exp(-lr2); + cr = pre * y / r; + dcr = -pre * y * (2.0 * lr2 + 1.0) / r2; + + x0 = r / cutoff; + env = 0.5 * (1.0 + cos(pi * x0)); + denv = -0.5 * sin(pi * x0) * pi / cutoff; + dcr = cr * denv + dcr * env; + cr = cr * env; + } else { + cr = 0.0; + dcr = 0.0; + } + +} + +void +ACERadialFunctions::evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j) { + if (nradbase_c > nradbase) + throw invalid_argument("nradbase_c couldn't be larger than nradbase"); + if (nradial_c > nradial) + throw invalid_argument("nradial_c couldn't be larger than nradial"); + if (mu_i > nelements) + throw invalid_argument("mu_i couldn't be larger than nelements"); + if (mu_j > nelements) + throw invalid_argument("mu_j couldn't be larger than nelements"); + + gr_vec.resize(r_vec.size(), nradbase_c); + dgr_vec.resize(r_vec.size(), nradbase_c); + d2gr_vec.resize(r_vec.size(), nradbase_c); + + fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + dfr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + d2fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); + + for (size_t i = 0; i < r_vec.size(); i++) { + DOUBLE_TYPE r = r_vec[i]; + this->evaluate(r, nradbase_c, nradial_c, mu_i, mu_j, true); + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr_vec(i, nr) = gr(nr); + dgr_vec(i, nr) = dgr(nr); + d2gr_vec(i, nr) = d2gr(nr); + } + + for (NS_TYPE nr = 0; nr < nradial_c; nr++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fr_vec(i, nr, l) = fr(nr, l); + dfr_vec(i, nr, l) = dfr(nr, l); + d2fr_vec(i, nr, l) = d2fr(nr, l); + + } + } + } + +} + +void SplineInterpolator::setupSplines(int num_of_functions, RadialFunctions func, + DOUBLE_TYPE *values, + DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff) { + + this->deltaSplineBins = deltaSplineBins; + this->cutoff = cutoff; + this->ntot = static_cast(cutoff / deltaSplineBins); + + DOUBLE_TYPE r, c[4]; + this->num_of_functions = num_of_functions; + this->values.resize(num_of_functions); + this->derivatives.resize(num_of_functions); + this->second_derivatives.resize(num_of_functions); + + Array1D f1g(num_of_functions); + Array1D f1gd1(num_of_functions); + f1g.fill(0); + f1gd1.fill(0); + + nlut = ntot; + DOUBLE_TYPE f0, f1, f0d1, f1d1; + int idx; + + // cutoff is global cutoff + rscalelookup = (DOUBLE_TYPE) nlut / cutoff; + invrscalelookup = 1.0 / rscalelookup; + + lookupTable.init(ntot + 1, num_of_functions, 4); + if (values == nullptr & num_of_functions > 0) + throw invalid_argument("SplineInterpolator::setupSplines: values could not be null"); + if (dvalues == nullptr & num_of_functions > 0) + throw invalid_argument("SplineInterpolator::setupSplines: dvalues could not be null"); + + for (int n = nlut; n >= 1; n--) { + r = invrscalelookup * DOUBLE_TYPE(n); + func(r); //populate values and dvalues arrays + for (int func_id = 0; func_id < num_of_functions; func_id++) { + f0 = values[func_id]; + f1 = f1g(func_id); + f0d1 = dvalues[func_id] * invrscalelookup; + f1d1 = f1gd1(func_id); + // evaluate coefficients + c[0] = f0; + c[1] = f0d1; + c[2] = 3.0 * (f1 - f0) - f1d1 - 2.0 * f0d1; + c[3] = -2.0 * (f1 - f0) + f1d1 + f0d1; + // store coefficients + for (idx = 0; idx <= 3; idx++) + lookupTable(n, func_id, idx) = c[idx]; + + // evaluate function values and derivatives at current position + f1g(func_id) = c[0]; + f1gd1(func_id) = c[1]; + } + } + + +} + + +void SplineInterpolator::calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives) { + DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2, w4l2; + DOUBLE_TYPE c[4]; + int func_id, idx; + DOUBLE_TYPE x = r * rscalelookup; + int nl = static_cast(floor(x)); + + if (nl <= 0) + throw std::invalid_argument("Encountered very small distance. Stopping."); + + if (nl < nlut) { + wl = x - DOUBLE_TYPE(nl); + wl2 = wl * wl; + wl3 = wl2 * wl; + w2l1 = 2.0 * wl; + w3l2 = 3.0 * wl2; + w4l2 = 6.0 * wl; + for (func_id = 0; func_id < num_of_functions; func_id++) { + for (idx = 0; idx <= 3; idx++) { + c[idx] = lookupTable(nl, func_id, idx); + } + values(func_id) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; + derivatives(func_id) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; + if (calc_second_derivatives) + second_derivatives(func_id) = (c[2] + c[3] * w4l2) * rscalelookup * rscalelookup * 2; + } + } else { // fill with zeroes + values.fill(0); + derivatives.fill(0); + if (calc_second_derivatives) + second_derivatives.fill(0); + } +} + +void SplineInterpolator::calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind) { + DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2; + DOUBLE_TYPE c[4]; + int idx; + DOUBLE_TYPE x = r * rscalelookup; + int nl = static_cast(floor(x)); + + if (nl <= 0) + throw std::invalid_argument("Encountered very small distance. Stopping."); + + if (nl < nlut) { + wl = x - DOUBLE_TYPE(nl); + wl2 = wl * wl; + wl3 = wl2 * wl; + w2l1 = 2.0 * wl; + w3l2 = 3.0 * wl2; + + for (idx = 0; idx <= 3; idx++) { + c[idx] = lookupTable(nl, func_ind, idx); + } + values(func_ind) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; + derivatives(func_ind) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; + + } else { // fill with zeroes + values(func_ind) = 0; + derivatives(func_ind) = 0; + } +} diff --git a/lib/pace/ace_radial.h b/lib/pace/ace_radial.h new file mode 100644 index 0000000000..e45cfaec79 --- /dev/null +++ b/lib/pace/ace_radial.h @@ -0,0 +1,324 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +#ifndef ACE_RADIAL_FUNCTIONS_H +#define ACE_RADIAL_FUNCTIONS_H + +#include "ace_arraynd.h" +#include "ace_types.h" +#include + +using namespace std; + +//typedef void (*RadialFunctions)(DOUBLE_TYPE x); +typedef std::function RadialFunctions; + +/** + * Class that implement spline interpolation and caching for radial functions + */ +class SplineInterpolator { +public: + DOUBLE_TYPE cutoff = 0; ///< cutoff + DOUBLE_TYPE deltaSplineBins = 0.001; + int ntot = 10000; ///< Number of bins for look-up tables. + int nlut = 10000; ///< number of nodes in look-up table + DOUBLE_TYPE invrscalelookup = 1; ///< inverse of conversion coefficient from distance to lookup table within cutoff range + DOUBLE_TYPE rscalelookup = 1; ///< conversion coefficient from distance to lookup table within cutoff range + int num_of_functions = 0;///< number of functions to spline-interpolation + + Array1D values;// = Array1D("values"); ///< shape: [func_ind] + Array1D derivatives;// = Array1D("derivatives");///< shape: [func_ind] + Array1D second_derivatives;// = Array1D("second_derivatives");///< shape: [func_ind] + + Array3D lookupTable = Array3D("lookupTable");///< shape: [ntot+1][func_ind][4] + + /** + * Setup splines + * + * @param num_of_functions number of functions + * @param func subroutine, that update `values` and `dvalues` arrays + * @param values values + * @param dvalues derivatives + */ + void setupSplines(int num_of_functions, RadialFunctions func, + DOUBLE_TYPE *values, + DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff); + + /** + * Populate `values` and `derivatives` arrays with a spline-interpolation for + * all functions + * + * @param r + * + * @return: populate 'values' and 'derivatives' + */ + void calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives = false); + + /** + * Populate `values` and `derivatives` arrays with a spline-interpolation for + * all functions + * + * @param r + * + * @return: populate 'values' and 'derivatives' + */ + void calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind); +}; + +/** + * Interface class for radial basis functions with rank=1 (g_k), R_nl (rank>1) and hard-core repulsion radial functions + */ +class AbstractRadialBasis { +public: + SPECIES_TYPE nelements = 0; ///< number of elements + Array2D cut = Array2D("cut"); ///< cutoffs, shape: [nelements][nelements] + Array2D dcut = Array2D("dcut"); ///< decay of cutoff, shape: [nelements][nelements] + DOUBLE_TYPE cutoff = 0; ///< cutoff + +// int ntot = 10000; ///< Number of bins for look-up tables. + DOUBLE_TYPE deltaSplineBins; + LS_TYPE lmax = 0; ///< maximum value of `l` + NS_TYPE nradial = 0; ///< maximum number `n` of radial functions \f$ R_{nl}(r) \f$ + NS_TYPE nradbase = 0; ///< number of radial basis functions \f$ g_k(r) \f$ + + // Arrays for look-up tables. + Array2D splines_gk; ///< array of spline interpolator to store g_k, shape: [nelements][nelements] + Array2D splines_rnl; ///< array of spline interpolator to store R_nl, shape: [nelements][nelements] + Array2D splines_hc; ///< array of spline interpolator to store R_nl shape: [nelements][nelements] + //-------------------------------------------------------------------------- + + string radbasename = "ChebExpCos"; ///< type of radial basis functions \f$ g_{k}(r) \f$ (default="ChebExpCos") + + /** + Arrays to store radial functions. + */ + Array1D gr = Array1D("gr"); ///< g_k(r) functions, shape: [nradbase] + Array1D dgr = Array1D("dgr"); ///< derivatives of g_k(r) functions, shape: [nradbase] + Array1D d2gr = Array1D("d2gr"); ///< derivatives of g_k(r) functions, shape: [nradbase] + + Array2D fr = Array2D("fr"); ///< R_nl(r) functions, shape: [nradial][lmax+1] + Array2D dfr = Array2D( + "dfr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] + Array2D d2fr = Array2D( + "d2fr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] + + + + DOUBLE_TYPE cr; ///< hard-core repulsion + DOUBLE_TYPE dcr; ///< derivative of hard-core repulsion + DOUBLE_TYPE d2cr; ///< derivative of hard-core repulsion + + Array5D crad = Array5D( + "crad"); ///< expansion coefficients of radial functions into radial basis function, see Eq. (27) of PRB, shape: [nelements][nelements][lmax + 1][nradial][nradbase] + Array2D lambda = Array2D( + "lambda"); ///< distance scaling parameter Eq.(24) of PRB, shape: [nelements][nelements] + + Array2D prehc = Array2D( + "prehc"); ///< hard-core repulsion coefficients (prefactor), shape: [nelements][nelements] + Array2D lambdahc = Array2D( + "lambdahc");; ///< hard-core repulsion coefficients (lambdahc), shape: [nelements][nelements] + + virtual void + evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) = 0; + + virtual void + init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename = "ChebExpCos") = 0; + + /** + * Function that sets up the look-up tables for spline-representation of radial functions. + */ + virtual void setuplookupRadspline() = 0; + + virtual AbstractRadialBasis *clone() const = 0; + + virtual ~AbstractRadialBasis() = default; +}; + + +/** +Class to store radial functions and their associated functions. \n +*/ +class ACERadialFunctions final : public AbstractRadialBasis { +public: + + //-------------------------------------------------------------------------- + + /** + Arrays to store Chebyshev polynomials. + */ + Array1D cheb = Array1D( + "cheb"); ///< Chebyshev polynomials of the first kind, shape: [nradbase+1] + Array1D dcheb = Array1D( + "dcheb"); ///< derivatives Chebyshev polynomials of the first kind, shape: [nradbase+1] + Array1D cheb2 = Array1D( + "cheb2"); ///< Chebyshev polynomials of the second kind, shape: [nradbase+1] + + //-------------------------------------------------------------------------- + + Array2D gr_vec; + Array2D dgr_vec; + Array2D d2gr_vec; + + Array3D fr_vec; + Array3D dfr_vec; + Array3D d2fr_vec; + //------------------------------------------------------------------------ + /** + * Default constructor + */ + ACERadialFunctions() = default; + + /** + * Parametrized constructor + * + * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase + * @param lmax maximum orbital moment - lmax + * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial + * @param ntot Number of bins for spline look-up tables. + * @param nelements numer of elements + * @param cutoff cutoff + * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") + */ + ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename = "ChebExpCos"); + + /** + * Initialize arrays for given parameters + * + * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase + * @param lmax maximum orbital moment - lmax + * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial + * @param ntot Number of bins for spline look-up tables. + * @param nelements numer of elements + * @param cutoff cutoff + * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") + */ + void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename = "ChebExpCos") final; + + /** + * Destructor + */ + ~ACERadialFunctions() final = default; + + /** + * Function that computes Chebyshev polynomials of first and second kind + * to setup the radial functions and the derivatives + * + * @param n maximum polynom order + * @param x + * + * @returns fills cheb, dcheb and cheb2 arrays + */ + void calcCheb(NS_TYPE n, DOUBLE_TYPE x); + + /** + * Function that computes radial basis functions \$f g_k(r) \$f, see Eq.(21) of PRB paper + * @param lam \$f \lambda \$f parameter, see eq. (24) of PRB paper + * @param cut cutoff + * @param dcut cutoff decay + * @param r distance + * + * @return function fills gr and dgr arrays + */ + void radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + /** + * Function that computes radial core repulsion \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f, + * and its derivative, see Eq.(27) of implementation notes. + * + * @param r distance + * @param pre prefactor: read from input, depends on pair of atoms mu_i mu_j + * @param lambda exponent: read from input, depends on pair of atoms mu_i mu_j + * @param cutoff cutoff distance: read from input, depends on pair of atoms mu_i mu_j + * @param cr (out) hard core repulsion + * @param dcr (out) derivative of hard core repulsion + */ + static void radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, + DOUBLE_TYPE &dcr); + + /** + * Function that sets up the look-up tables for spline-representation of radial functions. + */ + void setuplookupRadspline() final; + + /** + * Function that computes radial functions \f$ R_{nl}(r)\f$ (see Eq. 27 from PRB paper) + * and its derivatives for all range of n,l, + * ONLY if radial basis functions (gr and dgr) are computed. + * @param elei first species type + * @param elej second species type + * + * @return fills in fr, dfr arrays + */ + void radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej); + + /** + * Compute all radial functions R_nl(r), radial basis functions g_k(r) and hard-core repulsion function hc(r) + * + * @param r distance + * @param nradbase_c + * @param nradial_c + * @param mu_i + * @param mu_j + * + * @return update gr(k), dgr(k), fr(n,l), dfr(n,l), cr, dcr + */ + void evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) final; + + + void + evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j); + + void chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + void chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + void chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); + + /** + * Setup all radial functions for element pair mu_i-mu_j and distance r + * @param mu_i first specie type + * @param mu_j second specie type + * @param r distance + * @return update fr(nr, l), dfr(nr, l) + */ + void all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r); + + ACERadialFunctions *clone() const override { + return new ACERadialFunctions(*this); + }; +}; + +#endif \ No newline at end of file diff --git a/lib/pace/ace_recursive.cpp b/lib/pace/ace_recursive.cpp new file mode 100644 index 0000000000..c895418943 --- /dev/null +++ b/lib/pace/ace_recursive.cpp @@ -0,0 +1,1340 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 20.12.2020 + +#include "ace_recursive.h" + +#include "ace_abstract_basis.h" +#include "ace_types.h" + +/* ------------------------------------------------------------ + * ACEDAG Implementation + * (just the DAG construction, not the traversal) + * ------------------------------------------------------------ */ + +/* Notes on different Tags: + * rec1 - first basic implementation + * rec2 - avoid index arithmetic, contiguous layout, + * canonical evaluator in ACE.jl format + * rec3 - split nodes into interior and leaf nodes + */ + +void ACEDAG::init(Array2D xAspec, + Array2D AAspec, + Array1D orders, + Array2D jl_coeffs, + int _heuristic ) { + + // remember which heuristic we want to use! + heuristic = _heuristic; + + /* stage one of the graph is just extracting the A basis from + * the tensor product format into the linear list; all information + * for that is already stored in Aspec, and the only thing to do here is + * to construct zero-coefficients. Still we have to copy Aspec, since + * the one we have here will (may?) be deleted. */ + int num1 = xAspec.get_dim(0); + Aspec = xAspec; //YL: just copying the multiarray: Aspec = xAspec; + + /* fill the one-particle basis into the DAGmap + * DAGmap[ (i1,...,in) ] = iAA index where the (i1,...,in) basis functions + * lives. + */ + TDAGMAP DAGmap; + for (int iA = 0; iA < num1; iA++) { + vector a(1); + a[0] = iA; + DAGmap[a] = iA; + } + + /* For stage 2 we now want to construct the actual recursion; the + recursion info will be stored in DAGspec, while the + coefficients go into DAGcoeffs. These arrays are initialized to + length `num2`, but they will have to grow as we add additional + artificial nodes into the graph. + + initially we treat all nodes as having children, but then in a + second stage below we reorganize. */ + int num2 = AAspec.get_dim(0); + int ndensity = jl_coeffs.get_dim(1); + nodes_pre.resize(2*num2, 2); + coeffs_pre.resize(2*num2, ndensity); + + /* the first basis function we construct will get index num1, + * since there are already num1 one-particle basis functions + * to collect during stage 1 */ + dag_idx = num1; + /* main loop over AA basis set to transform into DAG */ + for (int iAA = 0; iAA < num2; iAA++) { + // create a vector representing the current basis function + int ord = orders(iAA); + vector aa(ord); + for (int t = 0; t < ord; t++) aa[t] = AAspec(iAA, t); + vector c(ndensity); + for (int p = 0; p < ndensity; p++) c[p] = jl_coeffs(iAA, p); + insert_node(DAGmap, aa, c); + } + + /* convert to 3-stage format through reordering + * interior nodes first, then leaf nodes */ + + // allocate storage + num_nodes = dag_idx; // store total size of dag + // num_nodes - num1 = number of many-body nodes. + nodes.resize(num_nodes - num1, 2); + coeffs.resize(num_nodes - num1, ndensity); + + // find out which nodes have children + haschild.resize(num_nodes - num1); + haschild.fill(false); + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (nodes_pre(iAA, 0) >= num1) + haschild(nodes_pre(iAA, 0)-num1) = true; + if (nodes_pre(iAA, 1) >= num1) + haschild(nodes_pre(iAA, 1)-num1) = true; + } + + // to reorder the graph we need a fresh map from preordered indices to + // postordered indices; for the 1-particle basis the order remains the same. + // TODO: doesn't need to be a map, could be a vector. + map neworder; + for (int iA = 0; iA < num1; iA++) + neworder[iA] = iA; + + // insert all interior nodes + num2_int = 0; + num2_leaf = 0; + dag_idx = num1; + int i1, i2, i1pre, i2pre; + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (haschild(iAA)) { + num2_int += 1; + // indices into AAbuf before reordering + i1pre = nodes_pre(iAA, 0); + i2pre = nodes_pre(iAA, 1); + // indices into AAbuf after reordering + i1 = neworder[i1pre]; + i2 = neworder[i2pre]; + // insert the current node : iAA is old order, dag_idx is new order + neworder[num1+iAA] = dag_idx; + nodes(dag_idx-num1, 0) = i1; + nodes(dag_idx-num1, 1) = i2; + for (int t = 0; t < ndensity; t++) + coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); + dag_idx++; + } + } + + // insert all leaf nodes + for (int iAA = 0; iAA < num_nodes - num1; iAA++) { + if (!haschild(iAA)) { + num2_leaf += 1; + // indices into AAbuf before reordering + i1pre = nodes_pre(iAA, 0); + i2pre = nodes_pre(iAA, 1); + // insert the current node : no need to remember the new order now + nodes(dag_idx-num1, 0) = neworder[i1pre]; + nodes(dag_idx-num1, 1) = neworder[i2pre]; + for (int t = 0; t < ndensity; t++) + coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); + dag_idx++; + } + } +#ifdef DEBUG + cout << "num2_int = " << num2_int << "; num2_leaf = " << num2_leaf << "\n"; +#endif + // free up memory that is no longer needed + nodes_pre.resize(0, 0); + coeffs_pre.resize(0, 0); + haschild.resize(0); + + /* finalize dag: allocate buffer storage */ + AAbuf.resize(num1 + num2_int); + w.resize(num_nodes); + // TODO: technically only need num1 + num2_int for w, this can save one + // memory access later, probably not worth the crazy code duplication. +} + +void ACEDAG::insert_node(TDAGMAP &DAGmap, vector a, vector c) { + /* start with a list of all possible partitions into 2 groups + * and check whether any of these nodes are already in the dag */ + auto partitions = find_2partitions(a); + int ndensity = c.size(); + int num1 = get_num1(); + + // TODO: first try to find partitions into nodes that are already parents + // that way we will get more leaf nodes! + for (TPARTITION const& p : partitions) { + /* this is the good case; the parent nodes are both already in the + * graph; add the new node and return. This is also the only place in the + * code where an actual insert happens. */ + if (DAGmap.count(p.first) && DAGmap.count(p.second)) { + if (nodes_pre.get_dim(0) < dag_idx + 1) { //check if array is sufficiently large + int newsize = (dag_idx * 3) / 2; + nodes_pre.resize(newsize, 2); // grow arrays if necessary + coeffs_pre.resize(newsize, ndensity); + } + int i1 = DAGmap[p.first]; + int i2 = DAGmap[p.second]; + nodes_pre(dag_idx - num1, 0) = i1; + nodes_pre(dag_idx - num1, 1) = i2; + DAGmap[a] = dag_idx; + for (int p = 0; p < ndensity; p++) + coeffs_pre(dag_idx - num1, p) = c[p]; + dag_idx += 1; + return; + } + } + + /* if we are here, then this means, the new node cannot yet be inserted. + * We first need to insert some intermediate auxiliary nodes. For this + * we use a simple heuristic: + * try to find a partition where one of the two nodes are already + * in the graph, if there are several, then we remember the longest + * (this is a very greedy heuristic!!) + * .... (continue below) .... + */ + TPARTITION longest; + int longest_length = 0; + for (auto const& p : partitions) { + int len = 0; + if (DAGmap.count(p.first)) { + len = p.first.size(); + } else if (DAGmap.count(p.second)) { + len = p.second.size(); + } + if ((len > 0) && (len > longest_length)) { + longest_length = len; + longest = p; + } + } + + /* sanity check */ + if (longest_length == 0) { + std::stringstream error_message; + error_message << "WARNING : something has gone horribly wrong! `longest_length == 0`! \n"; + error_message << "a = ["; + for (int t = 0; t < a.size(); t++) + error_message << a[t] << ", "; + error_message << "]\n"; + throw std::logic_error(error_message.str()); +// return; + } + + /* If there is a partition with one component already in the graph, + * then we only need to add in the other component. Note that there will + * always be at least one such partition, namely all those containing + * a one-element node e.g. (1,2,3,4) -> (1,) (2,3,4) then (1,) is + * a one-particle basis function and hence always in the graph. + * If heuristic == 0, then we just take one of those partitionas and move on. + * + * We also accept the found partition if longest_length > 1. + * And we also accept it if we have a 2- or 3-correlation. + */ + + if ( (heuristic == 0) + || (longest_length > 1) + || (a.size() <= 3)) { + /* insert the other node that isn't in the DAG yet + * this is an artificial node so it gets zero-coefficients + * This step is recursive, so more than one node might be inserted here */ + vector cz(ndensity); + for (int i = 0; i < ndensity; i++) cz[i] = 0.0; + TPARTITION p = longest; + if (DAGmap.count(p.first)) + insert_node(DAGmap, p.second, cz); + else + insert_node(DAGmap, p.first, cz); + } + + /* Second heuristic : heuristic == 1 + * Focus on inserting artificial 2-correlations + */ + else if (heuristic == 1) { + // and we also know that longest_length == 1 and nu = a.size >= 4. + int nu = a.size(); + // generate an artificial partition + vector a1(2); + for (int i = 0; i < 2; i++) a1[i] = a[i]; + vector a2(nu - 2); + for (int i = 0; i < nu - 2; i++) a2[i] = a[2 + i]; + vector cz(ndensity); + for (int i = 0; i < cz.size(); i++) cz[i] = 0.0; + // and insert both (we know neither are in the DAG yet) + insert_node(DAGmap, a1, cz); + insert_node(DAGmap, a2, cz); + } else { + cout << "WARNING : something has gone horribly wrong! \n"; + // TODO: Throw and error here?!? + return; + } + + + + /* now we should be ready to insert the entire tuple `a` since there is now + * an eligible parent pair. Here we recompute the partition of `a`, but + * that's a small price to pay for a clearer code. Maybe this can be + * optimized a bit by wrapping it all into a while loop or having a second + * version of `insert_node` ... */ + insert_node(DAGmap, a, c); +} + +TPARTITIONS ACEDAG::find_2partitions(vector v) { + int N = v.size(); + int zo; + TPARTITIONS partitions; + TPARTITION part; + /* This is a fun little hack to extract all subsets of the indices 1:N + * the number i will have binary representation with each digit indicating + * whether or not that index belongs to the selected subset */ + for (int i = 1; i < (1< v1(N1); + vector v2(N2); + int i1 =0, i2 = 0; + p = 1; + for (int n = 0; n < N; n++) { + zo = ((i / p) % 2); + p *= 2; + if (zo == 1) { + v1[i1] = v[n]; + i1 += 1; + } else { + v2[i2] = v[n]; + i2 += 1; + } + } + part = make_pair(v1, v2); + partitions.push_back(part); + } + return partitions; +} + +void ACEDAG::print() { + cout << "DAG Specification: \n" ; + cout << " n1 : " << get_num1() << "\n"; + cout << " n2 : " << get_num2() << "\n"; + cout << " num_nodes : " << num_nodes << "\n"; + cout << "--------------------\n"; + cout << "A-spec: \n"; + for (int iA = 0; iA < get_num1(); iA++) { + cout << iA << " : " << Aspec(iA, 0) << + Aspec(iA, 1) << Aspec(iA, 2) << Aspec(iA, 3) << "\n"; + } + + cout << "-----------\n"; + cout << "AA-tree\n"; + + for (int iAA = 0; iAA < get_num2(); iAA++) { + cout << iAA + get_num1() << " : " << + nodes(iAA, 0) << ", " << nodes(iAA, 1) << "\n"; + } +} + + +/* ------------------------------------------------------------ + * ACERecursiveEvaluator + * ------------------------------------------------------------ */ + + +void ACERecursiveEvaluator::set_basis(ACECTildeBasisSet &bas, int heuristic) { + basis_set = &bas; + init(basis_set, heuristic); +} + +void ACERecursiveEvaluator::init(ACECTildeBasisSet *basis_set, int heuristic) { + + ACEEvaluator::init(basis_set); + + + weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, + "weights"); + + weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); + + + DG_cache.init(1, basis_set->nradbase, "DG_cache"); + DG_cache.fill(0); + + R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); + R_cache.fill(0); + + DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); + DR_cache.fill(0); + + Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); + Y_cache.fill({0, 0}); + + DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); + DY_cache.fill({0.}); + + //hard-core repulsion + DCR_cache.init(1, "DCR_cache"); + DCR_cache.fill(0); + dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); + + /* convert to ACE.jl format to prepare for construction of DAG + * This will fill the arrays jl_Aspec, jl_AAspec, jl_orders + */ + acejlformat(); + + // test_acejlformat(); + + // now pass this info into the DAG + dag.init(jl_Aspec, jl_AAspec, jl_orders, jl_coeffs, heuristic); + + // finally empty the temporary arrays to clear up the memory... + // TODO +} + + +void ACERecursiveEvaluator::acejlformat() { + + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + int j, jj, func_ind, ms_ind; + + SPECIES_TYPE mu_i = 0;//TODO: multispecies + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + int AAidx = 0; + RANK_TYPE order, t; + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + /* transform basis into new format: + [A1 ... A_num1] + [(i1,i2)(i1,i2)(...)(i1,i2,i3)(...)] + where each ia represents an A_{ia} + */ + + /* compute max values for mu, n, l, m */ + SPECIES_TYPE maxmu = 0; //TODO: multispecies + NS_TYPE maxn = basis_set->nradmax; + LS_TYPE maxl = basis_set->lmax; + RANK_TYPE maxorder = basis_set->rankmax; + const DENSITY_TYPE ndensity = basis_set->ndensitymax; + + int num1 = 0; + + + /* create a 4D lookup table for the 1-p basis + * TODO: replace with a map?? + */ + Array4D A_lookup(int(maxmu+1), int(maxn), int(maxl+1), int(2*maxl+1)); + for (int mu = 0; mu < maxmu+1; mu++) + for (int n = 0; n < maxn; n++) + for (int l = 0; l < maxl+1; l++) + for (int m = 0; m < 2*maxl+1; m++) + A_lookup(mu, n, l, m) = -1; + int A_idx = 0; // linear index of A basis function (1-particle) + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; +// func->print(); + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + for (t = 0; t < order; t++) { + int iA = A_lookup(mus[t], ns[t]-1, ls[t], ms[t]+ls[t]); + if (iA == -1) { + A_lookup(mus[t], ns[t] - 1, ls[t], ms[t] + ls[t]) = A_idx; + A_idx += 1; + } + } + } + } + + /* create the reverse list: linear indixes to mu,l,m,n + this keeps only the basis functions we really need */ + num1 = A_idx; + Array2D & Aspec = jl_Aspec; + Aspec.resize(num1, 4); + // Array2D Aspec(num1, 4); + for (int mu = 0; mu <= maxmu; mu++) + for (int n = 1; n <= maxn; n++) + for (int l = 0; l <= maxl; l++) + for (int m = -l; m <= l; m++) { + int iA = A_lookup(mu, n-1, l, l+m); + if (iA != -1) { + Aspec(iA, 0) = mu; + Aspec(iA, 1) = n; + Aspec(iA, 2) = l; + Aspec(iA, 3) = m; + } + } + + /* ============ HALF-BASIS TRICK START ============ */ + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + if (!( (mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl) )) + continue; + + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + // find first positive and negative index + int pos_idx = order + 1; + int neg_idx = order + 1; + for (t = order-1; t >= 0; t--) + if (ms[t] > 0) pos_idx = t; + else if (ms[t] < 0) neg_idx = t; + + // if neg_idx < pos_idx then this means that ms is non-zero + // and that the first non-zero index is negative, hence this is + // a negative-sign tuple which we want to combine into + // its opposite. + if (neg_idx < pos_idx) { + // find the opposite tuple + int ms_ind2 = 0; + MS_TYPE *ms2; + bool found_opposite = false; + for (ms_ind2 = 0; ms_ind2 < func->num_ms_combs; ++ms_ind2) { + ms2 = &func->ms_combs[ms_ind2 * order]; + bool isopposite = true; + for (t = 0; t < order; t++) + if (ms[t] != -ms2[t]) { + isopposite = false; + break; + } + if (isopposite) { + found_opposite = true; + break; + } + } + + if (ms_ind == ms_ind2) { + cout << "WARNING - ms_ind == ms_ind2 \n"; + } + + // now we need to overwrite the coefficients + if (found_opposite) { + int sig = 1; + for (t = 0; t < order; t++) + if (ms[t] < 0) + sig *= -1; + for (int p = 0; p < ndensity; ++p) { + func->ctildes[ms_ind2 * ndensity + p] += + func->ctildes[ms_ind * ndensity + p]; + func->ctildes[ms_ind * ndensity + p] = 0.0; + } + } + } + } + } + + // /* ============ HALF-BASIS TRICK END ============ */ + + + /* count number of basis functions, keep only non-zero!! */ + int num2 = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + for (ms_ind = 0; ms_ind < (&basis[func_ind])->num_ms_combs; ++ms_ind, ++func_ms_ind) { + // check that the coefficients are actually non-zero + bool isnonzero = false; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + if (func->ctildes[ms_ind * ndensity + p] != 0.0) + isnonzero = true; + if (isnonzero) + num2++; + } + } + + + /* Now create the AA basis links into the A basis */ + num1 = A_idx; // total number of A-basis functions that we keep + // Array1D AAorders(num2); + Array1D & AAorders = jl_orders; + AAorders.resize(num2); + // Array2D AAspec(num2, maxorder); // specs of AA basis functions + Array2D & AAspec = jl_AAspec; + AAspec.resize(num2, maxorder); + jl_coeffs.resize(num2, ndensity); + AAidx = 0; // linear index into AA basis function + int len_flat = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + if (!((mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl))) //fool-proofing of functions + continue; + + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + // check that the coefficients are actually non-zero + bool iszero = true; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + if (func->ctildes[ms_ind * ndensity + p] != 0.0) + iszero = false; + if (iszero) continue; + + AAorders(AAidx) = order; + for (t = 0; t < order; t++) { + int Ait = A_lookup(int(mus[t]), int(ns[t]-1), int(ls[t]), int(ms[t])+int(ls[t])); + AAspec(AAidx, t) = Ait; + len_flat += 1; + } + for (t = order; t < maxorder; t++) AAspec(AAidx, t) = -1; + /* copy over the coefficients */ + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + jl_coeffs(AAidx, p) = func->ctildes[ms_ind * ndensity + p]; + AAidx += 1; + } + } + + // flatten the AAspec array + jl_AAspec_flat.resize(len_flat); + int idx_spec = 0; + for (int AAidx = 0; AAidx < jl_AAspec.get_dim(0); AAidx++) + for (int p = 0; p < jl_orders(AAidx); p++, idx_spec++) + jl_AAspec_flat(idx_spec) = jl_AAspec(AAidx, p); + +} + +void ACERecursiveEvaluator::test_acejlformat() { + + Array2D AAspec = jl_AAspec; + Array2D Aspec = jl_Aspec; + Array1D AAorders = jl_orders; + cout << "num2 = " << AAorders.get_dim(0) << "\n"; + int func_ms_ind = 0; + int func_ms_t_ind = 0;// index for dB + int j, jj, func_ind, ms_ind; + + SPECIES_TYPE mu_i = 0; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + RANK_TYPE order, t; + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + /* ==== test by printing the basis spec ====*/ + // TODO: convert this into an automatic consistency test + int iAA = 0; + for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { + ACECTildeBasisFunction *func = &basis[func_ind]; + order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; + // func->print(); + //loop over {ms} combinations in sum + for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { + ms = &func->ms_combs[ms_ind * order]; + + + cout << iAA << " : |"; + for (t = 0; t < order; t++) + cout << mus[t] << ";" << ns[t] << "," << ls[t] << "," << ms[t] << "|"; + cout << "\n"; + + cout << " ["; + for (t = 0; t < AAorders(iAA); t++) + cout << AAspec(iAA, int(t)) << ","; + cout << "]\n"; + cout << " |"; + for (t = 0; t < AAorders(iAA); t++) { + int iA = AAspec(iAA, t); + // cout << iA << ","; + cout << Aspec(iA, 0) << ";" + << Aspec(iA, 1) << "," + << Aspec(iA, 2) << "," + << Aspec(iA, 3) << "|"; + } + cout << "\n"; + iAA += 1; + } + } + /* ==== END TEST ==== */ + + +} + + + + +void ACERecursiveEvaluator::resize_neighbours_cache(int max_jnum) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); + } + if (R_cache.get_dim(0) < max_jnum) { + + //TODO: implement grow + R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + R_cache.fill(0); + + DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); + DR_cache.fill(0); + + DG_cache.resize(max_jnum, basis_set->nradbase); + DG_cache.fill(0); + + Y_cache.resize(max_jnum, basis_set->lmax + 1); + Y_cache.fill({0, 0}); + + DY_cache.resize(max_jnum, basis_set->lmax + 1); + DY_cache.fill({0}); + + //hard-core repulsion + DCR_cache.init(max_jnum, "DCR_cache"); + DCR_cache.fill(0); + } +} + + + +// double** r - atomic coordinates of atom I +// int* types - atomic types if atom I +// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; +// Usage: j = jlist_of_i[jj]; +// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; + +void +ACERecursiveEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { + if(basis_set== nullptr) { + throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); + } + per_atom_calc_timer.start(); +#ifdef PRINT_MAIN_STEPS + printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); +#endif + DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; + DOUBLE_TYPE r_norm; + DOUBLE_TYPE xn, yn, zn, r_xyz; + DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; + DOUBLE_TYPE *r_hat; + + SPECIES_TYPE mu_j; + RANK_TYPE r, rank, t; + NS_TYPE n; + LS_TYPE l; + MS_TYPE m, m_t; + + SPECIES_TYPE *mus; + NS_TYPE *ns; + LS_TYPE *ls; + MS_TYPE *ms; + + int j, jj, func_ind, ms_ind; + SHORT_INT_TYPE factor; + + ACEComplex Y{0}, Y_DR{0.}; + ACEComplex B{0.}; + ACEComplex dB{0}; + ACEComplex A_cache[basis_set->rankmax]; + + ACEComplex dA[basis_set->rankmax]; + int spec[basis_set->rankmax]; + + dB_flatten.fill({0.}); + + ACEDYcomponent grad_phi_nlm{0}, DY{0.}; + + //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme + ACEComplex A_forward_prod[basis_set->rankmax + 1]; + ACEComplex A_backward_prod[basis_set->rankmax + 1]; + + DOUBLE_TYPE inv_r_norm; + DOUBLE_TYPE r_norms[jnum]; + DOUBLE_TYPE inv_r_norms[jnum]; + DOUBLE_TYPE rhats[jnum][3];//normalized vector + SPECIES_TYPE elements[jnum]; + const DOUBLE_TYPE xtmp = x[i][0]; + const DOUBLE_TYPE ytmp = x[i][1]; + const DOUBLE_TYPE ztmp = x[i][2]; + DOUBLE_TYPE f_ji[3]; + + bool is_element_mapping = element_type_mapping.get_size() > 0; + SPECIES_TYPE mu_i; + if (is_element_mapping) + mu_i = element_type_mapping(type[i]); + else + mu_i = type[i]; + + const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; + const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; + + ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; + ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; + + DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; + DOUBLE_TYPE dF_drho_core; + + //TODO: lmax -> lmaxi (get per-species type) + const LS_TYPE lmaxi = basis_set->lmax; + + //TODO: nradmax -> nradiali (get per-species type) + const NS_TYPE nradiali = basis_set->nradmax; + + //TODO: nradbase -> nradbasei (get per-species type) + const NS_TYPE nradbasei = basis_set->nradbase; + + //TODO: get per-species type number of densities + const DENSITY_TYPE ndensity= basis_set->ndensitymax; + + neighbours_forces.resize(jnum, 3); + neighbours_forces.fill(0); + + //TODO: shift nullifications to place where arrays are used + weights.fill({0}); + weights_rank1.fill(0); + A.fill({0}); + A_rank1.fill(0); + rhos.fill(0); + dF_drho.fill(0); + +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); + basis_projections.init(total_basis_size, ndensity, "c_projections"); +#endif + + //proxy references to spherical harmonics and radial functions arrays + const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; + const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; + + const Array2D &fr = basis_set->radial_functions->fr; + const Array2D &dfr = basis_set->radial_functions->dfr; + + const Array1D &gr = basis_set->radial_functions->gr; + const Array1D &dgr = basis_set->radial_functions->dgr; + + loop_over_neighbour_timer.start(); + + int jj_actual = 0; + SPECIES_TYPE type_j = 0; + int neighbour_index_mapping[jnum]; // jj_actual -> jj + //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); + r_xyz = sqrt(xn * xn + yn * yn + zn * zn); + + if (r_xyz >= current_cutoff) + continue; + + inv_r_norm = 1 / r_xyz; + + r_norms[jj_actual] = r_xyz; + inv_r_norms[jj_actual] = inv_r_norm; + rhats[jj_actual][0] = xn * inv_r_norm; + rhats[jj_actual][1] = yn * inv_r_norm; + rhats[jj_actual][2] = zn * inv_r_norm; + elements[jj_actual] = mu_j; + neighbour_index_mapping[jj_actual] = jj; + jj_actual++; + } + + int jnum_actual = jj_actual; + + //ALGORITHM 1: Atomic base A + for (jj = 0; jj < jnum_actual; ++jj) { + r_norm = r_norms[jj]; + mu_j = elements[jj]; + r_hat = rhats[jj]; + + //proxies + Array2DLM &Y_jj = Y_cache(jj); + Array2DLM &DY_jj = DY_cache(jj); + + + basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); + basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); + //loop for computing A's + //rank = 1 + for (n = 0; n < basis_set->nradbase; n++) { + GR = gr(n); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("-neigh atom %d\n", jj); + printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); + printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); +#endif + DG_cache(jj, n) = dgr(n); + A_rank1(mu_j, n) += GR * Y00; + } + //loop for computing A's + // for rank > 1 + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + R = fr(n, l); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); +#endif + + DR_cache(jj, n, l) = dfr(n, l); + R_cache(jj, n, l) = R; + + for (m = 0; m <= l; m++) { + Y = ylm(l, m); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); +#endif + A_lm(l, m) += R * Y; //accumulation sum over neighbours + Y_jj(l, m) = Y; + DY_jj(l, m) = dylm(l, m); + } + } + } + + //hard-core repulsion + rho_core += basis_set->radial_functions->cr; + DCR_cache(jj) = basis_set->radial_functions->dcr; + + } //end loop over neighbours + + //complex conjugate A's (for NEGATIVE (-m) terms) + // for rank > 1 + for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { + for (n = 0; n < nradiali; n++) { + auto &A_lm = A(mu_j, n); + for (l = 0; l <= lmaxi; l++) { + //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm + for (m = 1; m <= l; m++) { + factor = m % 2 == 0 ? 1 : -1; + A_lm(l, -m) = A_lm(l, m).conjugated() * factor; + } + } + } + } //now A's are constructed + loop_over_neighbour_timer.stop(); + + // ==================== ENERGY ==================== + + energy_calc_timer.start(); +#ifdef EXTRA_C_PROJECTIONS + basis_projections_rank1.fill(0); + basis_projections.fill(0); +#endif + + //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation + //rank=1 + for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { + ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; +// ndensity = func->ndensity; +#ifdef PRINT_LOOPS_INDICES + printf("Num density = %d r = 0\n",(int) ndensity ); + print_C_tilde_B_basis_function(*func); +#endif + double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); +#ifdef DEBUG_ENERGY_CALCULATIONS + printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); + printf(" coeff[0] = %f\n", func->ctildes[0]); +#endif + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + rhos(p) += func->ctildes[p] * A_cur; +#ifdef EXTRA_C_PROJECTIONS + //aggregate C-projections separately + basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; +#endif + } + } // end loop for rank=1 + + // ================ START RECURSIVE EVALUATOR ==================== + // (rank > 1 only) + + /* STAGE 1: + * 1-particle basis is already evaluated, so we only need to + * copy it into the AA value buffer + */ + int num1 = dag.get_num1(); + for (int idx = 0; idx < num1; idx++) + dag.AAbuf(idx) = A( dag.Aspec(idx, 0), + dag.Aspec(idx, 1)-1, + dag.Aspec(idx, 2), + dag.Aspec(idx, 3) ); + + + if (recursive) { + /* STAGE 2: FORWARD PASS + * Forward pass: go through the dag and store all intermediate results + */ + + // rhos.fill(0); note the rhos are already reset and started filling above! + ACEComplex AAcur{0.0}; + int i1, i2; + + int * dag_nodes = dag.nodes.get_data(); + int idx_nodes = 0; + + DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); + int idx_coefs = 0; + + int num2_int = dag.get_num2_int(); + int num2_leaf = dag.get_num2_leaf(); + + // interior nodes (save AA) + for (int idx = num1; idx < num1+num2_int; idx++) { + i1 = dag_nodes[idx_nodes]; idx_nodes++; + i2 = dag_nodes[idx_nodes]; idx_nodes++; + AAcur = dag.AAbuf(i1) * dag.AAbuf(i2); + dag.AAbuf(idx) = AAcur; + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur.real_part_product(dag_coefs[idx_coefs]); + } + + // leaf nodes -> no need to store in AAbuf + DOUBLE_TYPE AAcur_re = 0.0; + for (int _idx = 0; _idx < num2_leaf; _idx++) { + i1 = dag_nodes[idx_nodes]; idx_nodes++; + i2 = dag_nodes[idx_nodes]; idx_nodes++; + AAcur_re = dag.AAbuf(i1).real_part_product(dag.AAbuf(i2)); + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur_re * dag_coefs[idx_coefs]; + } + + } else { + + /* non-recursive Julia-style evaluator implementation */ + // TODO: fix array access to enable bounds checking again??? + ACEComplex AAcur{1.0}; + int *AAspec = jl_AAspec_flat.get_data(); + DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); + int idx_spec = 0; + int idx_coefs = 0; + int order = 0; + int max_order = jl_AAspec.get_dim(1); + for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++) { + AAcur = 1.0; + order = jl_orders(iAA); + for (int r = 0; r < order; r++, idx_spec++) + AAcur *= dag.AAbuf( AAspec[idx_spec] ); + for (int p = 0; p < ndensity; p++, idx_coefs++) + rhos(p) += AAcur.real_part_product(coeffs[idx_coefs]); + } + } + + /* we now have rho and can evaluate lots of things. + -------- this is back to the original PACE code --------- */ + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("rhos = "); + for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); + drho_cut = basis_set->drho_core_cutoffs(mu_i); + + basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); + basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); + + dF_drho_core = evdwl * dfcut + 1; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) + dF_drho(p) *= fcut; + evdwl_cut = evdwl * fcut + rho_core; + + // E0 shift + evdwl_cut += basis_set->E0vals(mu_i); + + /* I've moved this from below the weight calculation + since I believe it only times the energy? the weights + are only needed for the forces? + But I believe we could add a third timer for computing just + the weights; this will allow us to check better where the + bottleneck is. + */ + energy_calc_timer.stop(); + + forces_calc_loop_timer.start(); + + +#ifdef DEBUG_FORCES_CALCULATIONS + printf("dFrhos = "); + for(DENSITY_TYPE p =0; pndensity; + for (DENSITY_TYPE p = 0; p < ndensity; ++p) { + //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 + weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; + } + } + + /* --------- we now continue with the recursive code --------- */ + + if (recursive) { + /* STAGE 2: BACKWARD PASS */ + int i1, i2; + ACEComplex AA1{0.0}; + ACEComplex AA2{0.0}; + ACEComplex wcur{0.0}; + int num2_int = dag.get_num2_int(); + int num2_leaf = dag.get_num2_leaf(); + /* to prepare for the backward we first need to zero the weights */ + dag.w.fill({0.0}); + + int * dag_nodes = dag.nodes.get_data(); + int idx_nodes = 2 * (num2_int + num2_leaf) - 1; + + DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); + int idx_coefs = ndensity * (num2_int + num2_leaf) - 1; + + for (int idx = num1+num2_int+num2_leaf - 1; idx >= num1; idx--) { + i2 = dag_nodes[idx_nodes]; idx_nodes--; + i1 = dag_nodes[idx_nodes]; idx_nodes--; + AA1 = dag.AAbuf(i1); + AA2 = dag.AAbuf(i2); + wcur = dag.w(idx); // [***] + for (int p = ndensity-1; p >= 0; p--, idx_coefs--) + wcur += dF_drho(p) * dag_coefs[idx_coefs]; + dag.w(i1) += wcur * AA2; // TODO: replace with explicit muladd? + dag.w(i2) += wcur * AA1; + } + + /* [***] + * Note that these weights don't really need to be stored for the + * leaf nodes. We tested splitting this for loop into two where + * for the leaf nodes the weight would just be initialized to 0.0 + * instead of reading from an array. The improvement was barely + * measurable, ca 3%, so we reverted to this simpler algorithm + */ + + + } else { + + // non-recursive ACE.jl style implemenation of gradients, but with + // a backward differentiation approach to the prod-A + // (cf. Algorithm 3 in the manuscript) + + dag.w.fill({0.0}); + ACEComplex AAf{1.0}, AAb{1.0}, theta{0.0}; + + int *AAspec = jl_AAspec_flat.get_data(); + DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); + int idx_spec = 0; + int idx_coefs = 0; + int order = 0; + int max_order = jl_AAspec.get_dim(1); + for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++ ) { + order = jl_orders(iAA); + theta = 0.0; + for (int p = 0; p < ndensity; p++, idx_coefs++) + theta += dF_drho(p) * coeffs[idx_coefs]; + dA[0] = 1.0; + AAf = 1.0; + for (int t = 0; t < order-1; t++, idx_spec++) { + spec[t] = AAspec[idx_spec]; + A_cache[t] = dag.AAbuf(spec[t]); + AAf *= A_cache[t]; + dA[t+1] = AAf; + } + spec[order-1] = AAspec[idx_spec]; idx_spec++; + A_cache[order-1] = dag.AAbuf(spec[order-1]); + AAb = 1.0; + for (int t = order-1; t >= 1; t--) { + AAb *= A_cache[t]; + dA[t-1] *= AAb; + dag.w(spec[t]) += theta * dA[t]; + } + dag.w(spec[0]) += theta * dA[0]; + } + + } + + /* STAGE 3: + * get the gradients from the 1-particle basis gradients and write them + * into the dF/drho derivatives. + */ + /* In order to reuse the original PACE code, we copy the weights back + * into the the PACE datastructure. */ + + for (int idx = 0; idx < num1; idx++) { + int m = dag.Aspec(idx, 3); + if (m >= 0) { + weights(dag.Aspec(idx, 0), // mu + dag.Aspec(idx, 1) - 1, // n + dag.Aspec(idx, 2), // l + m ) += dag.w(idx); + } else { + int factor = (m % 2 == 0 ? 1 : -1); + weights(dag.Aspec(idx, 0), // mu + dag.Aspec(idx, 1) - 1, // n + dag.Aspec(idx, 2), // l + -m ) += factor * dag.w(idx).conjugated(); + } + } + + + /* ------ From here we are now back to the original PACE code ---- */ + +// ==================== FORCES ==================== +#ifdef PRINT_MAIN_STEPS + printf("\nFORCE CALCULATION\n"); + printf("loop over neighbours\n"); +#endif + +// loop over neighbour atoms for force calculations + for (jj = 0; jj < jnum_actual; ++jj) { + mu_j = elements[jj]; + r_hat = rhats[jj]; + inv_r_norm = inv_r_norms[jj]; + + Array2DLM &Y_cache_jj = Y_cache(jj); + Array2DLM &DY_cache_jj = DY_cache(jj); + +#ifdef PRINT_LOOPS_INDICES + printf("\nneighbour atom #%d\n", jj); + printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); +#endif + + forces_calc_neighbour_timer.start(); + + f_ji[0] = f_ji[1] = f_ji[2] = 0; + +//for rank = 1 + for (n = 0; n < nradbasei; ++n) { + if (weights_rank1(mu_j, n) == 0) + continue; + auto &DG = DG_cache(jj, n); + DGR = DG * Y00; + DGR *= weights_rank1(mu_j, n); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); + printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); + printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); + printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); +#endif + f_ji[0] += DGR * r_hat[0]; + f_ji[1] += DGR * r_hat[1]; + f_ji[2] += DGR * r_hat[2]; + } + +//for rank > 1 + for (n = 0; n < nradiali; n++) { + for (l = 0; l <= lmaxi; l++) { + R_over_r = R_cache(jj, n, l) * inv_r_norm; + DR = DR_cache(jj, n, l); + + // for m>=0 + for (m = 0; m <= l; m++) { + ACEComplex w = weights(mu_j, n, l, m); + if (w == 0) + continue; + //counting for -m cases if m>0 + // if (m > 0) w *= 2; // not needed for recursive eval + + DY = DY_cache_jj(l, m); + Y_DR = Y_cache_jj(l, m) * DR; + + grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; + grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; + grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; +#ifdef DEBUG_FORCES_CALCULATIONS + printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, + grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, + grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, + grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); + + printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m, w.real, w.img); + //if (m>0) w*=2; + printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, + w.real_part_product(grad_phi_nlm.a[0]), + w.real_part_product(grad_phi_nlm.a[1]), + w.real_part_product(grad_phi_nlm.a[2]) + ); +#endif +// real-part multiplication only + f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); + f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); + f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); + } + } + } + + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); +#endif + + //hard-core repulsion + DCR = DCR_cache(jj); +#ifdef DEBUG_FORCES_CALCULATIONS + printf("DCR = %f\n",DCR); +#endif + f_ji[0] += dF_drho_core * DCR * r_hat[0]; + f_ji[1] += dF_drho_core * DCR * r_hat[1]; + f_ji[2] += dF_drho_core * DCR * r_hat[2]; +#ifdef PRINT_INTERMEDIATE_VALUES + printf("with core-repulsion\n"); + printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, + f_ji[0], f_ji[1], f_ji[2] + ); + printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); +#endif + + neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; + neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; + neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; + + forces_calc_neighbour_timer.stop(); + }// end loop over neighbour atoms for forces + + forces_calc_loop_timer.stop(); + + //now, energies and forces are ready + //energies(i) = evdwl + rho_core; + e_atom = evdwl_cut; + +#ifdef PRINT_INTERMEDIATE_VALUES + printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); +#endif + per_atom_calc_timer.stop(); +} \ No newline at end of file diff --git a/lib/pace/ace_recursive.h b/lib/pace/ace_recursive.h new file mode 100644 index 0000000000..78e74feb86 --- /dev/null +++ b/lib/pace/ace_recursive.h @@ -0,0 +1,247 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 20.12.2020 + +#ifndef ACE_RECURSIVE_H +#define ACE_RECURSIVE_H + +#include "ace_abstract_basis.h" +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_c_basis.h" +#include "ace_complex.h" +#include "ace_timing.h" +#include "ace_types.h" +#include "ace_evaluator.h" + +#include +#include +#include +#include +#include + +using namespace std; + + +typedef pair, vector > TPARTITION; +typedef list TPARTITIONS; + +typedef map, int> TDAGMAP; + +class ACEDAG { + + TPARTITIONS find_2partitions(vector v); + + void insert_node(TDAGMAP &dagmap, + vector node, + vector c); + + // the following fields are used only for *construction*, not evaluation + int dag_idx; // current index of dag node + Array2D nodes_pre; //TODO: YL: better to use vector<> + Array2D coeffs_pre; //TODO: YL: better to use vector<> + Array1D haschild; //TODO: YL: better to use vector<> + + /* which heuristic to choose for DAG construction? + * 0 : the simple original heuristic + * 1 : prioritize 2-correlation nodes and build the rest from those + */ + int heuristic = 0; + +public: + + ACEDAG() = default; + + void init(Array2D Aspec, Array2D AAspec, + Array1D orders, Array2D coeffs, + int heuristic ); + + Array1D AAbuf; + Array1D w; + + Array2D Aspec; + + // nodes in the graph + Array2D nodes; + Array2D coeffs; + + // total number of nodes in the dag + int num_nodes; + // number of interior nodes (with children) + int num2_int; + // number of leaf nodes (nc = no child) + int num2_leaf; + + + // number of 1-particle basis functions + // (these will be stored in the first num1 entries of AAbuf) + int get_num1() { return Aspec.get_dim(0); }; + // total number of n-correlation basis functions n > 1. + int get_num2() { return num_nodes - get_num1(); }; + int get_num2_int() { return num2_int; }; // with children + int get_num2_leaf() { return num2_leaf; }; // without children + + // debugging tool + void print(); +}; + + +/** + * Recursive Variant of the ACETildeEvaluator; should be 100% compatible + */ +class ACERecursiveEvaluator : public ACEEvaluator { + + /** + * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase] + */ + Array2D weights_rank1 = Array2D("weights_rank1"); + + /** + * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, + * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] + */ + Array4DLM weights = Array4DLM("weights"); + + /** + * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) + * shape:[max_jnum][nradbase] + */ + Array2D DG_cache = Array2D("DG_cache"); + + + /** + * cache for \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D R_cache = Array3D("R_cache"); + /** + * cache for derivatives of \f$ R_{nl}(r)\f$ + * shape:[max_jnum][nradbase][0..lmax] + */ + Array3D DR_cache = Array3D("DR_cache"); + /** + * cache for \f$ Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM Y_cache = Array3DLM("Y_cache"); + /** + * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ + * shape:[max_jnum][0..lmax][m] + */ + Array3DLM DY_cache = Array3DLM("dY_dense_cache"); + + /** + * cache for derivatives of hard-core repulsion + * shape:[max_jnum] + */ + Array1D DCR_cache = Array1D("DCR_cache"); + + /** + * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], + * shape:[func_ms_r_ind] + */ + Array1D dB_flatten = Array1D("dB_flatten"); + + /** + * pointer to the ACEBasisSet object + */ + ACECTildeBasisSet *basis_set = nullptr; + + /** + * Initialize internal arrays according to basis set sizes + * @param basis_set + */ + void init(ACECTildeBasisSet *basis_set, int heuristic); + + /* convert the PACE to the ACE.jl format to prepare for DAG construction*/ + Array2D jl_Aspec; + Array2D jl_AAspec; + Array1D jl_AAspec_flat; + Array1D jl_orders; + Array2D jl_coeffs; + void acejlformat(); + + /* the main event : the computational graph */ + ACEDAG dag; + + bool recursive = true; + +public: + + + ACERecursiveEvaluator() = default; + + explicit ACERecursiveEvaluator(ACECTildeBasisSet &bas, + bool recursive = true) { + set_recursive(recursive); + set_basis(bas); + } + + /** + * set the basis function to the ACE evaluator + * @param bas + */ + void set_basis(ACECTildeBasisSet &bas, int heuristic = 0); + + /** + * The key method to compute energy and forces for atom 'i'. + * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array + * + * @param i atom index + * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] + * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] + * @param jnum number of neighbours of atom_i + * @param jlist array of neighbour indices, shape: [jnum] + */ + void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; + + /** + * Resize all caches over neighbours atoms + * @param max_jnum maximum number of neighbours + */ + void resize_neighbours_cache(int max_jnum) override; + + /******* public functions related to recursive evaluator ********/ + + // print out the DAG for visual inspection + void print_dag() {dag.print();} + + // print out the jl format for visual inspection + // should be converted into a proper test + void test_acejlformat(); + + void set_recursive(bool tf) { recursive = tf; } + + /********************************/ + +}; + + +#endif //ACE_RECURSIVE_H \ No newline at end of file diff --git a/lib/pace/ace_spherical_cart.cpp b/lib/pace/ace_spherical_cart.cpp new file mode 100644 index 0000000000..f1f0fccced --- /dev/null +++ b/lib/pace/ace_spherical_cart.cpp @@ -0,0 +1,221 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Ralf Drautz, Yury Lysogorskiy + +#include + +#include "ace_spherical_cart.h" + +ACECartesianSphericalHarmonics::ACECartesianSphericalHarmonics(LS_TYPE lm) { + init(lm); +} + +void ACECartesianSphericalHarmonics::init(LS_TYPE lm) { + lmax = lm; + + alm.init(lmax, "alm"); + blm.init(lmax, "blm"); + cl.init(lmax + 1); + dl.init(lmax + 1); + + plm.init(lmax, "plm"); + dplm.init(lmax, "dplm"); + + ylm.init(lmax, "ylm"); + dylm.init(lmax, "dylm"); + + pre_compute(); +} + +/** +Destructor for ACECartesianSphericalHarmonics. + +@param None + +@returns None +*/ +ACECartesianSphericalHarmonics::~ACECartesianSphericalHarmonics() {} + + +void ACECartesianSphericalHarmonics::pre_compute() { + + DOUBLE_TYPE a, b; + DOUBLE_TYPE lsq, ld, l1, l2; + DOUBLE_TYPE msq; + + for (LS_TYPE l = 1; l <= lmax; l++) { + lsq = l * l; + ld = 2 * l; + l1 = (4 * lsq - 1); + l2 = lsq - ld + 1; + for (MS_TYPE m = 0; m < l - 1; m++) { + msq = m * m; + a = sqrt((DOUBLE_TYPE(l1)) / (DOUBLE_TYPE(lsq - msq))); + b = -sqrt((DOUBLE_TYPE(l2 - msq)) / (DOUBLE_TYPE(4 * l2 - 1))); + alm(l, m) = a; + blm(l, m) = b; + } + } + + for (LS_TYPE l = 1; l <= lmax; l++) { + cl(l) = -sqrt(1.0 + 0.5 / (DOUBLE_TYPE(l))); + dl(l) = sqrt(DOUBLE_TYPE(2 * (l - 1) + 3)); + } +} + + +void ACECartesianSphericalHarmonics::compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi) { + + // requires -1 <= rz <= 1 , NO CHECKING IS PERFORMED !!!!!!!!! + // prefactors include 1/sqrt(2) factor compared to reference + DOUBLE_TYPE t; + + // l=0, m=0 + //plm(0, 0) = Y00/sq1o4pi; //= sq1o4pi; + plm(0, 0) = Y00; //= 1; + dplm(0, 0) = 0.0; + + if (lmaxi > 0) { + + // l=1, m=0 + plm(1, 0) = Y00 * sq3 * rz; + dplm(1, 0) = Y00 * sq3; + + // l=1, m=1 + plm(1, 1) = -sq3o2 * Y00; + dplm(1, 1) = 0.0; + + // loop l = 2, lmax + for (LS_TYPE l = 2; l <= lmaxi; l++) { + for (MS_TYPE m = 0; m < l - 1; m++) { + plm(l, m) = alm(l, m) * (rz * plm(l - 1, m) + blm(l, m) * plm(l - 2, m)); + dplm(l, m) = alm(l, m) * (plm(l - 1, m) + rz * dplm(l - 1, m) + blm(l, m) * dplm(l - 2, m)); + } + t = dl(l) * plm(l - 1, l - 1); + plm(l, l - 1) = t * rz; + dplm(l, l - 1) = t; + plm(l, l) = cl(l) * plm(l - 1, l - 1); + dplm(l, l) = 0.0; + } + } +} //end compute_barplm + + +void ACECartesianSphericalHarmonics::compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi) { + + // requires rx^2 + ry^2 + rz^2 = 1 , NO CHECKING IS PERFORMED !!!!!!!!! + + DOUBLE_TYPE real; + DOUBLE_TYPE img; + MS_TYPE m; + ACEComplex phase; + ACEComplex phasem, mphasem1; + ACEComplex dyx, dyy, dyz; + ACEComplex rdy; + + phase.real = rx; + phase.img = ry; + //compute barplm + compute_barplm(rz, lmaxi); + + //m = 0 + m = 0; + for (LS_TYPE l = 0; l <= lmaxi; l++) { + + ylm(l, m).real = plm(l, m); + ylm(l, m).img = 0.0; + + dyz.real = dplm(l, m); + rdy.real = dyz.real * rz; + + dylm(l, m).a[0].real = -rdy.real * rx; + dylm(l, m).a[0].img = 0.0; + dylm(l, m).a[1].real = -rdy.real * ry; + dylm(l, m).a[1].img = 0.0; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = 0; + } + //m = 0 + m = 1; + for (LS_TYPE l = 1; l <= lmaxi; l++) { + + ylm(l, m) = phase * plm(l, m); + +// std::cout << "Re ylm(" << l << "," << m <<")= " << ylm(l, m).real << std::endl; +// std::cout << "Im ylm(" << l << "," << m <<")= " << ylm(l, m).img << std::endl; + + dyx.real = plm(l, m); + dyx.img = 0.0; + dyy.real = 0.0; + dyy.img = plm(l, m); + dyz.real = phase.real * dplm(l, m); + dyz.img = phase.img * dplm(l, m); + + rdy.real = rx * dyx.real + +rz * dyz.real; + rdy.img = ry * dyy.img + rz * dyz.img; + + dylm(l, m).a[0].real = dyx.real - rdy.real * rx; + dylm(l, m).a[0].img = -rdy.img * rx; + dylm(l, m).a[1].real = -rdy.real * ry; + dylm(l, m).a[1].img = dyy.img - rdy.img * ry; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = dyz.img - rdy.img * rz; + } + + // m > 1 + phasem = phase; + for (MS_TYPE m = 2; m <= lmaxi; m++) { + + mphasem1.real = phasem.real * DOUBLE_TYPE(m); + mphasem1.img = phasem.img * DOUBLE_TYPE(m); + phasem = phasem * phase; + + for (LS_TYPE l = m; l <= lmaxi; l++) { + + ylm(l, m).real = phasem.real * plm(l, m); + ylm(l, m).img = phasem.img * plm(l, m); + + dyx = mphasem1 * plm(l, m); + dyy.real = -dyx.img; + dyy.img = dyx.real; + dyz = phasem * dplm(l, m); + + rdy.real = rx * dyx.real + ry * dyy.real + rz * dyz.real; + rdy.img = rx * dyx.img + ry * dyy.img + rz * dyz.img; + + dylm(l, m).a[0].real = dyx.real - rdy.real * rx; + dylm(l, m).a[0].img = dyx.img - rdy.img * rx; + dylm(l, m).a[1].real = dyy.real - rdy.real * ry; + dylm(l, m).a[1].img = dyy.img - rdy.img * ry; + dylm(l, m).a[2].real = dyz.real - rdy.real * rz; + dylm(l, m).a[2].img = dyz.img - rdy.img * rz; + } + } + +} + diff --git a/lib/pace/ace_spherical_cart.h b/lib/pace/ace_spherical_cart.h new file mode 100644 index 0000000000..b2a0cb5913 --- /dev/null +++ b/lib/pace/ace_spherical_cart.h @@ -0,0 +1,134 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Ralf Drautz, Yury Lysogorskiy + +#ifndef ACE_SPHERICAL_CART_H +#define ACE_SPHERICAL_CART_H + +#include + +#include "ace_arraynd.h" +#include "ace_array2dlm.h" +#include "ace_complex.h" +#include "ace_types.h" + + +using namespace std; + +const DOUBLE_TYPE sq1o4pi = 0.28209479177387814347; // sqrt(1/(4*pi)) +const DOUBLE_TYPE sq4pi = 3.54490770181103176384; // sqrt(4*pi) +const DOUBLE_TYPE sq3 = 1.73205080756887719318;//sqrt(3), numpy +const DOUBLE_TYPE sq3o2 = 1.22474487139158894067;//sqrt(3/2), numpy + +//definition of common factor for spherical harmonics = Y00 +//const DOUBLE_TYPE Y00 = sq1o4pi; +const DOUBLE_TYPE Y00 = 1; + +/** +Class to store spherical harmonics and their associated functions. \n +All the associated members such as \f$ P_{lm}, Y_{lm}\f$ etc are one dimensional arrays of length (L+1)*(L+2)/2. \n +The value that corresponds to a particular l, m configuration can be accessed through a \code ylm(l,m) \endcode \n +*/ +class ACECartesianSphericalHarmonics { +public: + + /** + int, the number of spherical harmonics to be found + */ + LS_TYPE lmax; + + /** + * Default constructor + */ + ACECartesianSphericalHarmonics() = default; + + /** + * Parametrized constructor. Dynamically initialises all the arrays. + * @param lmax maximum orbital moment + */ + explicit ACECartesianSphericalHarmonics(LS_TYPE lmax); + + /** + * Initialize internal arrays and precompute necessary coefficients + * @param lm maximum orbital moment + */ + void init(LS_TYPE lm); + + /** + * Destructor + */ + ~ACECartesianSphericalHarmonics(); + + /** + * Precompute necessaary helper arrays Precomputes the value of \f$ a_{lm}, b_{lm}, c_l, d_l \f$ + */ + void pre_compute(); + + /** + Function that computes \f$ \bar{P}_{lm} \f$ for the corresponding lmax value + Input is \f$ \hat{r}_z \f$ which is the $z$-component of the bond direction. + + For each \f$ \hat{r}_z \f$, this computes the whole range of \f$ \bar{P}_{lm} \f$ values + and its derivatives upto the lmax specified, which is a member of the class. + + @param rz, DOUBLE_TYPE + + @returns None + */ + void compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi); + + /** + Function that computes \f$ Y_{lm} \f$ for the corresponding lmax value + Input is the bond-directon vector \f$ \hat{r}_x, \hat{r}_y, \hat{r}_z \f$ + + Each \f$ Y_{lm} \f$ value is a ACEComplex object with real and imaginary parts. This function also + finds the derivatives, which are stored in the Dycomponent class, with each component being a + ACEComplex object. + + @param rx, DOUBLE_TYPE + @param ry, DOUBLE_TYPE + @param rz, DOUBLE_TYPE + @param lmaxi, int + */ + void compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi); + + Array2DLM alm; + Array2DLM blm; + Array1D cl; + Array1D dl; + + Array2DLM plm; + Array2DLM dplm; + + Array2DLM ylm; ///< Values of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call + Array2DLM dylm;///< Values of gradients of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call + +}; + + +#endif diff --git a/lib/pace/ace_timing.h b/lib/pace/ace_timing.h new file mode 100644 index 0000000000..7f5243eb99 --- /dev/null +++ b/lib/pace/ace_timing.h @@ -0,0 +1,126 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Yury Lysogorskiy on 19.02.20. + +#ifndef ACE_TIMING_H +#define ACE_TIMING_H + +#include + +using namespace std::chrono; +using Clock = std::chrono::high_resolution_clock; +using TimePoint = std::chrono::time_point; +using Duration = Clock::duration; + +////////////////////////////////////////// +#ifdef FINE_TIMING +/** + * Helper class for timing the code. + * The timer should be initialized to reset measured time and + * then call "start" and "stop" before and after measured code. + * The measured time is stored in "duration" variable + */ +struct ACETimer { + Duration duration; ///< measured duration + TimePoint start_moment; ///< start moment of current measurement + + ACETimer() { init(); }; + + /** + * Reset timer + */ + void init() { duration = std::chrono::nanoseconds(0); } + + /** + * Start timer + */ + void start() { start_moment = Clock::now(); } + + /** + * Stop timer, update measured "duration" + */ + void stop() { duration += Clock::now() - start_moment; } + + /** + * Get duration in microseconds + */ + long as_microseconds() { return std::chrono::duration_cast(duration).count(); } + + /** + * Get duration in nanoseconds + */ + long as_nanoseconds() { return std::chrono::duration_cast(duration).count(); } + +}; + +#else // EMPTY Definitions +/** + * Helper class for timing the code. + * The timer should be initialized to reset measured time and + * then call "start" and "stop" before and after measured code. + * The measured time is stored in "duration" variable + */ +struct ACETimer { + Duration duration; ///< measured duration + TimePoint start_moment; ///< start moment of current measurement + + ACETimer() {}; + + /** + * Reset timer + */ + void init() {} + + /** + * Start timer + */ + void start() {} + + /** + * Stop timer, update measured "duration" + */ + void stop() {} + + /** + * Get duration in microseconds + */ + long as_microseconds() {return 0; } + + /** + * Get duration in nanoseconds + */ + long as_nanoseconds() {return 0; } + +}; + +#endif +////////////////////////////////////////// + + +#endif //ACE_TIMING_H diff --git a/lib/pace/ace_types.h b/lib/pace/ace_types.h new file mode 100644 index 0000000000..f9b3cf7267 --- /dev/null +++ b/lib/pace/ace_types.h @@ -0,0 +1,45 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Yury Lysogorskiy on 20.01.20. + +#ifndef ACE_TYPES_H +#define ACE_TYPES_H + +typedef char RANK_TYPE; +typedef int SPECIES_TYPE; +typedef short int NS_TYPE; +typedef short int LS_TYPE; + +typedef short int DENSITY_TYPE; + +typedef short int MS_TYPE; + +typedef short int SHORT_INT_TYPE; +typedef double DOUBLE_TYPE; + +#endif \ No newline at end of file diff --git a/lib/pace/ace_version.h b/lib/pace/ace_version.h new file mode 100644 index 0000000000..9d61e5c505 --- /dev/null +++ b/lib/pace/ace_version.h @@ -0,0 +1,39 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Lysogorskiy Yury on 07.04.2020. + +#ifndef ACE_VERSION_H +#define ACE_VERSION_H + +#define VERSION_YEAR 2021 +#define VERSION_MONTH 2 +#define VERSION_DAY 3 + +#endif //ACE_VERSION_Hls + diff --git a/lib/pace/ships_radial.cpp b/lib/pace/ships_radial.cpp new file mode 100644 index 0000000000..e948f03f21 --- /dev/null +++ b/lib/pace/ships_radial.cpp @@ -0,0 +1,388 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + +// Created by Christoph Ortner on 03.06.2020 + +#include "ships_radial.h" + +#include +#include +#include + + +using namespace std; + +void SHIPsRadPolyBasis::_init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, + DOUBLE_TYPE xl, DOUBLE_TYPE xr, + int pl, int pr, size_t maxn) { + this->p = p; + this->r0 = r0; + this->rcut = rcut; + this->xl = xl; + this->xr = xr; + this->pl = pl; + this->pr = pr; + this->maxn = maxn; + this->A.resize(maxn); + this->B.resize(maxn); + this->C.resize(maxn); + this->P.resize(maxn); + this->dP_dr.resize(maxn); +} + + +void SHIPsRadPolyBasis::fread(FILE *fptr) +{ + int res; //for fscanf result + int maxn, p, pl, pr, ntests; + double r0, xl, xr, a, b, c, rcut; + + // transform parameters + res = fscanf(fptr, "transform parameters: p=%d r0=%lf\n", &p, &r0); + if (res != 2) + throw invalid_argument("Couldn't read line: transform parameters: p=%d r0=%lf"); + // cutoff parameters + res = fscanf(fptr, "cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d\n", + &rcut, &xl, &xr, &pl, &pr); + if (res != 5) + throw invalid_argument("Couldn't read cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d"); + // basis size + res = fscanf(fptr, "recursion coefficients: maxn = %d\n", &maxn); + if (res != 1) + throw invalid_argument("Couldn't read recursion coefficients: maxn = %d"); + // initialize and allocate + this->_init(r0, p, rcut, xl, xr, pl, pr, maxn); + + // read basis coefficients + for (int i = 0; i < maxn; i++) { + res = fscanf(fptr, " %lf %lf %lf\n", &a, &b, &c); + if (res != 3) + throw invalid_argument("Couldn't read line: A_n B_n C_n"); + this->A(i) = DOUBLE_TYPE(a); + this->B(i) = DOUBLE_TYPE(b); + this->C(i) = DOUBLE_TYPE(c); + } + + // // check there are no consistency tests (I don't have time to fix this now) + // res = fscanf(fptr, "tests: ntests = %d\n", &ntests); + // if (res != 1) + // throw invalid_argument("Couldn't read line: tests: ntests = %d"); + // if (ntests != 0) + // throw invalid_argument("must have ntests = 0!"); + + // --------------------------------------------------------------------- + // run the consistency test this could be moved into a separate function + double r, Pn, dPn; + double err = 0.0; + + res = fscanf(fptr, "tests: ntests = %d\n", &ntests); + if (res != 1) + throw invalid_argument("Couldn't read line: tests: ntests = %d"); + for (size_t itest = 0; itest < ntests; itest++) { + // read an r argument + res = fscanf(fptr, " r=%lf\n", &r); + // printf("r = %lf \n", r); + if (res != 1) + throw invalid_argument("Couldn't read line: r=%lf"); + // printf("test %d, r=%f, maxn=%d \n", itest, r, maxn); + // evaluate the basis + this->calcP(r, maxn, SPECIES_TYPE(0), SPECIES_TYPE(0)); + // compare against the stored values + for (size_t n = 0; n < maxn; n++) { + res = fscanf(fptr, " %lf %lf\n", &Pn, &dPn); + if (res != 2) + throw invalid_argument("Couldn't read test value line: %lf %lf"); + err = max(err, abs(Pn - this->P(n)) + abs(dPn - this->dP_dr(n))); + // printf(" %d %e %e \n", int(n), + // abs(Pn - this->P(n)), + // abs(dPn - this->dP_dr(n))); + } + } + if (ntests > 0) + printf("Maximum Test error = %e\n", err); + // --------------------------------------------------------------------- + +} + + + + +size_t SHIPsRadPolyBasis::get_maxn() +{ + return this->maxn; +} + + +// Julia code: ((1+r0)/(1+r))^p +void SHIPsRadPolyBasis::transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const { + x_out = pow((1 + r0) / (1 + r), p); // ==pow( (1 + r) / (1 + r0), -p ); + dx_out = -p * pow((1 + r) / (1 + r0), -p - 1) / (1 + r0); +} + +void SHIPsRadPolyBasis::fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const { + if ( ((x < xl) && (pl > 0)) || ((x > xr) && (pr > 0)) ) { + f_out = 0.0; + df_out = 0.0; + } else { + f_out = pow(x - xl, pl) * pow(x - xr, pr); + df_out = pl * pow(x - xl, pl - 1) * pow(x - xr, pr) + pow(x - xl, pl) * pr * pow(x - xr, pr - 1); + } +} + + /* ------------------------------------------------------------------------ +Julia Code +P[1] = J.A[1] * _fcut_(J.pl, J.tl, J.pr, J.tr, t) +if length(J) == 1; return P; end +P[2] = (J.A[2] * t + J.B[2]) * P[1] +@inbounds for n = 3:length(J) + P[n] = (J.A[n] * t + J.B[n]) * P[n-1] + J.C[n] * P[n-2] +end +return P +------------------------------------------------------------------------ */ + +void SHIPsRadPolyBasis::calcP(DOUBLE_TYPE r, size_t maxn, + SPECIES_TYPE z1, SPECIES_TYPE z2) { + if (maxn > this->maxn) + throw invalid_argument("Given maxn couldn't be larger than global maxn"); + + if (maxn > P.get_size()) + throw invalid_argument("Given maxn couldn't be larger than global length of P"); + + DOUBLE_TYPE x, dx_dr; // dx -> dx/dr + transform(r, x, dx_dr); + // printf("r = %f, x = %f, fcut = %f \n", r, x, fcut(x)); + DOUBLE_TYPE f, df_dx; + fcut(x, f, df_dx); // df -> df/dx + + //fill with zeros + P.fill(0); + dP_dr.fill(0); + + P(0) = A(0) * f; + dP_dr(0) = A(0) * df_dx * dx_dr; // dP/dr; chain rule: df_cut/dr = df_cut/dx * dx/dr + if (maxn > 0) { + P(1) = (A(1) * x + B(1)) * P(0); + dP_dr(1) = A(1) * dx_dr * P(0) + (A(1) * x + B(1)) * dP_dr(0); + } + for (size_t n = 2; n < maxn; n++) { + P(n) = (A(n) * x + B(n)) * P(n - 1) + C(n) * P(n - 2); + dP_dr(n) = A(n) * dx_dr * P(n - 1) + (A(n) * x + B(n)) * dP_dr(n - 1) + C(n) * dP_dr(n - 2); + } +} + + +// ==================================================================== + + +bool SHIPsRadialFunctions::has_pair() { + return this->haspair; +} + +void SHIPsRadialFunctions::load(string fname) { + FILE * fptr = fopen(fname.data(), "r"); + size_t res = fscanf(fptr, "radbasename=ACE.jl.Basic\n"); + if (res != 0) + throw("SHIPsRadialFunctions::load : couldnt read radbasename=ACE.jl.Basic"); + this->fread(fptr); + fclose(fptr); +} + +void SHIPsRadialFunctions::fread(FILE *fptr){ + int res; + size_t maxn; + char hasE0, haspair; + DOUBLE_TYPE c; + + // check whether we have a pair potential + res = fscanf(fptr, "haspair: %c\n", &haspair); + if (res != 1) + throw("SHIPsRadialFunctions::load : couldn't read haspair"); + + // read the radial basis + this->radbasis.fread(fptr); + + // read the pair potential + if (haspair == 't') { + this->haspair=true; + fscanf(fptr, "begin repulsive potential\n"); + fscanf(fptr, "begin polypairpot\n"); + // read the basis parameters + pairbasis.fread(fptr); + maxn = pairbasis.get_maxn(); + // read the coefficients + fscanf(fptr, "coefficients\n"); + paircoeffs.resize(maxn); + for (size_t n = 0; n < maxn; n++) { + fscanf(fptr, "%lf\n", &c); + paircoeffs(n) = c; + } + fscanf(fptr, "end polypairpot\n"); + // read the spline parameters + fscanf(fptr, "spline parameters\n"); + fscanf(fptr, " e_0 + B exp(-A*(r/ri-1)) * (ri/r)\n"); + fscanf(fptr, "ri=%lf\n", &(this->ri)); + fscanf(fptr, "e0=%lf\n", &(this->e0)); + fscanf(fptr, "A=%lf\n", &(this->A)); + fscanf(fptr, "B=%lf\n", &(this->B)); + fscanf(fptr, "end repulsive potential\n"); + } +} + + +size_t SHIPsRadialFunctions::get_maxn() +{ + return this->radbasis.get_maxn(); +} + +DOUBLE_TYPE SHIPsRadialFunctions::get_rcut() +{ + return max(radbasis.rcut, pairbasis.rcut); +} + + +void SHIPsRadialFunctions::fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { + radbasis.calcP(r, maxn, z1, z2); + for (NS_TYPE n = 0; n < maxn; n++) { + gr(n) = radbasis.P(n); + dgr(n) = radbasis.dP_dr(n); + } +} + + +void SHIPsRadialFunctions::fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { + radbasis.calcP(r, maxn, z1, z2); + for (NS_TYPE n = 0; n < maxn; n++) { + for (LS_TYPE l = 0; l <= lmax; l++) { + fr(n, l) = radbasis.P(n); + dfr(n, l) = radbasis.dP_dr(n); + } + } +} + + +void SHIPsRadialFunctions::setuplookupRadspline() { +} + + +void SHIPsRadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, + SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, string radbasename) { + //mimic ACERadialFunctions::init + this->nradbase = nradb; + this->lmax = lmax; + this->nradial = nradial; + this->deltaSplineBins = deltaSplineBins; + this->nelements = nelements; + this->cutoff = cutoff; + this->radbasename = radbasename; + + gr.init(nradbase, "gr"); + dgr.init(nradbase, "dgr"); + + + fr.init(nradial, lmax + 1, "fr"); + dfr.init(nradial, lmax + 1, "dfr"); + + splines_gk.init(nelements, nelements, "splines_gk"); + splines_rnl.init(nelements, nelements, "splines_rnl"); + splines_hc.init(nelements, nelements, "splines_hc"); + + lambda.init(nelements, nelements, "lambda"); + lambda.fill(1.); + + cut.init(nelements, nelements, "cut"); + cut.fill(1.); + + dcut.init(nelements, nelements, "dcut"); + dcut.fill(1.); + + crad.init(nelements, nelements, (lmax + 1), nradial, nradbase, "crad"); + crad.fill(0.); + + //hard-core repulsion + prehc.init(nelements, nelements, "prehc"); + prehc.fill(0.); + + lambdahc.init(nelements, nelements, "lambdahc"); + lambdahc.fill(1.); +} + + +void SHIPsRadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, bool calc_second_derivatives) { + if (calc_second_derivatives) + throw invalid_argument("SHIPsRadialFunctions has not `calc_second_derivatives` option"); + + radbasis.calcP(r, nradbase_c, mu_i, mu_j); + for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { + gr(nr) = radbasis.P(nr); + dgr(nr) = radbasis.dP_dr(nr); + } + for (NS_TYPE nr = 0; nr < nradial_c; nr++) { + for (LS_TYPE l = 0; l <= this->lmax; l++) { + fr(nr, l) = radbasis.P(nr); + dfr(nr, l) = radbasis.dP_dr(nr); + } + } + + if (this->has_pair()) + this->evaluate_pair(r, mu_i, mu_j); + else { + cr = 0; + dcr = 0; + } +} + +void SHIPsRadialFunctions::evaluate_pair(DOUBLE_TYPE r, + SPECIES_TYPE mu_i, + SPECIES_TYPE mu_j, + bool calc_second_derivatives) { + // spline_hc.calcSplines(r); + // cr = spline_hc.values(0); + // dcr = spline_hc.derivatives(0); + + // the outer polynomial potential + if (r > ri) { + pairbasis.calcP(r, pairbasis.get_maxn(), mu_i, mu_j); + cr = 0; + dcr = 0; + for (size_t n = 0; n < pairbasis.get_maxn(); n++) { + cr += paircoeffs(n) * pairbasis.P(n); + dcr += paircoeffs(n) * pairbasis.dP_dr(n); + } + } + else { // the repulsive core part + cr = e0 + B * exp(-A * (r/ri - 1)) * (ri/r); + dcr = B * exp( - A * (r/ri-1) ) * ri * ( - A / ri / r - 1/(r*r) ); + } + // fix double-counting + cr *= 0.5; + dcr *= 0.5; +} + + + diff --git a/lib/pace/ships_radial.h b/lib/pace/ships_radial.h new file mode 100644 index 0000000000..60a82448cd --- /dev/null +++ b/lib/pace/ships_radial.h @@ -0,0 +1,158 @@ +/* + * Performant implementation of atomic cluster expansion and interface to LAMMPS + * + * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + * + * ^1: Ruhr-University Bochum, Bochum, Germany + * ^2: University of Cambridge, Cambridge, United Kingdom + * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + * ^4: University of British Columbia, Vancouver, BC, Canada + * + * + * See the LICENSE file. + * This FILENAME is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * You should have received a copy of the GNU General Public License + * along with this program. If not, see . + */ + + +// Created by Christoph Ortner on 03.06.2020 + +#ifndef SHIPs_RADIAL_FUNCTIONS_H +#define SHIPs_RADIAL_FUNCTIONS_H + +#include "ace_arraynd.h" +#include "ace_types.h" +#include "ace_radial.h" + +class SHIPsRadPolyBasis { + +public: + + // transform parameters + int p = 0; + DOUBLE_TYPE r0 = 0.0; + + // cutoff parameters + DOUBLE_TYPE rcut = 0.0; + DOUBLE_TYPE xl = 0.0; + DOUBLE_TYPE xr = 0.0; + int pl = 0; + int pr = 0; + + // basis size + size_t maxn = 0; + + // recursion parameters + Array1D A = Array1D("SHIPs radial basis: A"); + Array1D B = Array1D("SHIPs radial basis: B"); + Array1D C = Array1D("SHIPs radial basis: C"); + + // temporary storage for evaluating the basis + Array1D P = Array1D("SHIPs radial basis: P"); + Array1D dP_dr = Array1D("SHIPs radial basis: dP"); + +////////////////////////////////// + + SHIPsRadPolyBasis() = default; + + ~SHIPsRadPolyBasis() = default; + + // distance transform + void transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const; + + // cutoff function + void fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const; + + void fread(FILE *fptr); + + void _init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, + DOUBLE_TYPE xl, DOUBLE_TYPE xr, + int pl, int pr, size_t maxn); + + void calcP(DOUBLE_TYPE r, size_t maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); + + size_t get_maxn(); + +}; + + + + +class SHIPsRadialFunctions : public AbstractRadialBasis { +public: + + // radial basis + SHIPsRadPolyBasis radbasis; + + // pair potential basis + bool haspair = false; + SHIPsRadPolyBasis pairbasis; + + // pair potential coefficients + Array1D paircoeffs = Array1D("SHIPs pairpot coeffs: paircoeffs"); + + // spline parameters for repulsive core + DOUBLE_TYPE ri = 0.0; + DOUBLE_TYPE e0 = 0.0; + DOUBLE_TYPE A = 0.0; + DOUBLE_TYPE B = 0.0; + +////////////////////////////////// + + SHIPsRadialFunctions() = default; + + ~SHIPsRadialFunctions() override = default; + + + void fread(FILE *fptr); + + void load(string fname); + + size_t get_maxn(); + DOUBLE_TYPE get_rcut(); + + bool has_pair(); + + void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, + DOUBLE_TYPE cutoff, + string radbasename) override; + + void + evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false) override; + + void + evaluate_pair(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, + bool calc_second_derivatives = false); + + void setuplookupRadspline() override; + + SHIPsRadialFunctions *clone() const override { + return new SHIPsRadialFunctions(*this); + }; + + /** + * Helper method, that populate `fr` and `dfr` 2D-arrays (n,l) with P(n), dP_dr for given coordinate r + * @param r + * @param maxn + * @param z1 + * @param z2 + */ + void fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); + + void fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); +}; + + +#endif diff --git a/src/Makefile b/src/Makefile index a63c49e344..bec0a2b16b 100644 --- a/src/Makefile +++ b/src/Makefile @@ -63,7 +63,7 @@ PACKLIB = compress gpu kim kokkos latte message mpiio mscg poems \ python voronoi \ user-adios user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \ user-netcdf user-plumed user-qmmm user-quip user-scafacos \ - user-smd user-vtk user-mesont + user-smd user-vtk user-mesont user-pace PACKSYS = compress mpiio python user-lb @@ -71,7 +71,7 @@ PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ - user-smd user-vtk + user-smd user-vtk user-pace PACKALL = $(PACKAGE) $(PACKUSER) diff --git a/src/USER-PACE/Install.sh b/src/USER-PACE/Install.sh new file mode 100644 index 0000000000..4d87b0e3ed --- /dev/null +++ b/src/USER-PACE/Install.sh @@ -0,0 +1,68 @@ +# Install.sh file that integrates the settings from the lib folder into the conventional build process (make build?) + +# COPIED FROM src/KIM/Install.sh: + +# # Install/unInstall package files in LAMMPS +# # mode = 0/1/2 for uninstall/install/update + +# mode=$1 + +# # enforce using portable C locale +# LC_ALL=C +# export LC_ALL + +# # arg1 = file, arg2 = file it depends on + +# action () { +# if (test $mode = 0) then +# rm -f ../$1 +# elif (! cmp -s $1 ../$1) then +# if (test -z "$2" || test -e ../$2) then +# cp $1 .. +# if (test $mode = 2) then +# echo " updating src/$1" +# fi +# fi +# elif (test -n "$2") then +# if (test ! -e ../$2) then +# rm -f ../$1 +# fi +# fi +# } + +# # all package files with no dependencies + +# for file in *.cpp *.h; do +# test -f ${file} && action $file +# done + +# # edit 2 Makefile.package files to include/exclude package info + +# if (test $1 = 1) then + +# if (test -e ../Makefile.package) then +# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package +# sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package +# sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package +# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package +# fi + +# if (test -e ../Makefile.package.settings) then +# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings +# # multiline form needed for BSD sed on Macs +# sed -i -e '4 i \ +# include ..\/..\/lib\/kim\/Makefile.lammps +# ' ../Makefile.package.settings +# fi + +# elif (test $1 = 0) then + +# if (test -e ../Makefile.package) then +# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package +# fi + +# if (test -e ../Makefile.package.settings) then +# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings +# fi + +# fi diff --git a/src/USER-PACE/LICENSE b/src/USER-PACE/LICENSE new file mode 100644 index 0000000000..f288702d2f --- /dev/null +++ b/src/USER-PACE/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp new file mode 100644 index 0000000000..a515b7b4b0 --- /dev/null +++ b/src/USER-PACE/pair_pace.cpp @@ -0,0 +1,458 @@ +/* +Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + +^1: Ruhr-University Bochum, Bochum, Germany +^2: University of Cambridge, Cambridge, United Kingdom +^3: Sandia National Laboratories, Albuquerque, New Mexico, USA +^4: University of British Columbia, Vancouver, BC, Canada + + + This FILENAME is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + + +// +// Created by Lysogorskiy Yury on 27.02.20. +// + +#include +#include +#include +#include +#include "pair_pace.h" +#include "atom.h" +#include "neighbor.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "force.h" +#include "comm.h" +#include "memory.h" +#include "error.h" + + +#include "math_const.h" + +#include "ace_version.h" + +using namespace LAMMPS_NS; +using namespace MathConst; + +#define MAXLINE 1024 +#define DELTA 4 + +//added YL + +//keywords for ACE evaluator style +#define RECURSIVE_KEYWORD "recursive" +#define PRODUCT_KEYWORD "product" + + +int elements_num_pace = 104; +char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", + "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", + "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", + "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", + "Te", "I", "Xe", "Cs", "Ba", "La", "Ce", "Pr", "Nd", "Pm", "Sm", "Eu", "Gd", + "Tb", "Dy", "Ho", "Er", "Tm", "Yb", "Lu", "Hf", "Ta", "W", "Re", "Os", "Ir", + "Pt", "Au", "Hg", "Tl", "Pb", "Bi", "Po", "At", "Rn", "Fr", "Ra", "Ac", "Th", + "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" +}; + +int AtomicNumberByName_pace(char *elname) { + for (int i = 1; i < elements_num_pace; i++) + if (strcmp(elname, elements_pace[i]) == 0) + return i; + return -1; +} + + +/* ---------------------------------------------------------------------- */ +PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { + //single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; + + nelements = 0; + + ace = NULL; + potential_file_name = NULL; + elements = NULL; + map = NULL; +} + +/* ---------------------------------------------------------------------- + check if allocated, since class can be destructed when incomplete +------------------------------------------------------------------------- */ + +PairPACE::~PairPACE() { + if (copymode) return; + + if (elements) + for (int i = 0; i < nelements; i++) delete[] elements[i]; + delete[] elements; + + + delete[] potential_file_name; + + delete basis_set; + delete ace; + + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(map); + memory->destroy(scale); + } +} + +/* ---------------------------------------------------------------------- */ + +void PairPACE::compute(int eflag, int vflag) { + int i, j, ii, jj, inum, jnum; + double delx, dely, delz, evdwl; + double fij[3]; + int *ilist, *jlist, *numneigh, **firstneigh; + + ev_init(eflag, vflag); + + // downwards modified by YL + + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; + + // number of atoms in cell + int nlocal = atom->nlocal; + + int newton_pair = force->newton_pair; + + // number of atoms including ghost atoms + int nall = nlocal + atom->nghost; + + // inum: length of the neighborlists list + inum = list->inum; + + // ilist: list of "i" atoms for which neighbor lists exist + ilist = list->ilist; + + //numneigh: the length of each these neigbor list + numneigh = list->numneigh; + + // the pointer to the list of neighbors of "i" + firstneigh = list->firstneigh; + + if (inum != nlocal) { + char str[128]; + snprintf(str,128,"inum: %d nlocal: %d are different",inum, nlocal); + error->all(FLERR,str); + } + + + // Aidan Thompson told RD (26 July 2019) that practically always holds: + // inum = nlocal + // i = ilist(ii) < inum + // j = jlist(jj) < nall + // neighborlist contains neighbor atoms plus skin atoms, + // skin atoms can be removed by setting skin to zero but here + // they are disregarded anyway + + + //determine the maximum number of neighbours + int max_jnum = -1; + int nei = 0; + for (ii = 0; ii < list->inum; ii++) { + i = ilist[ii]; + jnum = numneigh[i]; + nei = nei + jnum; + if (jnum > max_jnum) + max_jnum = jnum; + } + + ace->resize_neighbours_cache(max_jnum); + + //loop over atoms + for (ii = 0; ii < list->inum; ii++) { + i = list->ilist[ii]; + const int itype = type[i]; + + const double xtmp = x[i][0]; + const double ytmp = x[i][1]; + const double ztmp = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // checking if neighbours are actually within cutoff range is done inside compute_atom + // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom + // by using 'ace->element_type_mapping' array + // x: [r0 ,r1, r2, ..., r100] + // i = 0 ,1 + // jnum(0) = 50 + // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] + try { + ace->compute_atom(i, x, type, jnum, jlist); + } catch (exception &e) { + error->all(FLERR, e.what()); + exit(EXIT_FAILURE); + } + // 'compute_atom' will update the `ace->e_atom` and `ace->neighbours_forces(jj, alpha)` arrays + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + const int jtype = type[j]; + j &= NEIGHMASK; + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + + fij[0] = scale[itype][jtype]*ace->neighbours_forces(jj, 0); + fij[1] = scale[itype][jtype]*ace->neighbours_forces(jj, 1); + fij[2] = scale[itype][jtype]*ace->neighbours_forces(jj, 2); + + + f[i][0] += fij[0]; + f[i][1] += fij[1]; + f[i][2] += fij[2]; + f[j][0] -= fij[0]; + f[j][1] -= fij[1]; + f[j][2] -= fij[2]; + + // tally per-atom virial contribution + if (vflag) + ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, + fij[0], fij[1], fij[2], + -delx, -dely, -delz); + } + + // tally energy contribution + if (eflag) { + // evdwl = energy of atom I + evdwl = scale[1][1]*ace->e_atom; + ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); + } + } + + if (vflag_fdotr) virial_fdotr_compute(); + + + // end modifications YL +} + +/* ---------------------------------------------------------------------- */ + +void PairPACE::allocate() { + allocated = 1; + int n = atom->ntypes; + + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(map, n + 1, "pair:map"); + memory->create(scale, n + 1, n + 1,"pair:scale"); +} + +/* ---------------------------------------------------------------------- + global settings +------------------------------------------------------------------------- */ + +void PairPACE::settings(int narg, char **arg) { + if (narg > 1) { + error->all(FLERR, + "Illegal pair_style command. Correct form:\n\tpair_style pace\nor\n\tpair_style pace "); + error->all(FLERR, RECURSIVE_KEYWORD); + error->all(FLERR, "or\n\tpair_style pace "); + error->all(FLERR, PRODUCT_KEYWORD); + } + recursive = true; // default evaluator style: RECURSIVE + if (narg > 0) { + if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) + recursive = true; + else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { + recursive = false; + } else { + error->all(FLERR, + "Illegal pair_style command: pair_style pace "); + error->all(FLERR, arg[0]); + error->all(FLERR, "\nCorrect form:\n\tpair_style pace\nor\n\tpair_style pace recursive"); + } + } + + if (comm->me == 0) { + if (screen) fprintf(screen, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); + if (logfile) fprintf(logfile, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); + + if (recursive) { + if (screen) fprintf(screen, "Recursive evaluator is used\n"); + if (logfile) fprintf(logfile, "Recursive evaluator is used\n"); + } else { + if (screen) fprintf(screen, "Product evaluator is used\n"); + if (logfile) fprintf(logfile, "Product evaluator is used\n"); + } + } + + +} + +/* ---------------------------------------------------------------------- + set coeffs for one or more type pairs +------------------------------------------------------------------------- */ + +void PairPACE::coeff(int narg, char **arg) { + + if (narg < 4) + error->all(FLERR, + "Incorrect args for pair coefficients. Correct form:\npair_coeff * * elem1 elem2 ..."); + + if (!allocated) allocate(); + + //number of provided elements in pair_coeff line + int ntypes_coeff = narg - 3; + + if (ntypes_coeff != atom->ntypes) { + char error_message[1024]; + snprintf(error_message, 1024, + "Incorrect args for pair coefficients. You provided %d elements in pair_coeff, but structure has %d atom types", + ntypes_coeff, atom->ntypes); + error->all(FLERR, error_message); + } + + char *type1 = arg[0]; + char *type2 = arg[1]; + char *potential_file_name = arg[2]; + char **elemtypes = &arg[3]; + + // insure I,J args are * * + + if (strcmp(type1, "*") != 0 || strcmp(type2, "*") != 0) + error->all(FLERR, "Incorrect args for pair coefficients"); + + + //load potential file + basis_set = new ACECTildeBasisSet(); + if (comm->me == 0) { + if (screen) fprintf(screen, "Loading %s\n", potential_file_name); + if (logfile) fprintf(logfile, "Loading %s\n", potential_file_name); + } + basis_set->load(potential_file_name); + + if (comm->me == 0) { + if (screen) fprintf(screen, "Total number of basis functions\n"); + if (logfile) fprintf(logfile, "Total number of basis functions\n"); + + for (SPECIES_TYPE mu = 0; mu < basis_set->nelements; mu++) { + int n_r1 = basis_set->total_basis_size_rank1[mu]; + int n = basis_set->total_basis_size[mu]; + if (screen) fprintf(screen, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); + if (logfile) fprintf(logfile, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); + } + } + + // read args that map atom types to pACE elements + // map[i] = which element the Ith atom type is, -1 if not mapped + // map[0] is not used + + ace = new ACERecursiveEvaluator(); + ace->set_recursive(recursive); + ace->element_type_mapping.init(atom->ntypes + 1); + + for (int i = 1; i <= atom->ntypes; i++) { + char *elemname = elemtypes[i - 1]; + int atomic_number = AtomicNumberByName_pace(elemname); + if (atomic_number == -1) { + char error_msg[1024]; + snprintf(error_msg, 1024, "String '%s' is not a valid element\n", elemname); + error->all(FLERR, error_msg); + } + SPECIES_TYPE mu = basis_set->get_species_index_by_name(elemname); + if (mu != -1) { + if (comm->me == 0) { + if (screen) + fprintf(screen, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); + if (logfile) + fprintf(logfile, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); + } + map[i] = mu; + ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator + } else { + char error_msg[1024]; + snprintf(error_msg, 1024, "Element %s is not supported by ACE-potential from file %s", elemname, + potential_file_name); + error->all(FLERR, error_msg); + } + } + + // clear setflag since coeff() called once with I,J = * * + int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + setflag[i][j] = 1; + scale[i][j] = 1.0; + } + } + + // set setflag i,j for type pairs where both are mapped to elements + + int count = 1; + for (int i = 1; i <= n; i++) + for (int j = i; j <= n; j++) + if (map[i] >= 0 && map[j] >= 0) { + setflag[i][j] = 1; + count++; + } + + if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); + + ace->set_basis(*basis_set, 1); +} + +/* ---------------------------------------------------------------------- + init specific to this pair style +------------------------------------------------------------------------- */ + +void PairPACE::init_style() { + if (atom->tag_enable == 0) + error->all(FLERR, "Pair style pACE requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR, "Pair style pACE requires newton pair on"); + + // request a full neighbor list + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; +} + +/* ---------------------------------------------------------------------- + init for one type pair i,j and corresponding j,i +------------------------------------------------------------------------- */ + +double PairPACE::init_one(int i, int j) { + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + //cutoff from the basis set's radial functions settings + scale[j][i] = scale[i][j]; + return basis_set->radial_functions->cut(map[i], map[j]); +} + +/* ---------------------------------------------------------------------- + extract method for extracting value of scale variable + ---------------------------------------------------------------------- */ +void *PairPACE::extract(const char *str, int &dim) +{ + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return NULL; +} + diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h new file mode 100644 index 0000000000..3fccbd98f0 --- /dev/null +++ b/src/USER-PACE/pair_pace.h @@ -0,0 +1,97 @@ +/* +Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, + Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, + Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 + +^1: Ruhr-University Bochum, Bochum, Germany +^2: University of Cambridge, Cambridge, United Kingdom +^3: Sandia National Laboratories, Albuquerque, New Mexico, USA +^4: University of British Columbia, Vancouver, BC, Canada + + + This FILENAME is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + + +// +// Created by Lysogorskiy Yury on 27.02.20. +// + + +#ifdef PAIR_CLASS + +PairStyle(pace,PairPACE) + +#else + +#ifndef LMP_PAIR_PACE_H +#define LMP_PAIR_PACE_H + +#include "pair.h" +#include "ace_evaluator.h" +#include "ace_recursive.h" +#include "ace_c_basis.h" + +namespace LAMMPS_NS { + + class PairPACE : public Pair { + public: + PairPACE(class LAMMPS *); + + virtual ~PairPACE(); + + virtual void compute(int, int); + + void settings(int, char **); + + void coeff(int, char **); + + virtual void init_style(); + + double init_one(int, int); + + void *extract(const char *, int &); + + // virtual double memory_usage(); + + protected: + ACECTildeBasisSet *basis_set = nullptr; + + ACERecursiveEvaluator *ace = nullptr; + + char *potential_file_name; + + virtual void allocate(); + + void read_files(char *, char *); + + inline int equal(double *x, double *y); + + + double rcutmax; // max cutoff for all elements + int nelements; // # of unique elements + char **elements; // names of unique elements + + int *map; // mapping from atom types to elements + int *jlist_local; + int *type_local; + double **scale; + + bool recursive = false; // "recursive" option for ACERecursiveEvaluator + }; + +} + +#endif +#endif \ No newline at end of file From 3de33027677ec318fe2d0f2f80a63ac35671ca07 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 12:20:24 +0200 Subject: [PATCH 024/100] remove source files from lib/pace; add lib/pace/Install.py to automatically download the source files from github/ICAMS/lammps-user-pace; add lib/pace/CMakeLists.txt to build libpace.a add lib/pace/README update src/USER-PACE/Install.sh --- lib/pace/CMakeLists.txt | 19 + lib/pace/Install.py | 112 +- lib/pace/LICENSE | 674 ----------- lib/pace/README | 9 + lib/pace/ace_abstract_basis.cpp | 184 --- lib/pace/ace_abstract_basis.h | 169 --- lib/pace/ace_array2dlm.h | 579 --------- lib/pace/ace_arraynd.h | 1949 ------------------------------- lib/pace/ace_c_basis.cpp | 980 ---------------- lib/pace/ace_c_basis.h | 155 --- lib/pace/ace_c_basisfunction.h | 251 ---- lib/pace/ace_complex.h | 266 ----- lib/pace/ace_contigous_array.h | 249 ---- lib/pace/ace_evaluator.cpp | 660 ----------- lib/pace/ace_evaluator.h | 230 ---- lib/pace/ace_flatten_basis.cpp | 130 --- lib/pace/ace_flatten_basis.h | 135 --- lib/pace/ace_radial.cpp | 566 --------- lib/pace/ace_radial.h | 324 ----- lib/pace/ace_recursive.cpp | 1340 --------------------- lib/pace/ace_recursive.h | 247 ---- lib/pace/ace_spherical_cart.cpp | 221 ---- lib/pace/ace_spherical_cart.h | 134 --- lib/pace/ace_timing.h | 126 -- lib/pace/ace_types.h | 45 - lib/pace/ace_version.h | 39 - lib/pace/ships_radial.cpp | 388 ------ lib/pace/ships_radial.h | 158 --- src/USER-PACE/Install.sh | 104 +- 29 files changed, 189 insertions(+), 10254 deletions(-) create mode 100644 lib/pace/CMakeLists.txt delete mode 100644 lib/pace/LICENSE delete mode 100644 lib/pace/ace_abstract_basis.cpp delete mode 100644 lib/pace/ace_abstract_basis.h delete mode 100644 lib/pace/ace_array2dlm.h delete mode 100644 lib/pace/ace_arraynd.h delete mode 100644 lib/pace/ace_c_basis.cpp delete mode 100644 lib/pace/ace_c_basis.h delete mode 100644 lib/pace/ace_c_basisfunction.h delete mode 100644 lib/pace/ace_complex.h delete mode 100644 lib/pace/ace_contigous_array.h delete mode 100644 lib/pace/ace_evaluator.cpp delete mode 100644 lib/pace/ace_evaluator.h delete mode 100644 lib/pace/ace_flatten_basis.cpp delete mode 100644 lib/pace/ace_flatten_basis.h delete mode 100644 lib/pace/ace_radial.cpp delete mode 100644 lib/pace/ace_radial.h delete mode 100644 lib/pace/ace_recursive.cpp delete mode 100644 lib/pace/ace_recursive.h delete mode 100644 lib/pace/ace_spherical_cart.cpp delete mode 100644 lib/pace/ace_spherical_cart.h delete mode 100644 lib/pace/ace_timing.h delete mode 100644 lib/pace/ace_types.h delete mode 100644 lib/pace/ace_version.h delete mode 100644 lib/pace/ships_radial.cpp delete mode 100644 lib/pace/ships_radial.h diff --git a/lib/pace/CMakeLists.txt b/lib/pace/CMakeLists.txt new file mode 100644 index 0000000000..2884c83cb9 --- /dev/null +++ b/lib/pace/CMakeLists.txt @@ -0,0 +1,19 @@ +cmake_minimum_required(VERSION 3.7) # CMake version check +project(aceevaluator) +set(CMAKE_CXX_STANDARD 11) # Enable c++11 standard + + +set(PACE_EVALUATOR_PATH ${CMAKE_CURRENT_LIST_DIR}/src/USER-PACE) +# message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") +set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) + +FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) +list(FILTER PACE_EVALUATOR_SOURCE_FILES EXCLUDE REGEX ".*pair_pace.*") +set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) + + +##### aceevaluator ##### +add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) +target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_compile_options(aceevaluator PRIVATE -O3) +set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index f87f5c14cb..640971e011 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -1 +1,111 @@ -# TODO \ No newline at end of file +# TODO#!/usr/bin/env python + +""" +Install.py tool to download, compile, and setup the pace library +used to automate the steps described in the README file in this dir +""" + +from __future__ import print_function +import sys, os, subprocess, shutil +from argparse import ArgumentParser + +sys.path.append('..') +from install_helpers import fullpath, geturl, checkmd5sum + +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + +# settings + +thisdir = fullpath('.') +version = "v.2021.2.3" + +# known checksums for different PACE versions. used to validate the download. +checksums = { \ + 'v.2021.2.3' : '9ebb087cba7e4ca041fde52f7e9e640c', \ + } + + +# help message + +HELP = """ +Syntax from src dir: make lib-pace args="-b" + or: make lib-pace args="-b -v version" +Syntax from lib dir: python Install.py -b + or: python Install.py -b -v version + +Examples: + +make lib-pace args="-b" # install default version of PACE lib +make lib-pace args="-b -v version" # install specified version of PACE lib + + +""" + +pgroup = parser.add_mutually_exclusive_group() +pgroup.add_argument("-b", "--build", action="store_true", + help="download and build base PACE library") +parser.add_argument("-v", "--version", default=version, choices=checksums.keys(), + help="set version of PACE library to download and build (default: %s)" % version) +parser.add_argument("-vv", "--verbose", action="store_true", + help="be more verbose about is happening while this script runs") + +args = parser.parse_args() + +# print help message and exit, if neither build nor path options are given +if not args.build: + parser.print_help() + sys.exit(HELP) + +buildflag = args.build + +verboseflag = args.verbose +version = args.version + + +archive_extension = "tar.gz" +url = "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/%s.%s" % (version, archive_extension) +unarchived_folder_name = "lammps-user-pace-%s"%(version) + +# download PACE tarball, unpack, build PACE +if buildflag: + + # download entire tarball + + print("Downloading pace tarball ...") + archive_filename = "%s.%s" % (version, archive_extension) + download_filename = "%s/%s" % (thisdir, archive_filename) + print("Downloading from ",url," to ",download_filename, end=" ") + geturl(url, download_filename) + print(" done") + + # verify downloaded archive integrity via md5 checksum, if known. + if version in checksums: + if not checkmd5sum(checksums[version], archive_filename): + sys.exit("Checksum for pace library does not match") + + print("Unpacking pace tarball ...") + src_folder = thisdir+"/src" + cmd = 'cd "%s"; rm -rf "%s"; tar -xvf %s; mv %s %s' % (thisdir, src_folder, archive_filename, unarchived_folder_name, src_folder) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + + # configure + + build_folder = "%s/build"%(thisdir) + print("Configuring libpace ...") + cmd = 'cd %s && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=Release' % (thisdir) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + if verboseflag: print(txt.decode("UTF-8")) + + # build + print("Building libpace ...") + cmd = 'cd "%s" && make -j2 && cp libpace.a %s/' % (build_folder, thisdir) + txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) + if verboseflag: + print(txt.decode("UTF-8")) + +# remove source files + + print("Removing pace build files and archive ...") + cmd = 'rm %s; rm -rf %s' % (download_filename, build_folder) + subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) \ No newline at end of file diff --git a/lib/pace/LICENSE b/lib/pace/LICENSE deleted file mode 100644 index f288702d2f..0000000000 --- a/lib/pace/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -. diff --git a/lib/pace/README b/lib/pace/README index e69de29bb2..e9a1ab820a 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -0,0 +1,9 @@ +This directory contains files required to use the USER-PACE package. + +You can type "make lib-pace" from the src directory to see help on +how to download and build this library via make commands, or you can +do the same thing by typing "python Install.py" from within this +directory. + + + diff --git a/lib/pace/ace_abstract_basis.cpp b/lib/pace/ace_abstract_basis.cpp deleted file mode 100644 index 3d8afafdaf..0000000000 --- a/lib/pace/ace_abstract_basis.cpp +++ /dev/null @@ -1,184 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Lysogorskiy Yury on 28.04.2020. - -#include "ace_abstract_basis.h" - -////embedding function -////case nemb = 1 only implementation -////F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) -//// !! no prefactor wpre -void Fexp(DOUBLE_TYPE x, DOUBLE_TYPE m, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { - DOUBLE_TYPE w = 1.e6; - DOUBLE_TYPE eps = 1e-10; - - DOUBLE_TYPE lambda = pow(1.0 / w, m - 1.0); - if (abs(x) > eps) { - DOUBLE_TYPE g; - DOUBLE_TYPE a = abs(x); - DOUBLE_TYPE am = pow(a, m); - DOUBLE_TYPE w3x3 = pow(w * a, 3); - DOUBLE_TYPE sign_factor = (signbit(x) ? -1 : 1); - if (w3x3 > 30.0) - g = 0.0; - else - g = exp(-w3x3); - - DOUBLE_TYPE omg = 1.0 - g; - F = sign_factor * (omg * am + lambda * g * a); - DOUBLE_TYPE dg = -3.0 * w * w * w * a * a * g; - DF = m * pow(a, m - 1.0) * omg - am * dg + lambda * dg * a + lambda * g; - } else { - F = lambda * x; - DF = lambda; - } -} - - -//Scaled-shifted embedding function -//F = sign(x)*( ( 1 - exp(-(w*x)^3) )*abs(x)^m + ((1/w)^(m-1))*exp(-(w*x)^3)*abs(x) ) -// !! no prefactor wpre -void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF) { - DOUBLE_TYPE eps = 1e-10; - DOUBLE_TYPE a, xoff, yoff, nx, exprho; - - if (abs(mexp - 1.0) < eps) { - F = rho; - DF = 1; - } else { - a = abs(rho); - exprho = exp(-a); - nx = 1. / mexp; - xoff = pow(nx, (nx / (1.0 - nx))) * exprho; - yoff = pow(nx, (1 / (1.0 - nx))) * exprho; - DOUBLE_TYPE sign_factor = (signbit(rho) ? -1 : 1); - F = sign_factor * (pow(xoff + a, mexp) - yoff); - DF = yoff + mexp * (-xoff + 1.0) * pow(xoff + a, mexp - 1.); - } -} - -void ACEAbstractBasisSet::inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, - DOUBLE_TYPE &fcut, DOUBLE_TYPE &dfcut) { - - DOUBLE_TYPE rho_low = rho_cut - drho_cut; - if (rho_core >= rho_cut) { - fcut = 0; - dfcut = 0; - } else if (rho_core <= rho_low) { - fcut = 1; - dfcut = 0; - } else { - fcut = 0.5 * (1 + cos(M_PI * (rho_core - rho_low) / drho_cut)); - dfcut = -0.5 * sin(M_PI * (rho_core - rho_low) / drho_cut) * M_PI / drho_cut; - } -} - -void ACEAbstractBasisSet::FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, - Array1D &derivatives, DENSITY_TYPE ndensity) { - DOUBLE_TYPE F, DF = 0, wpre, mexp; - for (int p = 0; p < ndensity; p++) { - wpre = FS_parameters.at(p * ndensity + 0); - mexp = FS_parameters.at(p * ndensity + 1); - if (this->npoti == "FinnisSinclair") - Fexp(rhos(p), mexp, F, DF); - else if (this->npoti == "FinnisSinclairShiftedScaled") - FexpShiftedScaled(rhos(p), mexp, F, DF); - value += F * wpre; // * weight (wpre) - derivatives(p) = DF * wpre;// * weight (wpre) - } -} - -void ACEAbstractBasisSet::_clean() { - - delete[] elements_name; - elements_name = nullptr; - delete radial_functions; - radial_functions = nullptr; -} - -ACEAbstractBasisSet::ACEAbstractBasisSet(const ACEAbstractBasisSet &other) { - ACEAbstractBasisSet::_copy_scalar_memory(other); - ACEAbstractBasisSet::_copy_dynamic_memory(other); -} - -ACEAbstractBasisSet &ACEAbstractBasisSet::operator=(const ACEAbstractBasisSet &other) { - if (this != &other) { - // deallocate old memory - ACEAbstractBasisSet::_clean(); - //copy scalar values - ACEAbstractBasisSet::_copy_scalar_memory(other); - //copy dynamic memory - ACEAbstractBasisSet::_copy_dynamic_memory(other); - } - return *this; -} - -ACEAbstractBasisSet::~ACEAbstractBasisSet() { - ACEAbstractBasisSet::_clean(); -} - -void ACEAbstractBasisSet::_copy_scalar_memory(const ACEAbstractBasisSet &src) { - deltaSplineBins = src.deltaSplineBins; - FS_parameters = src.FS_parameters; - npoti = src.npoti; - - nelements = src.nelements; - rankmax = src.rankmax; - ndensitymax = src.ndensitymax; - nradbase = src.nradbase; - lmax = src.lmax; - nradmax = src.nradmax; - cutoffmax = src.cutoffmax; - - spherical_harmonics = src.spherical_harmonics; - - rho_core_cutoffs = src.rho_core_cutoffs; - drho_core_cutoffs = src.drho_core_cutoffs; - - - E0vals = src.E0vals; -} - -void ACEAbstractBasisSet::_copy_dynamic_memory(const ACEAbstractBasisSet &src) {//allocate new memory - if (src.elements_name == nullptr) - throw runtime_error("Could not copy ACEAbstractBasisSet::elements_name - array not initialized"); - elements_name = new string[nelements]; - //copy - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - elements_name[mu] = src.elements_name[mu]; - } - radial_functions = src.radial_functions->clone(); -} - -SPECIES_TYPE ACEAbstractBasisSet::get_species_index_by_name(const string &elemname) { - for (SPECIES_TYPE t = 0; t < nelements; t++) { - if (this->elements_name[t] == elemname) - return t; - } - return -1; -} \ No newline at end of file diff --git a/lib/pace/ace_abstract_basis.h b/lib/pace/ace_abstract_basis.h deleted file mode 100644 index 165ea9496f..0000000000 --- a/lib/pace/ace_abstract_basis.h +++ /dev/null @@ -1,169 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Lysogorskiy Yury on 28.04.2020. - -#ifndef ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H -#define ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H - -#include -#include - -#include "ace_c_basisfunction.h" -#include "ace_contigous_array.h" -#include "ace_radial.h" -#include "ace_spherical_cart.h" -#include "ace_types.h" - -using namespace std; - -/** - * Abstract basis set class - */ -class ACEAbstractBasisSet { -public: - SPECIES_TYPE nelements = 0; ///< number of elements in basis set - RANK_TYPE rankmax = 0; ///< maximum value of rank - DENSITY_TYPE ndensitymax = 0; ///< maximum number of densities \f$ \rho^{(p)} \f$ - NS_TYPE nradbase = 0; ///< maximum number of radial \f$\textbf{basis}\f$ function \f$ g_{k}(r) \f$ - LS_TYPE lmax = 0; ///< \f$ l_\textrm{max} \f$ - maximum value of orbital moment \f$ l \f$ - NS_TYPE nradmax = 0; ///< maximum number \f$ n \f$ of radial function \f$ R_{nl}(r) \f$ - DOUBLE_TYPE cutoffmax = 0; ///< maximum value of cutoff distance among all species in basis set - DOUBLE_TYPE deltaSplineBins = 0; ///< Spline interpolation density - - string npoti = "FinnisSinclair"; ///< FS and embedding function combination - - string *elements_name = nullptr; ///< Array of elements name for mapping from index (0..nelements-1) to element symbol (string) - - AbstractRadialBasis *radial_functions = nullptr; ///< object to work with radial functions - ACECartesianSphericalHarmonics spherical_harmonics; ///< object to work with spherical harmonics in Cartesian representation - - - Array1D rho_core_cutoffs; ///< energy-based inner cut-off - Array1D drho_core_cutoffs; ///< decay of energy-based inner cut-off - - vector FS_parameters; ///< parameters for cluster functional, see Eq.(3) in implementation notes or Eq.(53) in PRB 99, 014104 (2019) - - // E0 values - Array1D E0vals; - - /** - * Default empty constructor - */ - ACEAbstractBasisSet() = default; - - // copy constructor, operator= and destructor (see. Rule of Three) - - /** - * Copy constructor (see. Rule of Three) - * @param other - */ - ACEAbstractBasisSet(const ACEAbstractBasisSet &other); - - /** - * operator= (see. Rule of Three) - * @param other - * @return - */ - ACEAbstractBasisSet &operator=(const ACEAbstractBasisSet &other); - - /** - * virtual destructor (see. Rule of Three) - */ - virtual ~ACEAbstractBasisSet(); - - /** - * Computing cluster functional \f$ F(\rho_i^{(1)}, \dots, \rho_i^{(P)}) \f$ - * and its derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ - * @param rhos array with densities \f$ \rho^{(p)} \f$ - * @param value (out) return value of cluster functional - * @param derivatives (out) array of derivatives \f$ (\partial F/\partial\rho_i^{(1)}, \dots, \partial F/\partial \rho_i^{(P)} ) \f$ - * @param ndensity number \f$ P \f$ of densities to use - */ - void FS_values_and_derivatives(Array1D &rhos, DOUBLE_TYPE &value, Array1D &derivatives, - DENSITY_TYPE ndensity); - - /** - * Computing hard core pairwise repulsive potential \f$ f_{cut}(\rho_i^{(\textrm{core})})\f$ and its derivative, - * see Eq.(29) of implementation notes - * @param rho_core value of \f$ \rho_i^{(\textrm{core})} \f$ - * @param rho_cut \f$ \rho_{cut}^{\mu_i} \f$ value - * @param drho_cut \f$ \Delta_{cut}^{\mu_i} \f$ value - * @param fcut (out) return inner cutoff function - * @param dfcut (out) return derivative of inner cutoff function - */ - static void inner_cutoff(DOUBLE_TYPE rho_core, DOUBLE_TYPE rho_cut, DOUBLE_TYPE drho_cut, DOUBLE_TYPE &fcut, - DOUBLE_TYPE &dfcut); - - - /** - * Virtual method to save potential to file - * @param filename file name - */ - virtual void save(const string &filename) = 0; - - /** - * Virtual method to load potential from file - * @param filename file name - */ - virtual void load(const string filename) = 0; - - /** - * Get the species index by its element name - * @param elemname element name - * @return species index - */ - SPECIES_TYPE get_species_index_by_name(const string &elemname); - - - // routines for copying and cleaning dynamic memory of the class (see. Rule of Three) - - /** - * Routine for clean the dynamically allocated memory\n - * IMPORTANT! It must be idempotent for safety. - */ - virtual void _clean(); - - /** - * Copy dynamic memory from src. Must be override and extended in derived classes! - * @param src source object to copy from - */ - virtual void _copy_dynamic_memory(const ACEAbstractBasisSet &src); - - /** - * Copy scalar values from src. Must be override and extended in derived classes! - * @param src source object to copy from - */ - virtual void _copy_scalar_memory(const ACEAbstractBasisSet &src); -}; - -void Fexp(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); - -void FexpShiftedScaled(DOUBLE_TYPE rho, DOUBLE_TYPE mexp, DOUBLE_TYPE &F, DOUBLE_TYPE &DF); - -#endif //ACE_EVALUATOR_ACE_ABSTRACT_BASIS_H diff --git a/lib/pace/ace_array2dlm.h b/lib/pace/ace_array2dlm.h deleted file mode 100644 index 2b38602bc7..0000000000 --- a/lib/pace/ace_array2dlm.h +++ /dev/null @@ -1,579 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 11.01.20. - - -#ifndef ACE_ARRAY2DLM_H -#define ACE_ARRAY2DLM_H - -#include -#include - -#include "ace_arraynd.h" -#include "ace_contigous_array.h" -#include "ace_types.h" - -using namespace std; - -/** - * Contiguous array to organize values by \f$ (l,m) \f$ indiced (orbital moment and its projection). - * Only \f$ l_\textrm{max}\f$ should be provided, \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array2DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - - bool is_proxy = false; ///< flag to show, if object is owning the memory or just represent it (proxying)dimensions - -public: - /** - * Default empty constructor - */ - Array2DLM() = default; - - /** - * Parametrized constructor - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array2DLM(LS_TYPE lmax, string array_name = "Array2DLM") { - init(lmax, array_name); - } - - - /** - * Constructor to create slices-proxy array, i.e. to provide access to the memory, but not to own it. - * @param lmax maximum value of \f$ l \f$ - * @param data_ptr pointer to original data - * @param array_name name of the array - */ - Array2DLM(LS_TYPE lmax, T *data_ptr, string array_name = "Array2DLM") { - this->lmax = lmax; - this->size = (lmax + 1) * (lmax + 1); - this->data = data_ptr; - this->array_name = array_name; - is_proxy = true; - }; - - /** - * Destructor - */ - ~Array2DLM() { - if (!is_proxy) { - if (data != nullptr) delete[] data; - } - data = nullptr; - } - - /** - * Initialize array, allocate memory - * @param lmax maximum value of l - * @param array_name name of the array - */ - void init(LS_TYPE lmax, string array_name = "Array2DLM") { - if (is_proxy) { - char s[1024]; - sprintf(s, "Could not re-initialize proxy-array %s\n", this->array_name.c_str()); - throw logic_error(s); - } - this->lmax = lmax; - this->array_name = array_name; - //for m = -l .. l - if (size != (lmax + 1) * (lmax + 1)) { - size = (lmax + 1) * (lmax + 1); - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0.0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - } - -#ifdef MULTIARRAY_INDICES_CHECK -/** - * Check if indices (l,m) are within array - */ - void check_indices(LS_TYPE l, MS_TYPE m) const { - - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - size_t ii = l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (l,m) for reading - * @param l - * @param m - * @return array value - */ - inline const T &operator()(LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(l, m); -#endif - //l^2 + l + m - return data[l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (l,m) for writing - * @param l - * @param m - * @return array value - */ - inline T &operator()(LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(l, m); -#endif - //l^2 + l + m - return data[l * (l + 1) + m]; - } - - /** - * Convert array to STL vector> container - * @return vector> container - */ - vector> to_vector() const { - vector> res; - res.resize(lmax + 1); - - for (int i = 0; i < lmax + 1; i++) { - res[i].resize(i + 1); - for (int j = 0; j < i + 1; j++) { - res[i][j] = operator()(i, j); - } - } - return res; - } -}; - -/** - * Contiguous array to organize values by \f$ (i_0, l , m) \f$ indices. - * Only \f$ d_{0}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array3DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - - - size_t dim[1] = {0}; ///< linear dimension \f$ d_{0} \f$ - - size_t s[1] = {0}; ///< strides for linear dimensions - - Array1D *> _proxy_slices; ///< slices representation -public: - /** - * Default empty constructor - */ - Array3DLM() = default; - - /** - * Parametrized constructor - * @param array_name name of the array - */ - Array3DLM(string array_name) { - this->array_name = array_name; - }; - - /** - * Parametrized constructor - * @param d0 maximum value of \f$ i_0 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array3DLM(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { - init(d0, lmax, array_name); - } - - /** - * Initialize array and its slices - * @param d0 maximum value of \f$ i_0 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - void init(size_t d0, LS_TYPE lmax, string array_name = "Array3DLM") { - this->array_name = array_name; - this->lmax = lmax; - dim[0] = d0; - s[0] = lmax * lmax; - if (size != s[0] * dim[0]) { - size = s[0] * dim[0]; - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - - _proxy_slices.set_array_name(array_name + "_proxy"); - //arrange proxy-slices - _clear_proxies(); - _proxy_slices.resize(dim[0]); - for (size_t i0 = 0; i0 < dim[0]; ++i0) { - _proxy_slices(i0) = new Array2DLM(this->lmax, &this->data[i0 * s[0]], - array_name + "_slice"); - } - } - - /** - * Release pointers to slices - */ - void _clear_proxies() { - for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) { - delete _proxy_slices(i0); - _proxy_slices(i0) = nullptr; - } - } - - /** - * Destructor, clear proxies - */ - ~Array3DLM() { - _clear_proxies(); - } - - /** - * Resize array to new dimensions - * @param d0 - * @param lmax - */ - void resize(size_t d0, LS_TYPE lmax) { - _clear_proxies(); - init(d0, lmax, this->array_name); - } - - /** - * Get array dimensions - * @param d dimension index - * @return dimension along axis 'd' - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - /** - * Check if indices (i0, l,m) are within array - */ - void check_indices(size_t i0, LS_TYPE l, MS_TYPE m) const { - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - - if ((i0 < 0) | (i0 >= dim[0])) { - fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - exit(EXIT_FAILURE); - } - - size_t ii = i0 * s[0] + l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (i0,l,m) for reading - * @param i0 - * @param l - * @param m - * @return array value - */ - inline const T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, l, m); -#endif - return data[i0 * s[0] + l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (i0,l,m) for writing - * @param i0 - * @param l - * @param m - * @return array value - */ - inline T &operator()(size_t i0, LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, l, m); -#endif - return data[i0 * s[0] + l * (l + 1) + m]; - } - - /** - * Return proxy Array2DLM pointing to i0, l=0, m=0 to read - * @param i0 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline const Array2DLM &operator()(size_t i0) const { - return *_proxy_slices(i0); - } - - /** - * Return proxy Array2DLM pointing to i0, l=0, m=0 to write - * @param i0 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline Array2DLM &operator()(size_t i0) { - return *_proxy_slices(i0); - } -}; - - -/** - * Contiguous array to organize values by \f$ (i_0, i_1, l , m) \f$ indices. - * Only \f$ d_{0}, d_{1}, l_\textrm{max}\f$ should be provided: \f$ m = -l, \dots,l \f$ - * for \f$ l = 0, \dots, l_\textrm{max}\f$ - * @tparam T type of values to store - */ -template -class Array4DLM : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - - LS_TYPE lmax = 0; ///< orbital dimension \f$ l_{max} \f$ - size_t dim[2] = {0, 0}; ///< linear dimension \f$ d_{0}, d_{1} \f$ - size_t s[2] = {0, 0}; ///< strides for linear dimensions - - Array2D *> _proxy_slices; ///< slices representation -public: - /** - * Default empty constructor - */ - Array4DLM() = default; - - /** - * Parametrized constructor - * @param array_name name of the array - */ - Array4DLM(string array_name) { - this->array_name = array_name; - }; - - /** - * Parametrized constructor - * @param d0 maximum value of \f$ i_0 \f$ - * @param d1 maximum value of \f$ i_1 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - explicit Array4DLM(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { - init(d0, d1, lmax, array_name); - } - - /** - * Initialize array, reallocate memory and its slices - * @param d0 maximum value of \f$ i_0 \f$ - * @param d1 maximum value of \f$ i_1 \f$ - * @param lmax maximum value of \f$ l \f$ - * @param array_name name of the array - */ - void init(size_t d0, size_t d1, LS_TYPE lmax, string array_name = "Array4DLM") { - this->array_name = array_name; - this->lmax = lmax; - dim[1] = d1; - dim[0] = d0; - s[1] = lmax * lmax; - s[0] = s[1] * dim[1]; - if (size != s[0] * dim[0]) { - size = s[0] * dim[0]; - if (data) delete[] data; - data = new T[size]{}; - memset(data, 0, size * sizeof(T)); - } else { - memset(data, 0, size * sizeof(T)); - } - - _proxy_slices.set_array_name(array_name + "_proxy"); - //release old memory if there is any - _clear_proxies(); - //arrange proxy-slices - _proxy_slices.resize(dim[0], dim[1]); - for (size_t i0 = 0; i0 < dim[0]; ++i0) - for (size_t i1 = 0; i1 < dim[1]; ++i1) { - _proxy_slices(i0, i1) = new Array2DLM(this->lmax, &this->data[i0 * s[0] + i1 * s[1]], - array_name + "_slice"); - } - } - - /** - * Release pointers to slices - */ - void _clear_proxies() { - - for (size_t i0 = 0; i0 < _proxy_slices.get_dim(0); ++i0) - for (size_t i1 = 0; i1 < _proxy_slices.get_dim(1); ++i1) { - delete _proxy_slices(i0, i1); - _proxy_slices(i0, i1) = nullptr; - } - } - - /** - * Destructor, clear proxies - */ - ~Array4DLM() { - _clear_proxies(); - } - - /** - * Deallocate memory, reallocate with the new dimensions - * @param d0 - * @param lmax - */ - void resize(size_t d0, size_t d1, LS_TYPE lmax) { - _clear_proxies(); - init(d0, d1, lmax, this->array_name); - } - - /** - * Get array dimensions - * @param d dimension index - * @return dimension along axis 'd' - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - /** - * Check if indices (i0, l,m) are within array - */ - void check_indices(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { - if ((l < 0) | (l > lmax)) { - fprintf(stderr, "%s: Index l = %d out of range (0, %d)\n", array_name.c_str(), l, lmax); - exit(EXIT_FAILURE); - } - - if ((m < -l) | (m > l)) { - fprintf(stderr, "%s: Index m = %d out of range (%d, %d)\n", array_name.c_str(), m, -l, l); - exit(EXIT_FAILURE); - } - - if ((i0 < 0) | (i0 >= dim[0])) { - fprintf(stderr, "%s: index i0 = %ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - exit(EXIT_FAILURE); - } - - - if ((i1 < 0) | (i1 >= dim[1])) { - fprintf(stderr, "%s: index i1 = %ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - exit(EXIT_FAILURE); - } - - size_t ii = i0 * s[0] + i1 * s[1] + l * (l + 1) + m; - if (ii >= size) { - fprintf(stderr, "%s: index = %ld out of range %ld\n", array_name.c_str(), ii, size); - exit(EXIT_FAILURE); - } - } -#endif - - /** - * Accessing the array value by index (i0,l,m) for reading - * @param i0 - * @param i1 - * @param l - * @param m - * @return array value - */ - inline const T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, l, m); -#endif - return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; - } - - /** - * Accessing the array value by index (i0,l,m) for writing - * @param i0 - * @param i1 - * @param l - * @param m - * @return array value - */ - inline T &operator()(size_t i0, size_t i1, LS_TYPE l, MS_TYPE m) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, l, m); -#endif - return data[i0 * s[0] + i1 * s[1] + l * (l + 1) + m]; - } - - /** - * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to read - * @param i0 - * @param i1 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline const Array2DLM &operator()(size_t i0, size_t i1) const { - return *_proxy_slices(i0, i1); - } - - /** - * Return proxy Array2DLM pointing to i0, i1, l=0, m=0 to write - * @param i0 - * @param i1 - * @return proxy Array2DLM pointing to i0, l=0, m=0 - */ - inline Array2DLM &operator()(size_t i0, size_t i1) { - return *_proxy_slices(i0, i1); - } -}; - -#endif //ACE_ARRAY2DLM_H \ No newline at end of file diff --git a/lib/pace/ace_arraynd.h b/lib/pace/ace_arraynd.h deleted file mode 100644 index 1044b5654e..0000000000 --- a/lib/pace/ace_arraynd.h +++ /dev/null @@ -1,1949 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -//automatically generate source code - -#ifndef ACE_MULTIARRAY_H -#define ACE_MULTIARRAY_H - -#include -#include -#include - -#include "ace_contigous_array.h" - -using namespace std; - - -/** - * Multidimensional (1 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array1D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[1] = {0}; ///< dimensions - size_t s[1] = {0}; ///< strides - int ndim = 1; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array1D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array1D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array1D(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { - init(d0, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0) { - - dim[0] = d0; - - s[0] = 1; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, const string &array_name = "Array1D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0) { - init(d0, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0) { - //check data size consistency - size_t new_size = d0; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0); -#endif - - return data[i0]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0); -#endif - - return data[i0]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array1D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector to_vector() const { - vector res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0] = operator()(i0); - - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector &vec) { - size_t d0 = 0; - d0 = vec.size(); - - - init(d0, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - operator()(i0) = vec.at(i0); - - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array1D(const vector &vec, const string &array_name = "Array1D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array1D &operator=(const vector &vec) { - this->set_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (2 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array2D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[2] = {0}; ///< dimensions - size_t s[2] = {0}; ///< strides - int ndim = 2; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array2D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array2D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array2D(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { - init(d0, d1, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1) { - - dim[0] = d0; - dim[1] = d1; - - s[1] = 1; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, const string &array_name = "Array2D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1) { - init(d0, d1, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1) { - //check data size consistency - size_t new_size = d0 * d1; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1); -#endif - - return data[i0 * s[0] + i1]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1); -#endif - - return data[i0 * s[0] + i1]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array2D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector> to_vector() const { - vector> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1] = operator()(i0, i1); - - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector> &vec) { - size_t d0 = 0; - size_t d1 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - - - } - - init(d0, d1, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - operator()(i0, i1) = vec.at(i0).at(i1); - - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array2D(const vector> &vec, const string &array_name = "Array2D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array2D &operator=(const vector> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array2D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (3 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array3D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[3] = {0}; ///< dimensions - size_t s[3] = {0}; ///< strides - int ndim = 3; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array3D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array3D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array3D(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { - init(d0, d1, d2, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - - s[2] = 1; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, const string &array_name = "Array3D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2) { - init(d0, d1, d2, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2) { - //check data size consistency - size_t new_size = d0 * d1 * d2; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array3D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>> to_vector() const { - vector>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2] = operator()(i0, i1, i2); - - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - - - } - } - - init(d0, d1, d2, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - operator()(i0, i1, i2) = vec.at(i0).at(i1).at(i2); - - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array3D(const vector>> &vec, const string &array_name = "Array3D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array3D &operator=(const vector>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array3D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (4 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array4D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[4] = {0}; ///< dimensions - size_t s[4] = {0}; ///< strides - int ndim = 4; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array4D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array4D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array4D(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { - init(d0, d1, d2, d3, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - - s[3] = 1; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, const string &array_name = "Array4D", T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3) { - init(d0, d1, d2, d3, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array4D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>> to_vector() const { - vector>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3] = operator()(i0, i1, i2, i3); - - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - - - } - } - } - - init(d0, d1, d2, d3, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - operator()(i0, i1, i2, i3) = vec.at(i0).at(i1).at(i2).at(i3); - - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array4D(const vector>>> &vec, const string &array_name = "Array4D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array4D &operator=(const vector>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array4D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (5 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array5D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[5] = {0}; ///< dimensions - size_t s[5] = {0}; ///< strides - int ndim = 5; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array5D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array5D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array5D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", - T *new_data = nullptr) { - init(d0, d1, d2, d3, d4, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - dim[4] = d4; - - s[4] = 1; - s[3] = s[4] * dim[4]; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, const string &array_name = "Array5D", - T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3, d4); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - init(d0, d1, d2, d3, d4, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3 * d4; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3, d4); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - if ((i4 < 0) | (i4 >= dim[4])) { - char buf[1024]; - sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array5D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>>> to_vector() const { - vector>>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3].resize(dim[4]); - - - for (int i4 = 0; i4 < dim[4]; i4++) { - res[i0][i1][i2][i3][i4] = operator()(i0, i1, i2, i3, i4); - - } - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - size_t d4 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - if (d3 > 0) { - d4 = vec.at(0).at(0).at(0).at(0).size(); - - - } - } - } - } - - init(d0, d1, d2, d3, d4, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) - throw std::invalid_argument("Vector size is not constant at dimension 4"); - - for (int i4 = 0; i4 < dim[4]; i4++) { - operator()(i0, i1, i2, i3, i4) = vec.at(i0).at(i1).at(i2).at(i3).at(i4); - - } - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array5D(const vector>>>> &vec, const string &array_name = "Array5D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array5D &operator=(const vector>>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array5D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -/** - * Multidimensional (6 - dimensional) array of type T with contiguous memory layout. - * If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @tparam T data type - */ -template -class Array6D : public ContiguousArrayND { - using ContiguousArrayND::array_name; - using ContiguousArrayND::data; - using ContiguousArrayND::size; - using ContiguousArrayND::is_proxy_; - - size_t dim[6] = {0}; ///< dimensions - size_t s[6] = {0}; ///< strides - int ndim = 6; ///< number of dimensions -public: - - /** - * Default empty constructor - */ - Array6D() = default; - - /** - * Parametrized constructor with array name - * @param array_name name of array (for error logging) - */ - Array6D(const string &array_name) { this->array_name = array_name; } - - /** - * Parametrized constructor - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - Array6D(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", - T *new_data = nullptr) { - init(d0, d1, d2, d3, d4, d5, array_name, new_data); - } - - /** - * Setup the dimensions and strides of array - * @param d0,... array sizes for different dimensions - */ - void set_dimensions(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - - dim[0] = d0; - dim[1] = d1; - dim[2] = d2; - dim[3] = d3; - dim[4] = d4; - dim[5] = d5; - - s[5] = 1; - s[4] = s[5] * dim[5]; - s[3] = s[4] * dim[4]; - s[2] = s[3] * dim[3]; - s[1] = s[2] * dim[2]; - s[0] = s[1] * dim[1]; - - size = s[0] * dim[0]; - }; - - /** - * Initialize array storage, dimensions and strides - * @param d0,... array sizes for different dimensions - * @param array_name string name of the array - */ - void init(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5, const string &array_name = "Array6D", - T *new_data = nullptr) { - this->array_name = array_name; - - size_t old_size = size; - set_dimensions(d0, d1, d2, d3, d4, d5); - - bool new_is_proxy = (new_data != nullptr); - - if (new_is_proxy) { - if (!is_proxy_) delete[] data; - data = new_data; - } else { - if (size != old_size) { - T *old_data = data; //preserve the pointer to the old data - data = new T[size]; // allocate new data - if (old_data != nullptr) { // - size_t min_size = old_size < size ? old_size : size; - memcpy(data, old_data, min_size * sizeof(T)); - if (!is_proxy_) delete[] old_data; - } - //memset(data, 0, size * sizeof(T)); - } else { - //memset(data, 0, size * sizeof(T)); - } - } - - is_proxy_ = new_is_proxy; - } - - /** - * Resize array - * @param d0,... array sizes for different dimensions - */ - void resize(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - init(d0, d1, d2, d3, d4, d5, this->array_name); - } - - /** - * Reshape array without reset the data - * @param d0,... array sizes for different dimensions - */ - void reshape(size_t d0, size_t d1, size_t d2, size_t d3, size_t d4, size_t d5) { - //check data size consistency - size_t new_size = d0 * d1 * d2 * d3 * d4 * d5; - if (new_size != size) - throw invalid_argument("Couldn't reshape array when the size is not conserved"); - set_dimensions(d0, d1, d2, d3, d4, d5); - } - - /** - * Get array size in dimension "d" - * @param d dimension index - */ - size_t get_dim(int d) const { - return dim[d]; - } - -#ifdef MULTIARRAY_INDICES_CHECK - - /** - * Check indices validity. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - void check_indices(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { - - if ((i0 < 0) | (i0 >= dim[0])) { - char buf[1024]; - sprintf(buf, "%s: index i0=%ld out of range (0, %ld)\n", array_name.c_str(), i0, dim[0] - 1); - throw std::out_of_range(buf); - } - - if ((i1 < 0) | (i1 >= dim[1])) { - char buf[1024]; - sprintf(buf, "%s: index i1=%ld out of range (0, %ld)\n", array_name.c_str(), i1, dim[1] - 1); - throw std::out_of_range(buf); - } - - if ((i2 < 0) | (i2 >= dim[2])) { - char buf[1024]; - sprintf(buf, "%s: index i2=%ld out of range (0, %ld)\n", array_name.c_str(), i2, dim[2] - 1); - throw std::out_of_range(buf); - } - - if ((i3 < 0) | (i3 >= dim[3])) { - char buf[1024]; - sprintf(buf, "%s: index i3=%ld out of range (0, %ld)\n", array_name.c_str(), i3, dim[3] - 1); - throw std::out_of_range(buf); - } - - if ((i4 < 0) | (i4 >= dim[4])) { - char buf[1024]; - sprintf(buf, "%s: index i4=%ld out of range (0, %ld)\n", array_name.c_str(), i4, dim[4] - 1); - throw std::out_of_range(buf); - } - - if ((i5 < 0) | (i5 >= dim[5])) { - char buf[1024]; - sprintf(buf, "%s: index i5=%ld out of range (0, %ld)\n", array_name.c_str(), i5, dim[5] - 1); - throw std::out_of_range(buf); - } - - } - -#endif - - /** - * Array access operator() for reading. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline const T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) const { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4, i5); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; - - } - - /** - * Array access operator() for writing. If preprocessor macro MULTIARRAY_INDICES_CHECK is defined, then the check of index will - * be performed before accessing memory. By default this is turned off. - * @param i0,... indices - */ - inline T &operator()(size_t i0, size_t i1, size_t i2, size_t i3, size_t i4, size_t i5) { -#ifdef MULTIARRAY_INDICES_CHECK - check_indices(i0, i1, i2, i3, i4, i5); -#endif - - return data[i0 * s[0] + i1 * s[1] + i2 * s[2] + i3 * s[3] + i4 * s[4] + i5]; - - } - - /** - * Array comparison operator - * @param other - */ - bool operator==(const Array6D &other) const { - //compare dimensions - for (int d = 0; d < ndim; d++) { - if (this->dim[d] != other.dim[d]) - return false; - } - return ContiguousArrayND::operator==(other); - } - - /** - * Convert to nested vector> container - * @return vector container - */ - vector>>>>> to_vector() const { - vector>>>>> res; - - res.resize(dim[0]); - - for (int i0 = 0; i0 < dim[0]; i0++) { - res[i0].resize(dim[1]); - - - for (int i1 = 0; i1 < dim[1]; i1++) { - res[i0][i1].resize(dim[2]); - - - for (int i2 = 0; i2 < dim[2]; i2++) { - res[i0][i1][i2].resize(dim[3]); - - - for (int i3 = 0; i3 < dim[3]; i3++) { - res[i0][i1][i2][i3].resize(dim[4]); - - - for (int i4 = 0; i4 < dim[4]; i4++) { - res[i0][i1][i2][i3][i4].resize(dim[5]); - - - for (int i5 = 0; i5 < dim[5]; i5++) { - res[i0][i1][i2][i3][i4][i5] = operator()(i0, i1, i2, i3, i4, i5); - - } - } - } - } - } - } - - - return res; - } // end to_vector() - - - /** - * Set values to vector> container - * @param vec container - */ - void set_vector(const vector>>>>> &vec) { - size_t d0 = 0; - size_t d1 = 0; - size_t d2 = 0; - size_t d3 = 0; - size_t d4 = 0; - size_t d5 = 0; - d0 = vec.size(); - - if (d0 > 0) { - d1 = vec.at(0).size(); - if (d1 > 0) { - d2 = vec.at(0).at(0).size(); - if (d2 > 0) { - d3 = vec.at(0).at(0).at(0).size(); - if (d3 > 0) { - d4 = vec.at(0).at(0).at(0).at(0).size(); - if (d4 > 0) { - d5 = vec.at(0).at(0).at(0).at(0).at(0).size(); - - - } - } - } - } - } - - init(d0, d1, d2, d3, d4, d5, array_name); - for (int i0 = 0; i0 < dim[0]; i0++) { - if (vec.at(i0).size() != d1) - throw std::invalid_argument("Vector size is not constant at dimension 1"); - - for (int i1 = 0; i1 < dim[1]; i1++) { - if (vec.at(i0).at(i1).size() != d2) - throw std::invalid_argument("Vector size is not constant at dimension 2"); - - for (int i2 = 0; i2 < dim[2]; i2++) { - if (vec.at(i0).at(i1).at(i2).size() != d3) - throw std::invalid_argument("Vector size is not constant at dimension 3"); - - for (int i3 = 0; i3 < dim[3]; i3++) { - if (vec.at(i0).at(i1).at(i2).at(i3).size() != d4) - throw std::invalid_argument("Vector size is not constant at dimension 4"); - - for (int i4 = 0; i4 < dim[4]; i4++) { - if (vec.at(i0).at(i1).at(i2).at(i3).at(i4).size() != d5) - throw std::invalid_argument("Vector size is not constant at dimension 5"); - - for (int i5 = 0; i5 < dim[5]; i5++) { - operator()(i0, i1, i2, i3, i4, i5) = vec.at(i0).at(i1).at(i2).at(i3).at(i4).at(i5); - - } - } - } - } - } - } - - } - - /** - * Parametrized constructor from vector> container - * @param vec container - * @param array_name array name - */ - Array6D(const vector>>>>> &vec, const string &array_name = "Array6D") { - this->set_vector(vec); - this->array_name = array_name; - } - - /** - * operator= to vector> container - * @param vec container - */ - Array6D &operator=(const vector>>>>> &vec) { - this->set_vector(vec); - return *this; - } - - - /** - * operator= to flatten vector container - * @param vec container - */ - Array6D &operator=(const vector &vec) { - this->set_flatten_vector(vec); - return *this; - } - - - vector get_shape() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = dim[d]; - return sh; - } - - vector get_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d]; - return sh; - } - - vector get_memory_strides() const { - vector sh(ndim); - for (int d = 0; d < ndim; d++) - sh[d] = s[d] * sizeof(T); - return sh; - } -}; - - -#endif //ACE_MULTIARRAY_H diff --git a/lib/pace/ace_c_basis.cpp b/lib/pace/ace_c_basis.cpp deleted file mode 100644 index d1c55700b7..0000000000 --- a/lib/pace/ace_c_basis.cpp +++ /dev/null @@ -1,980 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 1.04.20. - -#include "ace_c_basis.h" -#include "ships_radial.h" - -using namespace std; - -ACECTildeBasisSet::ACECTildeBasisSet(string filename) { - load(filename); -} - -ACECTildeBasisSet::ACECTildeBasisSet(const ACECTildeBasisSet &other) { - ACECTildeBasisSet::_copy_scalar_memory(other); - ACECTildeBasisSet::_copy_dynamic_memory(other); - pack_flatten_basis(); -} - - -ACECTildeBasisSet &ACECTildeBasisSet::operator=(const ACECTildeBasisSet &other) { - if (this != &other) { - _clean(); - _copy_scalar_memory(other); - _copy_dynamic_memory(other); - pack_flatten_basis(); - } - return *this; -} - - -ACECTildeBasisSet::~ACECTildeBasisSet() { - ACECTildeBasisSet::_clean(); -} - -void ACECTildeBasisSet::_clean() { - // call parent method - ACEFlattenBasisSet::_clean(); - _clean_contiguous_arrays(); - _clean_basis_arrays(); -} - -void ACECTildeBasisSet::_copy_scalar_memory(const ACECTildeBasisSet &src) { - ACEFlattenBasisSet::_copy_scalar_memory(src); - num_ctilde_max = src.num_ctilde_max; -} - -void ACECTildeBasisSet::_copy_dynamic_memory(const ACECTildeBasisSet &src) {//allocate new memory - ACEFlattenBasisSet::_copy_dynamic_memory(src); - - if (src.basis_rank1 == nullptr) - throw runtime_error("Could not copy ACECTildeBasisSet::basis_rank1 - array not initialized"); - if (src.basis == nullptr) throw runtime_error("Could not copy ACECTildeBasisSet::basis - array not initialized"); - - - basis_rank1 = new ACECTildeBasisFunction *[src.nelements]; - basis = new ACECTildeBasisFunction *[src.nelements]; - - //copy basis arrays - for (SPECIES_TYPE mu = 0; mu < src.nelements; ++mu) { - basis_rank1[mu] = new ACECTildeBasisFunction[src.total_basis_size_rank1[mu]]; - - for (size_t i = 0; i < src.total_basis_size_rank1[mu]; i++) { - basis_rank1[mu][i] = src.basis_rank1[mu][i]; - } - - - basis[mu] = new ACECTildeBasisFunction[src.total_basis_size[mu]]; - for (size_t i = 0; i < src.total_basis_size[mu]; i++) { - basis[mu][i] = src.basis[mu][i]; - } - } - //DON"T COPY CONTIGUOUS ARRAY, REBUILD THEM -} - -void ACECTildeBasisSet::_clean_contiguous_arrays() { - ACEFlattenBasisSet::_clean_contiguous_arrays(); - - delete[] full_c_tildes_rank1; - full_c_tildes_rank1 = nullptr; - - delete[] full_c_tildes; - full_c_tildes = nullptr; -} - -//re-pack the constituent dynamic arrays of all basis functions in contiguous arrays -void ACECTildeBasisSet::pack_flatten_basis() { - compute_array_sizes(basis_rank1, basis); - - //1. clean contiguous arrays - _clean_contiguous_arrays(); - //2. allocate contiguous arrays - delete[] full_ns_rank1; - full_ns_rank1 = new NS_TYPE[rank_array_total_size_rank1]; - delete[] full_ls_rank1; - full_ls_rank1 = new NS_TYPE[rank_array_total_size_rank1]; - delete[] full_mus_rank1; - full_mus_rank1 = new SPECIES_TYPE[rank_array_total_size_rank1]; - delete[] full_ms_rank1; - full_ms_rank1 = new MS_TYPE[rank_array_total_size_rank1]; - - delete[] full_c_tildes_rank1; - full_c_tildes_rank1 = new DOUBLE_TYPE[coeff_array_total_size_rank1]; - - - delete[] full_ns; - full_ns = new NS_TYPE[rank_array_total_size]; - delete[] full_ls; - full_ls = new LS_TYPE[rank_array_total_size]; - delete[] full_mus; - full_mus = new SPECIES_TYPE[rank_array_total_size]; - delete[] full_ms; - full_ms = new MS_TYPE[ms_array_total_size]; - - delete[] full_c_tildes; - full_c_tildes = new DOUBLE_TYPE[coeff_array_total_size]; - - - //3. copy the values from private C_tilde_B_basis_function arrays to new contigous space - //4. clean private memory - //5. reassign private array pointers - - //r = 0, rank = 1 - size_t rank_array_ind_rank1 = 0; - size_t coeff_array_ind_rank1 = 0; - size_t ms_array_ind_rank1 = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - for (int func_ind_r1 = 0; func_ind_r1 < total_basis_size_rank1[mu]; ++func_ind_r1) { - ACECTildeBasisFunction &func = basis_rank1[mu][func_ind_r1]; - - //copy values ns from c_tilde_basis_function private memory to contigous memory part - full_ns_rank1[rank_array_ind_rank1] = func.ns[0]; - - //copy values ls from c_tilde_basis_function private memory to contigous memory part - full_ls_rank1[rank_array_ind_rank1] = func.ls[0]; - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - full_mus_rank1[rank_array_ind_rank1] = func.mus[0]; - - //copy values ctildes from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_c_tildes_rank1[coeff_array_ind_rank1], func.ctildes, - func.ndensity * sizeof(DOUBLE_TYPE)); - - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ms_rank1[ms_array_ind_rank1], func.ms_combs, - func.num_ms_combs * - func.rank * sizeof(MS_TYPE)); - - //release memory of each ACECTildeBasisFunction if it is not proxy - func._clean(); - - func.mus = &full_mus_rank1[rank_array_ind_rank1]; - func.ns = &full_ns_rank1[rank_array_ind_rank1]; - func.ls = &full_ls_rank1[rank_array_ind_rank1]; - func.ms_combs = &full_ms_rank1[ms_array_ind_rank1]; - func.ctildes = &full_c_tildes_rank1[coeff_array_ind_rank1]; - func.is_proxy = true; - - rank_array_ind_rank1 += func.rank; - ms_array_ind_rank1 += func.rank * - func.num_ms_combs; - coeff_array_ind_rank1 += func.num_ms_combs * func.ndensity; - - } - } - - - //rank>1, r>0 - size_t rank_array_ind = 0; - size_t coeff_array_ind = 0; - size_t ms_array_ind = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - ACECTildeBasisFunction &func = basis[mu][func_ind]; - - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_mus[rank_array_ind], func.mus, - func.rank * sizeof(SPECIES_TYPE)); - - //copy values ns from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ns[rank_array_ind], func.ns, - func.rank * sizeof(NS_TYPE)); - //copy values ls from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ls[rank_array_ind], func.ls, - func.rank * sizeof(LS_TYPE)); - //copy values mus from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_ms[ms_array_ind], func.ms_combs, - func.num_ms_combs * - func.rank * sizeof(MS_TYPE)); - - //copy values ctildes from c_tilde_basis_function private memory to contigous memory part - memcpy(&full_c_tildes[coeff_array_ind], func.ctildes, - func.num_ms_combs * func.ndensity * sizeof(DOUBLE_TYPE)); - - - //release memory of each ACECTildeBasisFunction if it is not proxy - func._clean(); - - func.ns = &full_ns[rank_array_ind]; - func.ls = &full_ls[rank_array_ind]; - func.mus = &full_mus[rank_array_ind]; - func.ctildes = &full_c_tildes[coeff_array_ind]; - func.ms_combs = &full_ms[ms_array_ind]; - func.is_proxy = true; - - rank_array_ind += func.rank; - ms_array_ind += func.rank * - func.num_ms_combs; - coeff_array_ind += func.num_ms_combs * func.ndensity; - } - } -} - -void fwrite_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { - RANK_TYPE r; - fprintf(fptr, "ctilde_basis_func: "); - fprintf(fptr, "rank=%d ndens=%d mu0=%d ", func.rank, func.ndensity, func.mu0); - - fprintf(fptr, "mu=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.mus[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "n=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ns[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "l=("); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ls[r]); - fprintf(fptr, ")\n"); - - fprintf(fptr, "num_ms=%d\n", func.num_ms_combs); - - for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { - fprintf(fptr, "<"); - for (r = 0; r < func.rank; ++r) - fprintf(fptr, " %d ", func.ms_combs[m_ind * func.rank + r]); - fprintf(fptr, ">: "); - for (DENSITY_TYPE p = 0; p < func.ndensity; p++) - fprintf(fptr, " %.18f ", func.ctildes[m_ind * func.ndensity + p]); - fprintf(fptr, "\n"); - } - -} - -void ACECTildeBasisSet::save(const string &filename) { - FILE *fptr; - fptr = fopen(filename.c_str(), "w"); - - fprintf(fptr, "nelements=%d\n", nelements); - - //elements mapping - fprintf(fptr, "elements:"); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) - fprintf(fptr, " %s", elements_name[mu].c_str()); - fprintf(fptr, "\n\n"); - - fprintf(fptr, "lmax=%d\n\n", lmax); - - fprintf(fptr, "embedding-function: %s\n", npoti.c_str()); - - fprintf(fptr, "%ld FS parameters: ", FS_parameters.size()); - for (int i = 0; i < FS_parameters.size(); ++i) { - fprintf(fptr, " %f", FS_parameters.at(i)); - } - fprintf(fptr, "\n"); - - //hard-core energy cutoff repulsion - fprintf(fptr, "core energy-cutoff parameters: "); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - fprintf(fptr, "%.18f %.18f\n", rho_core_cutoffs(mu_i), drho_core_cutoffs(mu_i)); - - // save E0 values - fprintf(fptr, "E0:"); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - fprintf(fptr, " %.18f", E0vals(mu_i)); - fprintf(fptr, "\n"); - - - fprintf(fptr, "\n"); - - - fprintf(fptr, "radbasename=%s\n", radial_functions->radbasename.c_str()); - fprintf(fptr, "nradbase=%d\n", nradbase); - fprintf(fptr, "nradmax=%d\n", nradmax); - - - fprintf(fptr, "cutoffmax=%f\n", cutoffmax); - - fprintf(fptr, "deltaSplineBins=%f\n", deltaSplineBins); - - //hard-core repulsion - fprintf(fptr, "core repulsion parameters: "); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, "%.18f %.18f\n", radial_functions->prehc(mu_i, mu_j), radial_functions->lambdahc(mu_j, mu_j)); - - - - - - //TODO: radial functions - //radparameter - fprintf(fptr, "radparameter="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->lambda(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "cutoff="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->cut(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "dcut="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - fprintf(fptr, " %.18f", radial_functions->dcut(mu_i, mu_j)); - fprintf(fptr, "\n"); - - fprintf(fptr, "crad="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - for (NS_TYPE k = 0; k < nradbase; k++) { - for (NS_TYPE n = 0; n < nradmax; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fprintf(fptr, " %.18f", radial_functions->crad(mu_i, mu_j, n, l, k)); - } - fprintf(fptr, "\n"); - } - } - } - - fprintf(fptr, "\n"); - - fprintf(fptr, "rankmax=%d\n", rankmax); - fprintf(fptr, "ndensitymax=%d\n", ndensitymax); - fprintf(fptr, "\n"); - - //num_c_tilde_max - fprintf(fptr, "num_c_tilde_max=%d\n", num_ctilde_max); - fprintf(fptr, "num_ms_combinations_max=%d\n", num_ms_combinations_max); - - - //write total_basis_size and total_basis_size_rank1 - fprintf(fptr, "total_basis_size_rank1: "); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - fprintf(fptr, "%d ", total_basis_size_rank1[mu]); - } - fprintf(fptr, "\n"); - - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) - fwrite_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); - - fprintf(fptr, "total_basis_size: "); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - fprintf(fptr, "%d ", total_basis_size[mu]); - } - fprintf(fptr, "\n"); - - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) - fwrite_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); - - - fclose(fptr); -} - -void fread_c_tilde_b_basis_func(FILE *fptr, ACECTildeBasisFunction &func) { - RANK_TYPE r; - int res; - char buf[3][128]; - - res = fscanf(fptr, " ctilde_basis_func: "); - - res = fscanf(fptr, "rank=%s ndens=%s mu0=%s ", buf[0], buf[1], buf[2]); - if (res != 3) - throw invalid_argument("Could not read C-tilde basis function"); - - func.rank = (RANK_TYPE) stol(buf[0]); - func.ndensity = (DENSITY_TYPE) stol(buf[1]); - func.mu0 = (SPECIES_TYPE) stol(buf[2]); - - func.mus = new SPECIES_TYPE[func.rank]; - func.ns = new NS_TYPE[func.rank]; - func.ls = new LS_TYPE[func.rank]; - - res = fscanf(fptr, " mu=("); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.mus[r] = (SPECIES_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); // ")" - - res = fscanf(fptr, " n=("); // "n=" - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - - func.ns[r] = (NS_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); - - res = fscanf(fptr, " l=("); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ls[r] = (NS_TYPE) stol(buf[0]); - } - res = fscanf(fptr, " )"); - - res = fscanf(fptr, " num_ms=%s\n", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - - func.num_ms_combs = (SHORT_INT_TYPE) stoi(buf[0]); - - func.ms_combs = new MS_TYPE[func.rank * func.num_ms_combs]; - func.ctildes = new DOUBLE_TYPE[func.ndensity * func.num_ms_combs]; - - for (int m_ind = 0; m_ind < func.num_ms_combs; m_ind++) { - res = fscanf(fptr, " <"); - for (r = 0; r < func.rank; ++r) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ms_combs[m_ind * func.rank + r] = stoi(buf[0]); - } - res = fscanf(fptr, " >:"); - for (DENSITY_TYPE p = 0; p < func.ndensity; p++) { - res = fscanf(fptr, "%s", buf[0]); - if (res != 1) - throw invalid_argument("Could not read C-tilde basis function"); - func.ctildes[m_ind * func.ndensity + p] = stod(buf[0]); - } - } -} - -string -format_error_message(const char *buffer, const string &filename, const string &var_name, const string &expected) { - string err_message = "File '" + filename + "': couldn't read '" + var_name + "'"; - if (buffer) - err_message = err_message + ", read:'" + buffer + "'"; - if (!expected.empty()) - err_message = err_message + ". Expected format: '" + expected + "'"; - return err_message; -} - -void throw_error(const string &filename, const string &var_name, const string expected = "") { - throw invalid_argument(format_error_message(nullptr, filename, var_name, expected)); -} - -DOUBLE_TYPE stod_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stod(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -int stoi_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stoi(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -long int stol_err(const char *buffer, const string &filename, const string &var_name, const string expected = "") { - try { - return stol(buffer); - } catch (invalid_argument &exc) { - throw invalid_argument(format_error_message(buffer, filename, var_name, expected).c_str()); - } -} - -void ACECTildeBasisSet::load(const string filename) { - int res; - char buffer[1024], buffer2[1024]; - string radbasename = "ChebExpCos"; - - FILE *fptr; - fptr = fopen(filename.c_str(), "r"); - if (fptr == NULL) - throw invalid_argument("Could not open file " + filename); - - //read number of elements - res = fscanf(fptr, " nelements="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nelements", "nelements=[number]"); - nelements = stoi_err(buffer, filename, "nelements", "nelements=[number]"); - - //elements mapping - elements_name = new string[nelements]; - res = fscanf(fptr, " elements:"); - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "elements", "elements: Ele1 Ele2 ..."); - elements_name[mu] = buffer; - } - - // load angular basis - only need spherical harmonics parameter - res = fscanf(fptr, " lmax=%s\n", buffer); - if (res != 1) - throw_error(filename, "lmax", "lmax=[number]"); - lmax = stoi_err(buffer, filename, "lmax", "lmax=[number]"); - spherical_harmonics.init(lmax); - - - // reading "embedding-function:" - bool is_embedding_function_specified = false; - res = fscanf(fptr, " embedding-function: %s", buffer); - if (res == 0) { - //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); - this->npoti = "FinnisSinclair"; // default values - //printf("Warning! No embedding-function is specified, embedding-function: FinnisSinclair would be assumed\n"); - is_embedding_function_specified = false; - } else { - this->npoti = buffer; - is_embedding_function_specified = true; - } - int parameters_size; - res = fscanf(fptr, "%s FS parameters:", buffer); - if (res != 1) - throw_error(filename, "FS parameters size", "[number] FS parameters: par1 par2 ..."); - parameters_size = stoi_err(buffer, filename, "FS parameters size", "[number] FS parameters"); - FS_parameters.resize(parameters_size); - for (int i = 0; i < FS_parameters.size(); ++i) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); - FS_parameters[i] = stod_err(buffer, filename, "FS parameter", "[number] FS parameters: [par1] [par2] ..."); - } - - if (!is_embedding_function_specified) { - // assuming non-linear potential, and embedding function type is important - for (int j = 1; j < parameters_size; j += 2) - if (FS_parameters[j] != 1.0) { //if not ensure linearity of embedding function parameters - printf("ERROR! Your potential is non-linear\n"); - printf("Please specify 'embedding-function: FinnisSinclair' or 'embedding-function: FinnisSinclairShiftedScaled' before 'FS parameters size' line\n"); - throw_error(filename, "embedding-function", "FinnisSinclair or FinnisSinclairShiftedScaled"); - } - printf("Notice! No embedding-function is specified, but potential has linear embedding, default embedding-function: FinnisSinclair would be assumed\n"); - } - - //hard-core energy cutoff repulsion - res = fscanf(fptr, " core energy-cutoff parameters:"); - if (res != 0) - throw_error(filename, "core energy-cutoff parameters", "core energy-cutoff parameters: [par1] [par2]"); - - rho_core_cutoffs.init(nelements, "rho_core_cutoffs"); - drho_core_cutoffs.init(nelements, "drho_core_cutoffs"); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) { - res = fscanf(fptr, "%s %s", buffer, buffer2); - if (res != 2) - throw_error(filename, "core energy-cutoff parameters", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - rho_core_cutoffs(mu_i) = stod_err(buffer, filename, "rho core cutoff", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - drho_core_cutoffs(mu_i) = stod_err(buffer2, filename, "drho_core_cutoff", - "core energy-cutoff parameters: [rho_core_cut] [drho_core_cutoff] ..."); - } - - // atom energy shift E0 (energy of isolated atom) - E0vals.init(nelements); - - // reading "E0:" - res = fscanf(fptr, " E0: %s", buffer); - if (res == 0) { - //throw_error(filename, "E0", " E0: E0-species1 E0-species2 ..."); - E0vals.fill(0.0); - } else { - double E0 = atof(buffer); - E0vals(0) = E0; - - for (SPECIES_TYPE mu_i = 1; mu_i < nelements; ++mu_i) { - res = fscanf(fptr, " %lf", &E0); - if (res != 1) - throw_error(filename, "E0", " couldn't read one of the E0 values"); - E0vals(mu_i) = E0; - } - res = fscanf(fptr, "\n"); - if (res != 0) - printf("file %s : format seems broken near E0; trying to continue...\n", filename.c_str()); - } - - // check which radial basis we need to load - res = fscanf(fptr, " radbasename=%s\n", buffer); - if (res != 1) { - throw_error(filename, "radbasename", "rabbasename=ChebExpCos|ChebPow|ACE.jl.Basic"); - } else { - radbasename = buffer; - } - -// printf("radbasename = `%s`\n", radbasename.c_str()); - if (radbasename == "ChebExpCos" | radbasename == "ChebPow") { - _load_radial_ACERadial(fptr, filename, radbasename); - } else if (radbasename == "ACE.jl.Basic") { - _load_radial_SHIPsBasic(fptr, filename, radbasename); - } else { - throw invalid_argument( - ("File '" + filename + "': I don't know how to read radbasename = " + radbasename).c_str()); - } - - res = fscanf(fptr, " rankmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "rankmax", "rankmax=[number]"); - rankmax = stoi_err(buffer, filename, "rankmax", "rankmax=[number]"); - - res = fscanf(fptr, " ndensitymax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "ndensitymax", "ndensitymax=[number]"); - ndensitymax = stoi_err(buffer, filename, "ndensitymax", "ndensitymax=[number]"); - - // read the list of correlations to be put into the basis - //num_c_tilde_max - res = fscanf(fptr, " num_c_tilde_max="); - res = fscanf(fptr, "%s\n", buffer); - if (res != 1) - throw_error(filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); - num_ctilde_max = stol_err(buffer, filename, "num_c_tilde_max", "num_c_tilde_max=[number]"); - - res = fscanf(fptr, " num_ms_combinations_max="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); -// throw invalid_argument(("File '" + filename + "': couldn't read num_ms_combinations_max").c_str()); - num_ms_combinations_max = stol_err(buffer, filename, "num_ms_combinations_max", "num_ms_combinations_max=[number]"); - - //read total_basis_size_rank1 - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - basis_rank1 = new ACECTildeBasisFunction *[nelements]; - res = fscanf(fptr, " total_basis_size_rank1: "); - - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "total_basis_size_rank1", "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); -// throw invalid_argument(("File '" + filename + "': couldn't read total_basis_size_rank1").c_str()); - total_basis_size_rank1[mu] = stoi_err(buffer, filename, "total_basis_size_rank1", - "total_basis_size_rank1: [size_ele1] [size_ele2] ..."); - basis_rank1[mu] = new ACECTildeBasisFunction[total_basis_size_rank1[mu]]; - } - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size_rank1[mu]; ++func_ind) { - fread_c_tilde_b_basis_func(fptr, basis_rank1[mu][func_ind]); - } - - //read total_basis_size - res = fscanf(fptr, " total_basis_size: "); - total_basis_size = new SHORT_INT_TYPE[nelements]; - basis = new ACECTildeBasisFunction *[nelements]; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "total_basis_size", "total_basis_size: [size_ele1] [size_ele2] ..."); - total_basis_size[mu] = stoi_err(buffer, filename, "total_basis_size", - "total_basis_size: [size_ele1] [size_ele2] ..."); - basis[mu] = new ACECTildeBasisFunction[total_basis_size[mu]]; - } - for (SPECIES_TYPE mu = 0; mu < nelements; mu++) - for (SHORT_INT_TYPE func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - fread_c_tilde_b_basis_func(fptr, basis[mu][func_ind]); - } - - fclose(fptr); - -// radial_functions->radbasename = radbasename; - radial_functions->setuplookupRadspline(); - pack_flatten_basis(); -} - -void ACECTildeBasisSet::compute_array_sizes(ACECTildeBasisFunction **basis_rank1, ACECTildeBasisFunction **basis) { - //compute arrays sizes - rank_array_total_size_rank1 = 0; - //ms_array_total_size_rank1 = rank_array_total_size_rank1; - coeff_array_total_size_rank1 = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - if (total_basis_size_rank1[mu] > 0) { - rank_array_total_size_rank1 += total_basis_size_rank1[mu]; - - ACEAbstractBasisFunction &func = basis_rank1[mu][0];//TODO: get total density instead of density from first function - coeff_array_total_size_rank1 += total_basis_size_rank1[mu] * func.ndensity; - } - } - - rank_array_total_size = 0; - coeff_array_total_size = 0; - - ms_array_total_size = 0; - max_dB_array_size = 0; - - - max_B_array_size = 0; - - size_t cur_ms_size = 0; - size_t cur_ms_rank_size = 0; - - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - - cur_ms_size = 0; - cur_ms_rank_size = 0; - for (int func_ind = 0; func_ind < total_basis_size[mu]; ++func_ind) { - auto &func = basis[mu][func_ind]; - rank_array_total_size += func.rank; - ms_array_total_size += func.rank * func.num_ms_combs; - coeff_array_total_size += func.ndensity * func.num_ms_combs; - - cur_ms_size += func.num_ms_combs; - cur_ms_rank_size += func.rank * func.num_ms_combs; - } - - if (cur_ms_size > max_B_array_size) - max_B_array_size = cur_ms_size; - - if (cur_ms_rank_size > max_dB_array_size) - max_dB_array_size = cur_ms_rank_size; - } -} - -void ACECTildeBasisSet::_clean_basis_arrays() { - if (basis_rank1 != nullptr) - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - delete[] basis_rank1[mu]; - basis_rank1[mu] = nullptr; - } - - if (basis != nullptr) - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - delete[] basis[mu]; - basis[mu] = nullptr; - } - delete[] basis; - basis = nullptr; - - delete[] basis_rank1; - basis_rank1 = nullptr; -} - -//pack into 1D array with all basis functions -void ACECTildeBasisSet::flatten_basis(C_tilde_full_basis_vector2d &mu0_ctilde_basis_vector) { - - _clean_basis_arrays(); - basis_rank1 = new ACECTildeBasisFunction *[nelements]; - basis = new ACECTildeBasisFunction *[nelements]; - - delete[] total_basis_size_rank1; - delete[] total_basis_size; - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - total_basis_size = new SHORT_INT_TYPE[nelements]; - - - size_t tot_size_rank1 = 0; - size_t tot_size = 0; - - for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { - tot_size = 0; - tot_size_rank1 = 0; - - for (auto &func: mu0_ctilde_basis_vector[mu]) { - if (func.rank == 1) tot_size_rank1 += 1; - else tot_size += 1; - } - - total_basis_size_rank1[mu] = tot_size_rank1; - basis_rank1[mu] = new ACECTildeBasisFunction[tot_size_rank1]; - - total_basis_size[mu] = tot_size; - basis[mu] = new ACECTildeBasisFunction[tot_size]; - } - - - for (SPECIES_TYPE mu = 0; mu < this->nelements; ++mu) { - size_t ind_rank1 = 0; - size_t ind = 0; - - for (auto &func: mu0_ctilde_basis_vector[mu]) { - if (func.rank == 1) { //r=0, rank=1 - basis_rank1[mu][ind_rank1] = func; - ind_rank1 += 1; - } else { //r>0, rank>1 - basis[mu][ind] = func; - ind += 1; - } - } - - } -} - - -void ACECTildeBasisSet::_load_radial_ACERadial(FILE *fptr, - const string filename, - const string radbasename) { - int res; - char buffer[1024], buffer2[1024]; - - res = fscanf(fptr, " nradbase="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nradbase", "nradbase=[number]"); -// throw invalid_argument(("File '" + filename + "': couldn't read nradbase").c_str()); - nradbase = stoi_err(buffer, filename, "nradbase", "nradbase=[number]"); - - res = fscanf(fptr, " nradmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "nradmax", "nradmax=[number]"); - nradmax = stoi_err(buffer, filename, "nradmax", "nradmax=[number]"); - - res = fscanf(fptr, " cutoffmax="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "cutoffmax", "cutoffmax=[number]"); - cutoffmax = stod_err(buffer, filename, "cutoffmax", "cutoffmax=[number]"); - - - res = fscanf(fptr, " deltaSplineBins="); - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); -// throw invalid_argument(("File '" + filename + "': couldn't read ntot").c_str()); - deltaSplineBins = stod_err(buffer, filename, "deltaSplineBins", "deltaSplineBins=[spline density, Angstroms]"); - - - if (radial_functions == nullptr) - radial_functions = new ACERadialFunctions(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - else - radial_functions->init(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - - - //hard-core repulsion - res = fscanf(fptr, " core repulsion parameters:"); - if (res != 0) - throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); -// throw invalid_argument(("File '" + filename + "': couldn't read core repulsion parameters").c_str()); - - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s %s", buffer, buffer2); - if (res != 2) - throw_error(filename, "core repulsion parameters", "core repulsion parameters: [prehc lambdahc] ..."); - radial_functions->prehc(mu_i, mu_j) = stod_err(buffer, filename, "core repulsion parameters", - "core repulsion parameters: [prehc lambdahc] ..."); - radial_functions->lambdahc(mu_i, mu_j) = stod_err(buffer2, filename, "core repulsion parameters", - "core repulsion parameters: [prehc lambdahc] ..."); - } - - - - //read radial functions parameter - res = fscanf(fptr, " radparameter="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "radparameter", "radparameter=[param_ele1] [param_ele2]"); - radial_functions->lambda(mu_i, mu_j) = stod_err(buffer, filename, "radparameter", - "radparameter=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " cutoff="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "cutoff", "cutoff=[param_ele1] [param_ele2]"); - radial_functions->cut(mu_i, mu_j) = stod_err(buffer, filename, "cutoff", - "cutoff=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " dcut="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) { - res = fscanf(fptr, " %s", buffer); - if (res != 1) - throw_error(filename, "dcut", "dcut=[param_ele1] [param_ele2]"); - radial_functions->dcut(mu_i, mu_j) = stod_err(buffer, filename, "dcut", "dcut=[param_ele1] [param_ele2]"); - } - - - res = fscanf(fptr, " crad="); - for (SPECIES_TYPE mu_i = 0; mu_i < nelements; ++mu_i) - for (SPECIES_TYPE mu_j = 0; mu_j < nelements; ++mu_j) - for (NS_TYPE k = 0; k < nradbase; k++) - for (NS_TYPE n = 0; n < nradmax; n++) - for (LS_TYPE l = 0; l <= lmax; l++) { - res = fscanf(fptr, "%s", buffer); - if (res != 1) - throw_error(filename, "crad", "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); - radial_functions->crad(mu_i, mu_j, n, l, k) = stod_err(buffer, filename, "crad", - "crad=[crad_]...[crad_knl]: nradbase*nrad*(l+1) times"); - } -} - -void ACECTildeBasisSet::_load_radial_SHIPsBasic(FILE *fptr, - const string filename, - const string radbasename) { - // create a radial basis object, and read it from the file pointer - SHIPsRadialFunctions *ships_radial_functions = new SHIPsRadialFunctions(); - ships_radial_functions->fread(fptr); - - //mimic ships_radial_functions to ACERadialFunctions - ships_radial_functions->nradial = ships_radial_functions->get_maxn(); - ships_radial_functions->nradbase = ships_radial_functions->get_maxn(); - - nradbase = ships_radial_functions->get_maxn(); - nradmax = ships_radial_functions->get_maxn(); - cutoffmax = ships_radial_functions->get_rcut(); - deltaSplineBins = 0.001; - - ships_radial_functions->init(nradbase, lmax, nradmax, - deltaSplineBins, - nelements, - cutoffmax, radbasename); - - - if (radial_functions) delete radial_functions; - radial_functions = ships_radial_functions; - radial_functions->prehc.fill(0); - radial_functions->lambdahc.fill(1); - radial_functions->lambda.fill(0); - - - radial_functions->cut.fill(ships_radial_functions->get_rcut()); - radial_functions->dcut.fill(0); - - radial_functions->crad.fill(0); - -} \ No newline at end of file diff --git a/lib/pace/ace_c_basis.h b/lib/pace/ace_c_basis.h deleted file mode 100644 index ec6b9e8afc..0000000000 --- a/lib/pace/ace_c_basis.h +++ /dev/null @@ -1,155 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 1.04.20. - -#ifndef ACE_C_BASIS_H -#define ACE_C_BASIS_H - -#include "ace_flatten_basis.h" - -typedef vector> C_tilde_full_basis_vector2d; - -/** - * ACE basis set of C-tilde basis functions - */ -class ACECTildeBasisSet : public ACEFlattenBasisSet { -public: - - ACECTildeBasisFunction **basis_rank1 = nullptr; ///< two-dimensional array of first-rank basis function with indices: [species index][func index] - ACECTildeBasisFunction **basis = nullptr; ///< two-dimensional array of higher rank basis function with indices: [species index][func index] - - DOUBLE_TYPE *full_c_tildes_rank1 = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size_rank1 - DOUBLE_TYPE *full_c_tildes = nullptr; ///< C_tilde coefficients contiguous package, size: coeff_array_total_size - - //TODO: remove? - SHORT_INT_TYPE num_ctilde_max = 0; - - - /** - * Default constructor - */ - ACECTildeBasisSet() = default; - - /** - * Constructor from .ace file - */ - ACECTildeBasisSet(const string filename); - - /** - * Copy constructor (see. Rule of Three) - * @param other - */ - ACECTildeBasisSet(const ACECTildeBasisSet &other); - - /** - * operator= (see. Rule of Three) - * @param other - * @return - */ - ACECTildeBasisSet &operator=(const ACECTildeBasisSet &other); - - /** - * Destructor (see. Rule of Three) - */ - ~ACECTildeBasisSet() override; - - /** - * Cleaning dynamic memory of the class (see. Rule of Three) - */ - void _clean() override; - - /** - * Copying and cleaning dynamic memory of the class (see. Rule of Three) - * @param src - */ - void _copy_dynamic_memory(const ACECTildeBasisSet &src); - - /** - * Copying scalar variables - * @param src - */ - void _copy_scalar_memory(const ACECTildeBasisSet &src); - - /** - * Clean contiguous arrays (full_c_tildes_rank1, full_c_tildes) and those of base class - */ - void _clean_contiguous_arrays() override ; - - /** - * Save potential to .ace file - * @param filename .ace file name - */ - void save(const string &filename) override; - - /** - * Load potential from .ace - * @param filename .ace file name - */ - void load(const string filename) override; - - /** - * Load the ACE type radial basis - */ - void _load_radial_ACERadial(FILE *fptr, - const string filename, - const string radbasename); - - void _load_radial_SHIPsBasic(FILE * fptr, - const string filename, - const string radbasename ); - - /** - * Re-pack the constituent dynamic arrays of all basis functions in contiguous arrays - */ - void pack_flatten_basis() override; - - /** - * Computes flatten array sizes - * @param basis_rank1 two-dimensional array of first-rank ACECTildeBasisFunctions - * @param basis two-dimensional array of higher-rank ACECTildeBasisFunctions - */ - void compute_array_sizes(ACECTildeBasisFunction** basis_rank1, ACECTildeBasisFunction** basis); - - /** - * Clean basis arrays 'basis_rank1' and 'basis' - */ - void _clean_basis_arrays(); - - /** - * Pack two-dimensional vector of ACECTildeBasisFunction into 1D dynami array with all basis functions - * @param mu0_ctilde_basis_vector vector> - */ - void flatten_basis(C_tilde_full_basis_vector2d& mu0_ctilde_basis_vector); - - /** - * Empty stub implementation - */ - void flatten_basis() override{}; -}; - -#endif //ACE_C_BASIS_H diff --git a/lib/pace/ace_c_basisfunction.h b/lib/pace/ace_c_basisfunction.h deleted file mode 100644 index 4e2795590e..0000000000 --- a/lib/pace/ace_c_basisfunction.h +++ /dev/null @@ -1,251 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 26.02.20. - -#ifndef ACE_C_BASISFUNCTION_H -#define ACE_C_BASISFUNCTION_H - -#include -#include -#include -#include - -#include "ace_types.h" - -//macros for copying the member-array from "other" object for C-tilde and B-basis -#define basis_mem_copy(other, array, size, type) if(other.array) { \ - if(!is_proxy) delete[] array;\ - array = new type[(size)];\ - is_proxy = false;\ - memcpy(array, other.array, (size) * sizeof(type));\ -} - -/** - * Abstract basis function, that stores general quantities - */ -struct ACEAbstractBasisFunction { - /** - * flattened array of computed combinations of (m1, m2, ..., m_rank) - * which have non-zero general Clebsch-Gordan coefficient: - * \f$ \mathbf{m}_1, \dots, \mathbf{m}_\mathrm{num ms combs}\f$ = - * \f$ (m_1, m_2, \dots, m_{rank})_1, \dots, (m_1, m_2, \dots, m_{rank})_{\mathrm{num ms combs}} \f$, - * size = num_ms_combs * rank, - * effective shape: [num_ms_combs][rank] - */ - MS_TYPE *ms_combs = nullptr; - - /** - * species types of neighbours atoms \f$ \mathbf{\mu} = (\mu_1, \mu_2, \dots, \mu_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - SPECIES_TYPE *mus = nullptr; - - /** - * indices for radial part \f$ \mathbf{n} = (n_1, n_2, \dots, n_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - NS_TYPE *ns = nullptr; - - - /** - * indices for radial part \f$ \mathbf{l} = (l_1, l_2, \dots, l_{rank}) \f$, - * should be lexicographically sorted, - * size = rank, - * effective shape: [rank] - */ - LS_TYPE *ls = nullptr; - - SHORT_INT_TYPE num_ms_combs = 0; ///< number of different ms-combinations - - RANK_TYPE rank = 0; ///< number of atomic base functions "A"s in basis function product B - - DENSITY_TYPE ndensity = 0; ///< number of densities - - SPECIES_TYPE mu0 = 0; ///< species type of central atom - - /** - * whether ms array contains only "non-negative" ms-combinations. - * positive ms-combination is when the first non-zero m is positive (0 1 -1) - * negative ms-combination is when the first non-zero m is negative (0 -1 1) - */ - bool is_half_ms_basis = false; - - /* - * flag, whether object is "owner" (i.e. responsible for memory cleaning) of - * the ms, ns, ls, mus and other dynamically allocated arrases or just a proxy for them - */ - bool is_proxy = false; - - /** - * Copying static and dynamic memory variables from another ACEAbstractBasisFunction. - * Always copy the dynamic memory, even if the source is a proxy object - * @param other - */ - virtual void _copy_from(const ACEAbstractBasisFunction &other) { - rank = other.rank; - ndensity = other.ndensity; - mu0 = other.mu0; - num_ms_combs = other.num_ms_combs; - is_half_ms_basis = other.is_half_ms_basis; - is_proxy = false; - - basis_mem_copy(other, mus, rank, SPECIES_TYPE) - basis_mem_copy(other, ns, rank, NS_TYPE) - basis_mem_copy(other, ls, rank, LS_TYPE) - basis_mem_copy(other, ms_combs, num_ms_combs * rank, MS_TYPE) - } - - /** - * Clean the dynamically allocated memory if object is responsible for it - */ - virtual void _clean() { - //release memory if the structure is not proxy - if (!is_proxy) { - delete[] mus; - delete[] ns; - delete[] ls; - delete[] ms_combs; - } - - mus = nullptr; - ns = nullptr; - ls = nullptr; - ms_combs = nullptr; - } - -}; - -/** - * Representation of C-tilde basis function, i.e. the function that is summed up over a group of B-functions - * that differs only by intermediate coupling orbital moment \f$ L \f$ and coefficients. - */ -struct ACECTildeBasisFunction : public ACEAbstractBasisFunction { - - /** - * c_tilde coefficients for all densities, - * size = num_ms_combs*ndensity, - * effective shape [num_ms_combs][ndensity] - */ - DOUBLE_TYPE *ctildes = nullptr; - - /* - * Default constructor - */ - ACECTildeBasisFunction() = default; - - // Because the ACECTildeBasisFunction contains dynamically allocated arrays, the Rule of Three should be - // fulfilled, i.e. copy constructor (copy the dynamic arrays), operator= (release previous arrays and - // copy the new dynamic arrays) and destructor (release all dynamically allocated memory) - - /** - * Copy constructor, to fulfill the Rule of Three. - * Always copy the dynamic memory, even if the source is a proxy object. - */ - ACECTildeBasisFunction(const ACECTildeBasisFunction &other) { - _copy_from(other); - } - - /* - * operator=, to fulfill the Rule of Three. - * Always copy the dynamic memory, even if the source is a proxy object - */ - ACECTildeBasisFunction &operator=(const ACECTildeBasisFunction &other) { - _clean(); - _copy_from(other); - return *this; - } - - /* - * Destructor - */ - ~ACECTildeBasisFunction() { - _clean(); - } - - /** - * Copy from another object, always copy the memory, even if the source is a proxy object - * @param other - */ - void _copy_from(const ACECTildeBasisFunction &other) { - ACEAbstractBasisFunction::_copy_from(other); - is_proxy = false; - basis_mem_copy(other, ctildes, num_ms_combs * ndensity, DOUBLE_TYPE) - } - - /** - * Clean the dynamically allocated memory if object is responsible for it - */ - void _clean() override { - ACEAbstractBasisFunction::_clean(); - //release memory if the structure is not proxy - if (!is_proxy) { - delete[] ctildes; - } - ctildes = nullptr; - } - - /** - * Print the information about basis function to cout, in order to ease the output redirection. - */ - void print() const { - using namespace std; - cout << "ACECTildeBasisFunction: ndensity= " << (int) this->ndensity << ", mu0 = " << (int) this->mu0 << " "; - cout << " mus=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << (int) this->mus[r] << " "; - cout << "), ns=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ns[r] << " "; - cout << "), ls=("; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ls[r] << " "; - - cout << "), " << this->num_ms_combs << " m_s combinations: {" << endl; - - for (int i = 0; i < this->num_ms_combs; i++) { - cout << "\t< "; - for (RANK_TYPE r = 0; r < this->rank; r++) - cout << this->ms_combs[i * this->rank + r] << " "; - cout << " >: c_tilde="; - for (DENSITY_TYPE p = 0; p < this->ndensity; ++p) - cout << " " << this->ctildes[i * this->ndensity + p] << " "; - cout << endl; - } - if (this->is_proxy) - cout << "proxy "; - if (this->is_half_ms_basis) - cout << "half_ms_basis"; - cout << "}" << endl; - } -}; - -#endif //ACE_C_BASISFUNCTION_H diff --git a/lib/pace/ace_complex.h b/lib/pace/ace_complex.h deleted file mode 100644 index 5fdb4b5b93..0000000000 --- a/lib/pace/ace_complex.h +++ /dev/null @@ -1,266 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 26.02.20. - -#ifndef ACE_COMPLEX_H -#define ACE_COMPLEX_H - - -/** -A custom data structure for complex numbers and overloaded operations with them. -*/ -struct ACEComplex { -public: - /** - Double, real part of the complex number - */ - DOUBLE_TYPE real; - /** - Double, imaginary part of the complex number - */ - DOUBLE_TYPE img; - - ACEComplex &operator=(const ACEComplex &rhs) = default; - - ACEComplex &operator=(const DOUBLE_TYPE &rhs) { - this->real = rhs; - this->img = 0.; - return *this; - } - - /** - Overloading of arithmetical operator += ACEComplex - */ - ACEComplex &operator+=(const ACEComplex &rhs) { - this->real += rhs.real; - this->img += rhs.img; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator += DOUBLE_TYPE - */ - ACEComplex &operator+=(const DOUBLE_TYPE &rhs) { - this->real += rhs; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator *= DOUBLE_TYPE - */ - ACEComplex &operator*=(const DOUBLE_TYPE &rhs) { - this->real *= rhs; - this->img *= rhs; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator *= ACEComplex - */ - ACEComplex &operator*=(const ACEComplex &rhs) { - DOUBLE_TYPE old_real = this->real; - this->real = old_real * rhs.real - this->img * rhs.img; - this->img = old_real * rhs.img + this->img * rhs.real; - return *this; // return the result by reference - } - - /** - Overloading of arithmetical operator * ACEComplex - */ - ACEComplex operator*(const ACEComplex &cm2) const { - ACEComplex res{real * cm2.real - img * cm2.img, - real * cm2.img + img * cm2.real}; - return res; - } - - /* - * Return complex conjugated copy of itself - */ - ACEComplex conjugated() const { - ACEComplex res{real, -img}; - return res; - } - - /* - * Complex conjugate itself inplace - */ - void conjugate() { - img = -img; - } - - /* - * Multiplication by ACEComplex and return real-part only - */ - DOUBLE_TYPE real_part_product(const ACEComplex &cm2) const { - return real * cm2.real - img * cm2.img; - } - - /* - * Multiplication by DOUBLE_TYPE and return real-part only - */ - DOUBLE_TYPE real_part_product(const DOUBLE_TYPE &cm2) const { - return real * cm2; - } - - /* - * Overloading of arithmetical operator * by DOUBLE_TYPE - */ - ACEComplex operator*(const DOUBLE_TYPE &cm2) const { - ACEComplex res{real * cm2, - img * cm2}; - return res; - } - - /* - * Overloading of arithmetical operator + ACEComplex - */ - ACEComplex operator+(const ACEComplex &cm2) const { - ACEComplex res{real + cm2.real, - img + cm2.img}; - return res; - } - - /* - * Overloading of arithmetical operator + with DOUBLE_TYPE - */ - ACEComplex operator+(const DOUBLE_TYPE &cm2) const { - ACEComplex res{real + cm2, img}; - return res; - } - - /* - * Overloading of arithmetical operator == ACEComplex - */ - bool operator==(const ACEComplex &c2) const { - return (real == c2.real) && (img == c2.img); - } - - /* - * Overloading of arithmetical operator == DOUBLE_TYPE - */ - bool operator==(const DOUBLE_TYPE &d2) const { - return (real == d2) && (img == 0.); - } - - /* - * Overloading of arithmetical operator != ACEComplex - */ - bool operator!=(const ACEComplex &c2) const { - return (real != c2.real) || (img != c2.img); - } - - /* - * Overloading of arithmetical operator != DOUBLE_TYPE - */ - bool operator!=(const DOUBLE_TYPE &d2) const { - return (real != d2) || (img != 0.); - } - -}; - -/* - * double * complex for commutativity with complex * double - */ -inline ACEComplex operator*(const DOUBLE_TYPE &real, const ACEComplex &cm) { - return cm * real; -} - -/* - * double + complex for commutativity with complex + double - */ -inline ACEComplex operator+(const DOUBLE_TYPE &real, const ACEComplex &cm) { - return cm + real; -} - -/** -A structure to store the derivative of \f$ Y_{lm} \f$ -*/ -struct ACEDYcomponent { -public: - /** - complex, contains the three components of derivative of Ylm, - \f$ \frac{dY_{lm}}{dx}, \frac{dY_{lm}}{dy} and \frac{dY_{lm}}{dz}\f$ - */ - ACEComplex a[3]; - - /* - * Overloading of arithmetical operator*= DOUBLE_TYPE - */ - ACEDYcomponent &operator*=(const DOUBLE_TYPE &rhs) { - this->a[0] *= rhs; - this->a[1] *= rhs; - this->a[2] *= rhs; - return *this; - } - - /* - * Overloading of arithmetical operator * ACEComplex - */ - ACEDYcomponent operator*(const ACEComplex &rhs) const { - ACEDYcomponent res; - res.a[0] = this->a[0] * rhs; - res.a[1] = this->a[1] * rhs; - res.a[2] = this->a[2] * rhs; - return res; - } - - /* - * Overloading of arithmetical operator * DOUBLE_TYPE - */ - ACEDYcomponent operator*(const DOUBLE_TYPE &rhs) const { - ACEDYcomponent res; - res.a[0] = this->a[0] * rhs; - res.a[1] = this->a[1] * rhs; - res.a[2] = this->a[2] * rhs; - return res; - } - - /* - * Return conjugated copy of itself - */ - ACEDYcomponent conjugated() const { - ACEDYcomponent res; - res.a[0] = this->a[0].conjugated(); - res.a[1] = this->a[1].conjugated(); - res.a[2] = this->a[2].conjugated(); - return res; - } - - /* - * Conjugated itself in-place - */ - void conjugate() { - this->a[0].conjugate(); - this->a[1].conjugate(); - this->a[2].conjugate(); - } - -}; - - -#endif //ACE_COMPLEX_H diff --git a/lib/pace/ace_contigous_array.h b/lib/pace/ace_contigous_array.h deleted file mode 100644 index f008fa203f..0000000000 --- a/lib/pace/ace_contigous_array.h +++ /dev/null @@ -1,249 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 11.01.20. -#ifndef ACE_CONTIGUOUSARRAYND_H -#define ACE_CONTIGUOUSARRAYND_H - -#include - -#include "ace_types.h" - -using namespace std; - -/** - * Common predecessor class to represent multidimensional array of type T - * and store it in memory contiguous form - * - * @tparam T data type - */ -template -class ContiguousArrayND { -protected: - T *data = nullptr; ///< pointer to contiguous data - size_t size = 0; ///< total array size - string array_name = "Array"; /// 0) { - data = new T[size]; - for (size_t ind = 0; ind < size; ind++) - data[ind] = other.data[ind]; - } - } else { //is proxy, then copy the pointer - data = other.data; - } - } - - /** - * Overload operator= - * @param other another ContiguousArrayND - * @return itself - */ - - ContiguousArrayND &operator=(const ContiguousArrayND &other) { -#ifdef MULTIARRAY_LIFE_CYCLE - cout< 0) { - - if(data!=nullptr) delete[] data; - data = new T[size]; - - for (size_t ind = 0; ind < size; ind++) - data[ind] = other.data[ind]; - } - } else { //is proxy, then copy the pointer - data = other.data; - } - } - return *this; - } - - - //TODO: make destructor virtual, check the destructors in inherited classes - - /** - * Destructor - */ - ~ContiguousArrayND() { -#ifdef MULTIARRAY_LIFE_CYCLE - cout<array_name = name; - } - - /** - * Get total number of elements in array (its size) - * @return array size - */ - size_t get_size() const { - return size; - } - - /** - * Fill array with value - * @param value value to fill - */ - void fill(T value) { - for (size_t ind = 0; ind < size; ind++) - data[ind] = value; - } - - /** - * Get array data at absolute index ind for reading - * @param ind absolute index - * @return array value - */ - inline const T &get_data(size_t ind) const { -#ifdef MULTIARRAY_INDICES_CHECK - if ((ind < 0) | (ind >= size)) { - printf("%s: get_data ind=%d out of range (0, %d)\n", array_name, ind, size); - exit(EXIT_FAILURE); - } -#endif - return data[ind]; - } - - /** - * Get array data at absolute index ind for writing - * @param ind absolute index - * @return array value - */ - inline T &get_data(size_t ind) { -#ifdef MULTIARRAY_INDICES_CHECK - if ((ind < 0) | (ind >= size)) { - printf("%s: get_data ind=%ld out of range (0, %ld)\n", array_name.c_str(), ind, size); - exit(EXIT_FAILURE); - } -#endif - return data[ind]; - } - - /** - * Get array data pointer - * @return data array pointer - */ - inline T* get_data() const { - return data; - } - - /** - * Overload comparison operator== - * Compare the total size and array values elementwise. - * - * @param other another array - * @return - */ - bool operator==(const ContiguousArrayND &other) const { - if (this->size != other.size) - return false; - - for (size_t i = 0; i < this->size; ++i) - if (this->data[i] != other.data[i]) - return false; - - return true; - } - - - /** - * Convert to flatten vector container - * @return vector container - */ - vector to_flatten_vector() const { - vector res; - - res.resize(size); - size_t vec_ind = 0; - - for (int vec_ind = 0; vec_ind < size; vec_ind++) - res.at(vec_ind) = data[vec_ind]; - - return res; - } // end to_flatten_vector() - - - /** - * Set values from flatten vector container - * @param vec container - */ - void set_flatten_vector(const vector &vec) { - if (vec.size() != size) - throw std::invalid_argument("Flatten vector size is not consistent with expected size"); - for (size_t i = 0; i < size; i++) { - data[i] = vec[i]; - } - } - - bool is_proxy(){ - return is_proxy_; - } - -}; - - -#endif //ACE_CONTIGUOUSARRAYND_H \ No newline at end of file diff --git a/lib/pace/ace_evaluator.cpp b/lib/pace/ace_evaluator.cpp deleted file mode 100644 index 987f4502bf..0000000000 --- a/lib/pace/ace_evaluator.cpp +++ /dev/null @@ -1,660 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 31.01.20. - -#include "ace_evaluator.h" - -#include "ace_abstract_basis.h" -#include "ace_types.h" - -void ACEEvaluator::init(ACEAbstractBasisSet *basis_set) { - A.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, "A"); - A_rank1.init(basis_set->nelements, basis_set->nradbase, "A_rank1"); - - rhos.init(basis_set->ndensitymax + 1, "rhos"); // +1 density for core repulsion - dF_drho.init(basis_set->ndensitymax + 1, "dF_drho"); // +1 density for core repulsion -} - -void ACEEvaluator::init_timers() { - loop_over_neighbour_timer.init(); - forces_calc_loop_timer.init(); - forces_calc_neighbour_timer.init(); - energy_calc_timer.init(); - per_atom_calc_timer.init(); - total_time_calc_timer.init(); -} - -//================================================================================================================ - -void ACECTildeEvaluator::set_basis(ACECTildeBasisSet &bas) { - basis_set = &bas; - init(basis_set); -} - -void ACECTildeEvaluator::init(ACECTildeBasisSet *basis_set) { - - ACEEvaluator::init(basis_set); - - - weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, - "weights"); - - weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); - - - DG_cache.init(1, basis_set->nradbase, "DG_cache"); - DG_cache.fill(0); - - R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); - R_cache.fill(0); - - DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); - DR_cache.fill(0); - - Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); - Y_cache.fill({0, 0}); - - DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); - DY_cache.fill({0.}); - - //hard-core repulsion - DCR_cache.init(1, "DCR_cache"); - DCR_cache.fill(0); - dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); - - -} - -void ACECTildeEvaluator::resize_neighbours_cache(int max_jnum) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); - } - if (R_cache.get_dim(0) < max_jnum) { - - //TODO: implement grow - R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - R_cache.fill(0); - - DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - DR_cache.fill(0); - - DG_cache.resize(max_jnum, basis_set->nradbase); - DG_cache.fill(0); - - Y_cache.resize(max_jnum, basis_set->lmax + 1); - Y_cache.fill({0, 0}); - - DY_cache.resize(max_jnum, basis_set->lmax + 1); - DY_cache.fill({0}); - - //hard-core repulsion - DCR_cache.init(max_jnum, "DCR_cache"); - DCR_cache.fill(0); - } -} - - - -// double** r - atomic coordinates of atom I -// int* types - atomic types if atom I -// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; -// Usage: j = jlist_of_i[jj]; -// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; - -void -ACECTildeEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACECTildeEvaluator: basis set is not assigned"); - } - per_atom_calc_timer.start(); -#ifdef PRINT_MAIN_STEPS - printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); -#endif - DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; - DOUBLE_TYPE r_norm; - DOUBLE_TYPE xn, yn, zn, r_xyz; - DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; - DOUBLE_TYPE *r_hat; - - SPECIES_TYPE mu_j; - RANK_TYPE r, rank, t; - NS_TYPE n; - LS_TYPE l; - MS_TYPE m, m_t; - - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - int j, jj, func_ind, ms_ind; - SHORT_INT_TYPE factor; - - ACEComplex Y{0}, Y_DR{0.}; - ACEComplex B{0.}; - ACEComplex dB{0}; - ACEComplex A_cache[basis_set->rankmax]; - - dB_flatten.fill({0.}); - - ACEDYcomponent grad_phi_nlm{0}, DY{0.}; - - //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme - ACEComplex A_forward_prod[basis_set->rankmax + 1]; - ACEComplex A_backward_prod[basis_set->rankmax + 1]; - - DOUBLE_TYPE inv_r_norm; - DOUBLE_TYPE r_norms[jnum]; - DOUBLE_TYPE inv_r_norms[jnum]; - DOUBLE_TYPE rhats[jnum][3];//normalized vector - SPECIES_TYPE elements[jnum]; - const DOUBLE_TYPE xtmp = x[i][0]; - const DOUBLE_TYPE ytmp = x[i][1]; - const DOUBLE_TYPE ztmp = x[i][2]; - DOUBLE_TYPE f_ji[3]; - - bool is_element_mapping = element_type_mapping.get_size() > 0; - SPECIES_TYPE mu_i; - if (is_element_mapping) - mu_i = element_type_mapping(type[i]); - else - mu_i = type[i]; - - const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - - ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; - DOUBLE_TYPE dF_drho_core; - - //TODO: lmax -> lmaxi (get per-species type) - const LS_TYPE lmaxi = basis_set->lmax; - - //TODO: nradmax -> nradiali (get per-species type) - const NS_TYPE nradiali = basis_set->nradmax; - - //TODO: nradbase -> nradbasei (get per-species type) - const NS_TYPE nradbasei = basis_set->nradbase; - - //TODO: get per-species type number of densities - const DENSITY_TYPE ndensity= basis_set->ndensitymax; - - neighbours_forces.resize(jnum, 3); - neighbours_forces.fill(0); - - //TODO: shift nullifications to place where arrays are used - weights.fill({0}); - weights_rank1.fill(0); - A.fill({0}); - A_rank1.fill(0); - rhos.fill(0); - dF_drho.fill(0); - -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); - basis_projections.init(total_basis_size, ndensity, "c_projections"); -#endif - - //proxy references to spherical harmonics and radial functions arrays - const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; - const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; - - const Array2D &fr = basis_set->radial_functions->fr; - const Array2D &dfr = basis_set->radial_functions->dfr; - - const Array1D &gr = basis_set->radial_functions->gr; - const Array1D &dgr = basis_set->radial_functions->dgr; - - loop_over_neighbour_timer.start(); - - int jj_actual = 0; - SPECIES_TYPE type_j = 0; - int neighbour_index_mapping[jnum]; // jj_actual -> jj - //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); - r_xyz = sqrt(xn * xn + yn * yn + zn * zn); - - if (r_xyz >= current_cutoff) - continue; - - inv_r_norm = 1 / r_xyz; - - r_norms[jj_actual] = r_xyz; - inv_r_norms[jj_actual] = inv_r_norm; - rhats[jj_actual][0] = xn * inv_r_norm; - rhats[jj_actual][1] = yn * inv_r_norm; - rhats[jj_actual][2] = zn * inv_r_norm; - elements[jj_actual] = mu_j; - neighbour_index_mapping[jj_actual] = jj; - jj_actual++; - } - - int jnum_actual = jj_actual; - - //ALGORITHM 1: Atomic base A - for (jj = 0; jj < jnum_actual; ++jj) { - r_norm = r_norms[jj]; - mu_j = elements[jj]; - r_hat = rhats[jj]; - - //proxies - Array2DLM &Y_jj = Y_cache(jj); - Array2DLM &DY_jj = DY_cache(jj); - - - basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); - basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); - //loop for computing A's - //rank = 1 - for (n = 0; n < basis_set->nradbase; n++) { - GR = gr(n); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("-neigh atom %d\n", jj); - printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); - printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); -#endif - DG_cache(jj, n) = dgr(n); - A_rank1(mu_j, n) += GR * Y00; - } - //loop for computing A's - // for rank > 1 - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - R = fr(n, l); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); -#endif - - DR_cache(jj, n, l) = dfr(n, l); - R_cache(jj, n, l) = R; - - for (m = 0; m <= l; m++) { - Y = ylm(l, m); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); -#endif - A_lm(l, m) += R * Y; //accumulation sum over neighbours - Y_jj(l, m) = Y; - DY_jj(l, m) = dylm(l, m); - } - } - } - - //hard-core repulsion - rho_core += basis_set->radial_functions->cr; - DCR_cache(jj) = basis_set->radial_functions->dcr; - - } //end loop over neighbours - - //complex conjugate A's (for NEGATIVE (-m) terms) - // for rank > 1 - for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm - for (m = 1; m <= l; m++) { - factor = m % 2 == 0 ? 1 : -1; - A_lm(l, -m) = A_lm(l, m).conjugated() * factor; - } - } - } - } //now A's are constructed - loop_over_neighbour_timer.stop(); - - // ==================== ENERGY ==================== - - energy_calc_timer.start(); -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.fill(0); - basis_projections.fill(0); -#endif - - //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation - //rank=1 - for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { - ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; -// ndensity = func->ndensity; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = 0\n",(int) ndensity ); - print_C_tilde_B_basis_function(*func); -#endif - double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); - printf(" coeff[0] = %f\n", func->ctildes[0]); -#endif - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - rhos(p) += func->ctildes[p] * A_cur; -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; -#endif - } - } // end loop for rank=1 - - //rank>1 - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - //TODO: check if func->ctildes are zero, then skip -// ndensity = func->ndensity; - rank = func->rank; - r = rank - 1; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = %d\n",(int) ndensity, (int)r ); - print_C_tilde_B_basis_function(*func); -#endif - mus = func->mus; - ns = func->ns; - ls = func->ls; - - //loop over {ms} combinations in sum - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * rank]; // current ms-combination (of length = rank) - - //loop over m, collect B = product of A with given ms - A_forward_prod[0] = 1; - A_backward_prod[r] = 1; - - //fill forward A-product triangle - for (t = 0; t < rank; t++) { - //TODO: optimize ns[t]-1 -> ns[t] during functions construction - A_cache[t] = A(mus[t], ns[t] - 1, ls[t], ms[t]); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A(x=%d, n=%d, l=%d, m=%d)=(%f,%f)\n", mus[t], ns[t], ls[t], ms[t], A_cache[t].real, - A_cache[t].img); -#endif - A_forward_prod[t + 1] = A_forward_prod[t] * A_cache[t]; - } - - B = A_forward_prod[t]; - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("B = (%f, %f)\n", (B).real, (B).img); -#endif - //fill backward A-product triangle - for (t = r; t >= 1; t--) { - A_backward_prod[t - 1] = - A_backward_prod[t] * A_cache[t]; - } - - for (t = 0; t < rank; ++t, ++func_ms_t_ind) { - dB = A_forward_prod[t] * A_backward_prod[t]; //dB - product of all A's except t-th - dB_flatten(func_ms_t_ind) = dB; -#ifdef DEBUG_FORCES_CALCULATIONS - m_t = ms[t]; - printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); -#endif - } - - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //real-part only multiplication - rhos(p) += B.real_part_product(func->ctildes[ms_ind * ndensity + p]); - -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections(func_ind, p)+=B.real_part_product(func->ctildes[ms_ind * ndensity + p]); -#endif - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("rhos(%d) += %f\n", p, B.real_part_product(func->ctildes[ms_ind * ndensity + p])); - printf("Rho[i = %d][p = %d] = %f\n", i , p , rhos(p)); -#endif - } - }//end of loop over {ms} combinations in sum - }// end loop for rank>1 - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("rhos = "); - for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); - drho_cut = basis_set->drho_core_cutoffs(mu_i); - - basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); - basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); - - dF_drho_core = evdwl * dfcut + 1; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - dF_drho(p) *= fcut; - evdwl_cut = evdwl * fcut + rho_core; - - // E0 shift - evdwl_cut += basis_set->E0vals(mu_i); - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dFrhos = "); - for(DENSITY_TYPE p =0; pndensity; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; - } - } - - // rank>1 - func_ms_ind = 0; - func_ms_t_ind = 0;// index for dB - DOUBLE_TYPE theta = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; -// ndensity = func->ndensity; - rank = func->rank; - mus = func->mus; - ns = func->ns; - ls = func->ls; - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * rank]; - theta = 0; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - theta += dF_drho(p) * func->ctildes[ms_ind * ndensity + p]; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("(p=%d) theta += dF_drho[p] * func.ctildes[ms_ind * ndensity + p] = %f * %f = %f\n",p, dF_drho(p), func->ctildes[ms_ind * ndensity + p],dF_drho(p)*func->ctildes[ms_ind * ndensity + p]); - printf("theta=%f\n",theta); -#endif - } - - theta *= 0.5; // 0.5 factor due to possible double counting ??? - for (t = 0; t < rank; ++t, ++func_ms_t_ind) { - m_t = ms[t]; - factor = (m_t % 2 == 0 ? 1 : -1); - dB = dB_flatten(func_ms_t_ind); - weights(mus[t], ns[t] - 1, ls[t], m_t) += theta * dB; //Theta_array(func_ms_ind); - // update -m_t (that could also be positive), because the basis is half_basis - weights(mus[t], ns[t] - 1, ls[t], -m_t) += - theta * (dB).conjugated() * factor;// Theta_array(func_ms_ind); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dB(n,l,m)(%d,%d,%d) = (%f, %f)\n", ns[t], ls[t], m_t, (dB).real, (dB).img); - printf("theta = %f\n",theta); - printf("weights(n,l,m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], m_t, (theta * dB * 0.5).real, - (theta * dB * 0.5).img); - printf("weights(n,l,-m)(%d,%d,%d) += (%f, %f)\n", ns[t], ls[t], -m_t, - ( theta * (dB).conjugated() * factor * 0.5).real, - ( theta * (dB).conjugated() * factor * 0.5).img); -#endif - } - } - } - energy_calc_timer.stop(); - -// ==================== FORCES ==================== -#ifdef PRINT_MAIN_STEPS - printf("\nFORCE CALCULATION\n"); - printf("loop over neighbours\n"); -#endif - - forces_calc_loop_timer.start(); -// loop over neighbour atoms for force calculations - for (jj = 0; jj < jnum_actual; ++jj) { - mu_j = elements[jj]; - r_hat = rhats[jj]; - inv_r_norm = inv_r_norms[jj]; - - Array2DLM &Y_cache_jj = Y_cache(jj); - Array2DLM &DY_cache_jj = DY_cache(jj); - -#ifdef PRINT_LOOPS_INDICES - printf("\nneighbour atom #%d\n", jj); - printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); -#endif - - forces_calc_neighbour_timer.start(); - - f_ji[0] = f_ji[1] = f_ji[2] = 0; - -//for rank = 1 - for (n = 0; n < nradbasei; ++n) { - if (weights_rank1(mu_j, n) == 0) - continue; - auto &DG = DG_cache(jj, n); - DGR = DG * Y00; - DGR *= weights_rank1(mu_j, n); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); - printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); - printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); - printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); -#endif - f_ji[0] += DGR * r_hat[0]; - f_ji[1] += DGR * r_hat[1]; - f_ji[2] += DGR * r_hat[2]; - } - -//for rank > 1 - for (n = 0; n < nradiali; n++) { - for (l = 0; l <= lmaxi; l++) { - R_over_r = R_cache(jj, n, l) * inv_r_norm; - DR = DR_cache(jj, n, l); - - // for m>=0 - for (m = 0; m <= l; m++) { - ACEComplex w = weights(mu_j, n, l, m); - if (w == 0) - continue; - //counting for -m cases if m>0 - if (m > 0) w *= 2; - - DY = DY_cache_jj(l, m); - Y_DR = Y_cache_jj(l, m) * DR; - - grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; - grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; - grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, - grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, - grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, - grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); - - printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m,w.real, w.img); - //if (m>0) w*=2; - printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, - w.real_part_product(grad_phi_nlm.a[0]), - w.real_part_product(grad_phi_nlm.a[1]), - w.real_part_product(grad_phi_nlm.a[2]) - ); -#endif -// real-part multiplication only - f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); - f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); - f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); - } - } - } - - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); -#endif - - //hard-core repulsion - DCR = DCR_cache(jj); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("DCR = %f\n",DCR); -#endif - f_ji[0] += dF_drho_core * DCR * r_hat[0]; - f_ji[1] += dF_drho_core * DCR * r_hat[1]; - f_ji[2] += dF_drho_core * DCR * r_hat[2]; -#ifdef PRINT_INTERMEDIATE_VALUES - printf("with core-repulsion\n"); - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); - printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); -#endif - - neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; - neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; - neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; - - forces_calc_neighbour_timer.stop(); - }// end loop over neighbour atoms for forces - - forces_calc_loop_timer.stop(); - - //now, energies and forces are ready - //energies(i) = evdwl + rho_core; - e_atom = evdwl_cut; - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); -#endif - per_atom_calc_timer.stop(); -} \ No newline at end of file diff --git a/lib/pace/ace_evaluator.h b/lib/pace/ace_evaluator.h deleted file mode 100644 index 356ea52563..0000000000 --- a/lib/pace/ace_evaluator.h +++ /dev/null @@ -1,230 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 31.01.20. - -#ifndef ACE_EVALUATOR_H -#define ACE_EVALUATOR_H - -#include "ace_abstract_basis.h" -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_c_basis.h" -#include "ace_complex.h" -#include "ace_timing.h" -#include "ace_types.h" - -/** - * Basic evaluator class, that should accept the basis set and implement the "compute_atom" method using given basis set. - */ -class ACEEvaluator { -protected: - - Array2D A_rank1 = Array2D("A_rank1"); ///< 2D-array for storing A's for rank=1, shape: A(mu_j,n) - Array4DLM A = Array4DLM("A"); ///< 4D array with (l,m) last indices for storing A's for rank>1: A(mu_j, n, l, m) - - Array1D rhos = Array1D("rhos"); ///< densities \f$ \rho^{(p)} \f$(ndensity), p = 0 .. ndensity-1 - Array1D dF_drho = Array1D("dF_drho"); ///< derivatives of cluster functional wrt. densities, index = 0 .. ndensity-1 - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACEAbstractBasisSet *basis_set); - -public: - // set of timers for code profiling - - ACETimer loop_over_neighbour_timer; ///< timer for loop over neighbours when constructing A's for single central atom - ACETimer per_atom_calc_timer; ///< timer for single compute_atom call - - - ACETimer forces_calc_loop_timer; ///< timer for forces calculations for single central atom - ACETimer forces_calc_neighbour_timer; ///< timer for loop over neighbour atoms for force calculations - - ACETimer energy_calc_timer; ///< timer for energy calculation - ACETimer total_time_calc_timer; ///< timer for total calculations of all atoms within given atomic environment system - - /** - * Initialize all timers - */ - void init_timers(); - - /** - * Mapping from external atoms types, i.e. LAMMPS, to internal SPECIES_TYPE, used in basis functions - */ - Array1D element_type_mapping = Array1D("element_type_mapping"); - - - DOUBLE_TYPE e_atom = 0; ///< energy of current atom, including core-repulsion - - /** - * temporary array for the pair forces between current atom_i and its neighbours atom_k - * neighbours_forces(k,3), k = 0..num_of_neighbours(atom_i)-1 - */ - Array2D neighbours_forces = Array2D("neighbours_forces"); - - ACEEvaluator() = default; - - virtual ~ACEEvaluator() = default; - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - virtual void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) = 0; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - virtual void resize_neighbours_cache(int max_jnum) = 0; - -#ifdef EXTRA_C_PROJECTIONS - /** - * 2D array to store projections of basis function for rank = 1, shape: [func_ind][ndensity] - */ - Array2D basis_projections_rank1 = Array2D("basis_projections_rank1"); - - /** - * 2D array to store projections of basis function for rank > 1, shape: [func_ind][ndensity] - */ - Array2D basis_projections = Array2D("basis_projections"); -#endif -}; - -//TODO: split into separate file -/** - * Evaluator for C-tilde basis set, that should accept the basis set and implement the "compute_atom" method using given basis set. - */ -class ACECTildeEvaluator : public ACEEvaluator { - - /** - * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase] - */ - Array2D weights_rank1 = Array2D("weights_rank1"); - - /** - * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] - */ - Array4DLM weights = Array4DLM("weights"); - - /** - * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) - * shape:[max_jnum][nradbase] - */ - Array2D DG_cache = Array2D("DG_cache"); - - - /** - * cache for \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D R_cache = Array3D("R_cache"); - /** - * cache for derivatives of \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D DR_cache = Array3D("DR_cache"); - /** - * cache for \f$ Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM Y_cache = Array3DLM("Y_cache"); - /** - * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM DY_cache = Array3DLM("dY_dense_cache"); - - /** - * cache for derivatives of hard-core repulsion - * shape:[max_jnum] - */ - Array1D DCR_cache = Array1D("DCR_cache"); - - /** - * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], - * shape:[func_ms_r_ind] - */ - Array1D dB_flatten = Array1D("dB_flatten"); - - /** - * pointer to the ACEBasisSet object - */ - ACECTildeBasisSet *basis_set = nullptr; - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACECTildeBasisSet *basis_set); - -public: - - ACECTildeEvaluator() = default; - - explicit ACECTildeEvaluator(ACECTildeBasisSet &bas) { - set_basis(bas); - } - - /** - * set the basis function to the ACE evaluator - * @param bas - */ - void set_basis(ACECTildeBasisSet &bas); - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - void resize_neighbours_cache(int max_jnum) override; -}; - - -#endif //ACE_EVALUATOR_H \ No newline at end of file diff --git a/lib/pace/ace_flatten_basis.cpp b/lib/pace/ace_flatten_basis.cpp deleted file mode 100644 index 541785a202..0000000000 --- a/lib/pace/ace_flatten_basis.cpp +++ /dev/null @@ -1,130 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by yury on 28.04.2020. - -#include "ace_flatten_basis.h" - -ACEFlattenBasisSet::ACEFlattenBasisSet(const ACEFlattenBasisSet &other) { - _copy_scalar_memory(other); - _copy_dynamic_memory(other); -} - -ACEFlattenBasisSet &ACEFlattenBasisSet::operator=(const ACEFlattenBasisSet &other) { - if (this != &other) { - _clean(); - _copy_scalar_memory(other); - _copy_dynamic_memory(other); - } - return *this; -} - - -ACEFlattenBasisSet::~ACEFlattenBasisSet() { - ACEFlattenBasisSet::_clean(); -} - -void ACEFlattenBasisSet::_clean() { - //chained call of base class method - ACEAbstractBasisSet::_clean(); - _clean_contiguous_arrays(); - _clean_basissize_arrays(); - -} - -void ACEFlattenBasisSet::_clean_basissize_arrays() { - delete[] total_basis_size; - total_basis_size = nullptr; - - delete[] total_basis_size_rank1; - total_basis_size_rank1 = nullptr; -} - -void ACEFlattenBasisSet::_clean_contiguous_arrays() { - delete[] full_ns_rank1; - full_ns_rank1 = nullptr; - - delete[] full_ls_rank1; - full_ls_rank1 = nullptr; - - delete[] full_mus_rank1; - full_mus_rank1 = nullptr; - - delete[] full_ms_rank1; - full_ms_rank1 = nullptr; - - ////// - - delete[] full_ns; - full_ns = nullptr; - - delete[] full_ls; - full_ls = nullptr; - - delete[] full_mus; - full_mus = nullptr; - - delete[] full_ms; - full_ms = nullptr; -} - -void ACEFlattenBasisSet::_copy_scalar_memory(const ACEFlattenBasisSet &src) { - ACEAbstractBasisSet::_copy_scalar_memory(src); - - rank_array_total_size_rank1 = src.rank_array_total_size_rank1; - coeff_array_total_size_rank1 = src.coeff_array_total_size_rank1; - rank_array_total_size = src.rank_array_total_size; - ms_array_total_size = src.ms_array_total_size; - coeff_array_total_size = src.coeff_array_total_size; - - max_B_array_size = src.max_B_array_size; - max_dB_array_size = src.max_dB_array_size; - num_ms_combinations_max = src.num_ms_combinations_max; -} - -void ACEFlattenBasisSet::_copy_dynamic_memory(const ACEFlattenBasisSet &src) { //allocate new memory - - ACEAbstractBasisSet::_copy_dynamic_memory(src); - - if (src.total_basis_size_rank1 == nullptr) - throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size_rank1 - array not initialized"); - if (src.total_basis_size == nullptr) - throw runtime_error("Could not copy ACEFlattenBasisSet::total_basis_size - array not initialized"); - - delete[] total_basis_size_rank1; - total_basis_size_rank1 = new SHORT_INT_TYPE[nelements]; - delete[] total_basis_size; - total_basis_size = new SHORT_INT_TYPE[nelements]; - - //copy - for (SPECIES_TYPE mu = 0; mu < nelements; ++mu) { - total_basis_size_rank1[mu] = src.total_basis_size_rank1[mu]; - total_basis_size[mu] = src.total_basis_size[mu]; - } -} - diff --git a/lib/pace/ace_flatten_basis.h b/lib/pace/ace_flatten_basis.h deleted file mode 100644 index e21cbb749a..0000000000 --- a/lib/pace/ace_flatten_basis.h +++ /dev/null @@ -1,135 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Lysogroskiy Yury on 28.04.2020. - -#ifndef ACE_EVALUATOR_ACE_FLATTEN_BASIS_H -#define ACE_EVALUATOR_ACE_FLATTEN_BASIS_H - - -#include "ace_abstract_basis.h" -#include "ace_c_basisfunction.h" -#include "ace_radial.h" -#include "ace_spherical_cart.h" -#include "ace_types.h" - -/** - * Basis set with basis function attributes, i.e. \f$ \mathbf{n}, \mathbf{l}, \mathbf{m}\f$, etc. - * packed into contiguous arrays for the cache-friendly memory layout. - */ -class ACEFlattenBasisSet : public ACEAbstractBasisSet { -public: - //arrays and its sizes for rank = 1 basis functions for packed basis - - size_t rank_array_total_size_rank1 = 0; ///< size for full_ns_rank1, full_ls_rank1, full_Xs_rank1 - size_t coeff_array_total_size_rank1 = 0; ///< size for full coefficients array (depends on B or C-Tilde basis) - - NS_TYPE *full_ns_rank1 = nullptr; ///< ns contiguous package [rank_array_total_size_rank1] - LS_TYPE *full_ls_rank1 = nullptr; ///< ls contiguous package [rank_array_total_size_rank1] - SPECIES_TYPE *full_mus_rank1 = nullptr; ///< mus contiguous package [rank_array_total_size_rank1] - MS_TYPE *full_ms_rank1 = nullptr; ///< m_s contiguous package[rank_array_total_size_rank1] - - //arrays and its sizes for rank > 1 basis functions for packed basis - size_t rank_array_total_size = 0; ///< size for full_ns, full_ls, full_Xs - size_t ms_array_total_size = 0; ///< size for full_ms array - size_t coeff_array_total_size = 0;///< size for full coefficients arrays (depends on B- or C- basis) - - NS_TYPE *full_ns = nullptr; ///< ns contiguous package [rank_array_total_size] - LS_TYPE *full_ls = nullptr; ///< ls contiguous package [rank_array_total_size] - SPECIES_TYPE *full_mus = nullptr; ///< mus contiguous package [rank_array_total_size] - MS_TYPE *full_ms = nullptr; ///< //m_s contiguous package [ms_array_total_size] - - /** - * Rearrange basis functions in contiguous memory to optimize cache access - */ - virtual void pack_flatten_basis() = 0; - - virtual void flatten_basis() = 0; - - //1D flat array basis representation: [mu] - SHORT_INT_TYPE *total_basis_size_rank1 = nullptr; ///< per-species type array of total_basis_rank1[mu] sizes - SHORT_INT_TYPE *total_basis_size = nullptr; ///< per-species type array of total_basis[mu] sizes - - size_t max_B_array_size = 0; ///< maximum over elements array size for B[func_ind][ms_ind] - size_t max_dB_array_size = 0; ///< maximum over elements array size for dB[func_ind][ms_ind][r] - - SHORT_INT_TYPE num_ms_combinations_max = 0; ///< maximum number of ms combinations among all basis functions - - /** - * Default constructor - */ - ACEFlattenBasisSet() = default; - - /** - * Copy constructor (see Rule of Three) - * @param other - */ - ACEFlattenBasisSet(const ACEFlattenBasisSet &other); - - /** - * operator= (see Rule of Three) - * @param other - * @return - */ - ACEFlattenBasisSet &operator=(const ACEFlattenBasisSet &other); - - /** - * Destructor (see Rule of Three) - */ - ~ACEFlattenBasisSet() override; - - // routines for copying and cleaning dynamic memory of the class (see Rule of Three) - /** - * Cleaning dynamic memory of the class (see. Rule of Three), - * must be idempotent for safety - */ - void _clean() override; - - /** - * Copying scalar variables - * @param src - */ - void _copy_scalar_memory(const ACEFlattenBasisSet &src); - - /** - * Copying and cleaning dynamic memory of the class (see. Rule of Three) - * @param src - */ - void _copy_dynamic_memory(const ACEFlattenBasisSet &src); - - /** - * Clean contiguous arrays - */ - virtual void _clean_contiguous_arrays(); - - /** - * Release dynamic arrays with basis set sizes - */ - void _clean_basissize_arrays(); -}; - -#endif //ACE_EVALUATOR_ACE_FLATTEN_BASIS_H diff --git a/lib/pace/ace_radial.cpp b/lib/pace/ace_radial.cpp deleted file mode 100644 index 01348a719c..0000000000 --- a/lib/pace/ace_radial.cpp +++ /dev/null @@ -1,566 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -#include -#include -#include - -#include "ace_radial.h" - -const DOUBLE_TYPE pi = 3.14159265358979323846264338327950288419; // pi - -ACERadialFunctions::ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - init(nradb, lmax, nradial, deltaSplineBins, nelements, cutoff, radbasename); -} - -void ACERadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - this->nradbase = nradb; - this->lmax = lmax; - this->nradial = nradial; - this->deltaSplineBins = deltaSplineBins; - this->nelements = nelements; - this->cutoff = cutoff; - this->radbasename = radbasename; - - gr.init(nradbase, "gr"); - dgr.init(nradbase, "dgr"); - d2gr.init(nradbase, "d2gr"); - - - fr.init(nradial, lmax + 1, "fr"); - dfr.init(nradial, lmax + 1, "dfr"); - d2fr.init(nradial, lmax + 1, "d2fr"); - - - cheb.init(nradbase + 1, "cheb"); - dcheb.init(nradbase + 1, "dcheb"); - cheb2.init(nradbase + 1, "cheb2"); - - - splines_gk.init(nelements, nelements, "splines_gk"); - splines_rnl.init(nelements, nelements, "splines_rnl"); - splines_hc.init(nelements, nelements, "splines_hc"); - - lambda.init(nelements, nelements, "lambda"); - lambda.fill(1.); - - cut.init(nelements, nelements, "cut"); - cut.fill(1.); - - dcut.init(nelements, nelements, "dcut"); - dcut.fill(1.); - - crad.init(nelements, nelements, nradial, (lmax + 1), nradbase, "crad"); - crad.fill(0.); - - //hard-core repulsion - prehc.init(nelements, nelements, "prehc"); - prehc.fill(0.); - - lambdahc.init(nelements, nelements, "lambdahc"); - lambdahc.fill(1.); - -} - - -/** -Function that computes Chebyshev polynomials of first and second kind - to setup the radial functions and the derivatives - -@param n, x - -@returns cheb1, dcheb1 -*/ -void ACERadialFunctions::calcCheb(NS_TYPE n, DOUBLE_TYPE x) { - if (n < 0) { - char s[1024]; - sprintf(s, "The order n of the polynomials should be positive %d\n", n); - throw std::invalid_argument(s); - } - DOUBLE_TYPE twox = 2.0 * x; - cheb(0) = 1.; - dcheb(0) = 0.; - cheb2(0) = 1.; - - if (nradbase > 1) { - cheb(1) = x; - cheb2(1) = twox; - } - for (NS_TYPE m = 1; m <= n - 1; m++) { - cheb(m + 1) = twox * cheb(m) - cheb(m - 1); - cheb2(m + 1) = twox * cheb2(m) - cheb2(m - 1); - } - for (NS_TYPE m = 1; m <= n; m++) { - dcheb(m) = m * cheb2(m - 1); - } -#ifdef DEBUG_RADIAL - for ( NS_TYPE m=0; m<=n; m++ ) { - printf(" m %d cheb %f dcheb %f \n", m, cheb(m), dcheb(m)); - } -#endif -} - -/** -Function that computes radial basis. - -@param lam, nradbase, cut, dcut, r - -@returns gr, dgr -*/ -void ACERadialFunctions::radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - /*lam is given by the formula (24), that contains cut */ - - if (r < cut) { - if (radbasename == "ChebExpCos") { - chebExpCos(lam, cut, dcut, r); - } else if (radbasename == "ChebPow") { - chebPow(lam, cut, dcut, r); - } else if (radbasename == "ChebLinear") { - chebLinear(lam, cut, dcut, r); - } else { - throw invalid_argument("Unknown radial basis function name: " + radbasename); - } - } else { - gr.fill(0); - dgr.fill(0); - } -} - -/*** - * Radial function: ChebExpCos, cheb exp scaling including cos envelope - * @param lam function parameter - * @param cut cutoff distance - * @param r function input argument - * @return fills in gr and dgr arrays - */ -void -ACERadialFunctions::chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE y2, y1, x, dx; - DOUBLE_TYPE env, denv, fcut, dfcut; - /* scaled distance x and derivative*/ - y1 = exp(-lam * r / cut); - y2 = exp(-lam); - x = 1.0 - 2.0 * ((y1 - y2) / (1 - y2)); - dx = 2 * (lam / cut) * (y1 / (1 - y2)); - /* calculation of Chebyshev polynomials from the recursion */ - calcCheb(nradbase - 1, x); - gr(0) = cheb(0); - dgr(0) = dcheb(0) * dx; - for (NS_TYPE n = 2; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n - 1); - dgr(n - 1) = -0.5 * dcheb(n - 1) * dx; - } - env = 0.5 * (1.0 + cos(M_PI * r / cut)); - denv = -0.5 * sin(M_PI * r / cut) * M_PI / cut; - for (NS_TYPE n = 0; n < nradbase; n++) { - dgr(n) = gr(n) * denv + dgr(n) * env; - gr(n) = gr(n) * env; - } - // for radtype = 3 a smooth cut is already included in the basis function - dx = cut - dcut; - if (r > dx) { - fcut = 0.5 * (1.0 + cos(M_PI * (r - dx) / dcut)); - dfcut = -0.5 * sin(M_PI * (r - dx) / dcut) * M_PI / dcut; - for (NS_TYPE n = 0; n < nradbase; n++) { - dgr(n) = gr(n) * dfcut + dgr(n) * fcut; - gr(n) = gr(n) * fcut; - } - } -} - -/*** -* Radial function: ChebPow, Radial function: ChebPow -* - argument of Chebyshev polynomials -* x = 2.0*( 1.0 - (1.0 - r/rcut)^lam ) - 1.0 -* - radial function -* gr(n) = ( 1.0 - Cheb(n) )/2.0, n = 1,...,nradbase -* - the function fulfills: -* gr(n) = 0 at rcut -* dgr(n) = 0 at rcut for lam >= 1 -* second derivative zero at rcut for lam >= 2 -* -> the radial function does not require a separate cutoff function -* - corresponds to radial basis radtype=5 in Fortran code -* -* @param lam function parameter -* @param cut cutoff distance -* @param r function input argument -* @return fills in gr and dgr arrays -*/ -void -ACERadialFunctions::chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE y, dy, x, dx; - /* scaled distance x and derivative*/ - y = (1.0 - r / cut); - dy = pow(y, (lam - 1.0)); - y = dy * y; - dy = -lam / cut * dy; - - x = 2.0 * (1.0 - y) - 1.0; - dx = -2.0 * dy; - calcCheb(nradbase, x); - for (NS_TYPE n = 1; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n); - dgr(n - 1) = -0.5 * dcheb(n) * dx; - } -} - - -void -ACERadialFunctions::chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r) { - DOUBLE_TYPE x, dx; - /* scaled distance x and derivative*/ - x = (1.0 - r / cut); - dx = -1 / cut; - calcCheb(nradbase, x); - for (NS_TYPE n = 1; n <= nradbase; n++) { - gr(n - 1) = 0.5 - 0.5 * cheb(n); - dgr(n - 1) = -0.5 * dcheb(n) * dx; - } -} - -/** -Function that computes radial functions. - -@param nradbase, nelements, elei, elej - -@returns fr, dfr -*/ -void ACERadialFunctions::radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej) { - DOUBLE_TYPE frval, dfrval; - for (NS_TYPE n = 0; n < nradial; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - frval = 0.0; - dfrval = 0.0; - for (NS_TYPE k = 0; k < nradbase; k++) { - frval += crad(elei, elej, n, l, k) * gr(k); - dfrval += crad(elei, elej, n, l, k) * dgr(k); - } - fr(n, l) = frval; - dfr(n, l) = dfrval; - } - } -} - - -void ACERadialFunctions::all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r) { - DOUBLE_TYPE lam = lambda(mu_i, mu_j); - DOUBLE_TYPE r_cut = cut(mu_i, mu_j); - DOUBLE_TYPE dr_cut = dcut(mu_i, mu_j); - // set up radial functions - radbase(lam, r_cut, dr_cut, r); //update gr, dgr - radfunc(mu_i, mu_j); // update fr(nr, l), dfr(nr, l) -} - - -void ACERadialFunctions::setuplookupRadspline() { - using namespace std::placeholders; - DOUBLE_TYPE lam, r_cut, dr_cut; - DOUBLE_TYPE cr_c, dcr_c, pre, lamhc; - - // at r = rcut + eps the function and its derivatives is zero - for (SPECIES_TYPE elei = 0; elei < nelements; elei++) { - for (SPECIES_TYPE elej = 0; elej < nelements; elej++) { - - lam = lambda(elei, elej); - r_cut = cut(elei, elej); - dr_cut = dcut(elei, elej); - - splines_gk(elei, elej).setupSplines(gr.get_size(), - std::bind(&ACERadialFunctions::radbase, this, lam, r_cut, dr_cut, - _1),//update gr, dgr - gr.get_data(), - dgr.get_data(), deltaSplineBins, cutoff); - - splines_rnl(elei, elej).setupSplines(fr.get_size(), - std::bind(&ACERadialFunctions::all_radfunc, this, elei, elej, - _1), // update fr(nr, l), dfr(nr, l) - fr.get_data(), - dfr.get_data(), deltaSplineBins, cutoff); - - - pre = prehc(elei, elej); - lamhc = lambdahc(elei, elej); -// radcore(r, pre, lamhc, cutoff, cr_c, dcr_c); - splines_hc(elei, elej).setupSplines(1, - std::bind(&ACERadialFunctions::radcore, _1, pre, lamhc, cutoff, - std::ref(cr_c), std::ref(dcr_c)), - &cr_c, - &dcr_c, deltaSplineBins, cutoff); - } - } - -} - -/** -Function that gets radial function from look-up table using splines. - -@param r, nradbase_c, nradial_c, lmax, mu_i, mu_j - -@returns fr, dfr, gr, dgr, cr, dcr -*/ -void -ACERadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, bool calc_second_derivatives) { - auto &spline_gk = splines_gk(mu_i, mu_j); - auto &spline_rnl = splines_rnl(mu_i, mu_j); - auto &spline_hc = splines_hc(mu_i, mu_j); - - spline_gk.calcSplines(r, calc_second_derivatives); // populate splines_gk.values, splines_gk.derivatives; - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr(nr) = spline_gk.values(nr); - dgr(nr) = spline_gk.derivatives(nr); - if (calc_second_derivatives) - d2gr(nr) = spline_gk.second_derivatives(nr); - } - - spline_rnl.calcSplines(r, calc_second_derivatives); - for (size_t ind = 0; ind < fr.get_size(); ind++) { - fr.get_data(ind) = spline_rnl.values.get_data(ind); - dfr.get_data(ind) = spline_rnl.derivatives.get_data(ind); - if (calc_second_derivatives) - d2fr.get_data(ind) = spline_rnl.second_derivatives.get_data(ind); - } - - spline_hc.calcSplines(r, calc_second_derivatives); - cr = spline_hc.values(0); - dcr = spline_hc.derivatives(0); - if (calc_second_derivatives) - d2cr = spline_hc.second_derivatives(0); -} - - -void -ACERadialFunctions::radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, - DOUBLE_TYPE &dcr) { -/* pseudocode for hard core repulsion -in: - r: distance - pre: prefactor: read from input, depends on pair of atoms mu_i mu_j - lambda: exponent: read from input, depends on pair of atoms mu_i mu_j - cutoff: cutoff distance: read from input, depends on pair of atoms mu_i mu_j -out: -cr: hard core repulsion -dcr: derivative of hard core repulsion - - function - \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f - -*/ - - DOUBLE_TYPE r2, lr2, y, x0, env, denv; - -// repulsion strictly positive and decaying - pre = abs(pre); - lambda = abs(lambda); - - r2 = r * r; - lr2 = lambda * r2; - if (lr2 < 50.0) { - y = exp(-lr2); - cr = pre * y / r; - dcr = -pre * y * (2.0 * lr2 + 1.0) / r2; - - x0 = r / cutoff; - env = 0.5 * (1.0 + cos(pi * x0)); - denv = -0.5 * sin(pi * x0) * pi / cutoff; - dcr = cr * denv + dcr * env; - cr = cr * env; - } else { - cr = 0.0; - dcr = 0.0; - } - -} - -void -ACERadialFunctions::evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j) { - if (nradbase_c > nradbase) - throw invalid_argument("nradbase_c couldn't be larger than nradbase"); - if (nradial_c > nradial) - throw invalid_argument("nradial_c couldn't be larger than nradial"); - if (mu_i > nelements) - throw invalid_argument("mu_i couldn't be larger than nelements"); - if (mu_j > nelements) - throw invalid_argument("mu_j couldn't be larger than nelements"); - - gr_vec.resize(r_vec.size(), nradbase_c); - dgr_vec.resize(r_vec.size(), nradbase_c); - d2gr_vec.resize(r_vec.size(), nradbase_c); - - fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - dfr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - d2fr_vec.resize(r_vec.size(), fr.get_dim(0), fr.get_dim(1)); - - for (size_t i = 0; i < r_vec.size(); i++) { - DOUBLE_TYPE r = r_vec[i]; - this->evaluate(r, nradbase_c, nradial_c, mu_i, mu_j, true); - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr_vec(i, nr) = gr(nr); - dgr_vec(i, nr) = dgr(nr); - d2gr_vec(i, nr) = d2gr(nr); - } - - for (NS_TYPE nr = 0; nr < nradial_c; nr++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fr_vec(i, nr, l) = fr(nr, l); - dfr_vec(i, nr, l) = dfr(nr, l); - d2fr_vec(i, nr, l) = d2fr(nr, l); - - } - } - } - -} - -void SplineInterpolator::setupSplines(int num_of_functions, RadialFunctions func, - DOUBLE_TYPE *values, - DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff) { - - this->deltaSplineBins = deltaSplineBins; - this->cutoff = cutoff; - this->ntot = static_cast(cutoff / deltaSplineBins); - - DOUBLE_TYPE r, c[4]; - this->num_of_functions = num_of_functions; - this->values.resize(num_of_functions); - this->derivatives.resize(num_of_functions); - this->second_derivatives.resize(num_of_functions); - - Array1D f1g(num_of_functions); - Array1D f1gd1(num_of_functions); - f1g.fill(0); - f1gd1.fill(0); - - nlut = ntot; - DOUBLE_TYPE f0, f1, f0d1, f1d1; - int idx; - - // cutoff is global cutoff - rscalelookup = (DOUBLE_TYPE) nlut / cutoff; - invrscalelookup = 1.0 / rscalelookup; - - lookupTable.init(ntot + 1, num_of_functions, 4); - if (values == nullptr & num_of_functions > 0) - throw invalid_argument("SplineInterpolator::setupSplines: values could not be null"); - if (dvalues == nullptr & num_of_functions > 0) - throw invalid_argument("SplineInterpolator::setupSplines: dvalues could not be null"); - - for (int n = nlut; n >= 1; n--) { - r = invrscalelookup * DOUBLE_TYPE(n); - func(r); //populate values and dvalues arrays - for (int func_id = 0; func_id < num_of_functions; func_id++) { - f0 = values[func_id]; - f1 = f1g(func_id); - f0d1 = dvalues[func_id] * invrscalelookup; - f1d1 = f1gd1(func_id); - // evaluate coefficients - c[0] = f0; - c[1] = f0d1; - c[2] = 3.0 * (f1 - f0) - f1d1 - 2.0 * f0d1; - c[3] = -2.0 * (f1 - f0) + f1d1 + f0d1; - // store coefficients - for (idx = 0; idx <= 3; idx++) - lookupTable(n, func_id, idx) = c[idx]; - - // evaluate function values and derivatives at current position - f1g(func_id) = c[0]; - f1gd1(func_id) = c[1]; - } - } - - -} - - -void SplineInterpolator::calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives) { - DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2, w4l2; - DOUBLE_TYPE c[4]; - int func_id, idx; - DOUBLE_TYPE x = r * rscalelookup; - int nl = static_cast(floor(x)); - - if (nl <= 0) - throw std::invalid_argument("Encountered very small distance. Stopping."); - - if (nl < nlut) { - wl = x - DOUBLE_TYPE(nl); - wl2 = wl * wl; - wl3 = wl2 * wl; - w2l1 = 2.0 * wl; - w3l2 = 3.0 * wl2; - w4l2 = 6.0 * wl; - for (func_id = 0; func_id < num_of_functions; func_id++) { - for (idx = 0; idx <= 3; idx++) { - c[idx] = lookupTable(nl, func_id, idx); - } - values(func_id) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; - derivatives(func_id) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; - if (calc_second_derivatives) - second_derivatives(func_id) = (c[2] + c[3] * w4l2) * rscalelookup * rscalelookup * 2; - } - } else { // fill with zeroes - values.fill(0); - derivatives.fill(0); - if (calc_second_derivatives) - second_derivatives.fill(0); - } -} - -void SplineInterpolator::calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind) { - DOUBLE_TYPE wl, wl2, wl3, w2l1, w3l2; - DOUBLE_TYPE c[4]; - int idx; - DOUBLE_TYPE x = r * rscalelookup; - int nl = static_cast(floor(x)); - - if (nl <= 0) - throw std::invalid_argument("Encountered very small distance. Stopping."); - - if (nl < nlut) { - wl = x - DOUBLE_TYPE(nl); - wl2 = wl * wl; - wl3 = wl2 * wl; - w2l1 = 2.0 * wl; - w3l2 = 3.0 * wl2; - - for (idx = 0; idx <= 3; idx++) { - c[idx] = lookupTable(nl, func_ind, idx); - } - values(func_ind) = c[0] + c[1] * wl + c[2] * wl2 + c[3] * wl3; - derivatives(func_ind) = (c[1] + c[2] * w2l1 + c[3] * w3l2) * rscalelookup; - - } else { // fill with zeroes - values(func_ind) = 0; - derivatives(func_ind) = 0; - } -} diff --git a/lib/pace/ace_radial.h b/lib/pace/ace_radial.h deleted file mode 100644 index e45cfaec79..0000000000 --- a/lib/pace/ace_radial.h +++ /dev/null @@ -1,324 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -#ifndef ACE_RADIAL_FUNCTIONS_H -#define ACE_RADIAL_FUNCTIONS_H - -#include "ace_arraynd.h" -#include "ace_types.h" -#include - -using namespace std; - -//typedef void (*RadialFunctions)(DOUBLE_TYPE x); -typedef std::function RadialFunctions; - -/** - * Class that implement spline interpolation and caching for radial functions - */ -class SplineInterpolator { -public: - DOUBLE_TYPE cutoff = 0; ///< cutoff - DOUBLE_TYPE deltaSplineBins = 0.001; - int ntot = 10000; ///< Number of bins for look-up tables. - int nlut = 10000; ///< number of nodes in look-up table - DOUBLE_TYPE invrscalelookup = 1; ///< inverse of conversion coefficient from distance to lookup table within cutoff range - DOUBLE_TYPE rscalelookup = 1; ///< conversion coefficient from distance to lookup table within cutoff range - int num_of_functions = 0;///< number of functions to spline-interpolation - - Array1D values;// = Array1D("values"); ///< shape: [func_ind] - Array1D derivatives;// = Array1D("derivatives");///< shape: [func_ind] - Array1D second_derivatives;// = Array1D("second_derivatives");///< shape: [func_ind] - - Array3D lookupTable = Array3D("lookupTable");///< shape: [ntot+1][func_ind][4] - - /** - * Setup splines - * - * @param num_of_functions number of functions - * @param func subroutine, that update `values` and `dvalues` arrays - * @param values values - * @param dvalues derivatives - */ - void setupSplines(int num_of_functions, RadialFunctions func, - DOUBLE_TYPE *values, - DOUBLE_TYPE *dvalues, DOUBLE_TYPE deltaSplineBins, DOUBLE_TYPE cutoff); - - /** - * Populate `values` and `derivatives` arrays with a spline-interpolation for - * all functions - * - * @param r - * - * @return: populate 'values' and 'derivatives' - */ - void calcSplines(DOUBLE_TYPE r, bool calc_second_derivatives = false); - - /** - * Populate `values` and `derivatives` arrays with a spline-interpolation for - * all functions - * - * @param r - * - * @return: populate 'values' and 'derivatives' - */ - void calcSplines(DOUBLE_TYPE r, SHORT_INT_TYPE func_ind); -}; - -/** - * Interface class for radial basis functions with rank=1 (g_k), R_nl (rank>1) and hard-core repulsion radial functions - */ -class AbstractRadialBasis { -public: - SPECIES_TYPE nelements = 0; ///< number of elements - Array2D cut = Array2D("cut"); ///< cutoffs, shape: [nelements][nelements] - Array2D dcut = Array2D("dcut"); ///< decay of cutoff, shape: [nelements][nelements] - DOUBLE_TYPE cutoff = 0; ///< cutoff - -// int ntot = 10000; ///< Number of bins for look-up tables. - DOUBLE_TYPE deltaSplineBins; - LS_TYPE lmax = 0; ///< maximum value of `l` - NS_TYPE nradial = 0; ///< maximum number `n` of radial functions \f$ R_{nl}(r) \f$ - NS_TYPE nradbase = 0; ///< number of radial basis functions \f$ g_k(r) \f$ - - // Arrays for look-up tables. - Array2D splines_gk; ///< array of spline interpolator to store g_k, shape: [nelements][nelements] - Array2D splines_rnl; ///< array of spline interpolator to store R_nl, shape: [nelements][nelements] - Array2D splines_hc; ///< array of spline interpolator to store R_nl shape: [nelements][nelements] - //-------------------------------------------------------------------------- - - string radbasename = "ChebExpCos"; ///< type of radial basis functions \f$ g_{k}(r) \f$ (default="ChebExpCos") - - /** - Arrays to store radial functions. - */ - Array1D gr = Array1D("gr"); ///< g_k(r) functions, shape: [nradbase] - Array1D dgr = Array1D("dgr"); ///< derivatives of g_k(r) functions, shape: [nradbase] - Array1D d2gr = Array1D("d2gr"); ///< derivatives of g_k(r) functions, shape: [nradbase] - - Array2D fr = Array2D("fr"); ///< R_nl(r) functions, shape: [nradial][lmax+1] - Array2D dfr = Array2D( - "dfr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] - Array2D d2fr = Array2D( - "d2fr"); ///< derivatives of R_nl(r) functions, shape: [nradial][lmax+1] - - - - DOUBLE_TYPE cr; ///< hard-core repulsion - DOUBLE_TYPE dcr; ///< derivative of hard-core repulsion - DOUBLE_TYPE d2cr; ///< derivative of hard-core repulsion - - Array5D crad = Array5D( - "crad"); ///< expansion coefficients of radial functions into radial basis function, see Eq. (27) of PRB, shape: [nelements][nelements][lmax + 1][nradial][nradbase] - Array2D lambda = Array2D( - "lambda"); ///< distance scaling parameter Eq.(24) of PRB, shape: [nelements][nelements] - - Array2D prehc = Array2D( - "prehc"); ///< hard-core repulsion coefficients (prefactor), shape: [nelements][nelements] - Array2D lambdahc = Array2D( - "lambdahc");; ///< hard-core repulsion coefficients (lambdahc), shape: [nelements][nelements] - - virtual void - evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) = 0; - - virtual void - init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename = "ChebExpCos") = 0; - - /** - * Function that sets up the look-up tables for spline-representation of radial functions. - */ - virtual void setuplookupRadspline() = 0; - - virtual AbstractRadialBasis *clone() const = 0; - - virtual ~AbstractRadialBasis() = default; -}; - - -/** -Class to store radial functions and their associated functions. \n -*/ -class ACERadialFunctions final : public AbstractRadialBasis { -public: - - //-------------------------------------------------------------------------- - - /** - Arrays to store Chebyshev polynomials. - */ - Array1D cheb = Array1D( - "cheb"); ///< Chebyshev polynomials of the first kind, shape: [nradbase+1] - Array1D dcheb = Array1D( - "dcheb"); ///< derivatives Chebyshev polynomials of the first kind, shape: [nradbase+1] - Array1D cheb2 = Array1D( - "cheb2"); ///< Chebyshev polynomials of the second kind, shape: [nradbase+1] - - //-------------------------------------------------------------------------- - - Array2D gr_vec; - Array2D dgr_vec; - Array2D d2gr_vec; - - Array3D fr_vec; - Array3D dfr_vec; - Array3D d2fr_vec; - //------------------------------------------------------------------------ - /** - * Default constructor - */ - ACERadialFunctions() = default; - - /** - * Parametrized constructor - * - * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase - * @param lmax maximum orbital moment - lmax - * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial - * @param ntot Number of bins for spline look-up tables. - * @param nelements numer of elements - * @param cutoff cutoff - * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") - */ - ACERadialFunctions(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename = "ChebExpCos"); - - /** - * Initialize arrays for given parameters - * - * @param nradb number of radial basis function \f$ g_k(r) \f$ - nradbase - * @param lmax maximum orbital moment - lmax - * @param nradial maximum n-index of radial functions \f$ R_{nl}(r) \f$ - nradial - * @param ntot Number of bins for spline look-up tables. - * @param nelements numer of elements - * @param cutoff cutoff - * @param radbasename type of radial basis function \f$ g_k(r) \f$ (default: "ChebExpCos") - */ - void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename = "ChebExpCos") final; - - /** - * Destructor - */ - ~ACERadialFunctions() final = default; - - /** - * Function that computes Chebyshev polynomials of first and second kind - * to setup the radial functions and the derivatives - * - * @param n maximum polynom order - * @param x - * - * @returns fills cheb, dcheb and cheb2 arrays - */ - void calcCheb(NS_TYPE n, DOUBLE_TYPE x); - - /** - * Function that computes radial basis functions \$f g_k(r) \$f, see Eq.(21) of PRB paper - * @param lam \$f \lambda \$f parameter, see eq. (24) of PRB paper - * @param cut cutoff - * @param dcut cutoff decay - * @param r distance - * - * @return function fills gr and dgr arrays - */ - void radbase(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - /** - * Function that computes radial core repulsion \$f f_{core} = pre \exp( - \lambda r^2 ) / r \$f, - * and its derivative, see Eq.(27) of implementation notes. - * - * @param r distance - * @param pre prefactor: read from input, depends on pair of atoms mu_i mu_j - * @param lambda exponent: read from input, depends on pair of atoms mu_i mu_j - * @param cutoff cutoff distance: read from input, depends on pair of atoms mu_i mu_j - * @param cr (out) hard core repulsion - * @param dcr (out) derivative of hard core repulsion - */ - static void radcore(DOUBLE_TYPE r, DOUBLE_TYPE pre, DOUBLE_TYPE lambda, DOUBLE_TYPE cutoff, DOUBLE_TYPE &cr, - DOUBLE_TYPE &dcr); - - /** - * Function that sets up the look-up tables for spline-representation of radial functions. - */ - void setuplookupRadspline() final; - - /** - * Function that computes radial functions \f$ R_{nl}(r)\f$ (see Eq. 27 from PRB paper) - * and its derivatives for all range of n,l, - * ONLY if radial basis functions (gr and dgr) are computed. - * @param elei first species type - * @param elej second species type - * - * @return fills in fr, dfr arrays - */ - void radfunc(SPECIES_TYPE elei, SPECIES_TYPE elej); - - /** - * Compute all radial functions R_nl(r), radial basis functions g_k(r) and hard-core repulsion function hc(r) - * - * @param r distance - * @param nradbase_c - * @param nradial_c - * @param mu_i - * @param mu_j - * - * @return update gr(k), dgr(k), fr(n,l), dfr(n,l), cr, dcr - */ - void evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) final; - - - void - evaluate_range(vector r_vec, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j); - - void chebExpCos(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - void chebPow(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - void chebLinear(DOUBLE_TYPE lam, DOUBLE_TYPE cut, DOUBLE_TYPE dcut, DOUBLE_TYPE r); - - /** - * Setup all radial functions for element pair mu_i-mu_j and distance r - * @param mu_i first specie type - * @param mu_j second specie type - * @param r distance - * @return update fr(nr, l), dfr(nr, l) - */ - void all_radfunc(SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, DOUBLE_TYPE r); - - ACERadialFunctions *clone() const override { - return new ACERadialFunctions(*this); - }; -}; - -#endif \ No newline at end of file diff --git a/lib/pace/ace_recursive.cpp b/lib/pace/ace_recursive.cpp deleted file mode 100644 index c895418943..0000000000 --- a/lib/pace/ace_recursive.cpp +++ /dev/null @@ -1,1340 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 20.12.2020 - -#include "ace_recursive.h" - -#include "ace_abstract_basis.h" -#include "ace_types.h" - -/* ------------------------------------------------------------ - * ACEDAG Implementation - * (just the DAG construction, not the traversal) - * ------------------------------------------------------------ */ - -/* Notes on different Tags: - * rec1 - first basic implementation - * rec2 - avoid index arithmetic, contiguous layout, - * canonical evaluator in ACE.jl format - * rec3 - split nodes into interior and leaf nodes - */ - -void ACEDAG::init(Array2D xAspec, - Array2D AAspec, - Array1D orders, - Array2D jl_coeffs, - int _heuristic ) { - - // remember which heuristic we want to use! - heuristic = _heuristic; - - /* stage one of the graph is just extracting the A basis from - * the tensor product format into the linear list; all information - * for that is already stored in Aspec, and the only thing to do here is - * to construct zero-coefficients. Still we have to copy Aspec, since - * the one we have here will (may?) be deleted. */ - int num1 = xAspec.get_dim(0); - Aspec = xAspec; //YL: just copying the multiarray: Aspec = xAspec; - - /* fill the one-particle basis into the DAGmap - * DAGmap[ (i1,...,in) ] = iAA index where the (i1,...,in) basis functions - * lives. - */ - TDAGMAP DAGmap; - for (int iA = 0; iA < num1; iA++) { - vector a(1); - a[0] = iA; - DAGmap[a] = iA; - } - - /* For stage 2 we now want to construct the actual recursion; the - recursion info will be stored in DAGspec, while the - coefficients go into DAGcoeffs. These arrays are initialized to - length `num2`, but they will have to grow as we add additional - artificial nodes into the graph. - - initially we treat all nodes as having children, but then in a - second stage below we reorganize. */ - int num2 = AAspec.get_dim(0); - int ndensity = jl_coeffs.get_dim(1); - nodes_pre.resize(2*num2, 2); - coeffs_pre.resize(2*num2, ndensity); - - /* the first basis function we construct will get index num1, - * since there are already num1 one-particle basis functions - * to collect during stage 1 */ - dag_idx = num1; - /* main loop over AA basis set to transform into DAG */ - for (int iAA = 0; iAA < num2; iAA++) { - // create a vector representing the current basis function - int ord = orders(iAA); - vector aa(ord); - for (int t = 0; t < ord; t++) aa[t] = AAspec(iAA, t); - vector c(ndensity); - for (int p = 0; p < ndensity; p++) c[p] = jl_coeffs(iAA, p); - insert_node(DAGmap, aa, c); - } - - /* convert to 3-stage format through reordering - * interior nodes first, then leaf nodes */ - - // allocate storage - num_nodes = dag_idx; // store total size of dag - // num_nodes - num1 = number of many-body nodes. - nodes.resize(num_nodes - num1, 2); - coeffs.resize(num_nodes - num1, ndensity); - - // find out which nodes have children - haschild.resize(num_nodes - num1); - haschild.fill(false); - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (nodes_pre(iAA, 0) >= num1) - haschild(nodes_pre(iAA, 0)-num1) = true; - if (nodes_pre(iAA, 1) >= num1) - haschild(nodes_pre(iAA, 1)-num1) = true; - } - - // to reorder the graph we need a fresh map from preordered indices to - // postordered indices; for the 1-particle basis the order remains the same. - // TODO: doesn't need to be a map, could be a vector. - map neworder; - for (int iA = 0; iA < num1; iA++) - neworder[iA] = iA; - - // insert all interior nodes - num2_int = 0; - num2_leaf = 0; - dag_idx = num1; - int i1, i2, i1pre, i2pre; - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (haschild(iAA)) { - num2_int += 1; - // indices into AAbuf before reordering - i1pre = nodes_pre(iAA, 0); - i2pre = nodes_pre(iAA, 1); - // indices into AAbuf after reordering - i1 = neworder[i1pre]; - i2 = neworder[i2pre]; - // insert the current node : iAA is old order, dag_idx is new order - neworder[num1+iAA] = dag_idx; - nodes(dag_idx-num1, 0) = i1; - nodes(dag_idx-num1, 1) = i2; - for (int t = 0; t < ndensity; t++) - coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); - dag_idx++; - } - } - - // insert all leaf nodes - for (int iAA = 0; iAA < num_nodes - num1; iAA++) { - if (!haschild(iAA)) { - num2_leaf += 1; - // indices into AAbuf before reordering - i1pre = nodes_pre(iAA, 0); - i2pre = nodes_pre(iAA, 1); - // insert the current node : no need to remember the new order now - nodes(dag_idx-num1, 0) = neworder[i1pre]; - nodes(dag_idx-num1, 1) = neworder[i2pre]; - for (int t = 0; t < ndensity; t++) - coeffs(dag_idx-num1, t) = coeffs_pre(iAA, t); - dag_idx++; - } - } -#ifdef DEBUG - cout << "num2_int = " << num2_int << "; num2_leaf = " << num2_leaf << "\n"; -#endif - // free up memory that is no longer needed - nodes_pre.resize(0, 0); - coeffs_pre.resize(0, 0); - haschild.resize(0); - - /* finalize dag: allocate buffer storage */ - AAbuf.resize(num1 + num2_int); - w.resize(num_nodes); - // TODO: technically only need num1 + num2_int for w, this can save one - // memory access later, probably not worth the crazy code duplication. -} - -void ACEDAG::insert_node(TDAGMAP &DAGmap, vector a, vector c) { - /* start with a list of all possible partitions into 2 groups - * and check whether any of these nodes are already in the dag */ - auto partitions = find_2partitions(a); - int ndensity = c.size(); - int num1 = get_num1(); - - // TODO: first try to find partitions into nodes that are already parents - // that way we will get more leaf nodes! - for (TPARTITION const& p : partitions) { - /* this is the good case; the parent nodes are both already in the - * graph; add the new node and return. This is also the only place in the - * code where an actual insert happens. */ - if (DAGmap.count(p.first) && DAGmap.count(p.second)) { - if (nodes_pre.get_dim(0) < dag_idx + 1) { //check if array is sufficiently large - int newsize = (dag_idx * 3) / 2; - nodes_pre.resize(newsize, 2); // grow arrays if necessary - coeffs_pre.resize(newsize, ndensity); - } - int i1 = DAGmap[p.first]; - int i2 = DAGmap[p.second]; - nodes_pre(dag_idx - num1, 0) = i1; - nodes_pre(dag_idx - num1, 1) = i2; - DAGmap[a] = dag_idx; - for (int p = 0; p < ndensity; p++) - coeffs_pre(dag_idx - num1, p) = c[p]; - dag_idx += 1; - return; - } - } - - /* if we are here, then this means, the new node cannot yet be inserted. - * We first need to insert some intermediate auxiliary nodes. For this - * we use a simple heuristic: - * try to find a partition where one of the two nodes are already - * in the graph, if there are several, then we remember the longest - * (this is a very greedy heuristic!!) - * .... (continue below) .... - */ - TPARTITION longest; - int longest_length = 0; - for (auto const& p : partitions) { - int len = 0; - if (DAGmap.count(p.first)) { - len = p.first.size(); - } else if (DAGmap.count(p.second)) { - len = p.second.size(); - } - if ((len > 0) && (len > longest_length)) { - longest_length = len; - longest = p; - } - } - - /* sanity check */ - if (longest_length == 0) { - std::stringstream error_message; - error_message << "WARNING : something has gone horribly wrong! `longest_length == 0`! \n"; - error_message << "a = ["; - for (int t = 0; t < a.size(); t++) - error_message << a[t] << ", "; - error_message << "]\n"; - throw std::logic_error(error_message.str()); -// return; - } - - /* If there is a partition with one component already in the graph, - * then we only need to add in the other component. Note that there will - * always be at least one such partition, namely all those containing - * a one-element node e.g. (1,2,3,4) -> (1,) (2,3,4) then (1,) is - * a one-particle basis function and hence always in the graph. - * If heuristic == 0, then we just take one of those partitionas and move on. - * - * We also accept the found partition if longest_length > 1. - * And we also accept it if we have a 2- or 3-correlation. - */ - - if ( (heuristic == 0) - || (longest_length > 1) - || (a.size() <= 3)) { - /* insert the other node that isn't in the DAG yet - * this is an artificial node so it gets zero-coefficients - * This step is recursive, so more than one node might be inserted here */ - vector cz(ndensity); - for (int i = 0; i < ndensity; i++) cz[i] = 0.0; - TPARTITION p = longest; - if (DAGmap.count(p.first)) - insert_node(DAGmap, p.second, cz); - else - insert_node(DAGmap, p.first, cz); - } - - /* Second heuristic : heuristic == 1 - * Focus on inserting artificial 2-correlations - */ - else if (heuristic == 1) { - // and we also know that longest_length == 1 and nu = a.size >= 4. - int nu = a.size(); - // generate an artificial partition - vector a1(2); - for (int i = 0; i < 2; i++) a1[i] = a[i]; - vector a2(nu - 2); - for (int i = 0; i < nu - 2; i++) a2[i] = a[2 + i]; - vector cz(ndensity); - for (int i = 0; i < cz.size(); i++) cz[i] = 0.0; - // and insert both (we know neither are in the DAG yet) - insert_node(DAGmap, a1, cz); - insert_node(DAGmap, a2, cz); - } else { - cout << "WARNING : something has gone horribly wrong! \n"; - // TODO: Throw and error here?!? - return; - } - - - - /* now we should be ready to insert the entire tuple `a` since there is now - * an eligible parent pair. Here we recompute the partition of `a`, but - * that's a small price to pay for a clearer code. Maybe this can be - * optimized a bit by wrapping it all into a while loop or having a second - * version of `insert_node` ... */ - insert_node(DAGmap, a, c); -} - -TPARTITIONS ACEDAG::find_2partitions(vector v) { - int N = v.size(); - int zo; - TPARTITIONS partitions; - TPARTITION part; - /* This is a fun little hack to extract all subsets of the indices 1:N - * the number i will have binary representation with each digit indicating - * whether or not that index belongs to the selected subset */ - for (int i = 1; i < (1< v1(N1); - vector v2(N2); - int i1 =0, i2 = 0; - p = 1; - for (int n = 0; n < N; n++) { - zo = ((i / p) % 2); - p *= 2; - if (zo == 1) { - v1[i1] = v[n]; - i1 += 1; - } else { - v2[i2] = v[n]; - i2 += 1; - } - } - part = make_pair(v1, v2); - partitions.push_back(part); - } - return partitions; -} - -void ACEDAG::print() { - cout << "DAG Specification: \n" ; - cout << " n1 : " << get_num1() << "\n"; - cout << " n2 : " << get_num2() << "\n"; - cout << " num_nodes : " << num_nodes << "\n"; - cout << "--------------------\n"; - cout << "A-spec: \n"; - for (int iA = 0; iA < get_num1(); iA++) { - cout << iA << " : " << Aspec(iA, 0) << - Aspec(iA, 1) << Aspec(iA, 2) << Aspec(iA, 3) << "\n"; - } - - cout << "-----------\n"; - cout << "AA-tree\n"; - - for (int iAA = 0; iAA < get_num2(); iAA++) { - cout << iAA + get_num1() << " : " << - nodes(iAA, 0) << ", " << nodes(iAA, 1) << "\n"; - } -} - - -/* ------------------------------------------------------------ - * ACERecursiveEvaluator - * ------------------------------------------------------------ */ - - -void ACERecursiveEvaluator::set_basis(ACECTildeBasisSet &bas, int heuristic) { - basis_set = &bas; - init(basis_set, heuristic); -} - -void ACERecursiveEvaluator::init(ACECTildeBasisSet *basis_set, int heuristic) { - - ACEEvaluator::init(basis_set); - - - weights.init(basis_set->nelements, basis_set->nradmax + 1, basis_set->lmax + 1, - "weights"); - - weights_rank1.init(basis_set->nelements, basis_set->nradbase, "weights_rank1"); - - - DG_cache.init(1, basis_set->nradbase, "DG_cache"); - DG_cache.fill(0); - - R_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "R_cache"); - R_cache.fill(0); - - DR_cache.init(1, basis_set->nradmax, basis_set->lmax + 1, "DR_cache"); - DR_cache.fill(0); - - Y_cache.init(1, basis_set->lmax + 1, "Y_cache"); - Y_cache.fill({0, 0}); - - DY_cache.init(1, basis_set->lmax + 1, "dY_dense_cache"); - DY_cache.fill({0.}); - - //hard-core repulsion - DCR_cache.init(1, "DCR_cache"); - DCR_cache.fill(0); - dB_flatten.init(basis_set->max_dB_array_size, "dB_flatten"); - - /* convert to ACE.jl format to prepare for construction of DAG - * This will fill the arrays jl_Aspec, jl_AAspec, jl_orders - */ - acejlformat(); - - // test_acejlformat(); - - // now pass this info into the DAG - dag.init(jl_Aspec, jl_AAspec, jl_orders, jl_coeffs, heuristic); - - // finally empty the temporary arrays to clear up the memory... - // TODO -} - - -void ACERecursiveEvaluator::acejlformat() { - - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - int j, jj, func_ind, ms_ind; - - SPECIES_TYPE mu_i = 0;//TODO: multispecies - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - int AAidx = 0; - RANK_TYPE order, t; - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - /* transform basis into new format: - [A1 ... A_num1] - [(i1,i2)(i1,i2)(...)(i1,i2,i3)(...)] - where each ia represents an A_{ia} - */ - - /* compute max values for mu, n, l, m */ - SPECIES_TYPE maxmu = 0; //TODO: multispecies - NS_TYPE maxn = basis_set->nradmax; - LS_TYPE maxl = basis_set->lmax; - RANK_TYPE maxorder = basis_set->rankmax; - const DENSITY_TYPE ndensity = basis_set->ndensitymax; - - int num1 = 0; - - - /* create a 4D lookup table for the 1-p basis - * TODO: replace with a map?? - */ - Array4D A_lookup(int(maxmu+1), int(maxn), int(maxl+1), int(2*maxl+1)); - for (int mu = 0; mu < maxmu+1; mu++) - for (int n = 0; n < maxn; n++) - for (int l = 0; l < maxl+1; l++) - for (int m = 0; m < 2*maxl+1; m++) - A_lookup(mu, n, l, m) = -1; - int A_idx = 0; // linear index of A basis function (1-particle) - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; -// func->print(); - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - for (t = 0; t < order; t++) { - int iA = A_lookup(mus[t], ns[t]-1, ls[t], ms[t]+ls[t]); - if (iA == -1) { - A_lookup(mus[t], ns[t] - 1, ls[t], ms[t] + ls[t]) = A_idx; - A_idx += 1; - } - } - } - } - - /* create the reverse list: linear indixes to mu,l,m,n - this keeps only the basis functions we really need */ - num1 = A_idx; - Array2D & Aspec = jl_Aspec; - Aspec.resize(num1, 4); - // Array2D Aspec(num1, 4); - for (int mu = 0; mu <= maxmu; mu++) - for (int n = 1; n <= maxn; n++) - for (int l = 0; l <= maxl; l++) - for (int m = -l; m <= l; m++) { - int iA = A_lookup(mu, n-1, l, l+m); - if (iA != -1) { - Aspec(iA, 0) = mu; - Aspec(iA, 1) = n; - Aspec(iA, 2) = l; - Aspec(iA, 3) = m; - } - } - - /* ============ HALF-BASIS TRICK START ============ */ - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - if (!( (mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl) )) - continue; - - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - // find first positive and negative index - int pos_idx = order + 1; - int neg_idx = order + 1; - for (t = order-1; t >= 0; t--) - if (ms[t] > 0) pos_idx = t; - else if (ms[t] < 0) neg_idx = t; - - // if neg_idx < pos_idx then this means that ms is non-zero - // and that the first non-zero index is negative, hence this is - // a negative-sign tuple which we want to combine into - // its opposite. - if (neg_idx < pos_idx) { - // find the opposite tuple - int ms_ind2 = 0; - MS_TYPE *ms2; - bool found_opposite = false; - for (ms_ind2 = 0; ms_ind2 < func->num_ms_combs; ++ms_ind2) { - ms2 = &func->ms_combs[ms_ind2 * order]; - bool isopposite = true; - for (t = 0; t < order; t++) - if (ms[t] != -ms2[t]) { - isopposite = false; - break; - } - if (isopposite) { - found_opposite = true; - break; - } - } - - if (ms_ind == ms_ind2) { - cout << "WARNING - ms_ind == ms_ind2 \n"; - } - - // now we need to overwrite the coefficients - if (found_opposite) { - int sig = 1; - for (t = 0; t < order; t++) - if (ms[t] < 0) - sig *= -1; - for (int p = 0; p < ndensity; ++p) { - func->ctildes[ms_ind2 * ndensity + p] += - func->ctildes[ms_ind * ndensity + p]; - func->ctildes[ms_ind * ndensity + p] = 0.0; - } - } - } - } - } - - // /* ============ HALF-BASIS TRICK END ============ */ - - - /* count number of basis functions, keep only non-zero!! */ - int num2 = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - for (ms_ind = 0; ms_ind < (&basis[func_ind])->num_ms_combs; ++ms_ind, ++func_ms_ind) { - // check that the coefficients are actually non-zero - bool isnonzero = false; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - if (func->ctildes[ms_ind * ndensity + p] != 0.0) - isnonzero = true; - if (isnonzero) - num2++; - } - } - - - /* Now create the AA basis links into the A basis */ - num1 = A_idx; // total number of A-basis functions that we keep - // Array1D AAorders(num2); - Array1D & AAorders = jl_orders; - AAorders.resize(num2); - // Array2D AAspec(num2, maxorder); // specs of AA basis functions - Array2D & AAspec = jl_AAspec; - AAspec.resize(num2, maxorder); - jl_coeffs.resize(num2, ndensity); - AAidx = 0; // linear index into AA basis function - int len_flat = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - if (!((mus[0] <= maxmu) && (ns[0] <= maxn) && (ls[0] <= maxl))) //fool-proofing of functions - continue; - - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - // check that the coefficients are actually non-zero - bool iszero = true; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - if (func->ctildes[ms_ind * ndensity + p] != 0.0) - iszero = false; - if (iszero) continue; - - AAorders(AAidx) = order; - for (t = 0; t < order; t++) { - int Ait = A_lookup(int(mus[t]), int(ns[t]-1), int(ls[t]), int(ms[t])+int(ls[t])); - AAspec(AAidx, t) = Ait; - len_flat += 1; - } - for (t = order; t < maxorder; t++) AAspec(AAidx, t) = -1; - /* copy over the coefficients */ - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - jl_coeffs(AAidx, p) = func->ctildes[ms_ind * ndensity + p]; - AAidx += 1; - } - } - - // flatten the AAspec array - jl_AAspec_flat.resize(len_flat); - int idx_spec = 0; - for (int AAidx = 0; AAidx < jl_AAspec.get_dim(0); AAidx++) - for (int p = 0; p < jl_orders(AAidx); p++, idx_spec++) - jl_AAspec_flat(idx_spec) = jl_AAspec(AAidx, p); - -} - -void ACERecursiveEvaluator::test_acejlformat() { - - Array2D AAspec = jl_AAspec; - Array2D Aspec = jl_Aspec; - Array1D AAorders = jl_orders; - cout << "num2 = " << AAorders.get_dim(0) << "\n"; - int func_ms_ind = 0; - int func_ms_t_ind = 0;// index for dB - int j, jj, func_ind, ms_ind; - - SPECIES_TYPE mu_i = 0; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - RANK_TYPE order, t; - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - /* ==== test by printing the basis spec ====*/ - // TODO: convert this into an automatic consistency test - int iAA = 0; - for (func_ind = 0; func_ind < total_basis_size; ++func_ind) { - ACECTildeBasisFunction *func = &basis[func_ind]; - order = func->rank; mus = func->mus; ns = func->ns; ls = func->ls; - // func->print(); - //loop over {ms} combinations in sum - for (ms_ind = 0; ms_ind < func->num_ms_combs; ++ms_ind, ++func_ms_ind) { - ms = &func->ms_combs[ms_ind * order]; - - - cout << iAA << " : |"; - for (t = 0; t < order; t++) - cout << mus[t] << ";" << ns[t] << "," << ls[t] << "," << ms[t] << "|"; - cout << "\n"; - - cout << " ["; - for (t = 0; t < AAorders(iAA); t++) - cout << AAspec(iAA, int(t)) << ","; - cout << "]\n"; - cout << " |"; - for (t = 0; t < AAorders(iAA); t++) { - int iA = AAspec(iAA, t); - // cout << iA << ","; - cout << Aspec(iA, 0) << ";" - << Aspec(iA, 1) << "," - << Aspec(iA, 2) << "," - << Aspec(iA, 3) << "|"; - } - cout << "\n"; - iAA += 1; - } - } - /* ==== END TEST ==== */ - - -} - - - - -void ACERecursiveEvaluator::resize_neighbours_cache(int max_jnum) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); - } - if (R_cache.get_dim(0) < max_jnum) { - - //TODO: implement grow - R_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - R_cache.fill(0); - - DR_cache.resize(max_jnum, basis_set->nradmax, basis_set->lmax + 1); - DR_cache.fill(0); - - DG_cache.resize(max_jnum, basis_set->nradbase); - DG_cache.fill(0); - - Y_cache.resize(max_jnum, basis_set->lmax + 1); - Y_cache.fill({0, 0}); - - DY_cache.resize(max_jnum, basis_set->lmax + 1); - DY_cache.fill({0}); - - //hard-core repulsion - DCR_cache.init(max_jnum, "DCR_cache"); - DCR_cache.fill(0); - } -} - - - -// double** r - atomic coordinates of atom I -// int* types - atomic types if atom I -// int **firstneigh - ptr to 1st J int value of each I atom. Usage: jlist = firstneigh[i]; -// Usage: j = jlist_of_i[jj]; -// jnum - number of J neighbors for each I atom. jnum = numneigh[i]; - -void -ACERecursiveEvaluator::compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) { - if(basis_set== nullptr) { - throw std::invalid_argument("ACERecursiveEvaluator: basis set is not assigned"); - } - per_atom_calc_timer.start(); -#ifdef PRINT_MAIN_STEPS - printf("\n ATOM: ind = %d r_norm=(%f, %f, %f)\n",i, x[i][0], x[i][1], x[i][2]); -#endif - DOUBLE_TYPE evdwl = 0, evdwl_cut = 0, rho_core = 0; - DOUBLE_TYPE r_norm; - DOUBLE_TYPE xn, yn, zn, r_xyz; - DOUBLE_TYPE R, GR, DGR, R_over_r, DR, DCR; - DOUBLE_TYPE *r_hat; - - SPECIES_TYPE mu_j; - RANK_TYPE r, rank, t; - NS_TYPE n; - LS_TYPE l; - MS_TYPE m, m_t; - - SPECIES_TYPE *mus; - NS_TYPE *ns; - LS_TYPE *ls; - MS_TYPE *ms; - - int j, jj, func_ind, ms_ind; - SHORT_INT_TYPE factor; - - ACEComplex Y{0}, Y_DR{0.}; - ACEComplex B{0.}; - ACEComplex dB{0}; - ACEComplex A_cache[basis_set->rankmax]; - - ACEComplex dA[basis_set->rankmax]; - int spec[basis_set->rankmax]; - - dB_flatten.fill({0.}); - - ACEDYcomponent grad_phi_nlm{0}, DY{0.}; - - //size is +1 of max to avoid out-of-boundary array access in double-triangular scheme - ACEComplex A_forward_prod[basis_set->rankmax + 1]; - ACEComplex A_backward_prod[basis_set->rankmax + 1]; - - DOUBLE_TYPE inv_r_norm; - DOUBLE_TYPE r_norms[jnum]; - DOUBLE_TYPE inv_r_norms[jnum]; - DOUBLE_TYPE rhats[jnum][3];//normalized vector - SPECIES_TYPE elements[jnum]; - const DOUBLE_TYPE xtmp = x[i][0]; - const DOUBLE_TYPE ytmp = x[i][1]; - const DOUBLE_TYPE ztmp = x[i][2]; - DOUBLE_TYPE f_ji[3]; - - bool is_element_mapping = element_type_mapping.get_size() > 0; - SPECIES_TYPE mu_i; - if (is_element_mapping) - mu_i = element_type_mapping(type[i]); - else - mu_i = type[i]; - - const SHORT_INT_TYPE total_basis_size_rank1 = basis_set->total_basis_size_rank1[mu_i]; - const SHORT_INT_TYPE total_basis_size = basis_set->total_basis_size[mu_i]; - - ACECTildeBasisFunction *basis_rank1 = basis_set->basis_rank1[mu_i]; - ACECTildeBasisFunction *basis = basis_set->basis[mu_i]; - - DOUBLE_TYPE rho_cut, drho_cut, fcut, dfcut; - DOUBLE_TYPE dF_drho_core; - - //TODO: lmax -> lmaxi (get per-species type) - const LS_TYPE lmaxi = basis_set->lmax; - - //TODO: nradmax -> nradiali (get per-species type) - const NS_TYPE nradiali = basis_set->nradmax; - - //TODO: nradbase -> nradbasei (get per-species type) - const NS_TYPE nradbasei = basis_set->nradbase; - - //TODO: get per-species type number of densities - const DENSITY_TYPE ndensity= basis_set->ndensitymax; - - neighbours_forces.resize(jnum, 3); - neighbours_forces.fill(0); - - //TODO: shift nullifications to place where arrays are used - weights.fill({0}); - weights_rank1.fill(0); - A.fill({0}); - A_rank1.fill(0); - rhos.fill(0); - dF_drho.fill(0); - -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.init(total_basis_size_rank1, ndensity, "c_projections_rank1"); - basis_projections.init(total_basis_size, ndensity, "c_projections"); -#endif - - //proxy references to spherical harmonics and radial functions arrays - const Array2DLM &ylm = basis_set->spherical_harmonics.ylm; - const Array2DLM &dylm = basis_set->spherical_harmonics.dylm; - - const Array2D &fr = basis_set->radial_functions->fr; - const Array2D &dfr = basis_set->radial_functions->dfr; - - const Array1D &gr = basis_set->radial_functions->gr; - const Array1D &dgr = basis_set->radial_functions->dgr; - - loop_over_neighbour_timer.start(); - - int jj_actual = 0; - SPECIES_TYPE type_j = 0; - int neighbour_index_mapping[jnum]; // jj_actual -> jj - //loop over neighbours, compute distance, consider only atoms within with rradial_functions->cut(mu_i, mu_j); - r_xyz = sqrt(xn * xn + yn * yn + zn * zn); - - if (r_xyz >= current_cutoff) - continue; - - inv_r_norm = 1 / r_xyz; - - r_norms[jj_actual] = r_xyz; - inv_r_norms[jj_actual] = inv_r_norm; - rhats[jj_actual][0] = xn * inv_r_norm; - rhats[jj_actual][1] = yn * inv_r_norm; - rhats[jj_actual][2] = zn * inv_r_norm; - elements[jj_actual] = mu_j; - neighbour_index_mapping[jj_actual] = jj; - jj_actual++; - } - - int jnum_actual = jj_actual; - - //ALGORITHM 1: Atomic base A - for (jj = 0; jj < jnum_actual; ++jj) { - r_norm = r_norms[jj]; - mu_j = elements[jj]; - r_hat = rhats[jj]; - - //proxies - Array2DLM &Y_jj = Y_cache(jj); - Array2DLM &DY_jj = DY_cache(jj); - - - basis_set->radial_functions->evaluate(r_norm, basis_set->nradbase, nradiali, mu_i, mu_j); - basis_set->spherical_harmonics.compute_ylm(r_hat[0], r_hat[1], r_hat[2], lmaxi); - //loop for computing A's - //rank = 1 - for (n = 0; n < basis_set->nradbase; n++) { - GR = gr(n); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("-neigh atom %d\n", jj); - printf("gr(n=%d)(r=%f) = %f\n", n, r_norm, gr(n)); - printf("dgr(n=%d)(r=%f) = %f\n", n, r_norm, dgr(n)); -#endif - DG_cache(jj, n) = dgr(n); - A_rank1(mu_j, n) += GR * Y00; - } - //loop for computing A's - // for rank > 1 - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - R = fr(n, l); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("R(nl=%d,%d)(r=%f)=%f\n", n + 1, l, r_norm, R); -#endif - - DR_cache(jj, n, l) = dfr(n, l); - R_cache(jj, n, l) = R; - - for (m = 0; m <= l; m++) { - Y = ylm(l, m); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("Y(lm=%d,%d)=(%f, %f)\n", l, m, Y.real, Y.img); -#endif - A_lm(l, m) += R * Y; //accumulation sum over neighbours - Y_jj(l, m) = Y; - DY_jj(l, m) = dylm(l, m); - } - } - } - - //hard-core repulsion - rho_core += basis_set->radial_functions->cr; - DCR_cache(jj) = basis_set->radial_functions->dcr; - - } //end loop over neighbours - - //complex conjugate A's (for NEGATIVE (-m) terms) - // for rank > 1 - for (mu_j = 0; mu_j < basis_set->nelements; mu_j++) { - for (n = 0; n < nradiali; n++) { - auto &A_lm = A(mu_j, n); - for (l = 0; l <= lmaxi; l++) { - //fill in -m part in the outer loop using the same m <-> -m symmetry as for Ylm - for (m = 1; m <= l; m++) { - factor = m % 2 == 0 ? 1 : -1; - A_lm(l, -m) = A_lm(l, m).conjugated() * factor; - } - } - } - } //now A's are constructed - loop_over_neighbour_timer.stop(); - - // ==================== ENERGY ==================== - - energy_calc_timer.start(); -#ifdef EXTRA_C_PROJECTIONS - basis_projections_rank1.fill(0); - basis_projections.fill(0); -#endif - - //ALGORITHM 2: Basis functions B with iterative product and density rho(p) calculation - //rank=1 - for (int func_rank1_ind = 0; func_rank1_ind < total_basis_size_rank1; ++func_rank1_ind) { - ACECTildeBasisFunction *func = &basis_rank1[func_rank1_ind]; -// ndensity = func->ndensity; -#ifdef PRINT_LOOPS_INDICES - printf("Num density = %d r = 0\n",(int) ndensity ); - print_C_tilde_B_basis_function(*func); -#endif - double A_cur = A_rank1(func->mus[0], func->ns[0] - 1); -#ifdef DEBUG_ENERGY_CALCULATIONS - printf("A_r=1(x=%d, n=%d)=(%f)\n", func->mus[0], func->ns[0], A_cur); - printf(" coeff[0] = %f\n", func->ctildes[0]); -#endif - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - rhos(p) += func->ctildes[p] * A_cur; -#ifdef EXTRA_C_PROJECTIONS - //aggregate C-projections separately - basis_projections_rank1(func_rank1_ind, p)+= func->ctildes[p] * A_cur; -#endif - } - } // end loop for rank=1 - - // ================ START RECURSIVE EVALUATOR ==================== - // (rank > 1 only) - - /* STAGE 1: - * 1-particle basis is already evaluated, so we only need to - * copy it into the AA value buffer - */ - int num1 = dag.get_num1(); - for (int idx = 0; idx < num1; idx++) - dag.AAbuf(idx) = A( dag.Aspec(idx, 0), - dag.Aspec(idx, 1)-1, - dag.Aspec(idx, 2), - dag.Aspec(idx, 3) ); - - - if (recursive) { - /* STAGE 2: FORWARD PASS - * Forward pass: go through the dag and store all intermediate results - */ - - // rhos.fill(0); note the rhos are already reset and started filling above! - ACEComplex AAcur{0.0}; - int i1, i2; - - int * dag_nodes = dag.nodes.get_data(); - int idx_nodes = 0; - - DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); - int idx_coefs = 0; - - int num2_int = dag.get_num2_int(); - int num2_leaf = dag.get_num2_leaf(); - - // interior nodes (save AA) - for (int idx = num1; idx < num1+num2_int; idx++) { - i1 = dag_nodes[idx_nodes]; idx_nodes++; - i2 = dag_nodes[idx_nodes]; idx_nodes++; - AAcur = dag.AAbuf(i1) * dag.AAbuf(i2); - dag.AAbuf(idx) = AAcur; - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur.real_part_product(dag_coefs[idx_coefs]); - } - - // leaf nodes -> no need to store in AAbuf - DOUBLE_TYPE AAcur_re = 0.0; - for (int _idx = 0; _idx < num2_leaf; _idx++) { - i1 = dag_nodes[idx_nodes]; idx_nodes++; - i2 = dag_nodes[idx_nodes]; idx_nodes++; - AAcur_re = dag.AAbuf(i1).real_part_product(dag.AAbuf(i2)); - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur_re * dag_coefs[idx_coefs]; - } - - } else { - - /* non-recursive Julia-style evaluator implementation */ - // TODO: fix array access to enable bounds checking again??? - ACEComplex AAcur{1.0}; - int *AAspec = jl_AAspec_flat.get_data(); - DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); - int idx_spec = 0; - int idx_coefs = 0; - int order = 0; - int max_order = jl_AAspec.get_dim(1); - for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++) { - AAcur = 1.0; - order = jl_orders(iAA); - for (int r = 0; r < order; r++, idx_spec++) - AAcur *= dag.AAbuf( AAspec[idx_spec] ); - for (int p = 0; p < ndensity; p++, idx_coefs++) - rhos(p) += AAcur.real_part_product(coeffs[idx_coefs]); - } - } - - /* we now have rho and can evaluate lots of things. - -------- this is back to the original PACE code --------- */ - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("rhos = "); - for(DENSITY_TYPE p =0; prho_core_cutoffs(mu_i); - drho_cut = basis_set->drho_core_cutoffs(mu_i); - - basis_set->inner_cutoff(rho_core, rho_cut, drho_cut, fcut, dfcut); - basis_set->FS_values_and_derivatives(rhos, evdwl, dF_drho, ndensity); - - dF_drho_core = evdwl * dfcut + 1; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) - dF_drho(p) *= fcut; - evdwl_cut = evdwl * fcut + rho_core; - - // E0 shift - evdwl_cut += basis_set->E0vals(mu_i); - - /* I've moved this from below the weight calculation - since I believe it only times the energy? the weights - are only needed for the forces? - But I believe we could add a third timer for computing just - the weights; this will allow us to check better where the - bottleneck is. - */ - energy_calc_timer.stop(); - - forces_calc_loop_timer.start(); - - -#ifdef DEBUG_FORCES_CALCULATIONS - printf("dFrhos = "); - for(DENSITY_TYPE p =0; pndensity; - for (DENSITY_TYPE p = 0; p < ndensity; ++p) { - //for rank=1 (r=0) only 1 ms-combination exists (ms_ind=0), so index of func.ctildes is 0..ndensity-1 - weights_rank1(func->mus[0], func->ns[0] - 1) += dF_drho(p) * func->ctildes[p]; - } - } - - /* --------- we now continue with the recursive code --------- */ - - if (recursive) { - /* STAGE 2: BACKWARD PASS */ - int i1, i2; - ACEComplex AA1{0.0}; - ACEComplex AA2{0.0}; - ACEComplex wcur{0.0}; - int num2_int = dag.get_num2_int(); - int num2_leaf = dag.get_num2_leaf(); - /* to prepare for the backward we first need to zero the weights */ - dag.w.fill({0.0}); - - int * dag_nodes = dag.nodes.get_data(); - int idx_nodes = 2 * (num2_int + num2_leaf) - 1; - - DOUBLE_TYPE * dag_coefs = dag.coeffs.get_data(); - int idx_coefs = ndensity * (num2_int + num2_leaf) - 1; - - for (int idx = num1+num2_int+num2_leaf - 1; idx >= num1; idx--) { - i2 = dag_nodes[idx_nodes]; idx_nodes--; - i1 = dag_nodes[idx_nodes]; idx_nodes--; - AA1 = dag.AAbuf(i1); - AA2 = dag.AAbuf(i2); - wcur = dag.w(idx); // [***] - for (int p = ndensity-1; p >= 0; p--, idx_coefs--) - wcur += dF_drho(p) * dag_coefs[idx_coefs]; - dag.w(i1) += wcur * AA2; // TODO: replace with explicit muladd? - dag.w(i2) += wcur * AA1; - } - - /* [***] - * Note that these weights don't really need to be stored for the - * leaf nodes. We tested splitting this for loop into two where - * for the leaf nodes the weight would just be initialized to 0.0 - * instead of reading from an array. The improvement was barely - * measurable, ca 3%, so we reverted to this simpler algorithm - */ - - - } else { - - // non-recursive ACE.jl style implemenation of gradients, but with - // a backward differentiation approach to the prod-A - // (cf. Algorithm 3 in the manuscript) - - dag.w.fill({0.0}); - ACEComplex AAf{1.0}, AAb{1.0}, theta{0.0}; - - int *AAspec = jl_AAspec_flat.get_data(); - DOUBLE_TYPE *coeffs = jl_coeffs.get_data(); - int idx_spec = 0; - int idx_coefs = 0; - int order = 0; - int max_order = jl_AAspec.get_dim(1); - for (int iAA = 0; iAA < jl_AAspec.get_dim(0); iAA ++ ) { - order = jl_orders(iAA); - theta = 0.0; - for (int p = 0; p < ndensity; p++, idx_coefs++) - theta += dF_drho(p) * coeffs[idx_coefs]; - dA[0] = 1.0; - AAf = 1.0; - for (int t = 0; t < order-1; t++, idx_spec++) { - spec[t] = AAspec[idx_spec]; - A_cache[t] = dag.AAbuf(spec[t]); - AAf *= A_cache[t]; - dA[t+1] = AAf; - } - spec[order-1] = AAspec[idx_spec]; idx_spec++; - A_cache[order-1] = dag.AAbuf(spec[order-1]); - AAb = 1.0; - for (int t = order-1; t >= 1; t--) { - AAb *= A_cache[t]; - dA[t-1] *= AAb; - dag.w(spec[t]) += theta * dA[t]; - } - dag.w(spec[0]) += theta * dA[0]; - } - - } - - /* STAGE 3: - * get the gradients from the 1-particle basis gradients and write them - * into the dF/drho derivatives. - */ - /* In order to reuse the original PACE code, we copy the weights back - * into the the PACE datastructure. */ - - for (int idx = 0; idx < num1; idx++) { - int m = dag.Aspec(idx, 3); - if (m >= 0) { - weights(dag.Aspec(idx, 0), // mu - dag.Aspec(idx, 1) - 1, // n - dag.Aspec(idx, 2), // l - m ) += dag.w(idx); - } else { - int factor = (m % 2 == 0 ? 1 : -1); - weights(dag.Aspec(idx, 0), // mu - dag.Aspec(idx, 1) - 1, // n - dag.Aspec(idx, 2), // l - -m ) += factor * dag.w(idx).conjugated(); - } - } - - - /* ------ From here we are now back to the original PACE code ---- */ - -// ==================== FORCES ==================== -#ifdef PRINT_MAIN_STEPS - printf("\nFORCE CALCULATION\n"); - printf("loop over neighbours\n"); -#endif - -// loop over neighbour atoms for force calculations - for (jj = 0; jj < jnum_actual; ++jj) { - mu_j = elements[jj]; - r_hat = rhats[jj]; - inv_r_norm = inv_r_norms[jj]; - - Array2DLM &Y_cache_jj = Y_cache(jj); - Array2DLM &DY_cache_jj = DY_cache(jj); - -#ifdef PRINT_LOOPS_INDICES - printf("\nneighbour atom #%d\n", jj); - printf("rhat = (%f, %f, %f)\n", r_hat[0], r_hat[1], r_hat[2]); -#endif - - forces_calc_neighbour_timer.start(); - - f_ji[0] = f_ji[1] = f_ji[2] = 0; - -//for rank = 1 - for (n = 0; n < nradbasei; ++n) { - if (weights_rank1(mu_j, n) == 0) - continue; - auto &DG = DG_cache(jj, n); - DGR = DG * Y00; - DGR *= weights_rank1(mu_j, n); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("r=1: (n,l,m)=(%d, 0, 0)\n",n+1); - printf("\tGR(n=%d, r=%f)=%f\n",n+1,r_norm, gr(n)); - printf("\tDGR(n=%d, r=%f)=%f\n",n+1,r_norm, dgr(n)); - printf("\tdF+=(%f, %f, %f)\n",DGR * r_hat[0], DGR * r_hat[1], DGR * r_hat[2]); -#endif - f_ji[0] += DGR * r_hat[0]; - f_ji[1] += DGR * r_hat[1]; - f_ji[2] += DGR * r_hat[2]; - } - -//for rank > 1 - for (n = 0; n < nradiali; n++) { - for (l = 0; l <= lmaxi; l++) { - R_over_r = R_cache(jj, n, l) * inv_r_norm; - DR = DR_cache(jj, n, l); - - // for m>=0 - for (m = 0; m <= l; m++) { - ACEComplex w = weights(mu_j, n, l, m); - if (w == 0) - continue; - //counting for -m cases if m>0 - // if (m > 0) w *= 2; // not needed for recursive eval - - DY = DY_cache_jj(l, m); - Y_DR = Y_cache_jj(l, m) * DR; - - grad_phi_nlm.a[0] = Y_DR * r_hat[0] + DY.a[0] * R_over_r; - grad_phi_nlm.a[1] = Y_DR * r_hat[1] + DY.a[1] * R_over_r; - grad_phi_nlm.a[2] = Y_DR * r_hat[2] + DY.a[2] * R_over_r; -#ifdef DEBUG_FORCES_CALCULATIONS - printf("d_phi(n=%d, l=%d, m=%d) = ((%f,%f), (%f,%f), (%f,%f))\n",n+1,l,m, - grad_phi_nlm.a[0].real, grad_phi_nlm.a[0].img, - grad_phi_nlm.a[1].real, grad_phi_nlm.a[1].img, - grad_phi_nlm.a[2].real, grad_phi_nlm.a[2].img); - - printf("weights(n,l,m)(%d,%d,%d) = (%f,%f)\n", n+1, l, m, w.real, w.img); - //if (m>0) w*=2; - printf("dF(n,l,m)(%d, %d, %d) += (%f, %f, %f)\n", n + 1, l, m, - w.real_part_product(grad_phi_nlm.a[0]), - w.real_part_product(grad_phi_nlm.a[1]), - w.real_part_product(grad_phi_nlm.a[2]) - ); -#endif -// real-part multiplication only - f_ji[0] += w.real_part_product(grad_phi_nlm.a[0]); - f_ji[1] += w.real_part_product(grad_phi_nlm.a[1]); - f_ji[2] += w.real_part_product(grad_phi_nlm.a[2]); - } - } - } - - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); -#endif - - //hard-core repulsion - DCR = DCR_cache(jj); -#ifdef DEBUG_FORCES_CALCULATIONS - printf("DCR = %f\n",DCR); -#endif - f_ji[0] += dF_drho_core * DCR * r_hat[0]; - f_ji[1] += dF_drho_core * DCR * r_hat[1]; - f_ji[2] += dF_drho_core * DCR * r_hat[2]; -#ifdef PRINT_INTERMEDIATE_VALUES - printf("with core-repulsion\n"); - printf("f_ji(jj=%d, i=%d)=(%f, %f, %f)\n", jj, i, - f_ji[0], f_ji[1], f_ji[2] - ); - printf("neighbour_index_mapping[jj=%d]=%d\n",jj,neighbour_index_mapping[jj]); -#endif - - neighbours_forces(neighbour_index_mapping[jj], 0) = f_ji[0]; - neighbours_forces(neighbour_index_mapping[jj], 1) = f_ji[1]; - neighbours_forces(neighbour_index_mapping[jj], 2) = f_ji[2]; - - forces_calc_neighbour_timer.stop(); - }// end loop over neighbour atoms for forces - - forces_calc_loop_timer.stop(); - - //now, energies and forces are ready - //energies(i) = evdwl + rho_core; - e_atom = evdwl_cut; - -#ifdef PRINT_INTERMEDIATE_VALUES - printf("energies(i) = FS(...rho_p_accum...) = %f\n", evdwl); -#endif - per_atom_calc_timer.stop(); -} \ No newline at end of file diff --git a/lib/pace/ace_recursive.h b/lib/pace/ace_recursive.h deleted file mode 100644 index 78e74feb86..0000000000 --- a/lib/pace/ace_recursive.h +++ /dev/null @@ -1,247 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 20.12.2020 - -#ifndef ACE_RECURSIVE_H -#define ACE_RECURSIVE_H - -#include "ace_abstract_basis.h" -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_c_basis.h" -#include "ace_complex.h" -#include "ace_timing.h" -#include "ace_types.h" -#include "ace_evaluator.h" - -#include -#include -#include -#include -#include - -using namespace std; - - -typedef pair, vector > TPARTITION; -typedef list TPARTITIONS; - -typedef map, int> TDAGMAP; - -class ACEDAG { - - TPARTITIONS find_2partitions(vector v); - - void insert_node(TDAGMAP &dagmap, - vector node, - vector c); - - // the following fields are used only for *construction*, not evaluation - int dag_idx; // current index of dag node - Array2D nodes_pre; //TODO: YL: better to use vector<> - Array2D coeffs_pre; //TODO: YL: better to use vector<> - Array1D haschild; //TODO: YL: better to use vector<> - - /* which heuristic to choose for DAG construction? - * 0 : the simple original heuristic - * 1 : prioritize 2-correlation nodes and build the rest from those - */ - int heuristic = 0; - -public: - - ACEDAG() = default; - - void init(Array2D Aspec, Array2D AAspec, - Array1D orders, Array2D coeffs, - int heuristic ); - - Array1D AAbuf; - Array1D w; - - Array2D Aspec; - - // nodes in the graph - Array2D nodes; - Array2D coeffs; - - // total number of nodes in the dag - int num_nodes; - // number of interior nodes (with children) - int num2_int; - // number of leaf nodes (nc = no child) - int num2_leaf; - - - // number of 1-particle basis functions - // (these will be stored in the first num1 entries of AAbuf) - int get_num1() { return Aspec.get_dim(0); }; - // total number of n-correlation basis functions n > 1. - int get_num2() { return num_nodes - get_num1(); }; - int get_num2_int() { return num2_int; }; // with children - int get_num2_leaf() { return num2_leaf; }; // without children - - // debugging tool - void print(); -}; - - -/** - * Recursive Variant of the ACETildeEvaluator; should be 100% compatible - */ -class ACERecursiveEvaluator : public ACEEvaluator { - - /** - * Weights \f$ \omega_{i \mu n 0 0} \f$ for rank = 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase] - */ - Array2D weights_rank1 = Array2D("weights_rank1"); - - /** - * Weights \f$ \omega_{i \mu n l m} \f$ for rank > 1, see Eq.(10) from implementation notes, - * 'i' is fixed for the current atom, shape: [nelements][nradbase][l=0..lmax, m] - */ - Array4DLM weights = Array4DLM("weights"); - - /** - * cache for gradients of \f$ g(r)\f$: grad_phi(jj,n)=A2DLM(l,m) - * shape:[max_jnum][nradbase] - */ - Array2D DG_cache = Array2D("DG_cache"); - - - /** - * cache for \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D R_cache = Array3D("R_cache"); - /** - * cache for derivatives of \f$ R_{nl}(r)\f$ - * shape:[max_jnum][nradbase][0..lmax] - */ - Array3D DR_cache = Array3D("DR_cache"); - /** - * cache for \f$ Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM Y_cache = Array3DLM("Y_cache"); - /** - * cache for \f$ \nabla Y_{lm}(\hat{r})\f$ - * shape:[max_jnum][0..lmax][m] - */ - Array3DLM DY_cache = Array3DLM("dY_dense_cache"); - - /** - * cache for derivatives of hard-core repulsion - * shape:[max_jnum] - */ - Array1D DCR_cache = Array1D("DCR_cache"); - - /** - * Partial derivatives \f$ dB_{i \mu n l m t}^{(r)} \f$ with sequential numbering over [func_ind][ms_ind][r], - * shape:[func_ms_r_ind] - */ - Array1D dB_flatten = Array1D("dB_flatten"); - - /** - * pointer to the ACEBasisSet object - */ - ACECTildeBasisSet *basis_set = nullptr; - - /** - * Initialize internal arrays according to basis set sizes - * @param basis_set - */ - void init(ACECTildeBasisSet *basis_set, int heuristic); - - /* convert the PACE to the ACE.jl format to prepare for DAG construction*/ - Array2D jl_Aspec; - Array2D jl_AAspec; - Array1D jl_AAspec_flat; - Array1D jl_orders; - Array2D jl_coeffs; - void acejlformat(); - - /* the main event : the computational graph */ - ACEDAG dag; - - bool recursive = true; - -public: - - - ACERecursiveEvaluator() = default; - - explicit ACERecursiveEvaluator(ACECTildeBasisSet &bas, - bool recursive = true) { - set_recursive(recursive); - set_basis(bas); - } - - /** - * set the basis function to the ACE evaluator - * @param bas - */ - void set_basis(ACECTildeBasisSet &bas, int heuristic = 0); - - /** - * The key method to compute energy and forces for atom 'i'. - * Method will update the "e_atom" variable and "neighbours_forces(jj, alpha)" array - * - * @param i atom index - * @param x atomic positions array of the real and ghost atoms, shape: [atom_ind][3] - * @param type atomic types array of the real and ghost atoms, shape: [atom_ind] - * @param jnum number of neighbours of atom_i - * @param jlist array of neighbour indices, shape: [jnum] - */ - void compute_atom(int i, DOUBLE_TYPE **x, const SPECIES_TYPE *type, const int jnum, const int *jlist) override; - - /** - * Resize all caches over neighbours atoms - * @param max_jnum maximum number of neighbours - */ - void resize_neighbours_cache(int max_jnum) override; - - /******* public functions related to recursive evaluator ********/ - - // print out the DAG for visual inspection - void print_dag() {dag.print();} - - // print out the jl format for visual inspection - // should be converted into a proper test - void test_acejlformat(); - - void set_recursive(bool tf) { recursive = tf; } - - /********************************/ - -}; - - -#endif //ACE_RECURSIVE_H \ No newline at end of file diff --git a/lib/pace/ace_spherical_cart.cpp b/lib/pace/ace_spherical_cart.cpp deleted file mode 100644 index f1f0fccced..0000000000 --- a/lib/pace/ace_spherical_cart.cpp +++ /dev/null @@ -1,221 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Ralf Drautz, Yury Lysogorskiy - -#include - -#include "ace_spherical_cart.h" - -ACECartesianSphericalHarmonics::ACECartesianSphericalHarmonics(LS_TYPE lm) { - init(lm); -} - -void ACECartesianSphericalHarmonics::init(LS_TYPE lm) { - lmax = lm; - - alm.init(lmax, "alm"); - blm.init(lmax, "blm"); - cl.init(lmax + 1); - dl.init(lmax + 1); - - plm.init(lmax, "plm"); - dplm.init(lmax, "dplm"); - - ylm.init(lmax, "ylm"); - dylm.init(lmax, "dylm"); - - pre_compute(); -} - -/** -Destructor for ACECartesianSphericalHarmonics. - -@param None - -@returns None -*/ -ACECartesianSphericalHarmonics::~ACECartesianSphericalHarmonics() {} - - -void ACECartesianSphericalHarmonics::pre_compute() { - - DOUBLE_TYPE a, b; - DOUBLE_TYPE lsq, ld, l1, l2; - DOUBLE_TYPE msq; - - for (LS_TYPE l = 1; l <= lmax; l++) { - lsq = l * l; - ld = 2 * l; - l1 = (4 * lsq - 1); - l2 = lsq - ld + 1; - for (MS_TYPE m = 0; m < l - 1; m++) { - msq = m * m; - a = sqrt((DOUBLE_TYPE(l1)) / (DOUBLE_TYPE(lsq - msq))); - b = -sqrt((DOUBLE_TYPE(l2 - msq)) / (DOUBLE_TYPE(4 * l2 - 1))); - alm(l, m) = a; - blm(l, m) = b; - } - } - - for (LS_TYPE l = 1; l <= lmax; l++) { - cl(l) = -sqrt(1.0 + 0.5 / (DOUBLE_TYPE(l))); - dl(l) = sqrt(DOUBLE_TYPE(2 * (l - 1) + 3)); - } -} - - -void ACECartesianSphericalHarmonics::compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi) { - - // requires -1 <= rz <= 1 , NO CHECKING IS PERFORMED !!!!!!!!! - // prefactors include 1/sqrt(2) factor compared to reference - DOUBLE_TYPE t; - - // l=0, m=0 - //plm(0, 0) = Y00/sq1o4pi; //= sq1o4pi; - plm(0, 0) = Y00; //= 1; - dplm(0, 0) = 0.0; - - if (lmaxi > 0) { - - // l=1, m=0 - plm(1, 0) = Y00 * sq3 * rz; - dplm(1, 0) = Y00 * sq3; - - // l=1, m=1 - plm(1, 1) = -sq3o2 * Y00; - dplm(1, 1) = 0.0; - - // loop l = 2, lmax - for (LS_TYPE l = 2; l <= lmaxi; l++) { - for (MS_TYPE m = 0; m < l - 1; m++) { - plm(l, m) = alm(l, m) * (rz * plm(l - 1, m) + blm(l, m) * plm(l - 2, m)); - dplm(l, m) = alm(l, m) * (plm(l - 1, m) + rz * dplm(l - 1, m) + blm(l, m) * dplm(l - 2, m)); - } - t = dl(l) * plm(l - 1, l - 1); - plm(l, l - 1) = t * rz; - dplm(l, l - 1) = t; - plm(l, l) = cl(l) * plm(l - 1, l - 1); - dplm(l, l) = 0.0; - } - } -} //end compute_barplm - - -void ACECartesianSphericalHarmonics::compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi) { - - // requires rx^2 + ry^2 + rz^2 = 1 , NO CHECKING IS PERFORMED !!!!!!!!! - - DOUBLE_TYPE real; - DOUBLE_TYPE img; - MS_TYPE m; - ACEComplex phase; - ACEComplex phasem, mphasem1; - ACEComplex dyx, dyy, dyz; - ACEComplex rdy; - - phase.real = rx; - phase.img = ry; - //compute barplm - compute_barplm(rz, lmaxi); - - //m = 0 - m = 0; - for (LS_TYPE l = 0; l <= lmaxi; l++) { - - ylm(l, m).real = plm(l, m); - ylm(l, m).img = 0.0; - - dyz.real = dplm(l, m); - rdy.real = dyz.real * rz; - - dylm(l, m).a[0].real = -rdy.real * rx; - dylm(l, m).a[0].img = 0.0; - dylm(l, m).a[1].real = -rdy.real * ry; - dylm(l, m).a[1].img = 0.0; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = 0; - } - //m = 0 - m = 1; - for (LS_TYPE l = 1; l <= lmaxi; l++) { - - ylm(l, m) = phase * plm(l, m); - -// std::cout << "Re ylm(" << l << "," << m <<")= " << ylm(l, m).real << std::endl; -// std::cout << "Im ylm(" << l << "," << m <<")= " << ylm(l, m).img << std::endl; - - dyx.real = plm(l, m); - dyx.img = 0.0; - dyy.real = 0.0; - dyy.img = plm(l, m); - dyz.real = phase.real * dplm(l, m); - dyz.img = phase.img * dplm(l, m); - - rdy.real = rx * dyx.real + +rz * dyz.real; - rdy.img = ry * dyy.img + rz * dyz.img; - - dylm(l, m).a[0].real = dyx.real - rdy.real * rx; - dylm(l, m).a[0].img = -rdy.img * rx; - dylm(l, m).a[1].real = -rdy.real * ry; - dylm(l, m).a[1].img = dyy.img - rdy.img * ry; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = dyz.img - rdy.img * rz; - } - - // m > 1 - phasem = phase; - for (MS_TYPE m = 2; m <= lmaxi; m++) { - - mphasem1.real = phasem.real * DOUBLE_TYPE(m); - mphasem1.img = phasem.img * DOUBLE_TYPE(m); - phasem = phasem * phase; - - for (LS_TYPE l = m; l <= lmaxi; l++) { - - ylm(l, m).real = phasem.real * plm(l, m); - ylm(l, m).img = phasem.img * plm(l, m); - - dyx = mphasem1 * plm(l, m); - dyy.real = -dyx.img; - dyy.img = dyx.real; - dyz = phasem * dplm(l, m); - - rdy.real = rx * dyx.real + ry * dyy.real + rz * dyz.real; - rdy.img = rx * dyx.img + ry * dyy.img + rz * dyz.img; - - dylm(l, m).a[0].real = dyx.real - rdy.real * rx; - dylm(l, m).a[0].img = dyx.img - rdy.img * rx; - dylm(l, m).a[1].real = dyy.real - rdy.real * ry; - dylm(l, m).a[1].img = dyy.img - rdy.img * ry; - dylm(l, m).a[2].real = dyz.real - rdy.real * rz; - dylm(l, m).a[2].img = dyz.img - rdy.img * rz; - } - } - -} - diff --git a/lib/pace/ace_spherical_cart.h b/lib/pace/ace_spherical_cart.h deleted file mode 100644 index b2a0cb5913..0000000000 --- a/lib/pace/ace_spherical_cart.h +++ /dev/null @@ -1,134 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Ralf Drautz, Yury Lysogorskiy - -#ifndef ACE_SPHERICAL_CART_H -#define ACE_SPHERICAL_CART_H - -#include - -#include "ace_arraynd.h" -#include "ace_array2dlm.h" -#include "ace_complex.h" -#include "ace_types.h" - - -using namespace std; - -const DOUBLE_TYPE sq1o4pi = 0.28209479177387814347; // sqrt(1/(4*pi)) -const DOUBLE_TYPE sq4pi = 3.54490770181103176384; // sqrt(4*pi) -const DOUBLE_TYPE sq3 = 1.73205080756887719318;//sqrt(3), numpy -const DOUBLE_TYPE sq3o2 = 1.22474487139158894067;//sqrt(3/2), numpy - -//definition of common factor for spherical harmonics = Y00 -//const DOUBLE_TYPE Y00 = sq1o4pi; -const DOUBLE_TYPE Y00 = 1; - -/** -Class to store spherical harmonics and their associated functions. \n -All the associated members such as \f$ P_{lm}, Y_{lm}\f$ etc are one dimensional arrays of length (L+1)*(L+2)/2. \n -The value that corresponds to a particular l, m configuration can be accessed through a \code ylm(l,m) \endcode \n -*/ -class ACECartesianSphericalHarmonics { -public: - - /** - int, the number of spherical harmonics to be found - */ - LS_TYPE lmax; - - /** - * Default constructor - */ - ACECartesianSphericalHarmonics() = default; - - /** - * Parametrized constructor. Dynamically initialises all the arrays. - * @param lmax maximum orbital moment - */ - explicit ACECartesianSphericalHarmonics(LS_TYPE lmax); - - /** - * Initialize internal arrays and precompute necessary coefficients - * @param lm maximum orbital moment - */ - void init(LS_TYPE lm); - - /** - * Destructor - */ - ~ACECartesianSphericalHarmonics(); - - /** - * Precompute necessaary helper arrays Precomputes the value of \f$ a_{lm}, b_{lm}, c_l, d_l \f$ - */ - void pre_compute(); - - /** - Function that computes \f$ \bar{P}_{lm} \f$ for the corresponding lmax value - Input is \f$ \hat{r}_z \f$ which is the $z$-component of the bond direction. - - For each \f$ \hat{r}_z \f$, this computes the whole range of \f$ \bar{P}_{lm} \f$ values - and its derivatives upto the lmax specified, which is a member of the class. - - @param rz, DOUBLE_TYPE - - @returns None - */ - void compute_barplm(DOUBLE_TYPE rz, LS_TYPE lmaxi); - - /** - Function that computes \f$ Y_{lm} \f$ for the corresponding lmax value - Input is the bond-directon vector \f$ \hat{r}_x, \hat{r}_y, \hat{r}_z \f$ - - Each \f$ Y_{lm} \f$ value is a ACEComplex object with real and imaginary parts. This function also - finds the derivatives, which are stored in the Dycomponent class, with each component being a - ACEComplex object. - - @param rx, DOUBLE_TYPE - @param ry, DOUBLE_TYPE - @param rz, DOUBLE_TYPE - @param lmaxi, int - */ - void compute_ylm(DOUBLE_TYPE rx, DOUBLE_TYPE ry, DOUBLE_TYPE rz, LS_TYPE lmaxi); - - Array2DLM alm; - Array2DLM blm; - Array1D cl; - Array1D dl; - - Array2DLM plm; - Array2DLM dplm; - - Array2DLM ylm; ///< Values of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call - Array2DLM dylm;///< Values of gradients of all spherical harmonics after \code compute_ylm(rx,ry,rz, lmaxi) \endcode call - -}; - - -#endif diff --git a/lib/pace/ace_timing.h b/lib/pace/ace_timing.h deleted file mode 100644 index 7f5243eb99..0000000000 --- a/lib/pace/ace_timing.h +++ /dev/null @@ -1,126 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Yury Lysogorskiy on 19.02.20. - -#ifndef ACE_TIMING_H -#define ACE_TIMING_H - -#include - -using namespace std::chrono; -using Clock = std::chrono::high_resolution_clock; -using TimePoint = std::chrono::time_point; -using Duration = Clock::duration; - -////////////////////////////////////////// -#ifdef FINE_TIMING -/** - * Helper class for timing the code. - * The timer should be initialized to reset measured time and - * then call "start" and "stop" before and after measured code. - * The measured time is stored in "duration" variable - */ -struct ACETimer { - Duration duration; ///< measured duration - TimePoint start_moment; ///< start moment of current measurement - - ACETimer() { init(); }; - - /** - * Reset timer - */ - void init() { duration = std::chrono::nanoseconds(0); } - - /** - * Start timer - */ - void start() { start_moment = Clock::now(); } - - /** - * Stop timer, update measured "duration" - */ - void stop() { duration += Clock::now() - start_moment; } - - /** - * Get duration in microseconds - */ - long as_microseconds() { return std::chrono::duration_cast(duration).count(); } - - /** - * Get duration in nanoseconds - */ - long as_nanoseconds() { return std::chrono::duration_cast(duration).count(); } - -}; - -#else // EMPTY Definitions -/** - * Helper class for timing the code. - * The timer should be initialized to reset measured time and - * then call "start" and "stop" before and after measured code. - * The measured time is stored in "duration" variable - */ -struct ACETimer { - Duration duration; ///< measured duration - TimePoint start_moment; ///< start moment of current measurement - - ACETimer() {}; - - /** - * Reset timer - */ - void init() {} - - /** - * Start timer - */ - void start() {} - - /** - * Stop timer, update measured "duration" - */ - void stop() {} - - /** - * Get duration in microseconds - */ - long as_microseconds() {return 0; } - - /** - * Get duration in nanoseconds - */ - long as_nanoseconds() {return 0; } - -}; - -#endif -////////////////////////////////////////// - - -#endif //ACE_TIMING_H diff --git a/lib/pace/ace_types.h b/lib/pace/ace_types.h deleted file mode 100644 index f9b3cf7267..0000000000 --- a/lib/pace/ace_types.h +++ /dev/null @@ -1,45 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Yury Lysogorskiy on 20.01.20. - -#ifndef ACE_TYPES_H -#define ACE_TYPES_H - -typedef char RANK_TYPE; -typedef int SPECIES_TYPE; -typedef short int NS_TYPE; -typedef short int LS_TYPE; - -typedef short int DENSITY_TYPE; - -typedef short int MS_TYPE; - -typedef short int SHORT_INT_TYPE; -typedef double DOUBLE_TYPE; - -#endif \ No newline at end of file diff --git a/lib/pace/ace_version.h b/lib/pace/ace_version.h deleted file mode 100644 index 9d61e5c505..0000000000 --- a/lib/pace/ace_version.h +++ /dev/null @@ -1,39 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Lysogorskiy Yury on 07.04.2020. - -#ifndef ACE_VERSION_H -#define ACE_VERSION_H - -#define VERSION_YEAR 2021 -#define VERSION_MONTH 2 -#define VERSION_DAY 3 - -#endif //ACE_VERSION_Hls - diff --git a/lib/pace/ships_radial.cpp b/lib/pace/ships_radial.cpp deleted file mode 100644 index e948f03f21..0000000000 --- a/lib/pace/ships_radial.cpp +++ /dev/null @@ -1,388 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - -// Created by Christoph Ortner on 03.06.2020 - -#include "ships_radial.h" - -#include -#include -#include - - -using namespace std; - -void SHIPsRadPolyBasis::_init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, - DOUBLE_TYPE xl, DOUBLE_TYPE xr, - int pl, int pr, size_t maxn) { - this->p = p; - this->r0 = r0; - this->rcut = rcut; - this->xl = xl; - this->xr = xr; - this->pl = pl; - this->pr = pr; - this->maxn = maxn; - this->A.resize(maxn); - this->B.resize(maxn); - this->C.resize(maxn); - this->P.resize(maxn); - this->dP_dr.resize(maxn); -} - - -void SHIPsRadPolyBasis::fread(FILE *fptr) -{ - int res; //for fscanf result - int maxn, p, pl, pr, ntests; - double r0, xl, xr, a, b, c, rcut; - - // transform parameters - res = fscanf(fptr, "transform parameters: p=%d r0=%lf\n", &p, &r0); - if (res != 2) - throw invalid_argument("Couldn't read line: transform parameters: p=%d r0=%lf"); - // cutoff parameters - res = fscanf(fptr, "cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d\n", - &rcut, &xl, &xr, &pl, &pr); - if (res != 5) - throw invalid_argument("Couldn't read cutoff parameters: rcut=%lf xl=%lf xr=%lf pl=%d pr=%d"); - // basis size - res = fscanf(fptr, "recursion coefficients: maxn = %d\n", &maxn); - if (res != 1) - throw invalid_argument("Couldn't read recursion coefficients: maxn = %d"); - // initialize and allocate - this->_init(r0, p, rcut, xl, xr, pl, pr, maxn); - - // read basis coefficients - for (int i = 0; i < maxn; i++) { - res = fscanf(fptr, " %lf %lf %lf\n", &a, &b, &c); - if (res != 3) - throw invalid_argument("Couldn't read line: A_n B_n C_n"); - this->A(i) = DOUBLE_TYPE(a); - this->B(i) = DOUBLE_TYPE(b); - this->C(i) = DOUBLE_TYPE(c); - } - - // // check there are no consistency tests (I don't have time to fix this now) - // res = fscanf(fptr, "tests: ntests = %d\n", &ntests); - // if (res != 1) - // throw invalid_argument("Couldn't read line: tests: ntests = %d"); - // if (ntests != 0) - // throw invalid_argument("must have ntests = 0!"); - - // --------------------------------------------------------------------- - // run the consistency test this could be moved into a separate function - double r, Pn, dPn; - double err = 0.0; - - res = fscanf(fptr, "tests: ntests = %d\n", &ntests); - if (res != 1) - throw invalid_argument("Couldn't read line: tests: ntests = %d"); - for (size_t itest = 0; itest < ntests; itest++) { - // read an r argument - res = fscanf(fptr, " r=%lf\n", &r); - // printf("r = %lf \n", r); - if (res != 1) - throw invalid_argument("Couldn't read line: r=%lf"); - // printf("test %d, r=%f, maxn=%d \n", itest, r, maxn); - // evaluate the basis - this->calcP(r, maxn, SPECIES_TYPE(0), SPECIES_TYPE(0)); - // compare against the stored values - for (size_t n = 0; n < maxn; n++) { - res = fscanf(fptr, " %lf %lf\n", &Pn, &dPn); - if (res != 2) - throw invalid_argument("Couldn't read test value line: %lf %lf"); - err = max(err, abs(Pn - this->P(n)) + abs(dPn - this->dP_dr(n))); - // printf(" %d %e %e \n", int(n), - // abs(Pn - this->P(n)), - // abs(dPn - this->dP_dr(n))); - } - } - if (ntests > 0) - printf("Maximum Test error = %e\n", err); - // --------------------------------------------------------------------- - -} - - - - -size_t SHIPsRadPolyBasis::get_maxn() -{ - return this->maxn; -} - - -// Julia code: ((1+r0)/(1+r))^p -void SHIPsRadPolyBasis::transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const { - x_out = pow((1 + r0) / (1 + r), p); // ==pow( (1 + r) / (1 + r0), -p ); - dx_out = -p * pow((1 + r) / (1 + r0), -p - 1) / (1 + r0); -} - -void SHIPsRadPolyBasis::fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const { - if ( ((x < xl) && (pl > 0)) || ((x > xr) && (pr > 0)) ) { - f_out = 0.0; - df_out = 0.0; - } else { - f_out = pow(x - xl, pl) * pow(x - xr, pr); - df_out = pl * pow(x - xl, pl - 1) * pow(x - xr, pr) + pow(x - xl, pl) * pr * pow(x - xr, pr - 1); - } -} - - /* ------------------------------------------------------------------------ -Julia Code -P[1] = J.A[1] * _fcut_(J.pl, J.tl, J.pr, J.tr, t) -if length(J) == 1; return P; end -P[2] = (J.A[2] * t + J.B[2]) * P[1] -@inbounds for n = 3:length(J) - P[n] = (J.A[n] * t + J.B[n]) * P[n-1] + J.C[n] * P[n-2] -end -return P ------------------------------------------------------------------------- */ - -void SHIPsRadPolyBasis::calcP(DOUBLE_TYPE r, size_t maxn, - SPECIES_TYPE z1, SPECIES_TYPE z2) { - if (maxn > this->maxn) - throw invalid_argument("Given maxn couldn't be larger than global maxn"); - - if (maxn > P.get_size()) - throw invalid_argument("Given maxn couldn't be larger than global length of P"); - - DOUBLE_TYPE x, dx_dr; // dx -> dx/dr - transform(r, x, dx_dr); - // printf("r = %f, x = %f, fcut = %f \n", r, x, fcut(x)); - DOUBLE_TYPE f, df_dx; - fcut(x, f, df_dx); // df -> df/dx - - //fill with zeros - P.fill(0); - dP_dr.fill(0); - - P(0) = A(0) * f; - dP_dr(0) = A(0) * df_dx * dx_dr; // dP/dr; chain rule: df_cut/dr = df_cut/dx * dx/dr - if (maxn > 0) { - P(1) = (A(1) * x + B(1)) * P(0); - dP_dr(1) = A(1) * dx_dr * P(0) + (A(1) * x + B(1)) * dP_dr(0); - } - for (size_t n = 2; n < maxn; n++) { - P(n) = (A(n) * x + B(n)) * P(n - 1) + C(n) * P(n - 2); - dP_dr(n) = A(n) * dx_dr * P(n - 1) + (A(n) * x + B(n)) * dP_dr(n - 1) + C(n) * dP_dr(n - 2); - } -} - - -// ==================================================================== - - -bool SHIPsRadialFunctions::has_pair() { - return this->haspair; -} - -void SHIPsRadialFunctions::load(string fname) { - FILE * fptr = fopen(fname.data(), "r"); - size_t res = fscanf(fptr, "radbasename=ACE.jl.Basic\n"); - if (res != 0) - throw("SHIPsRadialFunctions::load : couldnt read radbasename=ACE.jl.Basic"); - this->fread(fptr); - fclose(fptr); -} - -void SHIPsRadialFunctions::fread(FILE *fptr){ - int res; - size_t maxn; - char hasE0, haspair; - DOUBLE_TYPE c; - - // check whether we have a pair potential - res = fscanf(fptr, "haspair: %c\n", &haspair); - if (res != 1) - throw("SHIPsRadialFunctions::load : couldn't read haspair"); - - // read the radial basis - this->radbasis.fread(fptr); - - // read the pair potential - if (haspair == 't') { - this->haspair=true; - fscanf(fptr, "begin repulsive potential\n"); - fscanf(fptr, "begin polypairpot\n"); - // read the basis parameters - pairbasis.fread(fptr); - maxn = pairbasis.get_maxn(); - // read the coefficients - fscanf(fptr, "coefficients\n"); - paircoeffs.resize(maxn); - for (size_t n = 0; n < maxn; n++) { - fscanf(fptr, "%lf\n", &c); - paircoeffs(n) = c; - } - fscanf(fptr, "end polypairpot\n"); - // read the spline parameters - fscanf(fptr, "spline parameters\n"); - fscanf(fptr, " e_0 + B exp(-A*(r/ri-1)) * (ri/r)\n"); - fscanf(fptr, "ri=%lf\n", &(this->ri)); - fscanf(fptr, "e0=%lf\n", &(this->e0)); - fscanf(fptr, "A=%lf\n", &(this->A)); - fscanf(fptr, "B=%lf\n", &(this->B)); - fscanf(fptr, "end repulsive potential\n"); - } -} - - -size_t SHIPsRadialFunctions::get_maxn() -{ - return this->radbasis.get_maxn(); -} - -DOUBLE_TYPE SHIPsRadialFunctions::get_rcut() -{ - return max(radbasis.rcut, pairbasis.rcut); -} - - -void SHIPsRadialFunctions::fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { - radbasis.calcP(r, maxn, z1, z2); - for (NS_TYPE n = 0; n < maxn; n++) { - gr(n) = radbasis.P(n); - dgr(n) = radbasis.dP_dr(n); - } -} - - -void SHIPsRadialFunctions::fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2) { - radbasis.calcP(r, maxn, z1, z2); - for (NS_TYPE n = 0; n < maxn; n++) { - for (LS_TYPE l = 0; l <= lmax; l++) { - fr(n, l) = radbasis.P(n); - dfr(n, l) = radbasis.dP_dr(n); - } - } -} - - -void SHIPsRadialFunctions::setuplookupRadspline() { -} - - -void SHIPsRadialFunctions::init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, - SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, string radbasename) { - //mimic ACERadialFunctions::init - this->nradbase = nradb; - this->lmax = lmax; - this->nradial = nradial; - this->deltaSplineBins = deltaSplineBins; - this->nelements = nelements; - this->cutoff = cutoff; - this->radbasename = radbasename; - - gr.init(nradbase, "gr"); - dgr.init(nradbase, "dgr"); - - - fr.init(nradial, lmax + 1, "fr"); - dfr.init(nradial, lmax + 1, "dfr"); - - splines_gk.init(nelements, nelements, "splines_gk"); - splines_rnl.init(nelements, nelements, "splines_rnl"); - splines_hc.init(nelements, nelements, "splines_hc"); - - lambda.init(nelements, nelements, "lambda"); - lambda.fill(1.); - - cut.init(nelements, nelements, "cut"); - cut.fill(1.); - - dcut.init(nelements, nelements, "dcut"); - dcut.fill(1.); - - crad.init(nelements, nelements, (lmax + 1), nradial, nradbase, "crad"); - crad.fill(0.); - - //hard-core repulsion - prehc.init(nelements, nelements, "prehc"); - prehc.fill(0.); - - lambdahc.init(nelements, nelements, "lambdahc"); - lambdahc.fill(1.); -} - - -void SHIPsRadialFunctions::evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, bool calc_second_derivatives) { - if (calc_second_derivatives) - throw invalid_argument("SHIPsRadialFunctions has not `calc_second_derivatives` option"); - - radbasis.calcP(r, nradbase_c, mu_i, mu_j); - for (NS_TYPE nr = 0; nr < nradbase_c; nr++) { - gr(nr) = radbasis.P(nr); - dgr(nr) = radbasis.dP_dr(nr); - } - for (NS_TYPE nr = 0; nr < nradial_c; nr++) { - for (LS_TYPE l = 0; l <= this->lmax; l++) { - fr(nr, l) = radbasis.P(nr); - dfr(nr, l) = radbasis.dP_dr(nr); - } - } - - if (this->has_pair()) - this->evaluate_pair(r, mu_i, mu_j); - else { - cr = 0; - dcr = 0; - } -} - -void SHIPsRadialFunctions::evaluate_pair(DOUBLE_TYPE r, - SPECIES_TYPE mu_i, - SPECIES_TYPE mu_j, - bool calc_second_derivatives) { - // spline_hc.calcSplines(r); - // cr = spline_hc.values(0); - // dcr = spline_hc.derivatives(0); - - // the outer polynomial potential - if (r > ri) { - pairbasis.calcP(r, pairbasis.get_maxn(), mu_i, mu_j); - cr = 0; - dcr = 0; - for (size_t n = 0; n < pairbasis.get_maxn(); n++) { - cr += paircoeffs(n) * pairbasis.P(n); - dcr += paircoeffs(n) * pairbasis.dP_dr(n); - } - } - else { // the repulsive core part - cr = e0 + B * exp(-A * (r/ri - 1)) * (ri/r); - dcr = B * exp( - A * (r/ri-1) ) * ri * ( - A / ri / r - 1/(r*r) ); - } - // fix double-counting - cr *= 0.5; - dcr *= 0.5; -} - - - diff --git a/lib/pace/ships_radial.h b/lib/pace/ships_radial.h deleted file mode 100644 index 60a82448cd..0000000000 --- a/lib/pace/ships_radial.h +++ /dev/null @@ -1,158 +0,0 @@ -/* - * Performant implementation of atomic cluster expansion and interface to LAMMPS - * - * Copyright 2021 (c) Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, - * Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, - * Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1 - * - * ^1: Ruhr-University Bochum, Bochum, Germany - * ^2: University of Cambridge, Cambridge, United Kingdom - * ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA - * ^4: University of British Columbia, Vancouver, BC, Canada - * - * - * See the LICENSE file. - * This FILENAME is free software: you can redistribute it and/or modify - * it under the terms of the GNU General Public License as published by - * the Free Software Foundation, either version 3 of the License, or - * (at your option) any later version. - - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * You should have received a copy of the GNU General Public License - * along with this program. If not, see . - */ - - -// Created by Christoph Ortner on 03.06.2020 - -#ifndef SHIPs_RADIAL_FUNCTIONS_H -#define SHIPs_RADIAL_FUNCTIONS_H - -#include "ace_arraynd.h" -#include "ace_types.h" -#include "ace_radial.h" - -class SHIPsRadPolyBasis { - -public: - - // transform parameters - int p = 0; - DOUBLE_TYPE r0 = 0.0; - - // cutoff parameters - DOUBLE_TYPE rcut = 0.0; - DOUBLE_TYPE xl = 0.0; - DOUBLE_TYPE xr = 0.0; - int pl = 0; - int pr = 0; - - // basis size - size_t maxn = 0; - - // recursion parameters - Array1D A = Array1D("SHIPs radial basis: A"); - Array1D B = Array1D("SHIPs radial basis: B"); - Array1D C = Array1D("SHIPs radial basis: C"); - - // temporary storage for evaluating the basis - Array1D P = Array1D("SHIPs radial basis: P"); - Array1D dP_dr = Array1D("SHIPs radial basis: dP"); - -////////////////////////////////// - - SHIPsRadPolyBasis() = default; - - ~SHIPsRadPolyBasis() = default; - - // distance transform - void transform(const DOUBLE_TYPE r, DOUBLE_TYPE &x_out, DOUBLE_TYPE &dx_out) const; - - // cutoff function - void fcut(const DOUBLE_TYPE x, DOUBLE_TYPE &f_out, DOUBLE_TYPE &df_out) const; - - void fread(FILE *fptr); - - void _init(DOUBLE_TYPE r0, int p, DOUBLE_TYPE rcut, - DOUBLE_TYPE xl, DOUBLE_TYPE xr, - int pl, int pr, size_t maxn); - - void calcP(DOUBLE_TYPE r, size_t maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); - - size_t get_maxn(); - -}; - - - - -class SHIPsRadialFunctions : public AbstractRadialBasis { -public: - - // radial basis - SHIPsRadPolyBasis radbasis; - - // pair potential basis - bool haspair = false; - SHIPsRadPolyBasis pairbasis; - - // pair potential coefficients - Array1D paircoeffs = Array1D("SHIPs pairpot coeffs: paircoeffs"); - - // spline parameters for repulsive core - DOUBLE_TYPE ri = 0.0; - DOUBLE_TYPE e0 = 0.0; - DOUBLE_TYPE A = 0.0; - DOUBLE_TYPE B = 0.0; - -////////////////////////////////// - - SHIPsRadialFunctions() = default; - - ~SHIPsRadialFunctions() override = default; - - - void fread(FILE *fptr); - - void load(string fname); - - size_t get_maxn(); - DOUBLE_TYPE get_rcut(); - - bool has_pair(); - - void init(NS_TYPE nradb, LS_TYPE lmax, NS_TYPE nradial, DOUBLE_TYPE deltaSplineBins, SPECIES_TYPE nelements, - DOUBLE_TYPE cutoff, - string radbasename) override; - - void - evaluate(DOUBLE_TYPE r, NS_TYPE nradbase_c, NS_TYPE nradial_c, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false) override; - - void - evaluate_pair(DOUBLE_TYPE r, SPECIES_TYPE mu_i, SPECIES_TYPE mu_j, - bool calc_second_derivatives = false); - - void setuplookupRadspline() override; - - SHIPsRadialFunctions *clone() const override { - return new SHIPsRadialFunctions(*this); - }; - - /** - * Helper method, that populate `fr` and `dfr` 2D-arrays (n,l) with P(n), dP_dr for given coordinate r - * @param r - * @param maxn - * @param z1 - * @param z2 - */ - void fill_Rnl(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); - - void fill_gk(DOUBLE_TYPE r, NS_TYPE maxn, SPECIES_TYPE z1, SPECIES_TYPE z2); -}; - - -#endif diff --git a/src/USER-PACE/Install.sh b/src/USER-PACE/Install.sh index 4d87b0e3ed..c099ddd2c4 100644 --- a/src/USER-PACE/Install.sh +++ b/src/USER-PACE/Install.sh @@ -1,68 +1,64 @@ -# Install.sh file that integrates the settings from the lib folder into the conventional build process (make build?) +# Install/unInstall package files in LAMMPS +# mode = 0/1/2 for uninstall/install/update -# COPIED FROM src/KIM/Install.sh: +mode=$1 -# # Install/unInstall package files in LAMMPS -# # mode = 0/1/2 for uninstall/install/update +# enforce using portable C locale +LC_ALL=C +export LC_ALL -# mode=$1 +# arg1 = file, arg2 = file it depends on -# # enforce using portable C locale -# LC_ALL=C -# export LC_ALL +action () { + if (test $mode = 0) then + rm -f ../$1 + elif (! cmp -s $1 ../$1) then + if (test -z "$2" || test -e ../$2) then + cp $1 .. + if (test $mode = 2) then + echo " updating src/$1" + fi + fi + elif (test -n "$2") then + if (test ! -e ../$2) then + rm -f ../$1 + fi + fi +} -# # arg1 = file, arg2 = file it depends on +# all package files with no dependencies -# action () { -# if (test $mode = 0) then -# rm -f ../$1 -# elif (! cmp -s $1 ../$1) then -# if (test -z "$2" || test -e ../$2) then -# cp $1 .. -# if (test $mode = 2) then -# echo " updating src/$1" -# fi -# fi -# elif (test -n "$2") then -# if (test ! -e ../$2) then -# rm -f ../$1 -# fi -# fi -# } +for file in *.cpp *.h; do + test -f ${file} && action $file +done -# # all package files with no dependencies +# edit 2 Makefile.package files to include/exclude package info -# for file in *.cpp *.h; do -# test -f ${file} && action $file -# done +if (test $1 = 1) then -# # edit 2 Makefile.package files to include/exclude package info + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*pace[^ \t]* //' ../Makefile.package + sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(pace_SYSINC) |' ../Makefile.package + sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(pace_SYSLIB) |' ../Makefile.package + sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(pace_SYSPATH) |' ../Makefile.package + fi -# if (test $1 = 1) then + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + # multiline form needed for BSD sed on Macs + sed -i -e '4 i \ +include ..\/..\/lib\/pace\/Makefile.lammps +' ../Makefile.package.settings + fi -# if (test -e ../Makefile.package) then -# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package -# sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(kim_SYSINC) |' ../Makefile.package -# sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(kim_SYSLIB) |' ../Makefile.package -# sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(kim_SYSPATH) |' ../Makefile.package -# fi +elif (test $1 = 0) then -# if (test -e ../Makefile.package.settings) then -# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings -# # multiline form needed for BSD sed on Macs -# sed -i -e '4 i \ -# include ..\/..\/lib\/kim\/Makefile.lammps -# ' ../Makefile.package.settings -# fi + if (test -e ../Makefile.package) then + sed -i -e 's/[^ \t]*pace[^ \t]* //' ../Makefile.package + fi -# elif (test $1 = 0) then + if (test -e ../Makefile.package.settings) then + sed -i -e '/^include.*pace.*$/d' ../Makefile.package.settings + fi -# if (test -e ../Makefile.package) then -# sed -i -e 's/[^ \t]*kim[^ \t]* //' ../Makefile.package -# fi - -# if (test -e ../Makefile.package.settings) then -# sed -i -e '/^include.*kim.*$/d' ../Makefile.package.settings -# fi - -# fi +fi From 0d1ccbe1b542fdcfb8259c23c501be756307798c Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 12:43:28 +0200 Subject: [PATCH 025/100] Move A.Thomson's modifications on doc and examples in: - doc/src/.rst - examples/USER/pace - potentials --- doc/src/Commands_pair.rst | 1 + doc/src/Packages_details.rst | 37 + doc/src/pair_pace.rst | 114 + examples/USER/pace/Cu-PBE-core-rep.ace | 1 + examples/USER/pace/in.pace.product | 38 + examples/USER/pace/in.pace.recursive | 38 + .../pace/log.03Feb2021.pace.product.g++.1 | 108 + .../pace/log.03Feb2021.pace.product.g++.4 | 108 + .../pace/log.03Feb2021.pace.recursive.g++.1 | 108 + .../pace/log.03Feb2021.pace.recursive.g++.4 | 108 + potentials/Cu-PBE-core-rep.ace | 8980 +++++++++++++++++ 11 files changed, 9641 insertions(+) create mode 100644 doc/src/pair_pace.rst create mode 120000 examples/USER/pace/Cu-PBE-core-rep.ace create mode 100644 examples/USER/pace/in.pace.product create mode 100644 examples/USER/pace/in.pace.recursive create mode 100644 examples/USER/pace/log.03Feb2021.pace.product.g++.1 create mode 100644 examples/USER/pace/log.03Feb2021.pace.product.g++.4 create mode 100644 examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 create mode 100644 examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 create mode 100644 potentials/Cu-PBE-core-rep.ace diff --git a/doc/src/Commands_pair.rst b/doc/src/Commands_pair.rst index 080f3eff20..1d15b93edf 100644 --- a/doc/src/Commands_pair.rst +++ b/doc/src/Commands_pair.rst @@ -215,6 +215,7 @@ OPT. * :doc:`oxrna2/stk ` * :doc:`oxrna2/xstk ` * :doc:`oxrna2/coaxstk ` + * :doc:`pace ` * :doc:`peri/eps ` * :doc:`peri/lps (o) ` * :doc:`peri/pmb (o) ` diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b662ae73c7..549ab3d8f0 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -90,6 +90,7 @@ page gives those details. * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` * :ref:`USER-OMP ` + * :ref:`USER-PACE ` * :ref:`USER-PHONON ` * :ref:`USER-PLUMED ` * :ref:`USER-PTM ` @@ -1349,6 +1350,42 @@ This package has :ref:`specific installation instructions ` on the ---------- +.. _PKG-USER-PACE: + +USER-PACE package +------------------- + +**Contents:** + +A pair style for the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. The USER-PACE +package provides an efficient implementation for running simulations +with ACE potentials. + +**Authors:** + +This package was written by Yury Lysogorskiy^1, +Cas van der Oord^2, Anton Bochkarev^1, +Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, +Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. + + ^1: Ruhr-University Bochum, Bochum, Germany + + ^2: University of Cambridge, Cambridge, United Kingdom + + ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA + + ^4: University of British Columbia, Vancouver, BC, Canada + +**Supporting info:** + +* src/USER-PACE: filenames -> commands +* :doc:`pair_style pace ` +* examples/USER/pace + +---------- + .. _PKG-USER-PLUMED: USER-PLUMED package diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst new file mode 100644 index 0000000000..1ebf6210cd --- /dev/null +++ b/doc/src/pair_pace.rst @@ -0,0 +1,114 @@ +.. index:: pair_style pace + +pair_style pace command +======================== + +Syntax +"""""" + +.. code-block:: LAMMPS + + pair_style pace ... keyword values ... + +* an optional keyword may be appended +* keyword = *product* or *recursive* + + .. parsed-literal:: + + *product* = use product algorithm for basis functions + *recursive* = use recursive algorithm for basis functions + +Examples +"""""""" + +.. code-block:: LAMMPS + + pair_style pace + pair_style pace product + pair_coeff * * Cu-PBE-core-rep.ace Cu + +Description +""""""""""" + +Pair style *pace* computes interactions using the Atomic Cluster +Expansion (ACE), which is a general expansion of the atomic energy in +multi-body basis functions. :ref:`(Drautz) `. +The *pace* pair style +provides an efficient implementation that +is described in this paper :ref:`(Lysogorskiy) `. + +In ACE, the total energy is decomposed into a sum over +atomic energies. The energy of atom *i* is expressed as a +linear or non-linear function of one or more density functions. +By projecting the +density onto a local atomic base, the lowest order contributions +to the energy can be expressed as a set of scalar polynomials in +basis function contributions summed over neighbor atoms. + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE coefficient file followed by N additional arguments +specifying the mapping of ACE elements to LAMMPS atom types, +where N is the number of LAMMPS atom types: + +* ACE coefficient file +* N element names = mapping of ACE elements to atom types + +Only a single pair_coeff command is used with the *pace* style which +specifies an ACE file that fully defines the potential. +Note that unlike for other potentials, cutoffs are +not set in the pair_style or pair_coeff command; they are specified in +the ACE file. + +The pair_style *mliap* may be followed by an optional keyword +*product* or *recursive*, which determines which of two algorithms + is used for the calculation of basis functions and derivatives. +The default is *recursive*. + +See the :doc:`pair_coeff ` doc page for alternate ways +to specify the path for the ACE coefficient file. + +Mixing, shift, table, tail correction, restart, rRESPA info +""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS with +user-specifiable parameters as described above. You never need to +specify a pair_coeff command with I != J arguments for this style. + +This pair style does not support the :doc:`pair_modify ` +shift, table, and tail options. + +This pair style does not write its information to :doc:`binary restart files `, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the *pair* keyword of the +:doc:`run_style respa ` command. It does not support the +*inner*\ , *middle*\ , *outer* keywords. + +---------- + +Restrictions +"""""""""""" + +This pair style is part of the USER-PACE package. It is only enabled if LAMMPS +was built with that package. +See the :doc:`Build package ` doc page for more info. + +Related commands +"""""""""""""""" + +:doc:`pair_style snap ` + +Default +""""""" + +recursive + +.. _Drautz20191: + +**(Drautz)** Drautz, Phys Rev B, 99, 014104 (2019). + +.. _Lysogorskiy20211: + +**(Lysogorskiy)** Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, TBD (2021). diff --git a/examples/USER/pace/Cu-PBE-core-rep.ace b/examples/USER/pace/Cu-PBE-core-rep.ace new file mode 120000 index 0000000000..4414592f78 --- /dev/null +++ b/examples/USER/pace/Cu-PBE-core-rep.ace @@ -0,0 +1 @@ +../../../potentials/Cu-PBE-core-rep.ace \ No newline at end of file diff --git a/examples/USER/pace/in.pace.product b/examples/USER/pace/in.pace.product new file mode 100644 index 0000000000..d70bb0f67c --- /dev/null +++ b/examples/USER/pace/in.pace.product @@ -0,0 +1,38 @@ +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box + +mass 1 26.98 + +group Al type 1 + +pair_style pace product +pair_coeff * * Cu-PBE-core-rep.ace Cu + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 + diff --git a/examples/USER/pace/in.pace.recursive b/examples/USER/pace/in.pace.recursive new file mode 100644 index 0000000000..dd655eb18d --- /dev/null +++ b/examples/USER/pace/in.pace.recursive @@ -0,0 +1,38 @@ +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +region box block 0 4 0 4 0 4 +create_box 1 box +create_atoms 1 box + +mass 1 26.98 + +group Al type 1 + +pair_style pace recursive +pair_coeff * * Cu-PBE-core-rep.ace Cu + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 + diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.1 b/examples/USER/pace/log.03Feb2021.pace.product.g++.1 new file mode 100644 index 0000000000..01ba9c25a4 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.product.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace product +ACE version: 2021.2.3 +Product evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 2.1827873e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 -2.910383e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 0 + 70 74.623347 -938.5575 -936.09782 55565.237 0 4.3655746e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.910383e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 0 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 11.4718 on 1 procs for 100 steps with 256 atoms + +Performance: 0.377 ns/day, 63.732 hours/ns, 8.717 timesteps/s +99.3% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 11.468 | 11.468 | 11.468 | 0.0 | 99.96 +Neigh | 0.001181 | 0.001181 | 0.001181 | 0.0 | 0.01 +Comm | 0.001207 | 0.001207 | 0.001207 | 0.0 | 0.01 +Output | 0.000876 | 0.000876 | 0.000876 | 0.0 | 0.01 +Modify | 0.000455 | 0.000455 | 0.000455 | 0.0 | 0.00 +Other | | 0.000397 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:11 diff --git a/examples/USER/pace/log.03Feb2021.pace.product.g++.4 b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 new file mode 100644 index 0000000000..052becb7d6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.product.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE product + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace product +ACE version: 2021.2.3 +Product evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -1.4551915e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 2.910383e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 2.1827873e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -1.4551915e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 7.2759576e-12 + 70 74.623347 -938.5575 -936.09782 55565.237 0 0 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -1.4551915e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 1.4551915e-11 +Loop time of 3.54317 on 4 procs for 100 steps with 256 atoms + +Performance: 1.219 ns/day, 19.684 hours/ns, 28.223 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.1375 | 3.3058 | 3.469 | 6.5 | 93.30 +Neigh | 0.000284 | 0.00031975 | 0.000352 | 0.0 | 0.01 +Comm | 0.071607 | 0.23492 | 0.40336 | 24.6 | 6.63 +Output | 0.001189 | 0.0012315 | 0.001347 | 0.2 | 0.03 +Modify | 0.000311 | 0.00032725 | 0.000351 | 0.0 | 0.01 +Other | | 0.0005298 | | | 0.01 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 new file mode 100644 index 0000000000..e6de3bd5c6 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.1 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.036 | 4.036 | 4.036 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 0 + 10 280.68558 -945.35055 -936.09878 46326.919 0 5.8207661e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 1.4551915e-11 + 30 160.53661 -941.38948 -936.09798 52222.083 0 7.2759576e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 -5.8207661e-11 + 50 59.165961 -938.04759 -936.0974 56850.103 0 0 + 60 53.124678 -937.84857 -936.09751 56878.948 0 8.7311491e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 -1.4551915e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 2.1827873e-11 + 90 142.02657 -940.77975 -936.09837 52001.1 0 2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 0 +Loop time of 9.31437 on 1 procs for 100 steps with 256 atoms + +Performance: 0.464 ns/day, 51.746 hours/ns, 10.736 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.3103 | 9.3103 | 9.3103 | 0.0 | 99.96 +Neigh | 0.001214 | 0.001214 | 0.001214 | 0.0 | 0.01 +Comm | 0.001176 | 0.001176 | 0.001176 | 0.0 | 0.01 +Output | 0.000827 | 0.000827 | 0.000827 | 0.0 | 0.01 +Modify | 0.000479 | 0.000479 | 0.000479 | 0.0 | 0.01 +Other | | 0.000363 | | | 0.00 + +Nlocal: 256.000 ave 256 max 256 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 2201.00 ave 2201 max 2201 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 43118.0 ave 43118 max 43118 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:09 diff --git a/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 new file mode 100644 index 0000000000..b816f8e570 --- /dev/null +++ b/examples/USER/pace/log.03Feb2021.pace.recursive.g++.4 @@ -0,0 +1,108 @@ +LAMMPS (24 Dec 2020) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) + using 1 OpenMP thread(s) per MPI task +# simple test of fcc Cu with ACE recursive + +units metal +atom_style atomic + +neighbor 0.3 bin +neigh_modify every 2 delay 10 check yes + +variable a equal 3.597 +lattice fcc $a +lattice fcc 3.597 +Lattice spacing in x,y,z = 3.5970000 3.5970000 3.5970000 +region box block 0 4 0 4 0 4 +create_box 1 box +Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (14.388000 14.388000 14.388000) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 256 atoms + create_atoms CPU = 0.000 seconds + +mass 1 26.98 + +group Al type 1 +256 atoms in group Al + +pair_style pace recursive +ACE version: 2021.2.3 +Recursive evaluator is used +pair_coeff * * Cu-PBE-core-rep.ace Cu +Loading Cu-PBE-core-rep.ace +Total number of basis functions + Cu: 16 (r=1) 726 (r>1) +Mapping LAMMPS atom type #1(Cu) -> ACE species type #0 + +velocity all create 300 8728 loop geom +timestep 0.0005 +fix 1 all nve + +compute eatom all pe/atom +compute energy all reduce sum c_eatom +variable delenergy equal c_energy-pe + +compute satom all stress/atom NULL +compute str all reduce sum c_satom[1] c_satom[2] c_satom[3] +variable delpress equal -(c_str[1]+c_str[2]+c_str[3])/(3*vol)-press + +thermo 10 +thermo_style custom step temp epair etotal press v_delenergy v_delpress + +run 100 +Neighbor list info ... + update every 2 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.7 + ghost atom cutoff = 7.7 + binsize = 3.85, bins = 4 4 4 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair pace, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.005 | 4.005 | 4.005 Mbytes +Step Temp E_pair TotEng Press v_delenergy v_delpress + 0 300 -945.9873 -936.0989 45359.818 0 -5.0931703e-11 + 10 280.68558 -945.35055 -936.09878 46326.919 0 1.4551915e-11 + 20 228.73618 -943.63789 -936.09844 48903.598 0 0 + 30 160.53661 -941.38948 -936.09798 52222.083 0 -2.910383e-11 + 40 97.732944 -939.31899 -936.09758 55176.875 0 0 + 50 59.165961 -938.04759 -936.0974 56850.103 0 -2.910383e-11 + 60 53.124678 -937.84857 -936.09751 56878.948 0 1.4551915e-11 + 70 74.623347 -938.5575 -936.09782 55565.237 0 3.6379788e-11 + 80 109.4762 -939.70663 -936.09815 53665.652 0 -7.2759576e-12 + 90 142.02657 -940.77975 -936.09837 52001.1 0 -2.910383e-11 + 100 161.73598 -941.42945 -936.09842 51114.997 0 7.2759576e-12 +Loop time of 2.91339 on 4 procs for 100 steps with 256 atoms + +Performance: 1.483 ns/day, 16.185 hours/ns, 34.324 timesteps/s +98.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.5753 | 2.723 | 2.8656 | 6.3 | 93.46 +Neigh | 0.000308 | 0.000365 | 0.00046 | 0.0 | 0.01 +Comm | 0.045106 | 0.18792 | 0.33552 | 24.1 | 6.45 +Output | 0.001213 | 0.001259 | 0.001388 | 0.2 | 0.04 +Modify | 0.000304 | 0.00033 | 0.00037 | 0.0 | 0.01 +Other | | 0.0005595 | | | 0.02 + +Nlocal: 64.0000 ave 71 max 57 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Nghost: 1373.00 ave 1380 max 1366 min +Histogram: 1 0 0 0 1 1 0 0 0 1 +Neighs: 0.00000 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 10779.5 ave 11978 max 9604 min +Histogram: 1 0 0 0 1 1 0 0 0 1 + +Total # of neighbors = 43118 +Ave neighs/atom = 168.42969 +Neighbor list builds = 1 +Dangerous builds = 0 + +Total wall time: 0:00:03 diff --git a/potentials/Cu-PBE-core-rep.ace b/potentials/Cu-PBE-core-rep.ace new file mode 100644 index 0000000000..338675f718 --- /dev/null +++ b/potentials/Cu-PBE-core-rep.ace @@ -0,0 +1,8980 @@ +nelements=1 +elements: Cu + +lmax=6 + +embedding-function: FinnisSinclairShiftedScaled +4 FS parameters: 1.000000 1.000000 1.000000 0.500000 +core energy-cutoff parameters: 100000.000000000000000000 250.000000000000000000 +E0: 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0.125820906632077067 From 29c78d022a1351f2f89d0bdd3dd274e0ad19ed08 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Wed, 7 Apr 2021 19:54:35 +0200 Subject: [PATCH 026/100] add lib/pace/Makefile.lammps --- lib/pace/Makefile.lammps | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 lib/pace/Makefile.lammps diff --git a/lib/pace/Makefile.lammps b/lib/pace/Makefile.lammps new file mode 100644 index 0000000000..17820716df --- /dev/null +++ b/lib/pace/Makefile.lammps @@ -0,0 +1,3 @@ +pace_SYSINC =-I../../lib/pace/src/USER-PACE +pace_SYSLIB = -L../../lib/pace/ -lpace +pace_SYSPATH = From feda2dc08dc11502dd24dd7c2bc835a21924be95 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Wed, 7 Apr 2021 14:07:58 -0600 Subject: [PATCH 027/100] Updated doc page and spelling --- doc/src/pair_pace.rst | 4 ++-- doc/utils/sphinx-config/false_positives.txt | 14 ++++++++++++++ 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 1ebf6210cd..36baaa7ef9 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -59,9 +59,9 @@ Note that unlike for other potentials, cutoffs are not set in the pair_style or pair_coeff command; they are specified in the ACE file. -The pair_style *mliap* may be followed by an optional keyword +The pair_style *pace* command may be followed by an optional keyword *product* or *recursive*, which determines which of two algorithms - is used for the calculation of basis functions and derivatives. +is used for the calculation of basis functions and derivatives. The default is *recursive*. See the :doc:`pair_coeff ` doc page for alternate ways diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 38a6971f4c..9689125753 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -268,6 +268,7 @@ blueviolet bn bni bo +Bochkarev Bochum bocs bodyflag @@ -343,6 +344,7 @@ Cao Capolungo Caro cartesian +Cas CasP Caswell Cates @@ -1069,6 +1071,7 @@ fuer fx fy fz +Gabor Gahler gainsboro Galindo @@ -1193,6 +1196,7 @@ Halperin Halver Hamaker Hamel +Hammerschmidt haptic Hara Harpertown @@ -1743,6 +1747,7 @@ lx ly Lybrand lyon +Lysogorskiy Lyulin lz Maaravi @@ -1801,8 +1806,10 @@ Materias mathbf mathjax matlab +Matous matplotlib Matsubara +Matteo Mattice Mattox Mattson @@ -1863,6 +1870,7 @@ MEMALIGN membered memcheck Mendelev +Menon mer Meremianin Mersenne @@ -1986,6 +1994,7 @@ mpiio mpirun mplayer mps +Mrovec Mryglod mscg MSCG @@ -2311,6 +2320,7 @@ oneway onn ons OO +Oord opencl openKIM openmp @@ -2331,6 +2341,7 @@ Orsi ortho orthonormal orthorhombic +Ortner oso Otype Ouldridge @@ -2620,6 +2631,7 @@ radians Rafferty rahman Rahman +Ralf Raman ramped ramping @@ -2726,6 +2738,7 @@ Rij RIj Rik Rin +Rinaldi Rino RiRj Risi @@ -2814,6 +2827,7 @@ Sandia sandybrown sanitizer Sanyal +Sarath sc scafacos SCAFACOS From 0151fd00c281aac40fdebd88b76b5ef80e3c2c81 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 17:37:30 -0400 Subject: [PATCH 028/100] correct CMake support for USER-PACE package and align with recent conventions for downloading external code --- cmake/Modules/Packages/USER-PACE.cmake | 34 +++++++++++++++++--------- 1 file changed, 23 insertions(+), 11 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index c9e8e1bcfe..008d32444c 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,14 +1,26 @@ -set(PACE_EVALUATOR_PATH ${LAMMPS_LIB_SOURCE_DIR}/pace) -message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") -set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) -FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) -set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "9ebb087cba7e4ca041fde52f7e9e640c" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +mark_as_advanced(PACELIB_URL) +mark_as_advanced(PACELIB_MD5) + +# download library sources to build folder +file(DOWNLOAD ${PACELIB_URL} libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) + +# uncompress downloaded sources +execute_process( + COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace* + COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz + WORKING_DIRECTORY ${CMAKE_BINARY_DIR} +) -##### aceevaluator ##### -add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) -target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) -target_compile_options(aceevaluator PRIVATE -O2) -set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) -target_link_libraries(lammps PRIVATE aceevaluator) \ No newline at end of file +file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE) +file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp) +list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) + +add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) +set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) +target_link_libraries(lammps PRIVATE pace) + From 7b34f025ee088212ee5d26ad62c993e8e7d80678 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 17:46:18 -0400 Subject: [PATCH 029/100] correct src/Makefile for USER-PACE --- src/Makefile | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/Makefile b/src/Makefile index bec0a2b16b..d5f0e600d6 100644 --- a/src/Makefile +++ b/src/Makefile @@ -55,7 +55,7 @@ PACKUSER = user-adios user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-c user-diffraction user-dpd user-drude user-eff user-fep user-h5md \ user-intel user-lb user-manifold user-meamc user-mesodpd user-mesont \ user-mgpt user-misc user-mofff user-molfile \ - user-netcdf user-omp user-phonon user-plumed user-ptm user-qmmm \ + user-netcdf user-omp user-phonon user-pace user-plumed user-ptm user-qmmm \ user-qtb user-quip user-reaction user-reaxc user-scafacos user-smd user-smtbq \ user-sdpd user-sph user-tally user-uef user-vtk user-yaff @@ -70,8 +70,8 @@ PACKSYS = compress mpiio python user-lb PACKINT = gpu kokkos message poems user-atc user-awpmd user-colvars user-mesont PACKEXT = kim latte mscg voronoi \ - user-adios user-h5md user-molfile user-netcdf user-plumed user-qmmm user-quip \ - user-smd user-vtk user-pace + user-adios user-h5md user-molfile user-netcdf user-pace user-plumed \ + user-qmmm user-quip user-smd user-vtk PACKALL = $(PACKAGE) $(PACKUSER) From 084c0713d6e69fad23459782978fa4c73889f82b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 18:05:00 -0400 Subject: [PATCH 030/100] resolve whitespace issues --- doc/src/Packages_details.rst | 4 ++-- doc/src/pair_pace.rst | 26 +++++++++++++------------- src/USER-PACE/pair_pace.cpp | 2 +- src/USER-PACE/pair_pace.h | 2 +- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 549ab3d8f0..1964a83717 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1363,9 +1363,9 @@ fit to a large archive of quantum mechanical (DFT) data. The USER-PACE package provides an efficient implementation for running simulations with ACE potentials. -**Authors:** +**Authors:** -This package was written by Yury Lysogorskiy^1, +This package was written by Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. diff --git a/doc/src/pair_pace.rst b/doc/src/pair_pace.rst index 36baaa7ef9..56ae0f32dc 100644 --- a/doc/src/pair_pace.rst +++ b/doc/src/pair_pace.rst @@ -15,8 +15,8 @@ Syntax .. parsed-literal:: - *product* = use product algorithm for basis functions - *recursive* = use recursive algorithm for basis functions + *product* = use product algorithm for basis functions + *recursive* = use recursive algorithm for basis functions Examples """""""" @@ -30,24 +30,24 @@ Examples Description """"""""""" -Pair style *pace* computes interactions using the Atomic Cluster -Expansion (ACE), which is a general expansion of the atomic energy in -multi-body basis functions. :ref:`(Drautz) `. -The *pace* pair style -provides an efficient implementation that +Pair style *pace* computes interactions using the Atomic Cluster +Expansion (ACE), which is a general expansion of the atomic energy in +multi-body basis functions. :ref:`(Drautz) `. +The *pace* pair style +provides an efficient implementation that is described in this paper :ref:`(Lysogorskiy) `. In ACE, the total energy is decomposed into a sum over -atomic energies. The energy of atom *i* is expressed as a -linear or non-linear function of one or more density functions. +atomic energies. The energy of atom *i* is expressed as a +linear or non-linear function of one or more density functions. By projecting the density onto a local atomic base, the lowest order contributions to the energy can be expressed as a set of scalar polynomials in basis function contributions summed over neighbor atoms. Only a single pair_coeff command is used with the *pace* style which -specifies an ACE coefficient file followed by N additional arguments -specifying the mapping of ACE elements to LAMMPS atom types, +specifies an ACE coefficient file followed by N additional arguments +specifying the mapping of ACE elements to LAMMPS atom types, where N is the number of LAMMPS atom types: * ACE coefficient file @@ -61,7 +61,7 @@ the ACE file. The pair_style *pace* command may be followed by an optional keyword *product* or *recursive*, which determines which of two algorithms -is used for the calculation of basis functions and derivatives. +is used for the calculation of basis functions and derivatives. The default is *recursive*. See the :doc:`pair_coeff ` doc page for alternate ways @@ -92,7 +92,7 @@ Restrictions """""""""""" This pair style is part of the USER-PACE package. It is only enabled if LAMMPS -was built with that package. +was built with that package. See the :doc:`Build package ` doc page for more info. Related commands diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index a515b7b4b0..ee1922d886 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -446,7 +446,7 @@ double PairPACE::init_one(int i, int j) { return basis_set->radial_functions->cut(map[i], map[j]); } -/* ---------------------------------------------------------------------- +/* ---------------------------------------------------------------------- extract method for extracting value of scale variable ---------------------------------------------------------------------- */ void *PairPACE::extract(const char *str, int &dim) diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 3fccbd98f0..76b08a65c0 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -94,4 +94,4 @@ namespace LAMMPS_NS { } #endif -#endif \ No newline at end of file +#endif From 2d1fc67b5df7d47c425565c96e208794e7c2a5bb Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:09:43 -0400 Subject: [PATCH 031/100] update .gitignore --- src/.gitignore | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/.gitignore b/src/.gitignore index 6fa3aef513..96a89ae667 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -32,6 +32,9 @@ /pair_kim.cpp /pair_kim.h +/pair_pace.cpp +/pair_pace.h + /superpose3d.h /kokkos.cpp From 2d4b05ffa6db866f30ae100754677ae6bdcd9d6d Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:13:10 -0400 Subject: [PATCH 032/100] refactor code to more closely match LAMMPS coding conventions - update indentation to 2 characters - remove dead code and unused class members - use convenience functions in many places - reuse code and members from Pair base class - declare local functions/variables static - PIMPL-ify access to the ACE evaluator library functions/classes - correct settings member variables to match implementation --- src/USER-PACE/pair_pace.cpp | 538 ++++++++++++++++-------------------- src/USER-PACE/pair_pace.h | 60 ++-- 2 files changed, 250 insertions(+), 348 deletions(-) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index ee1922d886..527f2a6f06 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -28,25 +28,33 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, // Created by Lysogorskiy Yury on 27.02.20. // -#include -#include -#include -#include #include "pair_pace.h" + #include "atom.h" -#include "neighbor.h" +#include "comm.h" +#include "error.h" +#include "force.h" +#include "math_const.h" +#include "memory.h" #include "neigh_list.h" #include "neigh_request.h" -#include "force.h" -#include "comm.h" -#include "memory.h" -#include "error.h" +#include "neighbor.h" +#include +#include -#include "math_const.h" - +#include "ace_evaluator.h" +#include "ace_recursive.h" +#include "ace_c_basis.h" #include "ace_version.h" +namespace LAMMPS_NS { + struct ACEImpl { + ACECTildeBasisSet *basis_set; + ACERecursiveEvaluator *ace; + }; +} + using namespace LAMMPS_NS; using namespace MathConst; @@ -59,9 +67,8 @@ using namespace MathConst; #define RECURSIVE_KEYWORD "recursive" #define PRODUCT_KEYWORD "product" - -int elements_num_pace = 104; -char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", +static int elements_num_pace = 104; +static char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N", "O", "F", "Ne", "Na", "Mg", "Al", "Si", "P", "S", "Cl", "Ar", "K", "Ca", "Sc", "Ti", "V", "Cr", "Mn", "Fe", "Co", "Ni", "Cu", "Zn", "Ga", "Ge", "As", "Se", "Br", "Kr", "Rb", "Sr", "Y", "Zr", "Nb", "Mo", "Tc", "Ru", "Rh", "Pd", "Ag", "Cd", "In", "Sn", "Sb", @@ -71,27 +78,26 @@ char const *const elements_pace[104] = {"X", "H", "He", "Li", "Be", "B", "C", "N "Pa", "U", "Np", "Pu", "Am", "Cm", "Bk", "Cf", "Es", "Fm", "Md", "No", "Lr" }; -int AtomicNumberByName_pace(char *elname) { - for (int i = 1; i < elements_num_pace; i++) - if (strcmp(elname, elements_pace[i]) == 0) - return i; - return -1; +static int AtomicNumberByName_pace(char *elname) { + for (int i = 1; i < elements_num_pace; i++) + if (strcmp(elname, elements_pace[i]) == 0) + return i; + return -1; } - /* ---------------------------------------------------------------------- */ PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { - //single_enable = 0; - restartinfo = 0; - one_coeff = 1; - manybody_flag = 1; + single_enable = 0; + restartinfo = 0; + one_coeff = 1; + manybody_flag = 1; - nelements = 0; + aceimpl = new ACEImpl; + aceimpl->ace = nullptr; + aceimpl->basis_set = nullptr; + recursive = false; - ace = NULL; - potential_file_name = NULL; - elements = NULL; - map = NULL; + scale = nullptr; } /* ---------------------------------------------------------------------- @@ -99,170 +105,157 @@ PairPACE::PairPACE(LAMMPS *lmp) : Pair(lmp) { ------------------------------------------------------------------------- */ PairPACE::~PairPACE() { - if (copymode) return; + if (copymode) return; - if (elements) - for (int i = 0; i < nelements; i++) delete[] elements[i]; - delete[] elements; + delete aceimpl->basis_set; + delete aceimpl->ace; + delete aceimpl; - - delete[] potential_file_name; - - delete basis_set; - delete ace; - - if (allocated) { - memory->destroy(setflag); - memory->destroy(cutsq); - memory->destroy(map); - memory->destroy(scale); - } + if (allocated) { + memory->destroy(setflag); + memory->destroy(cutsq); + memory->destroy(scale); + } } /* ---------------------------------------------------------------------- */ void PairPACE::compute(int eflag, int vflag) { - int i, j, ii, jj, inum, jnum; - double delx, dely, delz, evdwl; - double fij[3]; - int *ilist, *jlist, *numneigh, **firstneigh; + int i, j, ii, jj, inum, jnum; + double delx, dely, delz, evdwl; + double fij[3]; + int *ilist, *jlist, *numneigh, **firstneigh; - ev_init(eflag, vflag); + ev_init(eflag, vflag); - // downwards modified by YL + // downwards modified by YL - double **x = atom->x; - double **f = atom->f; - tagint *tag = atom->tag; - int *type = atom->type; + double **x = atom->x; + double **f = atom->f; + tagint *tag = atom->tag; + int *type = atom->type; - // number of atoms in cell - int nlocal = atom->nlocal; + // number of atoms in cell + int nlocal = atom->nlocal; - int newton_pair = force->newton_pair; + int newton_pair = force->newton_pair; - // number of atoms including ghost atoms - int nall = nlocal + atom->nghost; + // number of atoms including ghost atoms + int nall = nlocal + atom->nghost; - // inum: length of the neighborlists list - inum = list->inum; + // inum: length of the neighborlists list + inum = list->inum; - // ilist: list of "i" atoms for which neighbor lists exist - ilist = list->ilist; + // ilist: list of "i" atoms for which neighbor lists exist + ilist = list->ilist; - //numneigh: the length of each these neigbor list - numneigh = list->numneigh; + //numneigh: the length of each these neigbor list + numneigh = list->numneigh; - // the pointer to the list of neighbors of "i" - firstneigh = list->firstneigh; + // the pointer to the list of neighbors of "i" + firstneigh = list->firstneigh; - if (inum != nlocal) { - char str[128]; - snprintf(str,128,"inum: %d nlocal: %d are different",inum, nlocal); - error->all(FLERR,str); + if (inum != nlocal) + error->all(FLERR,fmt::format("inum: {} nlocal: {} are different",inum, nlocal)); + + // Aidan Thompson told RD (26 July 2019) that practically always holds: + // inum = nlocal + // i = ilist(ii) < inum + // j = jlist(jj) < nall + // neighborlist contains neighbor atoms plus skin atoms, + // skin atoms can be removed by setting skin to zero but here + // they are disregarded anyway + + + //determine the maximum number of neighbours + int max_jnum = -1; + int nei = 0; + for (ii = 0; ii < list->inum; ii++) { + i = ilist[ii]; + jnum = numneigh[i]; + nei = nei + jnum; + if (jnum > max_jnum) + max_jnum = jnum; + } + + aceimpl->ace->resize_neighbours_cache(max_jnum); + + //loop over atoms + for (ii = 0; ii < list->inum; ii++) { + i = list->ilist[ii]; + const int itype = type[i]; + + const double xtmp = x[i][0]; + const double ytmp = x[i][1]; + const double ztmp = x[i][2]; + + jlist = firstneigh[i]; + jnum = numneigh[i]; + + // checking if neighbours are actually within cutoff range is done inside compute_atom + // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom + // by using 'aceimpl->ace->element_type_mapping' array + // x: [r0 ,r1, r2, ..., r100] + // i = 0 ,1 + // jnum(0) = 50 + // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] + + try { + aceimpl->ace->compute_atom(i, x, type, jnum, jlist); + } catch (exception &e) { + error->one(FLERR, e.what()); + } + // 'compute_atom' will update the `aceimpl->ace->e_atom` and `aceimpl->ace->neighbours_forces(jj, alpha)` arrays + + for (jj = 0; jj < jnum; jj++) { + j = jlist[jj]; + const int jtype = type[j]; + j &= NEIGHMASK; + delx = x[j][0] - xtmp; + dely = x[j][1] - ytmp; + delz = x[j][2] - ztmp; + + fij[0] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 0); + fij[1] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 1); + fij[2] = scale[itype][jtype]*aceimpl->ace->neighbours_forces(jj, 2); + + f[i][0] += fij[0]; + f[i][1] += fij[1]; + f[i][2] += fij[2]; + f[j][0] -= fij[0]; + f[j][1] -= fij[1]; + f[j][2] -= fij[2]; + + // tally per-atom virial contribution + if (vflag) + ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, + fij[0], fij[1], fij[2], + -delx, -dely, -delz); } - - // Aidan Thompson told RD (26 July 2019) that practically always holds: - // inum = nlocal - // i = ilist(ii) < inum - // j = jlist(jj) < nall - // neighborlist contains neighbor atoms plus skin atoms, - // skin atoms can be removed by setting skin to zero but here - // they are disregarded anyway - - - //determine the maximum number of neighbours - int max_jnum = -1; - int nei = 0; - for (ii = 0; ii < list->inum; ii++) { - i = ilist[ii]; - jnum = numneigh[i]; - nei = nei + jnum; - if (jnum > max_jnum) - max_jnum = jnum; + // tally energy contribution + if (eflag) { + // evdwl = energy of atom I + evdwl = scale[1][1]*aceimpl->ace->e_atom; + ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); } + } - ace->resize_neighbours_cache(max_jnum); + if (vflag_fdotr) virial_fdotr_compute(); - //loop over atoms - for (ii = 0; ii < list->inum; ii++) { - i = list->ilist[ii]; - const int itype = type[i]; - - const double xtmp = x[i][0]; - const double ytmp = x[i][1]; - const double ztmp = x[i][2]; - - jlist = firstneigh[i]; - jnum = numneigh[i]; - - // checking if neighbours are actually within cutoff range is done inside compute_atom - // mapping from LAMMPS atom types ('type' array) to ACE species is done inside compute_atom - // by using 'ace->element_type_mapping' array - // x: [r0 ,r1, r2, ..., r100] - // i = 0 ,1 - // jnum(0) = 50 - // jlist(neigh ind of 0-atom) = [1,2,10,7,99,25, .. 50 element in total] - try { - ace->compute_atom(i, x, type, jnum, jlist); - } catch (exception &e) { - error->all(FLERR, e.what()); - exit(EXIT_FAILURE); - } - // 'compute_atom' will update the `ace->e_atom` and `ace->neighbours_forces(jj, alpha)` arrays - - for (jj = 0; jj < jnum; jj++) { - j = jlist[jj]; - const int jtype = type[j]; - j &= NEIGHMASK; - delx = x[j][0] - xtmp; - dely = x[j][1] - ytmp; - delz = x[j][2] - ztmp; - - fij[0] = scale[itype][jtype]*ace->neighbours_forces(jj, 0); - fij[1] = scale[itype][jtype]*ace->neighbours_forces(jj, 1); - fij[2] = scale[itype][jtype]*ace->neighbours_forces(jj, 2); - - - f[i][0] += fij[0]; - f[i][1] += fij[1]; - f[i][2] += fij[2]; - f[j][0] -= fij[0]; - f[j][1] -= fij[1]; - f[j][2] -= fij[2]; - - // tally per-atom virial contribution - if (vflag) - ev_tally_xyz(i, j, nlocal, newton_pair, 0.0, 0.0, - fij[0], fij[1], fij[2], - -delx, -dely, -delz); - } - - // tally energy contribution - if (eflag) { - // evdwl = energy of atom I - evdwl = scale[1][1]*ace->e_atom; - ev_tally_full(i, 2.0 * evdwl, 0.0, 0.0, 0.0, 0.0, 0.0); - } - } - - if (vflag_fdotr) virial_fdotr_compute(); - - - // end modifications YL + // end modifications YL } /* ---------------------------------------------------------------------- */ void PairPACE::allocate() { - allocated = 1; - int n = atom->ntypes; + allocated = 1; + int n = atom->ntypes; - memory->create(setflag, n + 1, n + 1, "pair:setflag"); - memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); - memory->create(map, n + 1, "pair:map"); - memory->create(scale, n + 1, n + 1,"pair:scale"); + memory->create(setflag, n + 1, n + 1, "pair:setflag"); + memory->create(cutsq, n + 1, n + 1, "pair:cutsq"); + memory->create(scale, n + 1, n + 1,"pair:scale"); + map = new int[n+1]; } /* ---------------------------------------------------------------------- @@ -270,41 +263,24 @@ void PairPACE::allocate() { ------------------------------------------------------------------------- */ void PairPACE::settings(int narg, char **arg) { - if (narg > 1) { - error->all(FLERR, - "Illegal pair_style command. Correct form:\n\tpair_style pace\nor\n\tpair_style pace "); - error->all(FLERR, RECURSIVE_KEYWORD); - error->all(FLERR, "or\n\tpair_style pace "); - error->all(FLERR, PRODUCT_KEYWORD); - } - recursive = true; // default evaluator style: RECURSIVE - if (narg > 0) { - if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) - recursive = true; - else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { - recursive = false; - } else { - error->all(FLERR, - "Illegal pair_style command: pair_style pace "); - error->all(FLERR, arg[0]); - error->all(FLERR, "\nCorrect form:\n\tpair_style pace\nor\n\tpair_style pace recursive"); - } - } - - if (comm->me == 0) { - if (screen) fprintf(screen, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); - if (logfile) fprintf(logfile, "ACE version: %d.%d.%d\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY); - - if (recursive) { - if (screen) fprintf(screen, "Recursive evaluator is used\n"); - if (logfile) fprintf(logfile, "Recursive evaluator is used\n"); - } else { - if (screen) fprintf(screen, "Product evaluator is used\n"); - if (logfile) fprintf(logfile, "Product evaluator is used\n"); - } - } + if (narg > 1) + error->all(FLERR,"Illegal pair_style command."); + recursive = true; // default evaluator style: RECURSIVE + if (narg > 0) { + if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) + recursive = true; + else if (strcmp(arg[0], PRODUCT_KEYWORD) == 0) { + recursive = false; + } else error->all(FLERR,"Illegal pair_style command"); + } + if (comm->me == 0) { + utils::logmesg(lmp,fmt::format("ACE version: {}.{}.{}\n", + VERSION_YEAR, VERSION_MONTH, VERSION_DAY)); + if (recursive) utils::logmesg(lmp,"Recursive evaluator is used\n"); + else utils::logmesg(lmp,"Product evaluator is used\n"); + } } /* ---------------------------------------------------------------------- @@ -313,110 +289,64 @@ void PairPACE::settings(int narg, char **arg) { void PairPACE::coeff(int narg, char **arg) { - if (narg < 4) - error->all(FLERR, - "Incorrect args for pair coefficients. Correct form:\npair_coeff * * elem1 elem2 ..."); + if (!allocated) allocate(); - if (!allocated) allocate(); + map_element2type(narg-3,arg+3); - //number of provided elements in pair_coeff line - int ntypes_coeff = narg - 3; + char *potential_file_name = arg[2]; + char **elemtypes = &arg[3]; - if (ntypes_coeff != atom->ntypes) { - char error_message[1024]; - snprintf(error_message, 1024, - "Incorrect args for pair coefficients. You provided %d elements in pair_coeff, but structure has %d atom types", - ntypes_coeff, atom->ntypes); - error->all(FLERR, error_message); + //load potential file + aceimpl->basis_set = new ACECTildeBasisSet(); + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Loading {}\n", potential_file_name)); + aceimpl->basis_set->load(potential_file_name); + + if (comm->me == 0) { + utils::logmesg(lmp,"Total number of basis functions\n"); + + for (SPECIES_TYPE mu = 0; mu < aceimpl->basis_set->nelements; mu++) { + int n_r1 = aceimpl->basis_set->total_basis_size_rank1[mu]; + int n = aceimpl->basis_set->total_basis_size[mu]; + utils::logmesg(lmp,fmt::format("\t{}: {} (r=1) {} (r>1)\n", aceimpl->basis_set->elements_name[mu], n_r1, n)); } + } - char *type1 = arg[0]; - char *type2 = arg[1]; - char *potential_file_name = arg[2]; - char **elemtypes = &arg[3]; + // read args that map atom types to pACE elements + // map[i] = which element the Ith atom type is, -1 if not mapped + // map[0] is not used - // insure I,J args are * * + aceimpl->ace = new ACERecursiveEvaluator(); + aceimpl->ace->set_recursive(recursive); + aceimpl->ace->element_type_mapping.init(atom->ntypes + 1); - if (strcmp(type1, "*") != 0 || strcmp(type2, "*") != 0) - error->all(FLERR, "Incorrect args for pair coefficients"); + const int n = atom->ntypes; + for (int i = 1; i <= n; i++) { + char *elemname = elemtypes[i - 1]; + int atomic_number = AtomicNumberByName_pace(elemname); + if (atomic_number == -1) + error->all(FLERR,fmt::format("'{}' is not a valid element\n", elemname)); - - //load potential file - basis_set = new ACECTildeBasisSet(); - if (comm->me == 0) { - if (screen) fprintf(screen, "Loading %s\n", potential_file_name); - if (logfile) fprintf(logfile, "Loading %s\n", potential_file_name); + SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname); + if (mu != -1) { + if (comm->me == 0) + utils::logmesg(lmp,fmt::format("Mapping LAMMPS atom type #{}({}) -> " + "ACE species type #{}\n", i, elemname, mu)); + map[i] = mu; + aceimpl->ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator + } else { + error->all(FLERR, fmt::format("Element {} is not supported by ACE-potential from file {}", elemname,potential_file_name)); } - basis_set->load(potential_file_name); + } - if (comm->me == 0) { - if (screen) fprintf(screen, "Total number of basis functions\n"); - if (logfile) fprintf(logfile, "Total number of basis functions\n"); - - for (SPECIES_TYPE mu = 0; mu < basis_set->nelements; mu++) { - int n_r1 = basis_set->total_basis_size_rank1[mu]; - int n = basis_set->total_basis_size[mu]; - if (screen) fprintf(screen, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); - if (logfile) fprintf(logfile, "\t%s: %d (r=1) %d (r>1)\n", basis_set->elements_name[mu].c_str(), n_r1, n); - } + // initialize scale factor + for (int i = 1; i <= n; i++) { + for (int j = i; j <= n; j++) { + scale[i][j] = 1.0; } + } - // read args that map atom types to pACE elements - // map[i] = which element the Ith atom type is, -1 if not mapped - // map[0] is not used - - ace = new ACERecursiveEvaluator(); - ace->set_recursive(recursive); - ace->element_type_mapping.init(atom->ntypes + 1); - - for (int i = 1; i <= atom->ntypes; i++) { - char *elemname = elemtypes[i - 1]; - int atomic_number = AtomicNumberByName_pace(elemname); - if (atomic_number == -1) { - char error_msg[1024]; - snprintf(error_msg, 1024, "String '%s' is not a valid element\n", elemname); - error->all(FLERR, error_msg); - } - SPECIES_TYPE mu = basis_set->get_species_index_by_name(elemname); - if (mu != -1) { - if (comm->me == 0) { - if (screen) - fprintf(screen, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); - if (logfile) - fprintf(logfile, "Mapping LAMMPS atom type #%d(%s) -> ACE species type #%d\n", i, elemname, mu); - } - map[i] = mu; - ace->element_type_mapping(i) = mu; // set up LAMMPS atom type to ACE species mapping for ace evaluator - } else { - char error_msg[1024]; - snprintf(error_msg, 1024, "Element %s is not supported by ACE-potential from file %s", elemname, - potential_file_name); - error->all(FLERR, error_msg); - } - } - - // clear setflag since coeff() called once with I,J = * * - int n = atom->ntypes; - for (int i = 1; i <= n; i++) { - for (int j = i; j <= n; j++) { - setflag[i][j] = 1; - scale[i][j] = 1.0; - } - } - - // set setflag i,j for type pairs where both are mapped to elements - - int count = 1; - for (int i = 1; i <= n; i++) - for (int j = i; j <= n; j++) - if (map[i] >= 0 && map[j] >= 0) { - setflag[i][j] = 1; - count++; - } - - if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients"); - - ace->set_basis(*basis_set, 1); + aceimpl->ace->set_basis(*aceimpl->basis_set, 1); } /* ---------------------------------------------------------------------- @@ -424,15 +354,15 @@ void PairPACE::coeff(int narg, char **arg) { ------------------------------------------------------------------------- */ void PairPACE::init_style() { - if (atom->tag_enable == 0) - error->all(FLERR, "Pair style pACE requires atom IDs"); - if (force->newton_pair == 0) - error->all(FLERR, "Pair style pACE requires newton pair on"); + if (atom->tag_enable == 0) + error->all(FLERR, "Pair style pACE requires atom IDs"); + if (force->newton_pair == 0) + error->all(FLERR, "Pair style pACE requires newton pair on"); - // request a full neighbor list - int irequest = neighbor->request(this, instance_me); - neighbor->requests[irequest]->half = 0; - neighbor->requests[irequest]->full = 1; + // request a full neighbor list + int irequest = neighbor->request(this, instance_me); + neighbor->requests[irequest]->half = 0; + neighbor->requests[irequest]->full = 1; } /* ---------------------------------------------------------------------- @@ -440,10 +370,10 @@ void PairPACE::init_style() { ------------------------------------------------------------------------- */ double PairPACE::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); - //cutoff from the basis set's radial functions settings - scale[j][i] = scale[i][j]; - return basis_set->radial_functions->cut(map[i], map[j]); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); + //cutoff from the basis set's radial functions settings + scale[j][i] = scale[i][j]; + return aceimpl->basis_set->radial_functions->cut(map[i], map[j]); } /* ---------------------------------------------------------------------- @@ -451,8 +381,8 @@ double PairPACE::init_one(int i, int j) { ---------------------------------------------------------------------- */ void *PairPACE::extract(const char *str, int &dim) { - dim = 2; - if (strcmp(str,"scale") == 0) return (void *) scale; - return NULL; + dim = 2; + if (strcmp(str,"scale") == 0) return (void *) scale; + return nullptr; } diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 76b08a65c0..b29ee3a7a9 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -39,58 +39,30 @@ PairStyle(pace,PairPACE) #define LMP_PAIR_PACE_H #include "pair.h" -#include "ace_evaluator.h" -#include "ace_recursive.h" -#include "ace_c_basis.h" namespace LAMMPS_NS { - class PairPACE : public Pair { - public: - PairPACE(class LAMMPS *); +class PairPACE : public Pair { + public: + PairPACE(class LAMMPS *); + virtual ~PairPACE(); - virtual ~PairPACE(); + virtual void compute(int, int); + void settings(int, char **); + void coeff(int, char **); + virtual void init_style(); + double init_one(int, int); - virtual void compute(int, int); + void *extract(const char *, int &); - void settings(int, char **); + protected: + struct ACEImpl *aceimpl; - void coeff(int, char **); - - virtual void init_style(); - - double init_one(int, int); - - void *extract(const char *, int &); - - // virtual double memory_usage(); - - protected: - ACECTildeBasisSet *basis_set = nullptr; - - ACERecursiveEvaluator *ace = nullptr; - - char *potential_file_name; - - virtual void allocate(); - - void read_files(char *, char *); - - inline int equal(double *x, double *y); - - - double rcutmax; // max cutoff for all elements - int nelements; // # of unique elements - char **elements; // names of unique elements - - int *map; // mapping from atom types to elements - int *jlist_local; - int *type_local; - double **scale; - - bool recursive = false; // "recursive" option for ACERecursiveEvaluator - }; + virtual void allocate(); + double **scale; + bool recursive; // "recursive" option for ACERecursiveEvaluator +}; } #endif From b57025523f58da4ceab22319986e06db4e29ac6a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:28:02 -0400 Subject: [PATCH 033/100] honor LAMMPS_POTENTIALS environment variable when loading potential file --- src/USER-PACE/pair_pace.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index 527f2a6f06..41551e454c 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -293,7 +293,7 @@ void PairPACE::coeff(int narg, char **arg) { map_element2type(narg-3,arg+3); - char *potential_file_name = arg[2]; + auto potential_file_name = utils::get_potential_file_path(arg[2]); char **elemtypes = &arg[3]; //load potential file From f6f383bf99b33e745be64d6734dd204d87a009f5 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:29:22 -0400 Subject: [PATCH 034/100] add .gitignore file to lib/pace folder --- lib/pace/.gitignore | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 lib/pace/.gitignore diff --git a/lib/pace/.gitignore b/lib/pace/.gitignore new file mode 100644 index 0000000000..0598083baa --- /dev/null +++ b/lib/pace/.gitignore @@ -0,0 +1,2 @@ +/src +/libpace.a From 8a233a5ec77292123670e5e0856bd032530e0fad Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 7 Apr 2021 19:30:38 -0400 Subject: [PATCH 035/100] add unit test reference data for USER-PACE --- .../tests/manybody-pair-pace_product.yaml | 156 ++++++++++++++++++ .../tests/manybody-pair-pace_recursive.yaml | 156 ++++++++++++++++++ 2 files changed, 312 insertions(+) create mode 100644 unittest/force-styles/tests/manybody-pair-pace_product.yaml create mode 100644 unittest/force-styles/tests/manybody-pair-pace_recursive.yaml diff --git a/unittest/force-styles/tests/manybody-pair-pace_product.yaml b/unittest/force-styles/tests/manybody-pair-pace_product.yaml new file mode 100644 index 0000000000..21c37c49be --- /dev/null +++ b/unittest/force-styles/tests/manybody-pair-pace_product.yaml @@ -0,0 +1,156 @@ +--- +lammps_version: 10 Mar 2021 +date_generated: Wed Apr 7 19:29:52 2021 +epsilon: 5e-13 +skip_tests: +prerequisites: ! | + pair pace +pre_commands: ! | + variable newton_pair delete + variable newton_pair index on +post_commands: ! "" +input_file: in.manybody +pair_style: pace product +pair_coeff: ! | + * * Cu-PBE-core-rep.ace Cu Cu Cu Cu Cu Cu Cu Cu +extract: ! "" +natoms: 64 +init_vdwl: -161.633164433256 +init_coul: 0 +init_stress: ! |2- + 4.9972088100615499e+00 6.2044830913935627e+00 9.1051638867046787e+00 -3.5472278350778463e+00 1.6694265484458743e+01 1.2476127820340779e+00 +init_forces: ! |2 + 1 -6.2219087614981250e-01 1.4663175178944543e+00 1.0137638901413766e+00 + 2 -1.1376106569501299e+00 -4.6174763313965872e-01 -9.1065044746775559e-01 + 3 2.1030321840370370e-01 -1.8491702608421043e-01 2.5692785978237719e-02 + 4 -8.7721996834879601e-01 1.5265564953914739e+00 6.4946175447488763e-01 + 5 -4.2522149043165169e-01 -3.7218018176382173e-01 -9.1663252333251566e-02 + 6 3.7791326544489656e-01 1.2266089287989812e+00 2.9557107319921827e-01 + 7 -5.3020873901893739e-01 -5.3124732660122731e-01 7.0401499321631211e-01 + 8 -4.7453371627778157e-02 2.6914766341308627e-01 -3.4048361271920741e-01 + 9 -1.5727338601129420e-01 -8.3756943998984656e-01 -1.0686980500960253e+00 + 10 4.1485698120166843e-03 -4.7811767918434078e-01 -1.0586891580297206e+00 + 11 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"" +input_file: in.manybody +pair_style: pace recursive +pair_coeff: ! | + * * Cu-PBE-core-rep.ace Cu Cu Cu Cu Cu Cu Cu Cu +extract: ! 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From d22d6ad45d97028977f916b92276d1cad819874a Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 11:52:49 +0200 Subject: [PATCH 036/100] cmake/USER-PACE.cmake: update PACELIB_URL and PACELIB_MD5 (new source files with whitespaces) lib/pace: add Makefile, Install.py use make remove the LICENSE from src/USER-PACE --- cmake/Modules/Packages/USER-PACE.cmake | 8 +- lib/pace/Install.py | 16 +- lib/pace/Makefile | 38 ++ src/USER-PACE/LICENSE | 674 ------------------------- 4 files changed, 46 insertions(+), 690 deletions(-) create mode 100644 lib/pace/Makefile delete mode 100644 src/USER-PACE/LICENSE diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index 008d32444c..b953278e75 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,11 +1,11 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "9ebb087cba7e4ca041fde52f7e9e640c" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "8041e3de7254815eb3ff0a11e2cc84ea" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) # download library sources to build folder -file(DOWNLOAD ${PACELIB_URL} libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) +file(DOWNLOAD ${PACELIB_URL} ./libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) # uncompress downloaded sources execute_process( @@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp) add_library(pace STATIC ${PACE_EVALUATOR_SOURCES}) -set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE}) +set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) target_link_libraries(lammps PRIVATE pace) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 640971e011..5f72157611 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -18,11 +18,11 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "v.2021.2.3" +version = "v.2021.2.3.upd" # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3' : '9ebb087cba7e4ca041fde52f7e9e640c', \ + 'v.2021.2.3.upd' : '8041e3de7254815eb3ff0a11e2cc84ea', \ } @@ -89,17 +89,9 @@ if buildflag: cmd = 'cd "%s"; rm -rf "%s"; tar -xvf %s; mv %s %s' % (thisdir, src_folder, archive_filename, unarchived_folder_name, src_folder) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) - # configure - - build_folder = "%s/build"%(thisdir) - print("Configuring libpace ...") - cmd = 'cd %s && mkdir build && cd build && cmake .. -DCMAKE_BUILD_TYPE=Release' % (thisdir) - txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) - if verboseflag: print(txt.decode("UTF-8")) - # build print("Building libpace ...") - cmd = 'cd "%s" && make -j2 && cp libpace.a %s/' % (build_folder, thisdir) + cmd = 'make lib -j2' txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) if verboseflag: print(txt.decode("UTF-8")) @@ -107,5 +99,5 @@ if buildflag: # remove source files print("Removing pace build files and archive ...") - cmd = 'rm %s; rm -rf %s' % (download_filename, build_folder) + cmd = 'rm %s; make clean-build' % (download_filename) subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True) \ No newline at end of file diff --git a/lib/pace/Makefile b/lib/pace/Makefile new file mode 100644 index 0000000000..baaef0b837 --- /dev/null +++ b/lib/pace/Makefile @@ -0,0 +1,38 @@ +SHELL = /bin/sh + +# ------ FILES ------ + +SRC_FILES = $(wildcard src/USER-PACE/*.cpp) +SRC = $(filter-out src/USER-PACE/pair_pace.cpp, $(SRC_FILES)) + +# ------ DEFINITIONS ------ + +LIB = libpace.a +OBJ = $(SRC:.cpp=.o) + + +# ------ SETTINGS ------ +CXXFLAGS = -O2 -fPIC -Isrc/USER-PACE + +ARCHIVE = ar +ARCHFLAG = -rc +DEPFLAGS = -M +USRLIB = +SYSLIB = + +# ------ MAKE PROCEDURE ------ + +lib: $(OBJ) + $(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ) + +# ------ COMPILE RULES ------ + +%.o: %.cpp + $(CXX) $(CXXFLAGS) -c $< -o $@ + +# ------ CLEAN ------ +clean-all: + -rm -f *~ $(OBJ) $(LIB) + +clean-build: + -rm -f *~ $(OBJ) \ No newline at end of file diff --git a/src/USER-PACE/LICENSE b/src/USER-PACE/LICENSE deleted file mode 100644 index f288702d2f..0000000000 --- a/src/USER-PACE/LICENSE +++ /dev/null @@ -1,674 +0,0 @@ - GNU GENERAL PUBLIC LICENSE - Version 3, 29 June 2007 - - Copyright (C) 2007 Free Software Foundation, Inc. - Everyone is permitted to copy and distribute verbatim copies - of this license document, but changing it is not allowed. - - Preamble - - The GNU General Public License is a free, copyleft license for -software and other kinds of works. - - The licenses for most software and other practical works are designed -to take away your freedom to share and change the works. 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From 73ee7805dc9dae77d2adf005925cf63ca4a69a7e Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 12:13:33 +0200 Subject: [PATCH 037/100] remove GPL3 license terms from src/USER-PACE/pair_pace.* delete lib/pace/CMakeLists.txt --- lib/pace/CMakeLists.txt | 19 ------------------- lib/pace/TODO | 30 ------------------------------ src/USER-PACE/pair_pace.cpp | 16 +--------------- src/USER-PACE/pair_pace.h | 16 +--------------- 4 files changed, 2 insertions(+), 79 deletions(-) delete mode 100644 lib/pace/CMakeLists.txt delete mode 100644 lib/pace/TODO diff --git a/lib/pace/CMakeLists.txt b/lib/pace/CMakeLists.txt deleted file mode 100644 index 2884c83cb9..0000000000 --- a/lib/pace/CMakeLists.txt +++ /dev/null @@ -1,19 +0,0 @@ -cmake_minimum_required(VERSION 3.7) # CMake version check -project(aceevaluator) -set(CMAKE_CXX_STANDARD 11) # Enable c++11 standard - - -set(PACE_EVALUATOR_PATH ${CMAKE_CURRENT_LIST_DIR}/src/USER-PACE) -# message("CMakeLists.txt DEBUG: PACE_EVALUATOR_PATH=${PACE_EVALUATOR_PATH}") -set(PACE_EVALUATOR_SRC_PATH ${PACE_EVALUATOR_PATH}) - -FILE(GLOB PACE_EVALUATOR_SOURCE_FILES ${PACE_EVALUATOR_SRC_PATH}/*.cpp) -list(FILTER PACE_EVALUATOR_SOURCE_FILES EXCLUDE REGEX ".*pair_pace.*") -set(PACE_EVALUATOR_INCLUDE_DIR ${PACE_EVALUATOR_SRC_PATH}) - - -##### aceevaluator ##### -add_library(aceevaluator ${PACE_EVALUATOR_SOURCE_FILES}) -target_include_directories(aceevaluator PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR}) -target_compile_options(aceevaluator PRIVATE -O3) -set_target_properties(aceevaluator PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE}) diff --git a/lib/pace/TODO b/lib/pace/TODO deleted file mode 100644 index 8021916923..0000000000 --- a/lib/pace/TODO +++ /dev/null @@ -1,30 +0,0 @@ -[TODO/DONE] pair_pace.cpp and pair_pace.h will have to go into src/USER-PACE and thus also need to conform to our requirements. - -[TODO] also src/USER-PACE would need to have an Install.sh file that integrates the settings from the lib folder into the conventional build process. -[TODO] there would have to be a lib/pace folder for building/interfacing to the library. - -[TODO] how you organize your repo is up to you. a better way to describe what you would have to do is to point you to examples. -which of the examples is relevant depends on what build system you are using for your "PACE" external package. - -If you are using CMake to build it, you can look at the KIM package -If you are using autoconf/automake, you can look at the USER-PLUMED package -If you are using neither (just a plain Makefile), you can look at the VORONOI or QUIP package -The following additional modifications are needed: - -[TODO] lib/pace: needs one or more Makefile.lammps, a README and an Install.py file -[TODO] src/Makefile: needs support for the USER-PACE package and compiling via lib-pace. Also the package needs to be added to the PACKEXT and PACKLIB variables - -[DONE] cmake/Modules/Packages/USER-PACE.cmake needs to be added -[DONE] cmake/CMakeLists.txt needs to include it in case the package is enabled. - -[TODO] doc/src/Build_extra.rst needs to include the build instructions for CMake and traditional make -[TODO] doc/src/Package_user.rst and doc/src/Package_details.rst needs to contain relevant information and links - - -Because of the different build systems, there are different steps required, but each of the examples I've pointed out are tested and used regularly and thus should be working sufficiently well. -Mind you the QUIP package is set up in such a way, that no automatic download is possible and a manual download and compilation is required. So that is the least preferred and least convenient option. - -We are happy to provide more details, but that requires that you first have something that already is following either of the suggested variants, so that we don't have to discuss in all generality. - -I would also suggest to close this pull request here, leave all files in place, but then start a new branch from the current master and then move the few things over you need to retain, -add the build environment files and then start working on getting it to do what it should. \ No newline at end of file diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index 41551e454c..c12753603a 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -7,21 +7,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, ^2: University of Cambridge, Cambridge, United Kingdom ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA ^4: University of British Columbia, Vancouver, BC, Canada - - - This FILENAME is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - */ +*/ // diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index b29ee3a7a9..37509cff5e 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -7,21 +7,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, ^2: University of Cambridge, Cambridge, United Kingdom ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA ^4: University of British Columbia, Vancouver, BC, Canada - - - This FILENAME is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - */ +*/ // From d1fd2f74d1046e4177b8714f4cf72ed47f7c87c8 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Thu, 8 Apr 2021 16:06:05 +0200 Subject: [PATCH 038/100] update PACELIB_URL (tackling some PGI warnings): v.2021.2.3.upd2 update lib/pace/Makefile: -O3 optimization --- cmake/Modules/Packages/USER-PACE.cmake | 4 ++-- lib/pace/Install.py | 4 ++-- lib/pace/Makefile | 5 ++--- 3 files changed, 6 insertions(+), 7 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index b953278e75..e8262f7d40 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "8041e3de7254815eb3ff0a11e2cc84ea" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd2.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "8fd1162724d349b930e474927197f20d" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 5f72157611..91aa8b3a46 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -18,11 +18,11 @@ parser = ArgumentParser(prog='Install.py', # settings thisdir = fullpath('.') -version = "v.2021.2.3.upd" +version = "v.2021.2.3.upd2" # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3.upd' : '8041e3de7254815eb3ff0a11e2cc84ea', \ + 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', \ } diff --git a/lib/pace/Makefile b/lib/pace/Makefile index baaef0b837..c2e1892ddd 100644 --- a/lib/pace/Makefile +++ b/lib/pace/Makefile @@ -12,11 +12,10 @@ OBJ = $(SRC:.cpp=.o) # ------ SETTINGS ------ -CXXFLAGS = -O2 -fPIC -Isrc/USER-PACE +CXXFLAGS = -O3 -fPIC -Isrc/USER-PACE ARCHIVE = ar ARCHFLAG = -rc -DEPFLAGS = -M USRLIB = SYSLIB = @@ -35,4 +34,4 @@ clean-all: -rm -f *~ $(OBJ) $(LIB) clean-build: - -rm -f *~ $(OBJ) \ No newline at end of file + -rm -f *~ $(OBJ) From 22a337b3935de957c94184d0859dfc3c0778903b Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 13:00:20 -0600 Subject: [PATCH 039/100] Updated READMEs in lib/pace and src/USER-PACE --- lib/pace/README | 13 +++++++++++-- src/USER-PACE/README | 23 +++++++++++++++++++++++ 2 files changed, 34 insertions(+), 2 deletions(-) create mode 100644 src/USER-PACE/README diff --git a/lib/pace/README b/lib/pace/README index e9a1ab820a..ddc6f7f7a7 100644 --- a/lib/pace/README +++ b/lib/pace/README @@ -1,9 +1,18 @@ -This directory contains files required to use the USER-PACE package. +This directory contains files required to use the USER-PACE package, +which provides the pace pair style, an efficient implementation of +the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. +This package was written by Yury Lysogorskiy and others +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +Ruhr University Bochum, Germany, http://www.icams.de You can type "make lib-pace" from the src directory to see help on how to download and build this library via make commands, or you can do the same thing by typing "python Install.py" from within this directory. +More information about the USER-PACE implementation of ACE +is available here: - +https://github.com/ICAMS/lammps-user-pace diff --git a/src/USER-PACE/README b/src/USER-PACE/README new file mode 100644 index 0000000000..476edaef76 --- /dev/null +++ b/src/USER-PACE/README @@ -0,0 +1,23 @@ +The USER-PACE package, +provides the pace pair style, an efficient implementation of +the Atomic Cluster Expansion potential (ACE). +ACE is a methodology for deriving a highly accurate classical potential +fit to a large archive of quantum mechanical (DFT) data. +This package was written by Yury Lysogorskiy and others +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +Ruhr University Bochum, Germany, http://www.icams.de + +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, +which must be done before building LAMMPS with this +package. Details of the download, build, and install process for +this package usng traditional make (not CMake) are given in the +lib/pace/README file, and scripts are +provided to help automate the process. Also see the LAMMPS manual for +general information on building LAMMPS with external libraries +using either traditional make or CMake. + +More information about the USER-PACE implementation of ACE +is available here: + +https://github.com/ICAMS/lammps-user-pace From a39dc9f9b224118e54330e67d6a240dfab91d352 Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 13:36:04 -0600 Subject: [PATCH 040/100] Added minimal info on downloading and building PACE library --- doc/src/Build_extras.rst | 32 ++++++++++++++++++++++++++++++++ doc/src/Packages_details.rst | 4 ++++ src/USER-PACE/README | 22 +++++++++++----------- 3 files changed, 47 insertions(+), 11 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 3af018c656..726374a012 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -52,6 +52,7 @@ This is the list of packages that may require additional steps. * :ref:`USER-MESONT ` * :ref:`USER-MOLFILE ` * :ref:`USER-NETCDF ` + * :ref:`USER-PACE ` * :ref:`USER-PLUMED ` * :ref:`USER-OMP ` * :ref:`USER-QMMM ` @@ -1247,6 +1248,37 @@ be built for the most part with all major versions of the C++ language. ---------- +.. _user-pace: + +USER-PACE package +----------------------------- + +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. + +.. tabs:: + + .. tab:: CMake build + + The library download and build will happen automatically when USER-PACE + is requested. + + .. tab:: Traditional make + + You can download and build the USER-PACE library + in one step from the ``lammps/src`` dir, using these commands, + which invoke the ``lib/pace/Install.py`` script. + + .. code-block:: bash + + $ make lib-pace # print help message + $ make lib-pace args="-b" # download and build the default version in lib/pace + + You should not need to edit the ``lib/pace/Makefile.lammps`` file. + +---------- + .. _user-plumed: USER-PLUMED package diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 1964a83717..b10983a35b 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -1378,6 +1378,10 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1. ^4: University of British Columbia, Vancouver, BC, Canada +**Install:** + +This package has :ref:`specific installation instructions ` on the :doc:`Build extras ` page. + **Supporting info:** * src/USER-PACE: filenames -> commands diff --git a/src/USER-PACE/README b/src/USER-PACE/README index 476edaef76..3d85c806e9 100644 --- a/src/USER-PACE/README +++ b/src/USER-PACE/README @@ -1,18 +1,18 @@ -The USER-PACE package, -provides the pace pair style, an efficient implementation of -the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical potential -fit to a large archive of quantum mechanical (DFT) data. +The USER-PACE package provides the pace pair style, +an efficient implementation of the Atomic Cluster Expansion +potential (ACE). + +ACE is a methodology for deriving a highly accurate classical +potential fit to a large archive of quantum mechanical (DFT) data. This package was written by Yury Lysogorskiy and others at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, -Ruhr University Bochum, Germany, http://www.icams.de +Ruhr University Bochum, Germany (http://www.icams.de). This package requires a library that can be downloaded and built -in lib/pace or somewhere else, -which must be done before building LAMMPS with this -package. Details of the download, build, and install process for -this package usng traditional make (not CMake) are given in the -lib/pace/README file, and scripts are +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. Details of the download, build, and +install process for this package using traditional make (not CMake) +are given in the lib/pace/README file, and scripts are provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. From 0aee75857a6e7fa320862255b81eff32f30c336f Mon Sep 17 00:00:00 2001 From: Aidan Thompson Date: Thu, 8 Apr 2021 14:09:19 -0600 Subject: [PATCH 041/100] Eliminated doc build warnings --- doc/src/Build_package.rst | 22 +++++++++++----------- doc/src/Packages_user.rst | 2 ++ doc/src/pair_style.rst | 5 +++-- 3 files changed, 16 insertions(+), 13 deletions(-) diff --git a/doc/src/Build_package.rst b/doc/src/Build_package.rst index f9fc52f8db..91531f51ec 100644 --- a/doc/src/Build_package.rst +++ b/doc/src/Build_package.rst @@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras ` page. These links take you to the extra instructions for those select packages: -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-NETCDF ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | :ref:`USER-SCAFACOS ` | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ -| :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | | -+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`COMPRESS ` | :ref:`GPU ` | :ref:`KIM ` | :ref:`KOKKOS ` | :ref:`LATTE ` | :ref:`MESSAGE ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`MSCG ` | :ref:`OPT ` | :ref:`POEMS ` | :ref:`PYTHON ` | :ref:`VORONOI ` | :ref:`USER-ADIOS ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-ATC ` | :ref:`USER-AWPMD ` | :ref:`USER-COLVARS ` | :ref:`USER-H5MD ` | :ref:`USER-INTEL ` | :ref:`USER-MOLFILE ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-NETCDF ` | :ref:`USER-PACE ` | :ref:`USER-PLUMED ` | :ref:`USER-OMP ` | :ref:`USER-QMMM ` | :ref:`USER-QUIP ` | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ +| :ref:`USER-SCAFACOS ` | :ref:`USER-SMD ` | :ref:`USER-VTK ` | | | | ++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+ The mechanism for including packages is simple but different for CMake versus make. diff --git a/doc/src/Packages_user.rst b/doc/src/Packages_user.rst index a3efaf15c8..00d1dfb67b 100644 --- a/doc/src/Packages_user.rst +++ b/doc/src/Packages_user.rst @@ -81,6 +81,8 @@ package: +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-OMP ` | OpenMP-enabled styles | :doc:`Speed omp ` | `Benchmarks `_ | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ +| :ref:`USER-PACE ` | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace ` | USER/pace | ext | ++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PHONON ` | phonon dynamical matrix | :doc:`fix phonon ` | USER/phonon | no | +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+ | :ref:`USER-PLUMED ` | :ref:`PLUMED ` free energy library | :doc:`fix plumed ` | USER/plumed | ext | diff --git a/doc/src/pair_style.rst b/doc/src/pair_style.rst index 89530895c4..a64fc67194 100644 --- a/doc/src/pair_style.rst +++ b/doc/src/pair_style.rst @@ -98,7 +98,7 @@ accelerated styles exist. * :doc:`zero ` - neighbor list but no interactions * :doc:`adp ` - angular dependent potential (ADP) of Mishin -* :doc:`agni ` - machine learned potential mapping atomic environment to forces +* :doc:`agni ` - AGNI machine-learning potential * :doc:`airebo ` - AIREBO potential of Stuart * :doc:`airebo/morse ` - AIREBO with Morse instead of LJ * :doc:`atm ` - Axilrod-Teller-Muto potential @@ -278,6 +278,7 @@ accelerated styles exist. * :doc:`oxrna2/hbond ` - * :doc:`oxrna2/stk ` - * :doc:`oxrna2/xstk ` - +* :doc:`pace ` - Atomic Cluster Expansion (ACE) machine-learning potential * :doc:`peri/eps ` - peridynamic EPS potential * :doc:`peri/lps ` - peridynamic LPS potential * :doc:`peri/pmb ` - peridynamic PMB potential @@ -295,7 +296,7 @@ accelerated styles exist. * :doc:`smd/ulsph ` - * :doc:`smtbq ` - * :doc:`mliap ` - Multiple styles of machine-learning potential -* :doc:`snap ` - SNAP quantum-accurate potential +* :doc:`snap ` - SNAP machine-learning potential * :doc:`soft ` - Soft (cosine) potential * :doc:`sph/heatconduction ` - * :doc:`sph/idealgas ` - From 7b45b691f4a926328f53fdcc95c9d78261656269 Mon Sep 17 00:00:00 2001 From: Yury Lysogorskiy Date: Fri, 9 Apr 2021 13:31:40 +0200 Subject: [PATCH 042/100] pair_pace.cpp: check that units are "metal" update ace-evaluator (download link + md5sum in cmake and make build systems): accept multilines comment at the beginning of potential.ace file add first comment line for potentials/Cu-PBE-core-rep.ace --- cmake/Modules/Packages/USER-PACE.cmake | 4 ++-- lib/pace/Install.py | 12 +++++++----- potentials/Cu-PBE-core-rep.ace | 2 ++ src/USER-PACE/pair_pace.cpp | 5 +++++ 4 files changed, 16 insertions(+), 7 deletions(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index e8262f7d40..df1fb023a5 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -1,6 +1,6 @@ -set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.2.3.upd2.tar.gz" CACHE STRING "URL for PACE evaluator library sources") -set(PACELIB_MD5 "8fd1162724d349b930e474927197f20d" CACHE STRING "MD5 checksum of PACE evaluator library tarball") +set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources") +set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball") mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) diff --git a/lib/pace/Install.py b/lib/pace/Install.py index 91aa8b3a46..08bbb331bb 100644 --- a/lib/pace/Install.py +++ b/lib/pace/Install.py @@ -12,20 +12,22 @@ from argparse import ArgumentParser sys.path.append('..') from install_helpers import fullpath, geturl, checkmd5sum -parser = ArgumentParser(prog='Install.py', - description="LAMMPS library build wrapper script") - # settings thisdir = fullpath('.') -version = "v.2021.2.3.upd2" +version = 'v.2021.4.9' # known checksums for different PACE versions. used to validate the download. checksums = { \ - 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', \ + 'v.2021.2.3.upd2' : '8fd1162724d349b930e474927197f20d', + 'v.2021.4.9' : '4db54962fbd6adcf8c18d46e1798ceb5', } +parser = ArgumentParser(prog='Install.py', + description="LAMMPS library build wrapper script") + + # help message HELP = """ diff --git a/potentials/Cu-PBE-core-rep.ace b/potentials/Cu-PBE-core-rep.ace index 338675f718..511bb9af7f 100644 --- a/potentials/Cu-PBE-core-rep.ace +++ b/potentials/Cu-PBE-core-rep.ace @@ -1,3 +1,5 @@ +# DATE: 2021-04-08 UNITS: metal CONTRIBUTOR: Yury Lysogorskiy CITATION: npj Comp. Mat., submitted (2021) + nelements=1 elements: Cu diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index c12753603a..f59291b33e 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -25,6 +25,7 @@ Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, #include "neigh_list.h" #include "neigh_request.h" #include "neighbor.h" +#include "update.h" #include #include @@ -252,6 +253,10 @@ void PairPACE::settings(int narg, char **arg) { if (narg > 1) error->all(FLERR,"Illegal pair_style command."); + // ACE potentials are parameterized in metal units + if (strcmp("metal",update->unit_style) != 0) + error->all(FLERR,"ACE potentials require 'metal' units"); + recursive = true; // default evaluator style: RECURSIVE if (narg > 0) { if (strcmp(arg[0], RECURSIVE_KEYWORD) == 0) From ded22bf8bc68cc20cc6333866fe447af0d7d3c02 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 11:36:10 -0400 Subject: [PATCH 043/100] Minor changes to dump_atom_gz/dump_atom_zstd --- src/COMPRESS/dump_atom_gz.cpp | 5 +---- src/COMPRESS/dump_atom_zstd.cpp | 4 ++-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 071af2167d..254e146800 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -11,16 +11,13 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_atom_gz.h" #include "domain.h" +#include "dump_atom_gz.h" #include "error.h" -#include "file_writer.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpAtomGZ::DumpAtomGZ(LAMMPS *lmp, int narg, char **arg) : diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index 300a4c81cb..dd744b5d49 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -43,7 +43,7 @@ DumpAtomZstd::~DumpAtomZstd() /* ---------------------------------------------------------------------- generic opening of a dump file - ASCII or binary or zstdipped + ASCII or binary or compressed some derived classes override this function ------------------------------------------------------------------------- */ @@ -180,7 +180,7 @@ int DumpAtomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; From 2682663df6ac7ee5092b2df090a95c5349074471 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 11:41:45 -0400 Subject: [PATCH 044/100] Use GzFileWriter in dump cfg/gz --- src/COMPRESS/dump_cfg_gz.cpp | 88 ++++++++----------- src/COMPRESS/dump_cfg_gz.h | 5 +- src/COMPRESS/dump_cfg_zstd.cpp | 3 +- unittest/formats/test_dump_cfg_compressed.cpp | 4 +- 4 files changed, 41 insertions(+), 59 deletions(-) diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 378baf502f..6bbf118789 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -11,41 +11,30 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_cfg_gz.h" #include "atom.h" #include "domain.h" +#include "dump_cfg_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; #define UNWRAPEXPAND 10.0 DumpCFGGZ::DumpCFGGZ(LAMMPS *lmp, int narg, char **arg) : DumpCFG(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump cfg/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpCFGGZ::~DumpCFGGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -95,17 +84,12 @@ void DumpCFGGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -127,30 +111,30 @@ void DumpCFGGZ::write_header(bigint n) if (atom->peri_flag) scale = atom->pdscale; else if (unwrapflag == 1) scale = UNWRAPEXPAND; - char str[64]; - sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT); - gzprintf(gzFp,str,n); - gzprintf(gzFp,"A = %g Angstrom (basic length-scale)\n",scale); - gzprintf(gzFp,"H0(1,1) = %g A\n",domain->xprd); - gzprintf(gzFp,"H0(1,2) = 0 A \n"); - gzprintf(gzFp,"H0(1,3) = 0 A \n"); - gzprintf(gzFp,"H0(2,1) = %g A \n",domain->xy); - gzprintf(gzFp,"H0(2,2) = %g A\n",domain->yprd); - gzprintf(gzFp,"H0(2,3) = 0 A \n"); - gzprintf(gzFp,"H0(3,1) = %g A \n",domain->xz); - gzprintf(gzFp,"H0(3,2) = %g A \n",domain->yz); - gzprintf(gzFp,"H0(3,3) = %g A\n",domain->zprd); - gzprintf(gzFp,".NO_VELOCITY.\n"); - gzprintf(gzFp,"entry_count = %d\n",nfield-2); + std::string header = fmt::format("Number of particles = {}\n", n); + header += fmt::format("A = {0:g} Angstrom (basic length-scale)\n", scale); + header += fmt::format("H0(1,1) = {0:g} A\n",domain->xprd); + header += fmt::format("H0(1,2) = 0 A \n"); + header += fmt::format("H0(1,3) = 0 A \n"); + header += fmt::format("H0(2,1) = {0:g} A \n",domain->xy); + header += fmt::format("H0(2,2) = {0:g} A\n",domain->yprd); + header += fmt::format("H0(2,3) = 0 A \n"); + header += fmt::format("H0(3,1) = {0:g} A \n",domain->xz); + header += fmt::format("H0(3,2) = {0:g} A \n",domain->yz); + header += fmt::format("H0(3,3) = {0:g} A\n",domain->zprd); + header += fmt::format(".NO_VELOCITY.\n"); + header += fmt::format("entry_count = {}\n",nfield-2); for (int i = 0; i < nfield-5; i++) - gzprintf(gzFp,"auxiliary[%d] = %s\n",i,auxname[i]); + header += fmt::format("auxiliary[{}] = {}\n",i,auxname[i]); + + writer.write(header.c_str(), header.length()); } /* ---------------------------------------------------------------------- */ void DumpCFGGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -160,11 +144,11 @@ void DumpCFGGZ::write() DumpCFG::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -175,16 +159,16 @@ int DumpCFGGZ::modify_param(int narg, char **arg) { int consumed = DumpCFG::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; } - diff --git a/src/COMPRESS/dump_cfg_gz.h b/src/COMPRESS/dump_cfg_gz.h index 0c6ed24f06..2844902a38 100644 --- a/src/COMPRESS/dump_cfg_gz.h +++ b/src/COMPRESS/dump_cfg_gz.h @@ -21,7 +21,7 @@ DumpStyle(cfg/gz,DumpCFGGZ) #define LMP_DUMP_CFG_GZ_H #include "dump_cfg.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpCFGGZ : public DumpCFG { virtual ~DumpCFGGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 459649c70a..978e695d1a 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -21,7 +21,6 @@ #include "domain.h" #include "dump_cfg_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -46,7 +45,7 @@ DumpCFGZstd::~DumpCFGZstd() /* ---------------------------------------------------------------------- generic opening of a dump file - ASCII or binary or zstdipped + ASCII or binary or compressed some derived classes override this function ------------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 20f902091b..6d5e8bcf04 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -234,7 +234,7 @@ TEST_F(DumpCfgCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.cfg"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -248,7 +248,7 @@ TEST_F(DumpCfgCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.cfg"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 77de0273be242bd6bae9bd0e59fd99a69ff1449d Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 12:37:14 -0400 Subject: [PATCH 045/100] Fix typo --- src/dump_local.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 53a82b496f..8b9b309aff 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -112,7 +112,7 @@ DumpLocal::DumpLocal(LAMMPS *lmp, int narg, char **arg) : label = utils::strdup("ENTRIES"); - // if wildcard expansion occurred, free earg memory from exapnd_args() + // if wildcard expansion occurred, free earg memory from expand_args() if (expand) { for (int i = 0; i < nfield; i++) delete [] earg[i]; From e0e031aa4324082c53654df333b82ea2d4b9b0c0 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 13:38:18 -0400 Subject: [PATCH 046/100] Correct dump_modify example in docs --- doc/src/dump_modify.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index 753cce703c..d072df5d4d 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -362,7 +362,7 @@ settings, reverting all values to their default format. compute 1 all property/local batom1 batom2 dump 1 all local 100 tmp.bonds index c_1[1] c_1[2] - dump_modify 1 format "%d %0.0f %0.0f" + dump_modify 1 format line "%d %0.0f %0.0f" will output the two atom IDs for atoms in each bond as integers. If the dump_modify command were omitted, they would appear as From 5c9a5ba8ac03f51ac1e3bf0457cc1742f003e4e7 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:48:38 -0400 Subject: [PATCH 047/100] Add missing code to allow customized formatting in dump local --- src/dump_local.cpp | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/src/dump_local.cpp b/src/dump_local.cpp index 8b9b309aff..dac8066236 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -225,6 +225,46 @@ int DumpLocal::modify_param(int narg, char **arg) delete [] label; label = utils::strdup(arg[1]); return 2; + } else if (strcmp(arg[0],"format") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + + if (strcmp(arg[1],"none") == 0) { + // just clear format_column_user allocated by this dump child class + for (int i = 0; i < nfield; i++) { + delete [] format_column_user[i]; + format_column_user[i] = nullptr; + } + return 2; + } else if (strcmp(arg[1],"int") == 0) { + delete [] format_int_user; + format_int_user = utils::strdup(arg[2]); + delete [] format_bigint_user; + int n = strlen(format_int_user) + 8; + format_bigint_user = new char[n]; + // replace "d" in format_int_user with bigint format specifier + // use of &str[1] removes leading '%' from BIGINT_FORMAT string + char *ptr = strchr(format_int_user,'d'); + if (ptr == nullptr) + error->all(FLERR, + "Dump_modify int format does not contain d character"); + char str[8]; + sprintf(str,"%s",BIGINT_FORMAT); + *ptr = '\0'; + sprintf(format_bigint_user,"%s%s%s",format_int_user,&str[1],ptr+1); + *ptr = 'd'; + + } else if (strcmp(arg[1],"float") == 0) { + delete [] format_float_user; + format_float_user = utils::strdup(arg[2]); + + } else { + int i = utils::inumeric(FLERR,arg[1],false,lmp) - 1; + if (i < 0 || i >= nfield) + error->all(FLERR,"Illegal dump_modify command"); + if (format_column_user[i]) delete [] format_column_user[i]; + format_column_user[i] = utils::strdup(arg[2]); + } + return 3; } return 0; } From dc71d8030694fb6c55588b94913182aa8f482f70 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:49:07 -0400 Subject: [PATCH 048/100] Add dump local tests --- unittest/formats/CMakeLists.txt | 5 + unittest/formats/test_dump_local.cpp | 195 +++++++++++++++++++++++++++ 2 files changed, 200 insertions(+) create mode 100644 unittest/formats/test_dump_local.cpp diff --git a/unittest/formats/CMakeLists.txt b/unittest/formats/CMakeLists.txt index be0d14c47d..4c6de98729 100644 --- a/unittest/formats/CMakeLists.txt +++ b/unittest/formats/CMakeLists.txt @@ -102,6 +102,11 @@ target_link_libraries(test_dump_cfg PRIVATE lammps GTest::GMock GTest::GTest) add_test(NAME DumpCfg COMMAND test_dump_cfg WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(DumpCfg PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") +add_executable(test_dump_local test_dump_local.cpp) +target_link_libraries(test_dump_local PRIVATE lammps GTest::GMock GTest::GTest) +add_test(NAME DumpLocal COMMAND test_dump_local WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +set_tests_properties(DumpLocal PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}") + if(BUILD_TOOLS) set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$") set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$") diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp new file mode 100644 index 0000000000..fb38ca08ad --- /dev/null +++ b/unittest/formats/test_dump_local.cpp @@ -0,0 +1,195 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#include "../testing/core.h" +#include "../testing/systems/melt.h" +#include "../testing/utils.h" +#include "fmt/format.h" +#include "output.h" +#include "thermo.h" +#include "utils.h" +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include + +using ::testing::Eq; + +char *BINARY2TXT_BINARY = nullptr; +bool verbose = false; + +class DumpLocalTest : public MeltTest { + std::string dump_style = "local"; + +public: + void enable_triclinic() + { + BEGIN_HIDE_OUTPUT(); + command("change_box all triclinic"); + END_HIDE_OUTPUT(); + } + + void generate_dump(std::string dump_file, std::string dump_options, std::string dump_modify_options, int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, dump_options)); + + if (!dump_modify_options.empty()) { + command(fmt::format("dump_modify id {}", dump_modify_options)); + } + + command(fmt::format("run {} post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void continue_dump(int ntimesteps) + { + BEGIN_HIDE_OUTPUT(); + command(fmt::format("run {} pre no post no", ntimesteps)); + END_HIDE_OUTPUT(); + } + + void SetUp() override { + MeltTest::SetUp(); + + BEGIN_HIDE_OUTPUT(); + command("compute comp all pair/local dist eng"); + END_HIDE_OUTPUT(); + } +}; + +TEST_F(DumpLocalTest, run0) +{ + auto dump_file = "dump_local_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 873); + + ASSERT_THAT(lines[0], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[1]), 0); + + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[3]), 864); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 2); + ASSERT_EQ(utils::split_words(lines[6]).size(), 2); + ASSERT_EQ(utils::split_words(lines[7]).size(), 2); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_line_run0) +{ + auto dump_file = "dump_local_format_line_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format line \"%d %20.8g\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.1876539 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_int_run0) +{ + auto dump_file = "dump_local_format_int_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format int \"%20d\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq(" 1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_float_run0) +{ + auto dump_file = "dump_local_format_float_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format float \"%20.5g\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.1877 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, format_column_run0) +{ + auto dump_file = "dump_local_format_column_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "format 1 \"%20d\"", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq(" 1 1.18765 ")); + delete_file(dump_file); +} + +TEST_F(DumpLocalTest, no_buffer_run0) +{ + auto dump_file = "dump_local_format_line_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "buffer no", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 873); + + ASSERT_THAT(lines[0], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[1]), 0); + + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[3]), 864); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 2); + ASSERT_EQ(utils::split_words(lines[6]).size(), 2); + ASSERT_EQ(utils::split_words(lines[7]).size(), 2); + ASSERT_THAT(lines[8], Eq("ITEM: ENTRIES index c_comp[1] ")); + ASSERT_EQ(utils::split_words(lines[9]).size(), 2); + ASSERT_THAT(lines[9], Eq("1 1.18765 ")); + delete_file(dump_file); +} + +int main(int argc, char **argv) +{ + MPI_Init(&argc, &argv); + ::testing::InitGoogleMock(&argc, argv); + + // handle arguments passed via environment variable + if (const char *var = getenv("TEST_ARGS")) { + std::vector env = utils::split_words(var); + for (auto arg : env) { + if (arg == "-v") { + verbose = true; + } + } + } + + BINARY2TXT_BINARY = getenv("BINARY2TXT_BINARY"); + + if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true; + + int rv = RUN_ALL_TESTS(); + MPI_Finalize(); + return rv; +} From d19cd8fb115bcab444b10742a692d913253a3231 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 14:49:45 -0400 Subject: [PATCH 049/100] Fix test --- unittest/formats/test_dump_atom.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/unittest/formats/test_dump_atom.cpp b/unittest/formats/test_dump_atom.cpp index 5161eece3e..669f4d38bd 100644 --- a/unittest/formats/test_dump_atom.cpp +++ b/unittest/formats/test_dump_atom.cpp @@ -135,7 +135,7 @@ TEST_F(DumpAtomTest, no_scale_run0) TEST_F(DumpAtomTest, no_buffer_no_scale_run0) { auto dump_file = "dump_no_buffer_no_scale_run0.melt"; - generate_dump(dump_file, "scale no", 0); + generate_dump(dump_file, "buffer no scale no", 0); ASSERT_FILE_EXISTS(dump_file); auto lines = read_lines(dump_file); From cf41ea6fafae8f9d69cd32429c433856f2c7b10f Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:42:28 -0400 Subject: [PATCH 050/100] Update dump local and local/gz --- src/COMPRESS/dump_local_gz.cpp | 118 ++++++++-------- src/COMPRESS/dump_local_gz.h | 5 +- src/COMPRESS/dump_local_zstd.cpp | 33 ++++- unittest/formats/test_dump_local.cpp | 66 +++++++++ .../formats/test_dump_local_compressed.cpp | 133 +++++++++++++++++- 5 files changed, 285 insertions(+), 70 deletions(-) diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index e8065a848a..a0a39b51e0 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -11,24 +11,18 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_local_gz.h" #include "domain.h" +#include "dump_local_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocal(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump local/gz only writes compressed files"); } @@ -38,12 +32,8 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : DumpLocalGZ::~DumpLocalGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -93,17 +83,12 @@ void DumpLocalGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +97,34 @@ void DumpLocalGZ::openfile() void DumpLocalGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF %s\n",label); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic) { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: %s %s\n",label,columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF {}\n{}\n", label, ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: {} {}\n", label, columns); + + writer.write(header.c_str(), header.length()); } } @@ -143,19 +133,28 @@ void DumpLocalGZ::write_header(bigint ndump) void DumpLocalGZ::write_data(int n, double *mybuf) { if (buffer_flag == 1) { - gzwrite(gzFp,mybuf,sizeof(char)*n); - + writer.write(mybuf, sizeof(char)*n); } else { - int i,j; + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; int m = 0; - for (i = 0; i < n; i++) { - for (j = 0; j < size_one; j++) { - if (vtype[j] == INT) - gzprintf(gzFp,vformat[j],static_cast (mybuf[m])); - else gzprintf(gzFp,vformat[j],mybuf[m]); + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } m++; } - gzprintf(gzFp,"\n"); + writer.write("\n", 1); } } } @@ -167,11 +166,11 @@ void DumpLocalGZ::write() DumpLocal::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -182,14 +181,15 @@ int DumpLocalGZ::modify_param(int narg, char **arg) { int consumed = DumpLocal::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.h b/src/COMPRESS/dump_local_gz.h index b3f7c7dcf8..7feb6a8945 100644 --- a/src/COMPRESS/dump_local_gz.h +++ b/src/COMPRESS/dump_local_gz.h @@ -21,7 +21,7 @@ DumpStyle(local/gz,DumpLocalGZ) #define LMP_DUMP_LOCAL_GZ_H #include "dump_local.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpLocalGZ : public DumpLocal { virtual ~DumpLocalGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index d26555d282..a4303f3b25 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -17,15 +17,13 @@ #ifdef LAMMPS_ZSTD -#include "dump_local_zstd.h" #include "domain.h" +#include "dump_local_zstd.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpLocalZstd::DumpLocalZstd(LAMMPS *lmp, int narg, char **arg) : @@ -42,7 +40,6 @@ DumpLocalZstd::~DumpLocalZstd() { } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -145,7 +142,31 @@ void DumpLocalZstd::write_header(bigint ndump) void DumpLocalZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, sizeof(char)*n); + if (buffer_flag == 1) { + writer.write(mybuf, sizeof(char)*n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump local/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ @@ -184,7 +205,7 @@ int DumpLocalZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/unittest/formats/test_dump_local.cpp b/unittest/formats/test_dump_local.cpp index fb38ca08ad..b122d71849 100644 --- a/unittest/formats/test_dump_local.cpp +++ b/unittest/formats/test_dump_local.cpp @@ -93,6 +93,18 @@ TEST_F(DumpLocalTest, run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, label_run0) +{ + auto dump_file = "dump_local_label_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "label ELEMENTS", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_THAT(lines[2], Eq("ITEM: NUMBER OF ELEMENTS")); + ASSERT_THAT(lines[8], Eq("ITEM: ELEMENTS index c_comp[1] ")); + delete_file(dump_file); +} + TEST_F(DumpLocalTest, format_line_run0) { auto dump_file = "dump_local_format_line_run0.melt"; @@ -170,6 +182,60 @@ TEST_F(DumpLocalTest, no_buffer_run0) delete_file(dump_file); } +TEST_F(DumpLocalTest, with_units_run0) +{ + auto dump_file = "dump_with_units_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "units yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: UNITS")); + ASSERT_THAT(lines[1], Eq("lj")); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, with_time_run0) +{ + auto dump_file = "dump_with_time_run0.melt"; + generate_dump(dump_file, "index c_comp[1]", "time yes", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + ASSERT_EQ(lines.size(), 875); + + ASSERT_THAT(lines[0], Eq("ITEM: TIME")); + ASSERT_THAT(std::stof(lines[1]), 0.0); + + ASSERT_THAT(lines[2], Eq("ITEM: TIMESTEP")); + ASSERT_EQ(std::stoi(lines[3]), 0); + + ASSERT_THAT(lines[4], Eq("ITEM: NUMBER OF ENTRIES")); + ASSERT_EQ(std::stoi(lines[5]), 864); +} + +TEST_F(DumpLocalTest, triclinic_run0) +{ + auto dump_file = "dump_local_triclinic_run0.melt"; + enable_triclinic(); + generate_dump(dump_file, "index c_comp[1]", "", 0); + + ASSERT_FILE_EXISTS(dump_file); + auto lines = read_lines(dump_file); + + ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp")); + ASSERT_EQ(utils::split_words(lines[5]).size(), 3); + ASSERT_EQ(utils::split_words(lines[6]).size(), 3); + ASSERT_EQ(utils::split_words(lines[7]).size(), 3); + delete_file(dump_file); +} + int main(int argc, char **argv) { MPI_Init(&argc, &argv); diff --git a/unittest/formats/test_dump_local_compressed.cpp b/unittest/formats/test_dump_local_compressed.cpp index 95656071fc..cd217354af 100644 --- a/unittest/formats/test_dump_local_compressed.cpp +++ b/unittest/formats/test_dump_local_compressed.cpp @@ -69,6 +69,135 @@ TEST_F(DumpLocalCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpLocalCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.local"; + auto base_name_0 = "no_buffer_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_time_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_time_run*.melt.local"; + auto base_name_0 = "with_time_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "time yes", "time yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "time yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_with_units_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_units_run*.melt.local"; + auto base_name_0 = "with_units_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "units yes", "units yes checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "units yes", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + +TEST_F(DumpLocalCompressTest, compressed_triclinic_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + enable_triclinic(); + + auto base_name = "triclinic_run*.melt.local"; + auto base_name_0 = "triclinic_run0.melt.local"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "index c_comp[1]"; + + if(compression_style == "local/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "", "checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpLocalCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); @@ -209,7 +338,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -224,7 +353,7 @@ TEST_F(DumpLocalCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.local"), fields)); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From eb3cddb028f475b3a3478dbba5abe358bfc4539a Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:46:18 -0400 Subject: [PATCH 051/100] Update docs to include format support in dump local variants --- doc/src/dump_modify.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/src/dump_modify.rst b/doc/src/dump_modify.rst index d072df5d4d..07f00c4030 100644 --- a/doc/src/dump_modify.rst +++ b/doc/src/dump_modify.rst @@ -308,9 +308,9 @@ performed with dump style *xtc*\ . ---------- -The *format* keyword can be used to change the default numeric format -output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and -*xyz* styles, and their MPIIO variants. Only the *line* or *none* +The *format* keyword can be used to change the default numeric format output +by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and +*xyz* styles, and their MPIIO variants. Only the *line* or *none* options can be used with the *atom* and *xyz* styles. All the specified format strings are C-style formats, e.g. as used by From c17ee12989b95e2fc160032494d19380230879f3 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 15:57:17 -0400 Subject: [PATCH 052/100] Update dump xyz/gz --- src/COMPRESS/dump_xyz_gz.cpp | 57 +++++++------------ src/COMPRESS/dump_xyz_gz.h | 5 +- src/COMPRESS/dump_xyz_zstd.cpp | 3 +- unittest/formats/test_dump_xyz_compressed.cpp | 4 +- 4 files changed, 27 insertions(+), 42 deletions(-) diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index c63d354e80..5c90c48d0f 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -15,19 +15,13 @@ #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZ(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump xyz/gz only writes compressed files"); } @@ -37,12 +31,8 @@ DumpXYZGZ::DumpXYZGZ(LAMMPS *lmp, int narg, char **arg) : DumpXYZGZ::~DumpXYZGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -92,17 +82,12 @@ void DumpXYZGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,8 +97,9 @@ void DumpXYZGZ::openfile() void DumpXYZGZ::write_header(bigint ndump) { if (me == 0) { - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - gzprintf(gzFp,"Atoms. Timestep: " BIGINT_FORMAT "\n",update->ntimestep); + std::string header = fmt::format("{}\n", ndump); + header += fmt::format("Atoms. Timestep: {}\n", update->ntimestep); + writer.write(header.c_str(), header.length()); } } @@ -121,7 +107,7 @@ void DumpXYZGZ::write_header(bigint ndump) void DumpXYZGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -131,11 +117,11 @@ void DumpXYZGZ::write() DumpXYZ::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -146,14 +132,15 @@ int DumpXYZGZ::modify_param(int narg, char **arg) { int consumed = DumpXYZ::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_xyz_gz.h b/src/COMPRESS/dump_xyz_gz.h index 834db488a5..2fce0a3f5a 100644 --- a/src/COMPRESS/dump_xyz_gz.h +++ b/src/COMPRESS/dump_xyz_gz.h @@ -21,7 +21,7 @@ DumpStyle(xyz/gz,DumpXYZGZ) #define LMP_DUMP_XYZ_GZ_H #include "dump_xyz.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpXYZGZ : public DumpXYZ { virtual ~DumpXYZGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 7c5b73d0ba..03edf561b1 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -19,7 +19,6 @@ #include "dump_xyz_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -158,7 +157,7 @@ int DumpXYZZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index dad7911b4c..b627cb5a99 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -195,7 +195,7 @@ TEST_F(DumpXYZCompressTest, compressed_modify_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.xyz"))); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -208,7 +208,7 @@ TEST_F(DumpXYZCompressTest, compressed_modify_multi_bad_param) command(fmt::format("dump id1 all {} 1 {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.xyz"))); END_HIDE_OUTPUT(); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 511f64fde4ab569d2ac9bde67c9e9c6d6aa7e3da Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 16:36:30 -0400 Subject: [PATCH 053/100] Update dump custom/gz --- src/COMPRESS/dump_atom_gz.cpp | 4 +- src/COMPRESS/dump_atom_zstd.cpp | 4 +- src/COMPRESS/dump_cfg_gz.cpp | 4 +- src/COMPRESS/dump_cfg_zstd.cpp | 4 +- src/COMPRESS/dump_custom_gz.cpp | 98 +++++++++---------- src/COMPRESS/dump_custom_gz.h | 5 +- src/COMPRESS/dump_custom_zstd.cpp | 7 +- src/COMPRESS/dump_local_gz.cpp | 5 +- src/COMPRESS/dump_local_zstd.cpp | 4 +- src/COMPRESS/dump_xyz_gz.cpp | 4 +- src/COMPRESS/dump_xyz_zstd.cpp | 4 +- .../formats/test_dump_custom_compressed.cpp | 33 ++++++- 12 files changed, 106 insertions(+), 70 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index 254e146800..b3b202e373 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -71,7 +71,9 @@ void DumpAtomGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index dd744b5d49..f739a53322 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -79,7 +79,9 @@ void DumpAtomZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 6bbf118789..23c0d82429 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -73,7 +73,9 @@ void DumpCFGGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 978e695d1a..5bc6ac86dc 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -81,7 +81,9 @@ void DumpCFGZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 4f03a4a232..5cecf22b5d 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -11,39 +11,28 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -#include "dump_custom_gz.h" #include "domain.h" +#include "dump_custom_gz.h" #include "error.h" #include "update.h" - #include - using namespace LAMMPS_NS; DumpCustomGZ::DumpCustomGZ(LAMMPS *lmp, int narg, char **arg) : DumpCustom(lmp, narg, arg) { - gzFp = nullptr; - - compression_level = Z_BEST_COMPRESSION; - if (!compressed) error->all(FLERR,"Dump custom/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpCustomGZ::~DumpCustomGZ() { - if (gzFp) gzclose(gzFp); - gzFp = nullptr; - fp = nullptr; } - /* ---------------------------------------------------------------------- generic opening of a dump file ASCII or binary or gzipped @@ -82,7 +71,9 @@ void DumpCustomGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; @@ -93,17 +84,12 @@ void DumpCustomGZ::openfile() // each proc with filewriter = 1 opens a file if (filewriter) { - std::string mode; - if (append_flag) { - mode = fmt::format("ab{}", compression_level); - } else { - mode = fmt::format("wb{}", compression_level); + try { + writer.open(filecurrent, append_flag); + } catch (FileWriterException &e) { + error->one(FLERR, e.what()); } - - gzFp = gzopen(filecurrent, mode.c_str()); - - if (gzFp == nullptr) error->one(FLERR,"Cannot open dump file"); - } else gzFp = nullptr; + } // delete string with timestep replaced @@ -112,29 +98,34 @@ void DumpCustomGZ::openfile() void DumpCustomGZ::write_header(bigint ndump) { + std::string header; + if ((multiproc) || (!multiproc && me == 0)) { if (unit_flag && !unit_count) { ++unit_count; - gzprintf(gzFp,"ITEM: UNITS\n%s\n",update->unit_style); + header = fmt::format("ITEM: UNITS\n{}\n",update->unit_style); } - if (time_flag) gzprintf(gzFp,"ITEM: TIME\n%.16g\n",compute_time()); - gzprintf(gzFp,"ITEM: TIMESTEP\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",update->ntimestep); - gzprintf(gzFp,"ITEM: NUMBER OF ATOMS\n"); - gzprintf(gzFp,BIGINT_FORMAT "\n",ndump); - if (domain->triclinic == 0) { - gzprintf(gzFp,"ITEM: BOX BOUNDS %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxxlo,boxxhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxylo,boxyhi); - gzprintf(gzFp,"%-1.16e %-1.16e\n",boxzlo,boxzhi); - } else { - gzprintf(gzFp,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxxlo,boxxhi,boxxy); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxylo,boxyhi,boxxz); - gzprintf(gzFp,"%-1.16e %-1.16e %-1.16e\n",boxzlo,boxzhi,boxyz); + if (time_flag) { + header += fmt::format("ITEM: TIME\n{0:.16g}\n", compute_time()); } - gzprintf(gzFp,"ITEM: ATOMS %s\n",columns); + + header += fmt::format("ITEM: TIMESTEP\n{}\n", update->ntimestep); + header += fmt::format("ITEM: NUMBER OF ATOMS\n{}\n", ndump); + if (domain->triclinic == 0) { + header += fmt::format("ITEM: BOX BOUNDS {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxxlo, boxxhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxylo, boxyhi); + header += fmt::format("{0:-1.16e} {1:-1.16e}\n", boxzlo, boxzhi); + } else { + header += fmt::format("ITEM: BOX BOUNDS xy xz yz {}\n", boundstr); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxxlo, boxxhi, boxxy); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxylo, boxyhi, boxxz); + header += fmt::format("{0:-1.16e} {1:-1.16e} {2:-1.16e}\n", boxzlo, boxzhi, boxyz); + } + header += fmt::format("ITEM: ATOMS {}\n", columns); + + writer.write(header.c_str(), header.length()); } } @@ -142,7 +133,7 @@ void DumpCustomGZ::write_header(bigint ndump) void DumpCustomGZ::write_data(int n, double *mybuf) { - gzwrite(gzFp,mybuf,sizeof(char)*n); + writer.write(mybuf, n); } /* ---------------------------------------------------------------------- */ @@ -152,11 +143,11 @@ void DumpCustomGZ::write() DumpCustom::write(); if (filewriter) { if (multifile) { - gzclose(gzFp); - gzFp = nullptr; + writer.close(); } else { - if (flush_flag) - gzflush(gzFp,Z_SYNC_FLUSH); + if (flush_flag && writer.isopen()) { + writer.flush(); + } } } } @@ -167,14 +158,15 @@ int DumpCustomGZ::modify_param(int narg, char **arg) { int consumed = DumpCustom::modify_param(narg, arg); if (consumed == 0) { - if (strcmp(arg[0],"compression_level") == 0) { - if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); - int min_level = Z_DEFAULT_COMPRESSION; - int max_level = Z_BEST_COMPRESSION; - compression_level = utils::inumeric(FLERR, arg[1], false, lmp); - if (compression_level < min_level || compression_level > max_level) - error->all(FLERR, fmt::format("Illegal dump_modify command: compression level must in the range of [{}, {}]", min_level, max_level)); - return 2; + try { + if (strcmp(arg[0],"compression_level") == 0) { + if (narg < 2) error->all(FLERR,"Illegal dump_modify command"); + int compression_level = utils::inumeric(FLERR, arg[1], false, lmp); + writer.setCompressionLevel(compression_level); + return 2; + } + } catch (FileWriterException &e) { + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_custom_gz.h b/src/COMPRESS/dump_custom_gz.h index 184f3563f1..db30b944ec 100644 --- a/src/COMPRESS/dump_custom_gz.h +++ b/src/COMPRESS/dump_custom_gz.h @@ -21,7 +21,7 @@ DumpStyle(custom/gz,DumpCustomGZ) #define LMP_DUMP_CUSTOM_GZ_H #include "dump_custom.h" -#include +#include "gz_file_writer.h" namespace LAMMPS_NS { @@ -31,8 +31,7 @@ class DumpCustomGZ : public DumpCustom { virtual ~DumpCustomGZ(); protected: - int compression_level; - gzFile gzFp; // file pointer for the compressed output stream + GzFileWriter writer; virtual void openfile(); virtual void write_header(bigint); diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index 3aa3f874ea..bd248bd0fc 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -20,7 +20,6 @@ #include "domain.h" #include "dump_custom_zstd.h" #include "error.h" -#include "file_writer.h" #include "update.h" #include @@ -79,7 +78,9 @@ void DumpCustomZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; @@ -184,7 +185,7 @@ int DumpCustomZstd::modify_param(int narg, char **arg) return 2; } } catch (FileWriterException &e) { - error->one(FLERR, e.what()); + error->one(FLERR, fmt::format("Illegal dump_modify command: {}", e.what())); } } return consumed; diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index a0a39b51e0..9b0ac0c344 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -27,7 +27,6 @@ DumpLocalGZ::DumpLocalGZ(LAMMPS *lmp, int narg, char **arg) : error->all(FLERR,"Dump local/gz only writes compressed files"); } - /* ---------------------------------------------------------------------- */ DumpLocalGZ::~DumpLocalGZ() @@ -72,7 +71,9 @@ void DumpLocalGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index a4303f3b25..05cd0bb1ae 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -78,7 +78,9 @@ void DumpLocalZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 5c90c48d0f..0697f19ce3 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -71,7 +71,9 @@ void DumpXYZGZ::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index 03edf561b1..cb75542337 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -78,7 +78,9 @@ void DumpXYZZstd::openfile() nameslist[numfiles] = utils::strdup(filecurrent); ++numfiles; } else { - remove(nameslist[fileidx]); + if (remove(nameslist[fileidx]) != 0) { + error->warning(FLERR, fmt::format("Could not delete {}", nameslist[fileidx])); + } delete[] nameslist[fileidx]; nameslist[fileidx] = utils::strdup(filecurrent); fileidx = (fileidx + 1) % maxfiles; diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index fb70206590..5ad231d440 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -58,6 +58,35 @@ TEST_F(DumpCustomCompressTest, compressed_run1) delete_file(converted_file); } +TEST_F(DumpCustomCompressTest, compressed_with_time_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "with_time_custom_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "time yes", "time yes checksum yes", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "time yes", 1); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); @@ -222,7 +251,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_bad_param) auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_bad_param_run0_*.melt.custom"), fields)); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 compression_level 12"); ); } @@ -234,7 +263,7 @@ TEST_F(DumpCustomCompressTest, compressed_modify_multi_bad_param) auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; command(fmt::format("dump id1 all {} 1 {} {}", compression_style, compressed_dump_filename("modify_multi_bad_param_run0_*.melt.custom"), fields)); - TEST_FAILURE(".*ERROR: Illegal dump_modify command: compression level must in the range of.*", + TEST_FAILURE(".*ERROR on proc 0: Illegal dump_modify command: Compression level must in the range of.*", command("dump_modify id1 pad 3 compression_level 12"); ); } From 234c75550722fa48ceff16456696e71628567124 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 17:08:57 -0400 Subject: [PATCH 054/100] Add missing types in dump local --- src/COMPRESS/dump_local_gz.cpp | 4 ++++ src/COMPRESS/dump_local_zstd.cpp | 4 ++++ src/dump_local.cpp | 8 ++++++++ 3 files changed, 16 insertions(+) diff --git a/src/COMPRESS/dump_local_gz.cpp b/src/COMPRESS/dump_local_gz.cpp index 9b0ac0c344..7ffb8d80ff 100644 --- a/src/COMPRESS/dump_local_gz.cpp +++ b/src/COMPRESS/dump_local_gz.cpp @@ -144,6 +144,10 @@ void DumpLocalGZ::write_data(int n, double *mybuf) int written = 0; if (vtype[j] == Dump::INT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } else { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); } diff --git a/src/COMPRESS/dump_local_zstd.cpp b/src/COMPRESS/dump_local_zstd.cpp index 05cd0bb1ae..4d7fe9361b 100644 --- a/src/COMPRESS/dump_local_zstd.cpp +++ b/src/COMPRESS/dump_local_zstd.cpp @@ -155,6 +155,10 @@ void DumpLocalZstd::write_data(int n, double *mybuf) int written = 0; if (vtype[j] == Dump::INT) { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); } else { written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); } diff --git a/src/dump_local.cpp b/src/dump_local.cpp index dac8066236..0f8d139f66 100644 --- a/src/dump_local.cpp +++ b/src/dump_local.cpp @@ -179,6 +179,8 @@ void DumpLocal::init_style() vformat[i] = utils::strdup(std::string(format_int_user) + " "); else if (vtype[i] == Dump::DOUBLE && format_float_user) vformat[i] = utils::strdup(std::string(format_float_user) + " "); + else if (vtype[i] == Dump::BIGINT && format_bigint_user) + vformat[i] = utils::strdup(std::string(format_bigint_user) + " "); else vformat[i] = utils::strdup(word + " "); ++i; } @@ -375,6 +377,10 @@ int DumpLocal::convert_string(int n, double *mybuf) for (j = 0; j < size_one; j++) { if (vtype[j] == Dump::INT) offset += sprintf(&sbuf[offset],vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) + offset += sprintf(&sbuf[offset],vformat[j],static_cast (mybuf[m])); else offset += sprintf(&sbuf[offset],vformat[j],mybuf[m]); m++; @@ -409,6 +415,8 @@ void DumpLocal::write_lines(int n, double *mybuf) for (i = 0; i < n; i++) { for (j = 0; j < size_one; j++) { if (vtype[j] == Dump::INT) fprintf(fp,vformat[j],static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) fprintf(fp,vformat[j],mybuf[m]); + else if (vtype[j] == Dump::BIGINT) fprintf(fp,vformat[j],static_cast(mybuf[m])); else fprintf(fp,vformat[j],mybuf[m]); m++; } From 242881af55578f6ca137865241415d3ba45a787b Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 17:45:45 -0400 Subject: [PATCH 055/100] Make dump custom/gz, custom/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_custom_gz.cpp | 30 ++++++++++++++++++- src/COMPRESS/dump_custom_zstd.cpp | 30 ++++++++++++++++++- .../formats/test_dump_custom_compressed.cpp | 29 ++++++++++++++++++ 3 files changed, 87 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_custom_gz.cpp b/src/COMPRESS/dump_custom_gz.cpp index 5cecf22b5d..9a3fc39d0a 100644 --- a/src/COMPRESS/dump_custom_gz.cpp +++ b/src/COMPRESS/dump_custom_gz.cpp @@ -133,7 +133,35 @@ void DumpCustomGZ::write_header(bigint ndump) void DumpCustomGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < nfield; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::STRING) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump custom/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_custom_zstd.cpp b/src/COMPRESS/dump_custom_zstd.cpp index bd248bd0fc..b3f0971bf5 100644 --- a/src/COMPRESS/dump_custom_zstd.cpp +++ b/src/COMPRESS/dump_custom_zstd.cpp @@ -146,7 +146,35 @@ void DumpCustomZstd::write_header(bigint ndump) void DumpCustomZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < nfield; j++) { + int written = 0; + if (vtype[j] == Dump::INT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } else if (vtype[j] == Dump::DOUBLE) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + } else if (vtype[j] == Dump::STRING) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + } else if (vtype[j] == Dump::BIGINT) { + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump custom/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_custom_compressed.cpp b/unittest/formats/test_dump_custom_compressed.cpp index 5ad231d440..cb45c1b837 100644 --- a/unittest/formats/test_dump_custom_compressed.cpp +++ b/unittest/formats/test_dump_custom_compressed.cpp @@ -87,6 +87,35 @@ TEST_F(DumpCustomCompressTest, compressed_with_time_run1) delete_file(converted_file); } +TEST_F(DumpCustomCompressTest, compressed_no_buffer_run1) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_custom_run1.melt"; + auto text_file = text_dump_filename(base_name); + auto compressed_file = compressed_dump_filename(base_name); + auto fields = "id type proc x y z ix iy iz xs ys zs xu yu zu xsu ysu zsu vx vy vz fx fy fz"; + + if(compression_style == "custom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, fields, fields, "buffer no", "buffer no checksum yes", 1); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, fields, "buffer no", 1); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpCustomCompressTest, compressed_triclinic_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From e5ee210f58a380b605a94f2539a67f34ecfe4807 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Fri, 9 Apr 2021 18:02:55 -0400 Subject: [PATCH 056/100] Make dump atom/gz, atom/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_atom_gz.cpp | 28 ++++++++++++++++++- src/COMPRESS/dump_atom_zstd.cpp | 28 ++++++++++++++++++- .../formats/test_dump_atom_compressed.cpp | 28 +++++++++++++++++++ 3 files changed, 82 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_atom_gz.cpp b/src/COMPRESS/dump_atom_gz.cpp index b3b202e373..7b54fd8e62 100644 --- a/src/COMPRESS/dump_atom_gz.cpp +++ b/src/COMPRESS/dump_atom_gz.cpp @@ -135,7 +135,33 @@ void DumpAtomGZ::write_header(bigint ndump) void DumpAtomGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = 0; + if (image_flag == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast (mybuf[m+5]), + static_cast (mybuf[m+6]), static_cast (mybuf[m+7])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump atom/gz output"); + } + + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_atom_zstd.cpp b/src/COMPRESS/dump_atom_zstd.cpp index f739a53322..b53ebb2269 100644 --- a/src/COMPRESS/dump_atom_zstd.cpp +++ b/src/COMPRESS/dump_atom_zstd.cpp @@ -143,7 +143,33 @@ void DumpAtomZstd::write_header(bigint ndump) void DumpAtomZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag == 1) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = 0; + if (image_flag == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4], static_cast (mybuf[m+5]), + static_cast (mybuf[m+6]), static_cast (mybuf[m+7])); + } else { + written = snprintf(vbuffer, VBUFFER_SIZE, format, + static_cast (mybuf[m]), static_cast (mybuf[m+1]), + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump atom/gz output"); + } + + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_atom_compressed.cpp b/unittest/formats/test_dump_atom_compressed.cpp index da68acee2a..aeb747004e 100644 --- a/unittest/formats/test_dump_atom_compressed.cpp +++ b/unittest/formats/test_dump_atom_compressed.cpp @@ -61,6 +61,34 @@ TEST_F(DumpAtomCompressTest, compressed_run0) delete_file(converted_file); } +TEST_F(DumpAtomCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto text_file = text_dump_filename("no_buffer_run0.melt"); + auto compressed_file = compressed_dump_filename("no_buffer_run0.melt"); + + if(compression_style == "atom/zstd") { + generate_text_and_compressed_dump(text_file, compressed_file, "", "", "buffer no", "buffer no checksum yes", 0); + } else { + generate_text_and_compressed_dump(text_file, compressed_file, "", "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file); + ASSERT_FILE_EXISTS(compressed_file); + + auto converted_file = convert_compressed_to_text(compressed_file); + + ASSERT_THAT(converted_file, Eq(converted_dump_filename("no_buffer_run0.melt"))); + ASSERT_FILE_EXISTS(converted_file); + ASSERT_FILE_EQUAL(text_file, converted_file); + delete_file(text_file); + delete_file(compressed_file); + delete_file(converted_file); +} + TEST_F(DumpAtomCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From 39a00e2901019e37d8bb3d50ffdbeedc9ed224f6 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 06:03:46 -0400 Subject: [PATCH 057/100] reformat --- doc/src/fix_qeq.rst | 125 ++++++++++++++++++++++++-------------------- 1 file changed, 67 insertions(+), 58 deletions(-) diff --git a/doc/src/fix_qeq.rst b/doc/src/fix_qeq.rst index 56fde059e8..c655076ce8 100644 --- a/doc/src/fix_qeq.rst +++ b/doc/src/fix_qeq.rst @@ -56,27 +56,28 @@ Examples Description """"""""""" -Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) ` (also known -as the matrix inversion method) and in :ref:`(Rick and Stuart) ` (also -known as the extended Lagrangian method) based on the -electronegativity equilization principle. +Perform the charge equilibration (QEq) method as described in +:ref:`(Rappe and Goddard) ` and formulated in :ref:`(Nakano) +` (also known as the matrix inversion method) and in +:ref:`(Rick and Stuart) ` (also known as the extended Lagrangian +method) based on the electronegativity equilization principle. These fixes can be used with any :doc:`pair style ` in LAMMPS, so long as per-atom charges are defined. The most typical use-case is in conjunction with a :doc:`pair style ` that performs charge equilibration periodically (e.g. every timestep), such -as the ReaxFF or Streitz-Mintmire potential. -But these fixes can also be used with -potentials that normally assume per-atom charges are fixed, e.g. a -:doc:`Buckingham ` or :doc:`LJ/Coulombic ` potential. +as the ReaxFF or Streitz-Mintmire potential. But these fixes can also +be used with potentials that normally assume per-atom charges are fixed, +e.g. a :doc:`Buckingham ` or :doc:`LJ/Coulombic ` +potential. -Because the charge equilibration calculation is effectively -independent of the pair style, these fixes can also be used to perform -a one-time assignment of charges to atoms. For example, you could -define the QEq fix, perform a zero-timestep run via the :doc:`run ` -command without any pair style defined which would set per-atom -charges (based on the current atom configuration), then remove the fix -via the :doc:`unfix ` command before performing further dynamics. +Because the charge equilibration calculation is effectively independent +of the pair style, these fixes can also be used to perform a one-time +assignment of charges to atoms. For example, you could define the QEq +fix, perform a zero-timestep run via the :doc:`run ` command +without any pair style defined which would set per-atom charges (based +on the current atom configuration), then remove the fix via the +:doc:`unfix ` command before performing further dynamics. .. note:: @@ -87,11 +88,14 @@ via the :doc:`unfix ` command before performing further dynamics. .. note:: - The :doc:`fix qeq/comb ` command must still be used - to perform charge equilibration with the :doc:`COMB potential `. The :doc:`fix qeq/reax ` - command can be used to perform charge equilibration with the :doc:`ReaxFF force field `, although fix qeq/shielded yields the - same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* - are the same. Eventually the fix qeq/reax command will be deprecated. + The :doc:`fix qeq/comb ` command must still be used to + perform charge equilibration with the :doc:`COMB potential + `. The :doc:`fix qeq/reax ` command can be + used to perform charge equilibration with the :doc:`ReaxFF force + field `, although fix qeq/shielded yields the same + results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance* + are the same. Eventually the fix qeq/reax command will be + deprecated. The QEq method minimizes the electrostatic energy of the system (or equalizes the derivative of energy with respect to charge of all the @@ -134,55 +138,57 @@ usually a good number. The *qeq/shielded* style describes partial charges on atoms also as point charges, but uses a shielded Coulomb potential to describe the interaction between a pair of charged particles. Interaction through -the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field ` paper. The shielding accounts for charge overlap +the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force +field ` paper. The shielding accounts for charge overlap between charged particles at small separation. This style is the same -as :doc:`fix qeq/reax `, and can be used with :doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and *gamma* -parameters from the *qfile* file are used. When using the string -*reax/c* as filename, these parameters are extracted directly from -an active *reax/c* pair style. This style solves partial -charges on atoms via the matrix inversion method. A tolerance of -1.0e-6 is usually a good number. +as :doc:`fix qeq/reax `, and can be used with +:doc:`pair_style reax/c `. Only the *chi*\ , *eta*\ , and +*gamma* parameters from the *qfile* file are used. When using the string +*reax/c* as filename, these parameters are extracted directly from an +active *reax/c* pair style. This style solves partial charges on atoms +via the matrix inversion method. A tolerance of 1.0e-6 is usually a +good number. The *qeq/slater* style describes partial charges on atoms as spherical charge densities centered around atoms via the Slater 1\ *s* orbital, so -that the interaction between a pair of charged particles is the -product of two Slater 1\ *s* orbitals. The expression for the Slater -1\ *s* orbital is given under equation (6) of the -:ref:`Streitz-Mintmire ` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and -*qcore* parameters from the *qfile* file are used. When using the string +that the interaction between a pair of charged particles is the product +of two Slater 1\ *s* orbitals. The expression for the Slater 1\ *s* +orbital is given under equation (6) of the :ref:`Streitz-Mintmire +` paper. Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore* +parameters from the *qfile* file are used. When using the string *coul/streitz* as filename, these parameters are extracted directly from -an active *coul/streitz* pair style. This style solves -partial charges on atoms via the matrix inversion method. A tolerance -of 1.0e-6 is usually a good number. Keyword *alpha* can be used to -change the Slater type orbital exponent. +an active *coul/streitz* pair style. This style solves partial charges +on atoms via the matrix inversion method. A tolerance of 1.0e-6 is +usually a good number. Keyword *alpha* can be used to change the Slater +type orbital exponent. The *qeq/dynamic* style describes partial charges on atoms as point -charges that interact through 1/r, but the extended Lagrangian method -is used to solve partial charges on atoms. Only the *chi* and *eta* +charges that interact through 1/r, but the extended Lagrangian method is +used to solve partial charges on atoms. Only the *chi* and *eta* parameters from the *qfile* file are used. Note that Coulomb -catastrophe can occur if repulsion between the pair of charged -particles is too weak. A tolerance of 1.0e-3 is usually a good -number. Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +catastrophe can occur if repulsion between the pair of charged particles +is too weak. A tolerance of 1.0e-3 is usually a good number. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. -The :ref:`\ *qeq/fire*\ ` style describes the same charge model and charge -solver as the *qeq/dynamic* style, but employs a FIRE minimization -algorithm to solve for equilibrium charges. -Keyword *qdamp* can be used to change the damping factor, while -keyword *qstep* can be used to change the time step size. +The :ref:`\ *qeq/fire*\ ` style describes the same charge model +and charge solver as the *qeq/dynamic* style, but employs a FIRE +minimization algorithm to solve for equilibrium charges. Keyword +*qdamp* can be used to change the damping factor, while keyword *qstep* +can be used to change the time step size. Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe different charge models, whereas the matrix inversion method and the extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are different solvers. -Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe -charges as point charges that interact through 1/r relationship, but -solve partial charges on atoms using different solvers. These three -styles should yield comparable results if -the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the -same. Style *qeq/point* is typically faster, *qeq/dynamic* scales -better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . +Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all +describe charges as point charges that interact through 1/r +relationship, but solve partial charges on atoms using different +solvers. These three styles should yield comparable results if the QEq +parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same. +Style *qeq/point* is typically faster, *qeq/dynamic* scales better on +larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . .. note:: @@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ . Restart, fix_modify, output, run start/stop, minimize info """"""""""""""""""""""""""""""""""""""""""""""""""""""""""" -No information about these fixes is written to :doc:`binary restart files `. No global scalar or vector or per-atom -quantities are stored by these fixes for access by various :doc:`output commands `. No parameter of these fixes can be used -with the *start/stop* keywords of the :doc:`run ` command. +No information about these fixes is written to :doc:`binary restart +files `. No global scalar or vector or per-atom quantities are +stored by these fixes for access by various :doc:`output commands +`. No parameter of these fixes can be used with the +*start/stop* keywords of the :doc:`run ` command. Thexe fixes are invoked during :doc:`energy minimization `. @@ -210,7 +218,8 @@ Restrictions """""""""""" These fixes are part of the QEQ package. They are only enabled if -LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. +LAMMPS was built with that package. See the :doc:`Build package +` doc page for more info. Related commands """""""""""""""" From e1418a341a6cc0f196ae958807160e250229b5c9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 06:05:41 -0400 Subject: [PATCH 058/100] ensure that only one of comb/comb3 is matched and called --- src/MANYBODY/fix_qeq_comb.cpp | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) diff --git a/src/MANYBODY/fix_qeq_comb.cpp b/src/MANYBODY/fix_qeq_comb.cpp index 910db90822..7c23e6c218 100644 --- a/src/MANYBODY/fix_qeq_comb.cpp +++ b/src/MANYBODY/fix_qeq_comb.cpp @@ -17,21 +17,21 @@ #include "fix_qeq_comb.h" -#include -#include -#include "pair_comb.h" -#include "pair_comb3.h" -#include "neigh_list.h" #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" #include "group.h" +#include "memory.h" +#include "neigh_list.h" #include "respa.h" #include "update.h" -#include "memory.h" -#include "error.h" +#include +#include +#include "pair_comb.h" +#include "pair_comb3.h" using namespace LAMMPS_NS; using namespace FixConst; @@ -85,9 +85,6 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), int nlocal = atom->nlocal; for (int i = 0; i < nlocal; i++) qf[i] = 0.0; - comb = nullptr; - comb3 = nullptr; - comm_forward = 1; } @@ -119,8 +116,9 @@ void FixQEQComb::init() if (!atom->q_flag) error->all(FLERR,"Fix qeq/comb requires atom attribute q"); - comb = (PairComb *) force->pair_match("^comb",0); comb3 = (PairComb3 *) force->pair_match("^comb3",0); + if (!comb3) comb = (PairComb *) force->pair_match("^comb",0); + if (comb == nullptr && comb3 == nullptr) error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb"); @@ -204,14 +202,17 @@ void FixQEQComb::post_force(int /*vflag*/) double *q = atom->q; int *mask = atom->mask; - if (comb) { + if (comb) { inum = comb->list->inum; ilist = comb->list->ilist; - } - if (comb3) { + } else if (comb3) { inum = comb3->list->inum; ilist = comb3->list->ilist; + } else { + inum = 0; + ilist = nullptr; } + for (ii = 0; ii < inum; ii++) { i = ilist[ii]; q1[i] = q2[i] = qf[i] = 0.0; @@ -227,8 +228,9 @@ void FixQEQComb::post_force(int /*vflag*/) } comm->forward_comm_fix(this); + enegtot = 0.0; if (comb) enegtot = comb->yasu_char(qf,igroup); - if (comb3) enegtot = comb3->combqeq(qf,igroup); + else if (comb3) enegtot = comb3->combqeq(qf,igroup); enegtot /= ngroup; enegchk = enegmax = 0.0; From bb0be962a91702abcd57b24651c898f60724555e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 16:44:46 -0400 Subject: [PATCH 059/100] eliminate use of s(n)printf() in QEQ package --- src/QEQ/fix_qeq.cpp | 30 ++++++++++++--------------- src/QEQ/fix_qeq_dynamic.cpp | 27 ++++++++++--------------- src/QEQ/fix_qeq_fire.cpp | 39 ++++++++++++++---------------------- src/QEQ/fix_qeq_point.cpp | 28 ++++++++++++-------------- src/QEQ/fix_qeq_shielded.cpp | 32 ++++++++++++++--------------- src/QEQ/fix_qeq_slater.cpp | 30 ++++++++++++--------------- 6 files changed, 80 insertions(+), 106 deletions(-) diff --git a/src/QEQ/fix_qeq.cpp b/src/QEQ/fix_qeq.cpp index a63e008b36..e592ed2af4 100644 --- a/src/QEQ/fix_qeq.cpp +++ b/src/QEQ/fix_qeq.cpp @@ -18,16 +18,16 @@ #include "fix_qeq.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neigh_list.h" -#include "update.h" +#include "error.h" #include "force.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "update.h" +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -386,13 +386,11 @@ int FixQEq::CG( double *b, double *x ) vector_sum( d, 1., p, beta, d, inum ); } - if (loop >= maxiter && comm->me == 0) { - char str[128]; - sprintf(str,"Fix qeq CG convergence failed (%g) after %d iterations " - "at " BIGINT_FORMAT " step",sqrt(sig_new)/b_norm,loop,update->ntimestep); - error->warning(FLERR,str); - } - + if ((comm->me == 0) && (loop >= maxiter)) + error->warning(FLERR,fmt::format("Fix qeq CG convergence failed ({}) " + "after {} iterations at step {}", + sqrt(sig_new)/b_norm,loop, + update->ntimestep)); return loop; } @@ -708,11 +706,9 @@ void FixQEq::read_file(char *file) FILE *fp; if (comm->me == 0) { fp = utils::open_potential(file,lmp,nullptr); - if (fp == nullptr) { - char str[128]; - snprintf(str,128,"Cannot open fix qeq parameter file %s",file); - error->one(FLERR,str); - } + if (fp == nullptr) + error->one(FLERR,fmt::format("Cannot open fix qeq parameter file {}: {}", + file,utils::getsyserror())); } // read each line out of file, skipping blank lines or leading '#' diff --git a/src/QEQ/fix_qeq_dynamic.cpp b/src/QEQ/fix_qeq_dynamic.cpp index b06bde223b..397393b786 100644 --- a/src/QEQ/fix_qeq_dynamic.cpp +++ b/src/QEQ/fix_qeq_dynamic.cpp @@ -17,20 +17,20 @@ #include "fix_qeq_dynamic.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" #include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "respa.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -154,14 +154,9 @@ void FixQEqDynamic::pre_force(int /*vflag*/) } } - if (comm->me == 0) { - if (iloop == maxiter) { - char str[128]; - sprintf(str,"Charges did not converge at step " BIGINT_FORMAT - ": %lg",update->ntimestep,enegchk); - error->warning(FLERR,str); - } - } + if ((comm->me == 0) && (iloop >= maxiter)) + error->warning(FLERR,fmt::format("Charges did not converge at step " + "{}: {}",update->ntimestep,enegchk)); if (force->kspace) force->kspace->qsum_qsq(); } diff --git a/src/QEQ/fix_qeq_fire.cpp b/src/QEQ/fix_qeq_fire.cpp index b33a7745e0..0bdf65dc18 100644 --- a/src/QEQ/fix_qeq_fire.cpp +++ b/src/QEQ/fix_qeq_fire.cpp @@ -17,22 +17,22 @@ #include "fix_qeq_fire.h" -#include - -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" +#include "kspace.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" #include "pair_comb.h" #include "pair_comb3.h" -#include "kspace.h" #include "respa.h" -#include "error.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace FixConst; @@ -47,7 +47,7 @@ using namespace FixConst; /* ---------------------------------------------------------------------- */ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : - FixQEq(lmp, narg, arg) + FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr) { qdamp = 0.20; qstep = 0.20; @@ -65,9 +65,6 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) : iarg += 2; } else error->all(FLERR,"Illegal fix qeq/fire command"); } - - comb = nullptr; - comb3 = nullptr; } /* ---------------------------------------------------------------------- */ @@ -94,9 +91,8 @@ void FixQEqFire::init() if (utils::strmatch(update->integrate_style,"^respa")) nlevels_respa = ((Respa *) update->integrate)->nlevels; - comb = (PairComb *) force->pair_match("comb",1); - comb3 = (PairComb3 *) force->pair_match("comb3",1); - + comb3 = (PairComb3 *) force->pair_match("^comb3",0); + if (!comb3) comb = (PairComb *) force->pair_match("^comb",0); } /* ---------------------------------------------------------------------- */ @@ -218,14 +214,9 @@ void FixQEqFire::pre_force(int /*vflag*/) if (enegchk < tolerance) break; } - if (comm->me == 0) { - if (iloop == maxiter) { - char str[128]; - sprintf(str,"Charges did not converge at step " BIGINT_FORMAT - ": %lg",update->ntimestep,enegchk); - error->warning(FLERR,str); - } - } + if ((comm->me == 0) && (iloop >= maxiter)) + error->warning(FLERR,fmt::format("Charges did not converge at step " + "{}: {}",update->ntimestep,enegchk)); if (force->kspace) force->kspace->qsum_qsq(); } diff --git a/src/QEQ/fix_qeq_point.cpp b/src/QEQ/fix_qeq_point.cpp index 3d71135ae1..ac31f906e0 100644 --- a/src/QEQ/fix_qeq_point.cpp +++ b/src/QEQ/fix_qeq_point.cpp @@ -16,20 +16,22 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_point.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" #include "kspace.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -158,13 +160,9 @@ void FixQEqPoint::compute_H() } } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/point has insufficient QEq matrix size"); - } + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/point has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill, H.m)); } /* ---------------------------------------------------------------------- */ diff --git a/src/QEQ/fix_qeq_shielded.cpp b/src/QEQ/fix_qeq_shielded.cpp index 356a747ed3..ad6202abd8 100644 --- a/src/QEQ/fix_qeq_shielded.cpp +++ b/src/QEQ/fix_qeq_shielded.cpp @@ -16,21 +16,23 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_shielded.h" -#include -#include + #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" -#include "respa.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; @@ -223,13 +225,9 @@ void FixQEqShielded::compute_H() } } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/shielded has insufficient QEq matrix size"); - } + if (m_fill >= H.m) + error->all(FLERR,fmt::format("Fix qeq/shielded has insufficient H matrix " + "size: m_fill={} H.m={}\n",m_fill,H.m)); } /* ---------------------------------------------------------------------- */ @@ -247,7 +245,7 @@ double FixQEqShielded::calculate_H( double r, double gamma ) Taper = Taper * r + Tap[0]; denom = r * r * r + gamma; - denom = pow(denom,0.3333333333333); + denom = pow(denom,1.0/3.0); return Taper * EV_TO_KCAL_PER_MOL / denom; } diff --git a/src/QEQ/fix_qeq_slater.cpp b/src/QEQ/fix_qeq_slater.cpp index 9b90f78d7a..326d71c93b 100644 --- a/src/QEQ/fix_qeq_slater.cpp +++ b/src/QEQ/fix_qeq_slater.cpp @@ -16,22 +16,23 @@ ------------------------------------------------------------------------- */ #include "fix_qeq_slater.h" -#include -#include #include "atom.h" #include "comm.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" +#include "error.h" #include "force.h" #include "group.h" -#include "pair.h" #include "kspace.h" -#include "respa.h" #include "math_const.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "pair.h" +#include "respa.h" +#include "update.h" + +#include +#include using namespace LAMMPS_NS; using namespace MathConst; @@ -207,14 +208,9 @@ void FixQEqSlater::compute_H() chizj[i] = zjtmp; } - if (m_fill >= H.m) { - char str[128]; - sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n", - m_fill, H.m ); - error->warning(FLERR,str); - error->all(FLERR,"Fix qeq/slater has insufficient QEq matrix size"); - } - + if (m_fill >= H.m) + error->all(FLERR,fmt::format(FLERR,"Fix qeq/slater has insufficient H " + "matrix size:m_fill={} H.m={}\n",m_fill,H.m)); } /* ---------------------------------------------------------------------- */ From 38d5798223a6946e688749b2d3dabe13810f659b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Sun, 11 Apr 2021 21:36:18 -0400 Subject: [PATCH 060/100] must not look for package metadata when using python module from source tree --- python/lammps/__init__.py | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index e6ffd779a9..93c46819c0 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -13,10 +13,16 @@ from .core import * from .data import * from .pylammps import * -# convert module string version to numeric version +# convert installed module string version to numeric version def get_version_number(): import time + from os.path import join from sys import version_info + + # must report 0 when inside LAMMPS source tree + if __file__.find(join('python', 'lammps', '__init__.py')) > 0: + return 0 + vstring = None if version_info.major == 3 and version_info.minor >= 8: from importlib.metadata import version From d81f03706cb8783020c990f6701933036c05e16f Mon Sep 17 00:00:00 2001 From: tc387 Date: Mon, 12 Apr 2021 01:30:36 -0500 Subject: [PATCH 061/100] Added an example using real units. --- .../charge_regulation/data.chreg-acid-real | 235 ++++++++++++++++++ .../misc/charge_regulation/in.chreg-acid-real | 44 ++++ .../log.11Apr21.chreg-acid-real.g++.1 | 145 +++++++++++ .../log.11Apr21.chreg-acid-real.g++.4 | 145 +++++++++++ 4 files changed, 569 insertions(+) create mode 100644 examples/USER/misc/charge_regulation/data.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/in.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid-real b/examples/USER/misc/charge_regulation/data.chreg-acid-real new file mode 100644 index 0000000000..1f005a155b --- /dev/null +++ b/examples/USER/misc/charge_regulation/data.chreg-acid-real @@ -0,0 +1,235 @@ +LAMMPS data file generated by get_input.py + +219 atoms +3 atom types +-180 180 xlo xhi +-180 180 ylo yhi +-180 180 zlo zhi + +Masses + +1 20 +2 20 +3 20 + +Atoms + +1 1 0 18.70795854 -60.24998141 144.0092784 +2 1 -1 -130.9166548 -58.17450505 59.42690807 +3 1 -1 -125.5489258 58.46696329 77.38308245 +4 1 -1 46.8178314 -169.1807517 143.6272062 +5 1 -1 -162.2028908 -135.2407217 -129.3455357 +6 1 -1 -69.93717134 136.6009615 -140.3684699 +7 1 -1 -92.39022725 0.88313303 -156.091658 +8 1 -1 150.5452585 -15.59052452 3.326246397 +9 1 -1 171.8072626 172.9794849 75.84528386 +10 1 -1 -3.808294794 171.5056017 -19.13183671 +11 1 -1 68.90552852 86.21187482 24.628687 +12 1 -1 -73.4512319 54.41387468 86.90435812 +13 1 -1 35.26889793 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-29.14739431 94.50860741 -51.527097 +122 2 1 -145.9322739 154.5384232 112.3421798 +123 2 1 -32.24342538 -22.90490626 -133.4101075 +124 2 1 155.0953371 97.30799449 -13.02231424 +125 2 1 -109.6079033 -42.89844953 -51.80376701 +126 2 1 -150.2770445 -55.20818421 147.7312972 +127 2 1 -26.96028917 151.3053234 51.82429115 +128 2 1 -42.51040448 55.12547194 -10.01649745 +129 2 1 -154.7332138 -166.4922488 75.56066422 +130 2 1 179.3252381 50.98353603 -103.842222 +131 2 1 -87.64561442 -167.4026399 -37.04977996 +132 2 1 -141.7543098 32.23109989 44.99445113 +133 2 1 121.3596596 -6.092779973 129.6856923 +134 2 1 124.4836766 -86.35531223 85.50625099 +135 2 1 140.6305506 -165.9843021 -35.3966949 +136 2 1 -89.51258901 36.2123163 54.25434215 +137 2 1 107.5306105 58.22419926 141.7457531 +138 2 1 -51.03564423 -166.277591 119.3103596 +139 2 1 106.3738063 153.673561 100.7747233 +140 2 1 -105.1662471 -49.88388187 -163.5658795 +141 2 1 -123.4063552 104.6405545 -157.1806703 +142 2 1 30.68517662 111.7365757 -128.0988407 +143 2 1 -70.66650991 -36.87088431 101.1920697 +144 2 1 59.85584345 28.56015074 -148.8751279 +145 2 1 76.34296857 -18.88899045 11.99663247 +146 2 1 -127.898772 9.029786744 -155.2067979 +147 2 1 -61.47407783 106.6906337 -32.24644961 +148 2 1 -41.82882356 105.2048819 95.67134776 +149 2 1 64.70518204 -125.5606981 -130.2221179 +150 2 1 -95.86998176 64.01110464 -62.69889224 +151 2 1 -3.893149866 -170.4938796 -173.9425756 +152 2 1 -142.5571999 -115.9852755 -42.33527796 +153 2 1 -170.1094774 67.22933296 -69.41406448 +154 2 1 -135.7002446 -117.3853245 -77.66219554 +155 2 1 97.68794466 -176.3481416 64.0577303 +156 2 1 98.30084322 -179.1048324 157.6098802 +157 2 1 -61.74657154 71.45180441 36.21267022 +158 2 1 148.9924395 8.130617629 2.580809806 +159 2 1 -7.179797893 131.8852645 48.92705878 +160 2 1 166.7210737 111.3028256 122.5151765 +161 2 1 160.4061661 105.4292149 147.9164951 +162 2 1 70.35573238 -156.217711 -37.86968306 +163 2 1 37.82167168 128.9612675 113.5371453 +164 2 1 -149.4650805 40.2544478 -89.16446826 +165 2 1 23.15794976 -35.62998186 -128.5225995 +166 2 1 148.5909499 65.59167763 44.47571026 +167 2 1 38.20567747 91.06090259 167.2556933 +168 2 1 -173.8935359 124.3001041 -123.4154022 +169 2 1 -113.0780192 -112.7185827 -75.51909042 +170 2 1 -47.52814398 -162.0232543 -40.84518679 +171 2 1 164.6580923 96.26106544 -67.52475023 +172 2 1 -166.687599 -28.28821753 -80.04284273 +173 2 1 9.786487166 -133.5748603 -110.4924395 +174 2 1 73.69685916 -130.6229707 -12.1566579 +175 2 1 90.69039384 -12.53964183 -156.8650452 +176 2 1 -1.065055548 123.2458955 9.207883208 +177 2 1 175.3144942 -62.38332615 89.50309521 +178 2 1 -135.5554643 -135.3786299 -12.22599884 +179 2 1 -65.15130962 -12.87802388 -85.25728639 +180 2 1 -161.9760397 -159.2069523 72.10033228 +181 2 1 -116.5200037 9.430944126 5.8294178 +182 2 1 -28.85454266 -176.0245493 -141.7245957 +183 2 1 63.2968571 -114.4145268 -168.891953 +184 2 1 -61.61686575 -158.2947391 162.9099557 +185 2 1 51.43661765 119.3411567 4.253266919 +186 2 1 50.78017633 47.93871152 129.5527454 +187 2 1 151.0842128 -27.15258927 -161.0800505 +188 2 1 -63.76595621 -118.2333675 -55.31381078 +189 2 1 -103.5498203 -55.20725862 -73.28180307 +190 2 1 -165.1300235 72.52455317 27.04945294 +191 2 1 68.10471264 124.0704131 -0.252243467 +192 2 1 79.29794618 142.8637277 -42.01908928 +193 2 1 167.6806551 20.41616629 -147.6924841 +194 2 1 -135.8036012 64.48710622 102.1923975 +195 2 1 98.55703781 -115.0070794 78.85760695 +196 2 1 15.16187488 19.73322691 -170.7866955 +197 2 1 151.0729333 50.92372407 -173.3272023 +198 2 1 42.92899709 -139.8564977 161.7836767 +199 2 1 -123.3797296 144.2768906 93.18435951 +200 2 1 83.46684339 160.4439871 16.84583748 +201 2 1 -9.982765467 138.2373541 -55.3263136 +202 2 1 -161.6023131 -141.5797686 -64.66795638 +203 2 1 2.63144963 -54.92560391 117.5540027 +204 2 1 -70.31638318 175.5673808 -103.3383852 +205 2 1 -4.543770763 -40.50287551 98.39515078 +206 2 1 19.2926167 -2.671035153 112.1413205 +207 2 1 76.93260202 177.3949067 -126.2787212 +208 2 1 131.8183006 132.4167597 131.6586696 +209 2 1 -82.9844547 -85.47123292 92.81285561 +210 3 -1 115.4743016 -5.981969165 65.81311346 +211 3 -1 -86.91538943 171.1823129 -45.00079 +212 3 -1 174.0893311 141.4009485 159.8631805 +213 3 -1 164.8739505 64.21237704 -8.113691614 +214 3 -1 -75.49748308 40.97887837 158.0779944 +215 3 -1 45.16399203 72.25791157 159.9861897 +216 3 -1 105.7676225 -56.05853127 3.624467826 +217 3 -1 166.8523536 -151.4993186 -151.6124408 +218 3 -1 -43.30886503 46.05330597 155.3934201 +219 3 -1 -5.592027058 2.85325065 11.39381158 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER/misc/charge_regulation/in.chreg-acid-real new file mode 100644 index 0000000000..195b163d96 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in.chreg-acid-real @@ -0,0 +1,44 @@ +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} + +variable cut_long equal 12.5*${sigma} +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +velocity all create ${temperature} 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_coeff * * ${epsilon} ${sigma} +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +run 2000 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 new file mode 100644 index 0000000000..3b766d662d --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 @@ -0,0 +1,145 @@ +LAMMPS (10 Feb 2021) +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real +Reading data file ... + orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.002 seconds + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable epsilon equal 0.0019872067*${temperature} +variable epsilon equal 0.0019872067*298 +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} +variable timestep equal 0.005*2000 + +variable cut_long equal 12.5*${sigma} +variable cut_long equal 12.5*7.2 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +variable cut_lj equal 2^(1.0/6.0)*7.2 +velocity all create ${temperature} 8008 loop geom +velocity all create 298 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 90 +pair_coeff * * ${epsilon} ${sigma} +pair_coeff * * 0.5921875966 ${sigma} +pair_coeff * * 0.5921875966 7.2 +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 298 $(v_tunit) 123 +fix fT all langevin 298 298 2000 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +timestep 10 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.019408615 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00012527706 + estimated relative force accuracy = 3.7726815e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 2197 512 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 93 + ghost atom cutoff = 93 + binsize = 46.5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -6.4798431 298 0 0 1 99 0 0 109 10 + 100 -6.9219668 306.44177 100 77 15 85 0 0 94 9 + 200 -6.8175255 306.64254 200 164 23 77 0 0 87 10 + 300 -5.2482381 331.67831 300 248 21 79 0 0 85 6 + 400 -7.4531538 285.3495 400 326 17 83 0 0 89 6 + 500 -6.9662528 286.2123 500 408 14 86 0 0 95 9 + 600 -6.528214 291.41762 600 492 14 86 0 0 95 9 + 700 -6.290871 271.50948 700 567 14 86 0 0 96 10 + 800 -6.4944741 300.66261 800 650 23 77 0 0 83 6 + 900 -8.0414672 305.6179 900 731 25 75 0 0 84 9 + 1000 -8.5694583 297.69733 1000 810 25 75 0 0 83 8 + 1100 -8.9364878 292.52429 1100 891 22 78 0 0 88 10 + 1200 -8.733737 316.79814 1200 963 21 79 0 0 88 9 + 1300 -8.0946506 350.85016 1300 1043 21 79 0 0 88 9 + 1400 -7.1835794 283.90836 1400 1128 17 83 0 0 93 10 + 1500 -6.5673667 306.70066 1500 1208 23 77 0 0 87 10 + 1600 -7.0819412 272.07245 1600 1288 21 79 0 0 89 10 + 1700 -5.8907481 301.00694 1700 1365 28 72 0 0 84 12 + 1800 -4.9932405 282.95729 1800 1447 24 76 0 0 82 6 + 1900 -4.3273176 296.96436 1900 1527 22 78 0 0 86 8 + 2000 -4.4859306 299.76741 2000 1600 26 74 0 0 81 7 +Loop time of 1.15911 on 1 procs for 2000 steps with 188 atoms + +Performance: 1490.798 ns/day, 0.016 hours/ns, 1725.460 timesteps/s +99.5% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.036171 | 0.036171 | 0.036171 | 0.0 | 3.12 +Kspace | 0.37716 | 0.37716 | 0.37716 | 0.0 | 32.54 +Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 1.93 +Comm | 0.005311 | 0.005311 | 0.005311 | 0.0 | 0.46 +Output | 0.000745 | 0.000745 | 0.000745 | 0.0 | 0.06 +Modify | 0.71566 | 0.71566 | 0.71566 | 0.0 | 61.74 +Other | | 0.001663 | | | 0.14 + +Nlocal: 188.000 ave 188 max 188 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 411.000 ave 411 max 411 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1268.00 ave 1268 max 1268 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 1268 +Ave neighs/atom = 6.7446809 +Neighbor list builds = 2195 +Dangerous builds = 15 +Total wall time: 0:00:01 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 new file mode 100644 index 0000000000..7ab22c1f36 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 @@ -0,0 +1,145 @@ +LAMMPS (10 Feb 2021) +# Charge regulation lammps for simple weak electrolyte + +units real +atom_style charge +neighbor 3.0 bin +read_data data.chreg-acid-real +Reading data file ... + orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 219 atoms + read_data CPU = 0.002 seconds + +#real units +variable sigma equal 7.2 # particle diameter 0.72 nm +variable temperature equal 298 # temperature 298 K +variable kb index 0.0019872067 # kB in Kcal/mol/K +variable epsilon equal ${kb}*${temperature} +variable epsilon equal 0.0019872067*${temperature} +variable epsilon equal 0.0019872067*298 +variable tunit equal 2000 # time unit is 2000 fs +variable timestep equal 0.005*${tunit} +variable timestep equal 0.005*2000 + +variable cut_long equal 12.5*${sigma} +variable cut_long equal 12.5*7.2 +variable nevery equal 100 +variable nmc equal 100 +variable pH equal 7.0 +variable pKa equal 6.0 +variable pIm equal 3.0 +variable pIp equal 3.0 + +variable cut_lj equal 2^(1.0/6.0)*${sigma} +variable cut_lj equal 2^(1.0/6.0)*7.2 +velocity all create ${temperature} 8008 loop geom +velocity all create 298 8008 loop geom + +pair_style lj/cut/coul/long ${cut_lj} ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 ${cut_long} +pair_style lj/cut/coul/long 8.08172674782749 90 +pair_coeff * * ${epsilon} ${sigma} +pair_coeff * * 0.5921875966 ${sigma} +pair_coeff * * 0.5921875966 7.2 +kspace_style pppm 1.0e-3 +dielectric 78 +pair_modify shift yes + +######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ########### +fix fnve all nve +compute dtemp all temp +compute_modify dtemp dynamic yes +fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 $(v_temperature) $(v_tunit) 123 +fix fT all langevin 298 298 $(v_tunit) 123 +fix fT all langevin 298 298 2000 123 +fix_modify fT temp dtemp + +fix chareg all charge/regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT +fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 seed 2345 tempfixid fT +thermo 100 +thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] +timestep ${timestep} +timestep 10 +run 2000 +PPPM initialization ... + using 12-bit tables for long-range coulomb (../kspace.cpp:339) + G vector (1/distance) = 0.019408615 + grid = 8 8 8 + stencil order = 5 + estimated absolute RMS force accuracy = 0.00012527706 + estimated relative force accuracy = 3.7726815e-07 + using double precision KISS FFT + 3d grid and FFT values/proc = 1053 128 +0 atoms in group FixChargeRegulation:exclusion_group:chareg +WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 93 + ghost atom cutoff = 93 + binsize = 46.5, bins = 8 8 8 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes +Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] + 0 -6.4798431 298 0 0 1 99 0 0 109 10 + 100 -7.9144028 317.49717 100 73 15 85 0 0 94 9 + 200 -5.9183735 315.31348 200 157 24 76 0 0 86 10 + 300 -6.7851544 295.82718 300 243 21 79 0 0 86 7 + 400 -6.3777493 297.53619 400 316 16 84 0 0 91 7 + 500 -6.0281518 287.62012 500 398 15 85 0 0 93 8 + 600 -8.4403907 301.30302 600 483 14 86 0 0 94 8 + 700 -9.6450828 305.33793 700 563 15 85 0 0 96 11 + 800 -6.1034312 307.18396 800 646 20 80 0 0 85 5 + 900 -7.3098915 295.21039 900 729 24 76 0 0 86 10 + 1000 -6.721795 316.34459 1000 803 25 75 0 0 84 9 + 1100 -7.389073 326.53025 1100 882 23 77 0 0 87 10 + 1200 -9.6721231 327.15878 1200 958 20 80 0 0 89 9 + 1300 -7.4738885 295.09338 1300 1045 20 80 0 0 88 8 + 1400 -7.8136191 297.62074 1400 1127 18 82 0 0 92 10 + 1500 -7.6522652 284.20977 1500 1204 24 76 0 0 85 9 + 1600 -8.473883 293.37704 1600 1283 22 78 0 0 92 14 + 1700 -5.7030629 327.53233 1700 1366 26 74 0 0 83 9 + 1800 -6.1817998 278.22073 1800 1447 21 79 0 0 84 5 + 1900 -5.3113964 293.69193 1900 1526 24 76 0 0 85 9 + 2000 -5.5827334 307.91424 2000 1599 26 74 0 0 80 6 +Loop time of 0.547632 on 4 procs for 2000 steps with 186 atoms + +Performance: 3155.407 ns/day, 0.008 hours/ns, 3652.091 timesteps/s +99.5% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.008417 | 0.01004 | 0.010817 | 1.0 | 1.83 +Kspace | 0.17103 | 0.17157 | 0.17208 | 0.1 | 31.33 +Neigh | 0.004536 | 0.0052815 | 0.005857 | 0.7 | 0.96 +Comm | 0.023141 | 0.02398 | 0.02617 | 0.8 | 4.38 +Output | 0.000556 | 0.00063325 | 0.000864 | 0.0 | 0.12 +Modify | 0.33403 | 0.33441 | 0.33471 | 0.1 | 61.07 +Other | | 0.001711 | | | 0.31 + +Nlocal: 46.5000 ave 48 max 44 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 241.500 ave 244 max 238 min +Histogram: 1 0 0 0 0 1 0 0 1 1 +Neighs: 303.750 ave 333 max 286 min +Histogram: 2 0 0 0 1 0 0 0 0 1 + +Total # of neighbors = 1215 +Ave neighs/atom = 6.5322581 +Neighbor list builds = 2196 +Dangerous builds = 12 +Total wall time: 0:00:00 From 7d95943b7e2ddb500addba2f69e78d7821eed3b5 Mon Sep 17 00:00:00 2001 From: tc387 Date: Mon, 12 Apr 2021 01:46:39 -0500 Subject: [PATCH 062/100] increased bin size in example input file to avoid dangerous builds --- .../misc/charge_regulation/in.chreg-acid-real | 2 +- .../log.11Apr21.chreg-acid-real.g++.1 | 66 +++++++------- .../log.11Apr21.chreg-acid-real.g++.4 | 88 +++++++++---------- 3 files changed, 78 insertions(+), 78 deletions(-) diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER/misc/charge_regulation/in.chreg-acid-real index 195b163d96..d7225f33ea 100644 --- a/examples/USER/misc/charge_regulation/in.chreg-acid-real +++ b/examples/USER/misc/charge_regulation/in.chreg-acid-real @@ -2,7 +2,7 @@ units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real #real units diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 index 3b766d662d..6e50ea5ef3 100644 --- a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 @@ -3,7 +3,7 @@ LAMMPS (10 Feb 2021) units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real Reading data file ... orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) @@ -83,16 +83,16 @@ WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulo Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 93 - ghost atom cutoff = 93 - binsize = 46.5, bins = 8 8 8 + master list distance cutoff = 100 + ghost atom cutoff = 100 + binsize = 50, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard -Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 Mbytes +Per MPI rank memory allocation (min/avg/max) = 3.708 | 3.708 | 3.708 Mbytes Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 0 -6.4798431 298 0 0 1 99 0 0 109 10 100 -6.9219668 306.44177 100 77 15 85 0 0 94 9 @@ -104,42 +104,42 @@ Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] 700 -6.290871 271.50948 700 567 14 86 0 0 96 10 800 -6.4944741 300.66261 800 650 23 77 0 0 83 6 900 -8.0414672 305.6179 900 731 25 75 0 0 84 9 - 1000 -8.5694583 297.69733 1000 810 25 75 0 0 83 8 - 1100 -8.9364878 292.52429 1100 891 22 78 0 0 88 10 - 1200 -8.733737 316.79814 1200 963 21 79 0 0 88 9 - 1300 -8.0946506 350.85016 1300 1043 21 79 0 0 88 9 - 1400 -7.1835794 283.90836 1400 1128 17 83 0 0 93 10 - 1500 -6.5673667 306.70066 1500 1208 23 77 0 0 87 10 - 1600 -7.0819412 272.07245 1600 1288 21 79 0 0 89 10 - 1700 -5.8907481 301.00694 1700 1365 28 72 0 0 84 12 - 1800 -4.9932405 282.95729 1800 1447 24 76 0 0 82 6 - 1900 -4.3273176 296.96436 1900 1527 22 78 0 0 86 8 - 2000 -4.4859306 299.76741 2000 1600 26 74 0 0 81 7 -Loop time of 1.15911 on 1 procs for 2000 steps with 188 atoms + 1000 -8.5694583 298.73349 1000 810 25 75 0 0 83 8 + 1100 -8.6677368 269.67435 1100 894 22 78 0 0 87 9 + 1200 -8.2246183 284.14886 1200 969 22 78 0 0 88 10 + 1300 -7.7674621 320.04838 1300 1040 23 77 0 0 85 8 + 1400 -9.5186335 303.48091 1400 1124 18 82 0 0 93 11 + 1500 -5.8437493 271.40712 1500 1204 25 75 0 0 83 8 + 1600 -5.9149181 268.24708 1600 1285 23 77 0 0 90 13 + 1700 -6.5047738 303.79732 1700 1369 27 73 0 0 84 11 + 1800 -7.3010139 308.98213 1800 1450 22 78 0 0 83 5 + 1900 -6.3505397 306.94357 1900 1527 22 78 0 0 86 8 + 2000 -5.7144173 287.06184 2000 1605 27 73 0 0 80 7 +Loop time of 1.17189 on 1 procs for 2000 steps with 187 atoms -Performance: 1490.798 ns/day, 0.016 hours/ns, 1725.460 timesteps/s -99.5% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 1474.535 ns/day, 0.016 hours/ns, 1706.638 timesteps/s +99.6% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.036171 | 0.036171 | 0.036171 | 0.0 | 3.12 -Kspace | 0.37716 | 0.37716 | 0.37716 | 0.0 | 32.54 -Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 1.93 -Comm | 0.005311 | 0.005311 | 0.005311 | 0.0 | 0.46 -Output | 0.000745 | 0.000745 | 0.000745 | 0.0 | 0.06 -Modify | 0.71566 | 0.71566 | 0.71566 | 0.0 | 61.74 -Other | | 0.001663 | | | 0.14 +Pair | 0.035807 | 0.035807 | 0.035807 | 0.0 | 3.06 +Kspace | 0.37689 | 0.37689 | 0.37689 | 0.0 | 32.16 +Neigh | 0.008694 | 0.008694 | 0.008694 | 0.0 | 0.74 +Comm | 0.004793 | 0.004793 | 0.004793 | 0.0 | 0.41 +Output | 0.000746 | 0.000746 | 0.000746 | 0.0 | 0.06 +Modify | 0.74292 | 0.74292 | 0.74292 | 0.0 | 63.39 +Other | | 0.00205 | | | 0.17 -Nlocal: 188.000 ave 188 max 188 min +Nlocal: 187.000 ave 187 max 187 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 411.000 ave 411 max 411 min +Nghost: 437.000 ave 437 max 437 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 1268.00 ave 1268 max 1268 min +Neighs: 1500.00 ave 1500 max 1500 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 1268 -Ave neighs/atom = 6.7446809 -Neighbor list builds = 2195 -Dangerous builds = 15 +Total # of neighbors = 1500 +Ave neighs/atom = 8.0213904 +Neighbor list builds = 2080 +Dangerous builds = 0 Total wall time: 0:00:01 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 index 7ab22c1f36..927e29c1f3 100644 --- a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 @@ -3,7 +3,7 @@ LAMMPS (10 Feb 2021) units real atom_style charge -neighbor 3.0 bin +neighbor 10.0 bin read_data data.chreg-acid-real Reading data file ... orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000) @@ -83,9 +83,9 @@ WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulo Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 93 - ghost atom cutoff = 93 - binsize = 46.5, bins = 8 8 8 + master list distance cutoff = 100 + ghost atom cutoff = 100 + binsize = 50, bins = 8 8 8 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/long, perpetual attributes: half, newton on @@ -95,51 +95,51 @@ Neighbor list info ... Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 Mbytes Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8] 0 -6.4798431 298 0 0 1 99 0 0 109 10 - 100 -7.9144028 317.49717 100 73 15 85 0 0 94 9 - 200 -5.9183735 315.31348 200 157 24 76 0 0 86 10 - 300 -6.7851544 295.82718 300 243 21 79 0 0 86 7 - 400 -6.3777493 297.53619 400 316 16 84 0 0 91 7 - 500 -6.0281518 287.62012 500 398 15 85 0 0 93 8 - 600 -8.4403907 301.30302 600 483 14 86 0 0 94 8 - 700 -9.6450828 305.33793 700 563 15 85 0 0 96 11 - 800 -6.1034312 307.18396 800 646 20 80 0 0 85 5 - 900 -7.3098915 295.21039 900 729 24 76 0 0 86 10 - 1000 -6.721795 316.34459 1000 803 25 75 0 0 84 9 - 1100 -7.389073 326.53025 1100 882 23 77 0 0 87 10 - 1200 -9.6721231 327.15878 1200 958 20 80 0 0 89 9 - 1300 -7.4738885 295.09338 1300 1045 20 80 0 0 88 8 - 1400 -7.8136191 297.62074 1400 1127 18 82 0 0 92 10 - 1500 -7.6522652 284.20977 1500 1204 24 76 0 0 85 9 - 1600 -8.473883 293.37704 1600 1283 22 78 0 0 92 14 - 1700 -5.7030629 327.53233 1700 1366 26 74 0 0 83 9 - 1800 -6.1817998 278.22073 1800 1447 21 79 0 0 84 5 - 1900 -5.3113964 293.69193 1900 1526 24 76 0 0 85 9 - 2000 -5.5827334 307.91424 2000 1599 26 74 0 0 80 6 -Loop time of 0.547632 on 4 procs for 2000 steps with 186 atoms + 100 -7.6327126 304.68909 100 73 15 85 0 0 94 9 + 200 -6.1699041 272.19597 200 156 24 76 0 0 87 11 + 300 -7.7876571 288.90801 300 240 20 80 0 0 87 7 + 400 -6.3239918 274.65708 400 315 16 84 0 0 90 6 + 500 -5.3978659 257.49208 500 398 15 85 0 0 93 8 + 600 -5.6433949 322.52048 600 477 18 82 0 0 90 8 + 700 -6.5351367 269.20244 700 558 18 82 0 0 91 9 + 800 -6.2093085 315.21326 800 638 24 76 0 0 83 7 + 900 -7.0795998 311.93228 900 719 28 72 0 0 82 10 + 1000 -6.4668438 281.72674 1000 796 27 73 0 0 81 8 + 1100 -6.2377994 318.48594 1100 875 25 75 0 0 84 9 + 1200 -6.6305072 304.9091 1200 950 23 77 0 0 87 10 + 1300 -5.9624552 286.05027 1300 1029 22 78 0 0 86 8 + 1400 -4.4695814 261.81053 1400 1111 20 80 0 0 90 10 + 1500 -5.6928652 293.72403 1500 1191 24 76 0 0 86 10 + 1600 -6.8715413 290.47065 1600 1275 22 78 0 0 90 12 + 1700 -6.5067505 292.74735 1700 1356 25 75 0 0 85 10 + 1800 -5.3902702 307.79012 1800 1434 22 78 0 0 83 5 + 1900 -5.1407153 318.48918 1900 1510 21 79 0 0 87 8 + 2000 -4.9514719 281.87771 2000 1589 25 75 0 0 82 7 +Loop time of 0.562889 on 4 procs for 2000 steps with 189 atoms -Performance: 3155.407 ns/day, 0.008 hours/ns, 3652.091 timesteps/s -99.5% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 3069.876 ns/day, 0.008 hours/ns, 3553.097 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.008417 | 0.01004 | 0.010817 | 1.0 | 1.83 -Kspace | 0.17103 | 0.17157 | 0.17208 | 0.1 | 31.33 -Neigh | 0.004536 | 0.0052815 | 0.005857 | 0.7 | 0.96 -Comm | 0.023141 | 0.02398 | 0.02617 | 0.8 | 4.38 -Output | 0.000556 | 0.00063325 | 0.000864 | 0.0 | 0.12 -Modify | 0.33403 | 0.33441 | 0.33471 | 0.1 | 61.07 -Other | | 0.001711 | | | 0.31 +Pair | 0.008399 | 0.010383 | 0.011765 | 1.2 | 1.84 +Kspace | 0.17501 | 0.17543 | 0.1757 | 0.1 | 31.17 +Neigh | 0.001833 | 0.0021325 | 0.002293 | 0.4 | 0.38 +Comm | 0.023099 | 0.024255 | 0.026645 | 0.9 | 4.31 +Output | 0.000465 | 0.000546 | 0.000783 | 0.0 | 0.10 +Modify | 0.3464 | 0.34669 | 0.34698 | 0.0 | 61.59 +Other | | 0.003452 | | | 0.61 -Nlocal: 46.5000 ave 48 max 44 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Nghost: 241.500 ave 244 max 238 min -Histogram: 1 0 0 0 0 1 0 0 1 1 -Neighs: 303.750 ave 333 max 286 min -Histogram: 2 0 0 0 1 0 0 0 0 1 +Nlocal: 47.2500 ave 57 max 41 min +Histogram: 1 1 0 1 0 0 0 0 0 1 +Nghost: 285.750 ave 303 max 263 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Neighs: 403.500 ave 548 max 324 min +Histogram: 2 0 0 1 0 0 0 0 0 1 -Total # of neighbors = 1215 -Ave neighs/atom = 6.5322581 -Neighbor list builds = 2196 -Dangerous builds = 12 +Total # of neighbors = 1614 +Ave neighs/atom = 8.5396825 +Neighbor list builds = 2081 +Dangerous builds = 0 Total wall time: 0:00:00 From bc25fa82688cb7506143454774115f0471dada1f Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 09:59:02 -0400 Subject: [PATCH 063/100] full integration into documentation build system --- doc/src/Commands_fix.rst | 1 + doc/src/fix.rst | 1 + doc/src/fix_charge_regulation.rst | 14 ++++++++++---- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/doc/src/Commands_fix.rst b/doc/src/Commands_fix.rst index 4793568288..671716e89d 100644 --- a/doc/src/Commands_fix.rst +++ b/doc/src/Commands_fix.rst @@ -46,6 +46,7 @@ OPT. * :doc:`bond/react ` * :doc:`bond/swap ` * :doc:`box/relax ` + * :doc:`charge/regulation ` * :doc:`client/md ` * :doc:`cmap ` * :doc:`colvars ` diff --git a/doc/src/fix.rst b/doc/src/fix.rst index 2e516faa4e..109bfb00be 100644 --- a/doc/src/fix.rst +++ b/doc/src/fix.rst @@ -189,6 +189,7 @@ accelerated styles exist. * :doc:`bond/react ` - apply topology changes to model reactions * :doc:`bond/swap ` - Monte Carlo bond swapping * :doc:`box/relax ` - relax box size during energy minimization +* :doc:`charge/regulation ` - Monte Carlo sampling of charge regulation * :doc:`client/md ` - MD client for client/server simulations * :doc:`cmap ` - enables CMAP cross-terms of the CHARMM force field * :doc:`colvars ` - interface to the collective variables "Colvars" library diff --git a/doc/src/fix_charge_regulation.rst b/doc/src/fix_charge_regulation.rst index fb63c8d7a5..ef91db1e59 100644 --- a/doc/src/fix_charge_regulation.rst +++ b/doc/src/fix_charge_regulation.rst @@ -225,7 +225,7 @@ quantities: Restrictions """""""""""" -This fix is part of the USER-MISC package. It is only enabled if LAMMPS +This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package ` doc page for more info. @@ -243,7 +243,9 @@ the LJ potential must be shifted so that it vanishes at the cutoff. This can be easily achieved using the :doc:`pair_modify ` command, i.e., by using: *pair_modify shift yes*. -Note: Region restrictions are not yet implemented. +.. note:: + + Region restrictions are not yet implemented. Related commands """""""""""""""" @@ -253,7 +255,11 @@ Related commands Default """"""" -pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = 100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = [1/3, 1/3, 1/3], group-ID = all + +pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; +acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery = +100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves = +[1/3, 1/3, 1/3], group-ID = all ---------- @@ -267,4 +273,4 @@ pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0; acid_type .. _Landsgesell: -**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007–3020 (2020). +**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020). From 9658b8e645f1fb611e52e1771e3a4b4cd6be7224 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:05:52 -0400 Subject: [PATCH 064/100] move fix charge/regulation to MC package (examples stay in place for now) --- doc/src/Packages_details.rst | 6 +++++- src/{USER-MISC => MC}/fix_charge_regulation.cpp | 0 src/{USER-MISC => MC}/fix_charge_regulation.h | 0 src/USER-MISC/README | 1 - 4 files changed, 5 insertions(+), 2 deletions(-) rename src/{USER-MISC => MC}/fix_charge_regulation.cpp (100%) rename src/{USER-MISC => MC}/fix_charge_regulation.h (100%) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index b662ae73c7..d5c011012d 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -585,7 +585,7 @@ MC package Several fixes and a pair style that have Monte Carlo (MC) or MC-like attributes. These include fixes for creating, breaking, and swapping bonds, for performing atomic swaps, and performing grand-canonical MC -(GCMC) in conjunction with dynamics. +(GCMC) or similar processes in conjunction with dynamics. **Supporting info:** @@ -593,8 +593,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC * :doc:`fix atom/swap ` * :doc:`fix bond/break ` * :doc:`fix bond/create ` +* :doc:`fix bond/create/angle ` * :doc:`fix bond/swap ` +* :doc:`fix charge/regulation ` * :doc:`fix gcmc ` +* :doc:`fix tfmc ` +* :doc:`fix widom ` * :doc:`pair_style dsmc ` * https://lammps.sandia.gov/movies.html#gcmc diff --git a/src/USER-MISC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp similarity index 100% rename from src/USER-MISC/fix_charge_regulation.cpp rename to src/MC/fix_charge_regulation.cpp diff --git a/src/USER-MISC/fix_charge_regulation.h b/src/MC/fix_charge_regulation.h similarity index 100% rename from src/USER-MISC/fix_charge_regulation.h rename to src/MC/fix_charge_regulation.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index ef25a0c116..314fe6146e 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -53,7 +53,6 @@ dihedral_style table/cut, Mike Salerno, ksalerno@pha.jhu.edu, 11 May 18 fix accelerate/cos, Zheng Gong (ENS de Lyon), z.gong@outlook.com, 24 Apr 20 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 -fix charge_regulation, Tine Curk and Jiaxing Yuan, tcurk5@gmail.com, 02 Feb 2021 fix electron/stopping/fit, James Stewart (SNL), jstewa .at. sandia.gov, 23 Sep 2020 fix electron/stopping, Konstantin Avchaciov, k.avchachov at gmail.com, 26 Feb 2019 fix ffl, David Wilkins (EPFL Lausanne), david.wilkins @ epfl.ch, 28 Sep 2018 From 0c79673d931091f8628c2f705c5133c39a471fed Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:14:31 -0400 Subject: [PATCH 065/100] make fix charge/regulation compatible with USER-INTEL package --- src/MC/fix_charge_regulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 5479082158..0aa3def153 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -45,7 +45,6 @@ #include #include - using namespace LAMMPS_NS; using namespace FixConst; using namespace MathConst; @@ -1082,6 +1081,7 @@ double FixChargeRegulation::energy_full() { if (force->kspace) force->kspace->compute(eflag, vflag); + if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag); if (modify->n_post_force) modify->post_force(vflag); if (modify->n_end_of_step) modify->end_of_step(); update->eflag_global = update->ntimestep; From a572142e6f4088eddf0f48e8a5d76232a0ee23ec Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:10 -0400 Subject: [PATCH 066/100] fix inconsistent new/delete --- src/MC/fix_charge_regulation.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 0aa3def153..797d7fb5b0 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -130,7 +130,7 @@ FixChargeRegulation::~FixChargeRegulation() { delete random_equal; delete random_unequal; - delete idftemp; + delete[] idftemp; if (group) { int igroupall = group->find("all"); From 65ba022c2a0ce3ab6e4822bfdc279679e511822c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:24 -0400 Subject: [PATCH 067/100] simplify --- src/MC/fix_charge_regulation.cpp | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 797d7fb5b0..47adad3f6d 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -1295,10 +1295,7 @@ void FixChargeRegulation::options(int narg, char **arg) { } else if (strcmp(arg[iarg], "tempfixid") == 0) { if (iarg + 2 > narg) error->all(FLERR, "Illegal fix charge/regulation command"); - int n = strlen(arg[iarg + 1]) + 1; - delete[] idftemp; - idftemp = new char[n]; - strcpy(idftemp, arg[iarg + 1]); + idftemp = utils::strdup(arg[iarg+1]); setThermoTemperaturePointer(); iarg += 2; } else if (strcmp(arg[iarg], "rxd") == 0) { @@ -1371,9 +1368,7 @@ void FixChargeRegulation::options(int narg, char **arg) { ngroupsmax * sizeof(char *), "fix_charge_regulation:groupstrings"); } - int n = strlen(arg[iarg + 1]) + 1; - groupstrings[ngroups] = new char[n]; - strcpy(groupstrings[ngroups], arg[iarg + 1]); + groupstrings[ngroups] = utils::strdup(arg[iarg+1]); ngroups++; iarg += 2; } else error->all(FLERR, "Illegal fix charge/regulation command"); From 82e1c4fb121c7e5c33f40406b0ed0c6f1b831121 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:25:39 -0400 Subject: [PATCH 068/100] silence compiler warnings --- src/MC/fix_charge_regulation.cpp | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 47adad3f6d..34391b86fb 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -14,6 +14,7 @@ /* ---------------------------------------------------------------------- Contributing author: Tine Curk (tcurk5@gmail.com) and Jiaxing Yuan (yuanjiaxing123@hotmail.com) ------------------------------------------------------------------------- */ + #include "fix_charge_regulation.h" #include "angle.h" @@ -652,7 +653,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; - int mask1_tmp, mask2_tmp; + int mask1_tmp = 0, mask2_tmp = 0; double *dummyp = nullptr; int m1 = -1, m2 = -1; @@ -724,12 +725,6 @@ void FixChargeRegulation::backward_ions() { atom->mask[m2] = mask2_tmp; } } - } else { - // reassign original charge and mask - if (m1 >= 0) { - atom->q[m1] = 1; - atom->mask[m1] = mask1_tmp; - } } } } @@ -738,7 +733,7 @@ void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp; + double *dummyp = nullptr; int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted if (salt_charge[0] <= -salt_charge[1]) { @@ -792,7 +787,7 @@ void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp; // dummy pointer + double *dummyp = nullptr; // dummy pointer int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions double qq[salt_charge_ratio + 1]; // charge array for all deleted ions int mask_tmp[salt_charge_ratio + 1]; // temporary mask array From c324d754a0644f2a50c5b376ca3318b8fc1a3396 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 10:51:44 -0400 Subject: [PATCH 069/100] when installing the LAMMPS python package create a valid version id --- python/install.py | 8 +++++--- python/lammps/__init__.py | 2 +- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/python/install.py b/python/install.py index 6e4c509f07..fbff02a1b5 100644 --- a/python/install.py +++ b/python/install.py @@ -10,7 +10,7 @@ build target in the conventional and CMake based build systems # copy LAMMPS shared library and lammps package to system dirs from __future__ import print_function -import sys,os,shutil +import sys,os,shutil,time from argparse import ArgumentParser parser = ArgumentParser(prog='install.py', @@ -80,13 +80,15 @@ if args.dir: sys.exit() -# extract version string from header +# extract LAMMPS version string from header +# and convert to python packaging compatible version def get_lammps_version(header): with open(header, 'r') as f: line = f.readline() start_pos = line.find('"')+1 end_pos = line.find('"', start_pos) - return "".join(line[start_pos:end_pos].split()) + t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y") + return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday) verstr = get_lammps_version(args.version) diff --git a/python/lammps/__init__.py b/python/lammps/__init__.py index 93c46819c0..2c0e7a6fe3 100644 --- a/python/lammps/__init__.py +++ b/python/lammps/__init__.py @@ -38,7 +38,7 @@ def get_version_number(): if not vstring: return 0 - t = time.strptime(vstring, "%d%b%Y") + t = time.strptime(vstring, "%Y.%m.%d") return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday __version__ = get_version_number() From 5605a237cf74184581cb1cffca17cba9b6b617c8 Mon Sep 17 00:00:00 2001 From: julient31 Date: Mon, 12 Apr 2021 10:27:20 -0600 Subject: [PATCH 070/100] working on the typedef correction --- src/KOKKOS/atom_kokkos.h | 9 ++- src/KOKKOS/atom_vec_spin_kokkos.cpp | 27 +++++-- src/KOKKOS/kokkos_type.h | 108 ++++++++++++++++++---------- 3 files changed, 95 insertions(+), 49 deletions(-) diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index 908958ab14..f5649f927e 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -56,9 +56,12 @@ class AtomKokkos : public Atom { // SPIN package - DAT::tdual_sp_array k_sp; - DAT::tdual_fm_array k_fm; - DAT::tdual_fm_long_array k_fm_long; + // DAT::tdual_sp_array k_sp; + // DAT::tdual_fm_array k_fm; + // DAT::tdual_fm_long_array k_fm_long; + DAT::tdual_float_1d_4 k_sp; + DAT::tdual_f_array k_fm; + DAT::tdual_f_array k_fm_long; // USER-DPD package DAT::tdual_efloat_1d k_uCond, k_uMech, k_uChem, k_uCG, k_uCGnew, diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index e513ff2ffa..5e3ff19831 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -189,7 +189,8 @@ struct AtomVecSpinKokkos_PackComm { AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, - const typename DAT::tdual_sp_array &sp, + // const typename DAT::tdual_sp_array &sp, + const typename DAT::tdual_float_1d_4 &sp, const typename DAT::tdual_xfloat_2d &buf, const typename DAT::tdual_int_2d &list, const int & iswap, @@ -1269,12 +1270,18 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); + // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_sp,space); + perform_async_copy(atomKK->k_sp,space); + // if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_fm,space); + perform_async_copy(atomKK->k_fm,space); + // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - perform_async_copy(atomKK->k_fm_long,space); + perform_async_copy(atomKK->k_fm_long,space); } else { if ((mask & X_MASK) && atomKK->k_x.need_sync()) perform_async_copy(atomKK->k_x,space); @@ -1290,12 +1297,18 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); + // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) + // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - perform_async_copy(atomKK->k_sp,space); + perform_async_copy(atomKK->k_sp,space); + // if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) + // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) - perform_async_copy(atomKK->k_fm,space); + perform_async_copy(atomKK->k_fm,space); + // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) + // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - perform_async_copy(atomKK->k_fm_long,space); + perform_async_copy(atomKK->k_fm_long,space); } } diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index e0e1dc8269..b0fbdf1f9f 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -773,33 +773,50 @@ typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; //3d SP_FLOAT array n*4 #ifdef LMP_KOKKOS_NO_LEGACY -typedef Kokkos::DualView tdual_sp_array; +// typedef Kokkos::DualView tdual_sp_array; +typedef Kokkos::DualView tdual_float_1d_4; #else -typedef Kokkos::DualView tdual_sp_array; +// typedef Kokkos::DualView tdual_sp_array; +typedef Kokkos::DualView tdual_float_1d_4; #endif -typedef tdual_sp_array::t_dev t_sp_array; -typedef tdual_sp_array::t_dev_const t_sp_array_const; -typedef tdual_sp_array::t_dev_um t_sp_array_um; -typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; -typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; +// typedef tdual_sp_array::t_dev t_sp_array; +// typedef tdual_sp_array::t_dev_const t_sp_array_const; +// typedef tdual_sp_array::t_dev_um t_sp_array_um; +// typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; +// typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; +typedef tdual_float_1d_4::t_dev t_sp_array; +typedef tdual_float_1d_4::t_dev_const t_sp_array_const; +typedef tdual_float_1d_4::t_dev_um t_sp_array_um; +typedef tdual_float_1d_4::t_dev_const_um t_sp_array_const_um; +typedef tdual_float_1d_4::t_dev_const_randomread t_sp_array_randomread; //3d FM_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_array; -typedef tdual_fm_array::t_dev t_fm_array; -typedef tdual_fm_array::t_dev_const t_fm_array_const; -typedef tdual_fm_array::t_dev_um t_fm_array_um; -typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; -typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; +// typedef Kokkos::DualView tdual_fm_array; +// typedef tdual_fm_array::t_dev t_fm_array; +// typedef tdual_fm_array::t_dev_const t_fm_array_const; +// typedef tdual_fm_array::t_dev_um t_fm_array_um; +// typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; +// typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; +typedef tdual_f_array::t_dev t_fm_array; +typedef tdual_f_array::t_dev_const t_fm_array_const; +typedef tdual_f_array::t_dev_um t_fm_array_um; +typedef tdual_f_array::t_dev_const_um t_fm_array_const_um; +typedef tdual_f_array::t_dev_const_randomread t_fm_array_randomread; //3d FML_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_long_array; -typedef tdual_fm_long_array::t_dev t_fm_long_array; -typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; -typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; -typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; -typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; +// typedef Kokkos::DualView tdual_fm_long_array; +// typedef tdual_fm_long_array::t_dev t_fm_long_array; +// typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; +// typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; +// typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; +// typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; +typedef tdual_f_array::t_dev t_fm_long_array; +typedef tdual_f_array::t_dev_const t_fm_long_array_const; +typedef tdual_f_array::t_dev_um t_fm_long_array_um; +typedef tdual_f_array::t_dev_const_um t_fm_long_array_const_um; +typedef tdual_f_array::t_dev_const_randomread t_fm_long_array_randomread; //Energy Types //1d E_FLOAT array n @@ -1040,30 +1057,43 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types //2d X_FLOAT array n*4 -typedef Kokkos::DualView tdual_sp_array; -typedef tdual_sp_array::t_host t_sp_array; -typedef tdual_sp_array::t_host_const t_sp_array_const; -typedef tdual_sp_array::t_host_um t_sp_array_um; -typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; -typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; +// typedef Kokkos::DualView tdual_sp_array; +// typedef tdual_sp_array::t_host t_sp_array; +// typedef tdual_sp_array::t_host_const t_sp_array_const; +// typedef tdual_sp_array::t_host_um t_sp_array_um; +// typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; +// typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; +typedef tdual_float_1d_4::t_host t_sp_array; +typedef tdual_float_1d_4::t_host_const t_sp_array_const; +typedef tdual_float_1d_4::t_host_um t_sp_array_um; +typedef tdual_float_1d_4::t_host_const_um t_sp_array_const_um; +typedef tdual_float_1d_4::t_host_const_randomread t_sp_array_randomread; //2d F_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_array; -//typedef Kokkos::DualView tdual_f_array; -typedef tdual_fm_array::t_host t_fm_array; -typedef tdual_fm_array::t_host_const t_fm_array_const; -typedef tdual_fm_array::t_host_um t_fm_array_um; -typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; -typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; +// typedef Kokkos::DualView tdual_fm_array; +// typedef tdual_fm_array::t_host t_fm_array; +// typedef tdual_fm_array::t_host_const t_fm_array_const; +// typedef tdual_fm_array::t_host_um t_fm_array_um; +// typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; +// typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; +typedef tdual_f_array::t_host t_fm_array; +typedef tdual_f_array::t_host_const t_fm_array_const; +typedef tdual_f_array::t_host_um t_fm_array_um; +typedef tdual_f_array::t_host_const_um t_fm_array_const_um; +typedef tdual_f_array::t_host_const_randomread t_fm_array_randomread; //2d F_FLOAT array n*3 -typedef Kokkos::DualView tdual_fm_long_array; -//typedef Kokkos::DualView tdual_f_array; -typedef tdual_fm_long_array::t_host t_fm_long_array; -typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; -typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; -typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; -typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; +// typedef Kokkos::DualView tdual_fm_long_array; +// typedef tdual_fm_long_array::t_host t_fm_long_array; +// typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; +// typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; +// typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; +// typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; +typedef tdual_f_array::t_host t_fm_long_array; +typedef tdual_f_array::t_host_const t_fm_long_array_const; +typedef tdual_f_array::t_host_um t_fm_long_array_um; +typedef tdual_f_array::t_host_const_um t_fm_long_array_const_um; +typedef tdual_f_array::t_host_const_randomread t_fm_long_array_randomread; //Energy Types From ee38452f14d3cd1d8549cae15223443606c7dd46 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:17 -0400 Subject: [PATCH 071/100] fix bug causing a failed download when using cmake -B --- cmake/Modules/Packages/USER-PACE.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cmake/Modules/Packages/USER-PACE.cmake b/cmake/Modules/Packages/USER-PACE.cmake index df1fb023a5..66f228017c 100644 --- a/cmake/Modules/Packages/USER-PACE.cmake +++ b/cmake/Modules/Packages/USER-PACE.cmake @@ -5,7 +5,7 @@ mark_as_advanced(PACELIB_URL) mark_as_advanced(PACELIB_MD5) # download library sources to build folder -file(DOWNLOAD ${PACELIB_URL} ./libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) +file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5}) # uncompress downloaded sources execute_process( From 04248c2ccdf41f8e2977e72ce99f1a45715e3463 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:35 -0400 Subject: [PATCH 072/100] finalize CMake build docs --- doc/src/Build_extras.rst | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 726374a012..12bb33f264 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1255,14 +1255,23 @@ USER-PACE package This package requires a library that can be downloaded and built in lib/pace or somewhere else, which must be done before building -LAMMPS with this package. +LAMMPS with this package. The code for the library can be found +at: `https://github.com/ICAMS/lammps-user-pace/ `_ .. tabs:: .. tab:: CMake build - The library download and build will happen automatically when USER-PACE - is requested. + By default the library will be downloaded from the git repository + and built automatically when the USER-PACE package is enabled with + ``-D PKG_USER-PACE=yes``. The location for the sources may be + customized by setting the variable ``PACELIB_URL`` when + configuring with CMake (e.g. to use a local archive on machines + without internet access). Since CMake checks the validity of the + archive with ``md5sum`` you may also need to set ``PACELIB_MD5`` + if you provide a different library version than what is downloaded + automatically. + .. tab:: Traditional make From f1e5d1115169ecbdb8977ed3bfd57d24667b2d51 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 14:52:53 -0400 Subject: [PATCH 073/100] add LAMMPS distribution header --- src/USER-PACE/pair_pace.cpp | 13 +++++++++++++ src/USER-PACE/pair_pace.h | 10 ++++++++++ 2 files changed, 23 insertions(+) diff --git a/src/USER-PACE/pair_pace.cpp b/src/USER-PACE/pair_pace.cpp index f59291b33e..d6eda0f511 100644 --- a/src/USER-PACE/pair_pace.cpp +++ b/src/USER-PACE/pair_pace.cpp @@ -1,3 +1,16 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + https://lammps.sandia.gov/, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + /* Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, diff --git a/src/USER-PACE/pair_pace.h b/src/USER-PACE/pair_pace.h index 37509cff5e..4d5ddcb9e8 100644 --- a/src/USER-PACE/pair_pace.h +++ b/src/USER-PACE/pair_pace.h @@ -1,3 +1,13 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + This software is distributed under the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + /* Copyright 2021 Yury Lysogorskiy^1, Cas van der Oord^2, Anton Bochkarev^1, Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1, From d08d59acb3cd4e271cc8d106ead2865636d3128c Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 15:00:21 -0400 Subject: [PATCH 074/100] whitespace fix --- src/pair_coul_cut.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/pair_coul_cut.cpp b/src/pair_coul_cut.cpp index 428c12c2e0..629d39a9c5 100644 --- a/src/pair_coul_cut.cpp +++ b/src/pair_coul_cut.cpp @@ -260,7 +260,7 @@ void PairCoulCut::read_restart(FILE *fp) MPI_Bcast(&scale[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { - if (me == 0) + if (me == 0) utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world); } From 47814292a119f42bd77881e1854c5fae23449695 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 12 Apr 2021 19:57:27 -0400 Subject: [PATCH 075/100] Make dump cfg/gz, cfg/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_cfg_gz.cpp | 67 ++++++++++++++++++- src/COMPRESS/dump_cfg_zstd.cpp | 67 ++++++++++++++++++- unittest/formats/test_dump_cfg_compressed.cpp | 33 +++++++++ 3 files changed, 165 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_cfg_gz.cpp b/src/COMPRESS/dump_cfg_gz.cpp index 23c0d82429..c5942c1fc5 100644 --- a/src/COMPRESS/dump_cfg_gz.cpp +++ b/src/COMPRESS/dump_cfg_gz.cpp @@ -136,7 +136,72 @@ void DumpCFGGZ::write_header(bigint n) void DumpCFGGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + if (unwrapflag == 0) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } else if (unwrapflag == 1) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2 && j <= 4) { + double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5; + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord); + } else if (j >= 5) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_cfg_zstd.cpp b/src/COMPRESS/dump_cfg_zstd.cpp index 5bc6ac86dc..0ea92f3807 100644 --- a/src/COMPRESS/dump_cfg_zstd.cpp +++ b/src/COMPRESS/dump_cfg_zstd.cpp @@ -148,7 +148,72 @@ void DumpCFGZstd::write_header(bigint n) void DumpCFGZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + if (unwrapflag == 0) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } else if (unwrapflag == 1) { + int m = 0; + for (int i = 0; i < n; i++) { + for (int j = 0; j < size_one; j++) { + int written = 0; + if (j == 0) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%f \n", mybuf[m]); + } else if (j == 1) { + written = snprintf(vbuffer, VBUFFER_SIZE, "%s \n", typenames[(int) mybuf[m]]); + } else if (j >= 2 && j <= 4) { + double unwrap_coord = (mybuf[m] - 0.5)/UNWRAPEXPAND + 0.5; + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], unwrap_coord); + } else if (j >= 5) { + if (vtype[j] == Dump::INT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + else if (vtype[j] == Dump::DOUBLE) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], mybuf[m]); + else if (vtype[j] == Dump::STRING) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], typenames[(int) mybuf[m]]); + else if (vtype[j] == Dump::BIGINT) + written = snprintf(vbuffer, VBUFFER_SIZE, vformat[j], static_cast (mybuf[m])); + } + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump cfg/gz output"); + } + m++; + } + writer.write("\n", 1); + } + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_cfg_compressed.cpp b/unittest/formats/test_dump_cfg_compressed.cpp index 6d5e8bcf04..1a00f9520e 100644 --- a/unittest/formats/test_dump_cfg_compressed.cpp +++ b/unittest/formats/test_dump_cfg_compressed.cpp @@ -66,6 +66,39 @@ TEST_F(DumpCfgCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpCfgCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.cfg"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + + auto base_name_0 = "no_buffer_run0.melt.cfg"; + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + auto fields = "mass type xs ys zs id proc procp1 x y z ix iy iz vx vy vz fx fy fz"; + + if(compression_style == "cfg/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, fields, fields, "buffer no", "buffer no", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, fields, "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpCfgCompressTest, compressed_unwrap_run0) { if (!COMPRESS_BINARY) GTEST_SKIP(); From dba3cce883b8c89fa5a012818990f4d851532bc1 Mon Sep 17 00:00:00 2001 From: Richard Berger Date: Mon, 12 Apr 2021 20:03:58 -0400 Subject: [PATCH 076/100] Make dump xyz/gz, xyz/zstd compatible to 'buffer no' option --- src/COMPRESS/dump_xyz_gz.cpp | 19 +++++++++++- src/COMPRESS/dump_xyz_zstd.cpp | 19 +++++++++++- unittest/formats/test_dump_xyz_compressed.cpp | 31 +++++++++++++++++++ 3 files changed, 67 insertions(+), 2 deletions(-) diff --git a/src/COMPRESS/dump_xyz_gz.cpp b/src/COMPRESS/dump_xyz_gz.cpp index 0697f19ce3..abd6e7fa78 100644 --- a/src/COMPRESS/dump_xyz_gz.cpp +++ b/src/COMPRESS/dump_xyz_gz.cpp @@ -109,7 +109,24 @@ void DumpXYZGZ::write_header(bigint ndump) void DumpXYZGZ::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = snprintf(vbuffer, VBUFFER_SIZE, format, + typenames[static_cast (mybuf[m+1])], + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump xyz/gz output"); + } + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/src/COMPRESS/dump_xyz_zstd.cpp b/src/COMPRESS/dump_xyz_zstd.cpp index cb75542337..74e482717b 100644 --- a/src/COMPRESS/dump_xyz_zstd.cpp +++ b/src/COMPRESS/dump_xyz_zstd.cpp @@ -120,7 +120,24 @@ void DumpXYZZstd::write_header(bigint ndump) void DumpXYZZstd::write_data(int n, double *mybuf) { - writer.write(mybuf, n); + if (buffer_flag) { + writer.write(mybuf, n); + } else { + constexpr size_t VBUFFER_SIZE = 256; + char vbuffer[VBUFFER_SIZE]; + int m = 0; + for (int i = 0; i < n; i++) { + int written = snprintf(vbuffer, VBUFFER_SIZE, format, + typenames[static_cast (mybuf[m+1])], + mybuf[m+2],mybuf[m+3],mybuf[m+4]); + if (written > 0) { + writer.write(vbuffer, written); + } else if (written < 0) { + error->one(FLERR, "Error while writing dump xyz/gz output"); + } + m += size_one; + } + } } /* ---------------------------------------------------------------------- */ diff --git a/unittest/formats/test_dump_xyz_compressed.cpp b/unittest/formats/test_dump_xyz_compressed.cpp index b627cb5a99..d9aa8e370d 100644 --- a/unittest/formats/test_dump_xyz_compressed.cpp +++ b/unittest/formats/test_dump_xyz_compressed.cpp @@ -60,6 +60,37 @@ TEST_F(DumpXYZCompressTest, compressed_run0) delete_file(converted_file_0); } +TEST_F(DumpXYZCompressTest, compressed_no_buffer_run0) +{ + if (!COMPRESS_BINARY) GTEST_SKIP(); + + auto base_name = "no_buffer_run*.melt.xyz"; + auto base_name_0 = "no_buffer_run0.melt.xyz"; + auto text_files = text_dump_filename(base_name); + auto compressed_files = compressed_dump_filename(base_name); + auto text_file_0 = text_dump_filename(base_name_0); + auto compressed_file_0 = compressed_dump_filename(base_name_0); + + if(compression_style == "xyz/zstd") { + generate_text_and_compressed_dump(text_files, compressed_files, "", "", "buffer no", "buffer no", 0); + } else { + generate_text_and_compressed_dump(text_files, compressed_files, "", "buffer no", 0); + } + + TearDown(); + + ASSERT_FILE_EXISTS(text_file_0); + ASSERT_FILE_EXISTS(compressed_file_0); + + auto converted_file_0 = convert_compressed_to_text(compressed_file_0); + + ASSERT_FILE_EXISTS(converted_file_0); + ASSERT_FILE_EQUAL(text_file_0, converted_file_0); + delete_file(text_file_0); + delete_file(compressed_file_0); + delete_file(converted_file_0); +} + TEST_F(DumpXYZCompressTest, compressed_multi_file_run1) { if (!COMPRESS_BINARY) GTEST_SKIP(); From e49e505b9f096bb1e954e99e51544353eff4ceb8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:16:02 -0400 Subject: [PATCH 077/100] make utility function private --- src/USER-COLVARS/ndx_group.h | 1 + 1 file changed, 1 insertion(+) diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index ceca1f9570..944638017d 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -31,6 +31,7 @@ class Ndx2Group : protected Pointers { public: Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {}; void command(int, char **); + private: void create(const std::string &, const std::vector &); }; From d8c68dec6f9f38e162cf428a231c70c44bc866ae Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:32:26 -0400 Subject: [PATCH 078/100] whitespace fixes --- doc/src/Build_extras.rst | 8 ++++---- src/COMPRESS/gz_file_writer.cpp | 2 +- src/MC/fix_charge_regulation.cpp | 2 +- src/USER-PACE/README | 20 ++++++++++---------- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/doc/src/Build_extras.rst b/doc/src/Build_extras.rst index 12bb33f264..d375d33e56 100644 --- a/doc/src/Build_extras.rst +++ b/doc/src/Build_extras.rst @@ -1253,8 +1253,8 @@ be built for the most part with all major versions of the C++ language. USER-PACE package ----------------------------- -This package requires a library that can be downloaded and built -in lib/pace or somewhere else, which must be done before building +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building LAMMPS with this package. The code for the library can be found at: `https://github.com/ICAMS/lammps-user-pace/ `_ @@ -1276,8 +1276,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ triclinic; + triclinic = domain->triclinic; int ipe = modify->find_compute("thermo_pe"); c_pe = modify->compute[ipe]; diff --git a/src/USER-PACE/README b/src/USER-PACE/README index 3d85c806e9..c701a615f7 100644 --- a/src/USER-PACE/README +++ b/src/USER-PACE/README @@ -1,23 +1,23 @@ -The USER-PACE package provides the pace pair style, -an efficient implementation of the Atomic Cluster Expansion +The USER-PACE package provides the pace pair style, +an efficient implementation of the Atomic Cluster Expansion potential (ACE). -ACE is a methodology for deriving a highly accurate classical -potential fit to a large archive of quantum mechanical (DFT) data. +ACE is a methodology for deriving a highly accurate classical +potential fit to a large archive of quantum mechanical (DFT) data. This package was written by Yury Lysogorskiy and others -at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, +at ICAMS, the Interdisciplinary Centre for Advanced Materials Simulation, Ruhr University Bochum, Germany (http://www.icams.de). -This package requires a library that can be downloaded and built -in lib/pace or somewhere else, which must be done before building -LAMMPS with this package. Details of the download, build, and -install process for this package using traditional make (not CMake) +This package requires a library that can be downloaded and built +in lib/pace or somewhere else, which must be done before building +LAMMPS with this package. Details of the download, build, and +install process for this package using traditional make (not CMake) are given in the lib/pace/README file, and scripts are provided to help automate the process. Also see the LAMMPS manual for general information on building LAMMPS with external libraries using either traditional make or CMake. -More information about the USER-PACE implementation of ACE +More information about the USER-PACE implementation of ACE is available here: https://github.com/ICAMS/lammps-user-pace From 02612047c34aac6dd90082b7c90c85df001cdf9e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Mon, 12 Apr 2021 23:57:30 -0400 Subject: [PATCH 079/100] must set CMAKE_EXPORT_COMPILE_COMMANDS ON for using iwyu --- cmake/CMakeLists.txt | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index f567a15d25..a11c7575d2 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -269,6 +269,7 @@ endif() set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool") mark_as_advanced(ENABLE_IWYU) if(ENABLE_IWYU) + set(CMAKE_EXPORT_COMPILE_COMMANDS ON) find_program(IWYU_EXE NAMES include-what-you-use iwyu) find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py) if (IWYU_EXE AND IWYU_TOOL) From fab571cf6bc1a1ba3aaa5b261f0244fda49a46b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 00:32:11 -0400 Subject: [PATCH 080/100] IWYU reported header updates --- src/body.cpp | 1 - src/compute.cpp | 1 - src/compute_chunk_spread_atom.cpp | 2 ++ src/compute_reduce.cpp | 2 ++ src/compute_temp_region.cpp | 9 ++++----- src/fix.cpp | 1 - src/fix_controller.cpp | 2 -- src/fix_enforce2d.cpp | 7 +++---- src/fix_lineforce.cpp | 1 - src/fix_nph_sphere.cpp | 2 -- src/fix_npt_sphere.cpp | 2 -- src/fix_nve_limit.cpp | 11 +++++------ src/fix_nve_noforce.cpp | 6 +++--- src/fix_planeforce.cpp | 1 - src/fix_store_force.cpp | 8 ++++---- src/fix_vector.cpp | 2 -- src/group.cpp | 1 - src/imbalance_store.cpp | 2 -- src/imbalance_var.cpp | 2 -- src/info.cpp | 1 - src/library.cpp | 1 - src/math_eigen.cpp | 4 +++- src/math_special.cpp | 2 -- src/my_pool_chunk.cpp | 1 - src/npair_full_bin_atomonly.cpp | 6 +++--- src/npair_half_bin_atomonly_newton.cpp | 6 +++--- src/npair_half_size_bin_newtoff.cpp | 6 +++--- src/npair_half_size_bin_newton.cpp | 6 +++--- src/npair_half_size_bin_newton_tri.cpp | 6 +++--- src/npair_half_size_multi_newtoff.cpp | 6 +++--- src/npair_half_size_multi_newton.cpp | 6 +++--- src/npair_half_size_multi_newton_tri.cpp | 6 +++--- src/npair_half_size_nsq_newtoff.cpp | 6 +++--- src/npair_half_size_nsq_newton.cpp | 6 +++--- src/npair_halffull_newtoff.cpp | 6 +++--- src/npair_halffull_newton.cpp | 6 +++--- src/npair_skip.cpp | 6 +++--- src/npair_skip_respa.cpp | 6 +++--- src/npair_skip_size.cpp | 6 +++--- src/npair_skip_size_off2on.cpp | 6 +++--- src/npair_skip_size_off2on_oneside.cpp | 6 +++--- src/output.cpp | 3 --- src/pair_lj96_cut.cpp | 15 +++++++-------- src/pair_lj_relres.cpp | 1 - src/reader.cpp | 2 -- src/region_sphere.cpp | 1 - src/tokenizer.cpp | 1 - src/universe.cpp | 2 -- src/variable.cpp | 1 - src/write_coeff.cpp | 1 - src/write_data.cpp | 1 - src/write_restart.cpp | 1 - 52 files changed, 84 insertions(+), 119 deletions(-) diff --git a/src/body.cpp b/src/body.cpp index 89bb2fc1d9..2c4121b0cc 100644 --- a/src/body.cpp +++ b/src/body.cpp @@ -12,7 +12,6 @@ ------------------------------------------------------------------------- */ #include "body.h" -#include using namespace LAMMPS_NS; diff --git a/src/compute.cpp b/src/compute.cpp index 81e317076c..46bd0d0fc8 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -22,7 +22,6 @@ #include "modify.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/compute_chunk_spread_atom.cpp b/src/compute_chunk_spread_atom.cpp index d817141064..f552454e72 100644 --- a/src/compute_chunk_spread_atom.cpp +++ b/src/compute_chunk_spread_atom.cpp @@ -23,6 +23,8 @@ #include "modify.h" #include "update.h" +#include + using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ diff --git a/src/compute_reduce.cpp b/src/compute_reduce.cpp index 30b4fcb98a..6e961df47a 100644 --- a/src/compute_reduce.cpp +++ b/src/compute_reduce.cpp @@ -25,6 +25,8 @@ #include "update.h" #include "variable.h" +#include + using namespace LAMMPS_NS; #define BIG 1.0e20 diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index 036f118a30..535a0166c5 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -13,15 +13,14 @@ #include "compute_temp_region.h" -#include #include "atom.h" -#include "update.h" -#include "force.h" #include "domain.h" -#include "region.h" +#include "error.h" +#include "force.h" #include "group.h" #include "memory.h" -#include "error.h" +#include "region.h" +#include "update.h" using namespace LAMMPS_NS; diff --git a/src/fix.cpp b/src/fix.cpp index 32a76cc125..14c04bf4b5 100644 --- a/src/fix.cpp +++ b/src/fix.cpp @@ -21,7 +21,6 @@ #include "memory.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_controller.cpp b/src/fix_controller.cpp index 21d1ccf751..c611dee271 100644 --- a/src/fix_controller.cpp +++ b/src/fix_controller.cpp @@ -21,8 +21,6 @@ #include "update.h" #include "variable.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_enforce2d.cpp b/src/fix_enforce2d.cpp index 1284a9b78c..11e041fcf4 100644 --- a/src/fix_enforce2d.cpp +++ b/src/fix_enforce2d.cpp @@ -12,14 +12,13 @@ ------------------------------------------------------------------------- */ #include "fix_enforce2d.h" -#include + #include "atom.h" -#include "update.h" #include "domain.h" +#include "error.h" #include "modify.h" #include "respa.h" -#include "error.h" - +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_lineforce.cpp b/src/fix_lineforce.cpp index 6a77442ea4..d95aacfd93 100644 --- a/src/fix_lineforce.cpp +++ b/src/fix_lineforce.cpp @@ -19,7 +19,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nph_sphere.cpp b/src/fix_nph_sphere.cpp index 20e072d5b5..1266cb2b9d 100644 --- a/src/fix_nph_sphere.cpp +++ b/src/fix_nph_sphere.cpp @@ -16,8 +16,6 @@ #include "error.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_npt_sphere.cpp b/src/fix_npt_sphere.cpp index a6dfeba425..8bbd43d4cf 100644 --- a/src/fix_npt_sphere.cpp +++ b/src/fix_npt_sphere.cpp @@ -16,8 +16,6 @@ #include "error.h" #include "modify.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_limit.cpp b/src/fix_nve_limit.cpp index 58db5e25d9..58dc023991 100644 --- a/src/fix_nve_limit.cpp +++ b/src/fix_nve_limit.cpp @@ -13,16 +13,15 @@ #include "fix_nve_limit.h" -#include -#include #include "atom.h" -#include "force.h" -#include "update.h" -#include "respa.h" -#include "modify.h" #include "comm.h" #include "error.h" +#include "force.h" +#include "modify.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_nve_noforce.cpp b/src/fix_nve_noforce.cpp index 61528a0024..e6bca3b608 100644 --- a/src/fix_nve_noforce.cpp +++ b/src/fix_nve_noforce.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "fix_nve_noforce.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" #include "error.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_planeforce.cpp b/src/fix_planeforce.cpp index 783d26ac9e..fe6f3d6500 100644 --- a/src/fix_planeforce.cpp +++ b/src/fix_planeforce.cpp @@ -19,7 +19,6 @@ #include "update.h" #include -#include using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_store_force.cpp b/src/fix_store_force.cpp index 1541294f6c..7ebd4db75a 100644 --- a/src/fix_store_force.cpp +++ b/src/fix_store_force.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "fix_store_force.h" -#include + #include "atom.h" -#include "update.h" -#include "respa.h" -#include "memory.h" #include "error.h" +#include "memory.h" +#include "respa.h" +#include "update.h" using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp index afd3778841..71a8bb3d3c 100644 --- a/src/fix_vector.cpp +++ b/src/fix_vector.cpp @@ -22,8 +22,6 @@ #include "update.h" #include "variable.h" -#include - using namespace LAMMPS_NS; using namespace FixConst; diff --git a/src/group.cpp b/src/group.cpp index ebab78dd0f..0143008a72 100644 --- a/src/group.cpp +++ b/src/group.cpp @@ -35,7 +35,6 @@ #include #include #include -#include using namespace LAMMPS_NS; diff --git a/src/imbalance_store.cpp b/src/imbalance_store.cpp index 879b434bfd..e72ef4d50b 100644 --- a/src/imbalance_store.cpp +++ b/src/imbalance_store.cpp @@ -16,8 +16,6 @@ #include "atom.h" #include "error.h" -#include - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/imbalance_var.cpp b/src/imbalance_var.cpp index d2a4f0d691..64f98a6a26 100644 --- a/src/imbalance_var.cpp +++ b/src/imbalance_var.cpp @@ -20,8 +20,6 @@ #include "memory.h" #include "variable.h" -#include - using namespace LAMMPS_NS; /* -------------------------------------------------------------------- */ diff --git a/src/info.cpp b/src/info.cpp index 948073bb10..f1ee327191 100644 --- a/src/info.cpp +++ b/src/info.cpp @@ -39,7 +39,6 @@ #include "pair.h" #include "pair_hybrid.h" #include "region.h" -#include "universe.h" #include "update.h" #include "variable.h" diff --git a/src/library.cpp b/src/library.cpp index 300aafc293..c51006f8d8 100644 --- a/src/library.cpp +++ b/src/library.cpp @@ -31,7 +31,6 @@ #include "group.h" #include "info.h" #include "input.h" -#include "integrate.h" #include "memory.h" #include "modify.h" #include "molecule.h" diff --git a/src/math_eigen.cpp b/src/math_eigen.cpp index ab00e42ae0..10caccd0e5 100644 --- a/src/math_eigen.cpp +++ b/src/math_eigen.cpp @@ -18,7 +18,9 @@ #include "math_eigen.h" #include "math_eigen_impl.h" -#include +#include +#include +#include using std::vector; using std::array; diff --git a/src/math_special.cpp b/src/math_special.cpp index 243d5a05f3..8d48158e72 100644 --- a/src/math_special.cpp +++ b/src/math_special.cpp @@ -4,8 +4,6 @@ #include // IWYU pragma: keep #include -#include "error.h" - using namespace LAMMPS_NS; static constexpr int nmaxfactorial = 167; diff --git a/src/my_pool_chunk.cpp b/src/my_pool_chunk.cpp index d866804adc..d824b0557b 100644 --- a/src/my_pool_chunk.cpp +++ b/src/my_pool_chunk.cpp @@ -14,7 +14,6 @@ #include "my_pool_chunk.h" #include -#include #if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32) #define LAMMPS_MEMALIGN 64 diff --git a/src/npair_full_bin_atomonly.cpp b/src/npair_full_bin_atomonly.cpp index 4e05c2c17a..8ace197e30 100644 --- a/src/npair_full_bin_atomonly.cpp +++ b/src/npair_full_bin_atomonly.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_full_bin_atomonly.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_bin_atomonly_newton.cpp b/src/npair_half_bin_atomonly_newton.cpp index 2dd0bd0b96..2007bda728 100644 --- a/src/npair_half_bin_atomonly_newton.cpp +++ b/src/npair_half_bin_atomonly_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_bin_atomonly_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newtoff.cpp b/src/npair_half_size_bin_newtoff.cpp index 2d406d533c..5b9eee3672 100644 --- a/src/npair_half_size_bin_newtoff.cpp +++ b/src/npair_half_size_bin_newtoff.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newton.cpp b/src/npair_half_size_bin_newton.cpp index 820b293414..9cf4e744ab 100644 --- a/src/npair_half_size_bin_newton.cpp +++ b/src/npair_half_size_bin_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_bin_newton_tri.cpp b/src/npair_half_size_bin_newton_tri.cpp index ea878ef440..83f903c864 100644 --- a/src/npair_half_size_bin_newton_tri.cpp +++ b/src/npair_half_size_bin_newton_tri.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_bin_newton_tri.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newtoff.cpp b/src/npair_half_size_multi_newtoff.cpp index d57542f562..f1bc93de38 100644 --- a/src/npair_half_size_multi_newtoff.cpp +++ b/src/npair_half_size_multi_newtoff.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newton.cpp b/src/npair_half_size_multi_newton.cpp index 01065876af..22a02899ca 100644 --- a/src/npair_half_size_multi_newton.cpp +++ b/src/npair_half_size_multi_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_multi_newton_tri.cpp b/src/npair_half_size_multi_newton_tri.cpp index 361c0ba260..268ca81f3d 100644 --- a/src/npair_half_size_multi_newton_tri.cpp +++ b/src/npair_half_size_multi_newton_tri.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_multi_newton_tri.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_nsq_newtoff.cpp b/src/npair_half_size_nsq_newtoff.cpp index 38594ebcb1..79302042a6 100644 --- a/src/npair_half_size_nsq_newtoff.cpp +++ b/src/npair_half_size_nsq_newtoff.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_nsq_newtoff.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_half_size_nsq_newton.cpp b/src/npair_half_size_nsq_newton.cpp index 9010ca9a86..1ac6223afa 100644 --- a/src/npair_half_size_nsq_newton.cpp +++ b/src/npair_half_size_nsq_newton.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_half_size_nsq_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" +#include "error.h" #include "group.h" #include "my_page.h" -#include "error.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_halffull_newtoff.cpp b/src/npair_halffull_newtoff.cpp index e2965b4a46..52f981e843 100644 --- a/src/npair_halffull_newtoff.cpp +++ b/src/npair_halffull_newtoff.cpp @@ -12,10 +12,10 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newtoff.h" -#include "neigh_list.h" -#include "atom_vec.h" -#include "my_page.h" + #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_halffull_newton.cpp b/src/npair_halffull_newton.cpp index 99b5493f3e..cf15af8f18 100644 --- a/src/npair_halffull_newton.cpp +++ b/src/npair_halffull_newton.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_halffull_newton.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip.cpp b/src/npair_skip.cpp index 45540ab2fa..6046464ecf 100644 --- a/src/npair_skip.cpp +++ b/src/npair_skip.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_respa.cpp b/src/npair_skip_respa.cpp index 3479a5d8ce..d24a30794e 100644 --- a/src/npair_skip_respa.cpp +++ b/src/npair_skip_respa.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_respa.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size.cpp b/src/npair_skip_size.cpp index d3810e6acc..40b70aed21 100644 --- a/src/npair_skip_size.cpp +++ b/src/npair_skip_size.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size_off2on.cpp b/src/npair_skip_size_off2on.cpp index 0d7630aaa9..994910852b 100644 --- a/src/npair_skip_size_off2on.cpp +++ b/src/npair_skip_size_off2on.cpp @@ -12,11 +12,11 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size_off2on.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/npair_skip_size_off2on_oneside.cpp b/src/npair_skip_size_off2on_oneside.cpp index eab98de035..30ee2ff6ba 100644 --- a/src/npair_skip_size_off2on_oneside.cpp +++ b/src/npair_skip_size_off2on_oneside.cpp @@ -12,12 +12,12 @@ ------------------------------------------------------------------------- */ #include "npair_skip_size_off2on_oneside.h" -#include "neigh_list.h" + #include "atom.h" -#include "atom_vec.h" #include "domain.h" -#include "my_page.h" #include "error.h" +#include "my_page.h" +#include "neigh_list.h" using namespace LAMMPS_NS; diff --git a/src/output.cpp b/src/output.cpp index 988ef04409..d7be9b8cd6 100644 --- a/src/output.cpp +++ b/src/output.cpp @@ -14,18 +14,15 @@ #include "output.h" #include "style_dump.h" // IWYU pragma: keep -#include "atom.h" #include "comm.h" #include "domain.h" #include "dump.h" #include "error.h" -#include "force.h" #include "group.h" #include "info.h" #include "input.h" #include "memory.h" #include "modify.h" -#include "neighbor.h" #include "thermo.h" #include "update.h" #include "variable.h" diff --git a/src/pair_lj96_cut.cpp b/src/pair_lj96_cut.cpp index 65f2d40e00..92cbb47440 100644 --- a/src/pair_lj96_cut.cpp +++ b/src/pair_lj96_cut.cpp @@ -17,20 +17,19 @@ #include "pair_lj96_cut.h" -#include -#include #include "atom.h" #include "comm.h" +#include "error.h" #include "force.h" -#include "neighbor.h" -#include "neigh_list.h" -#include "neigh_request.h" -#include "update.h" -#include "respa.h" #include "math_const.h" #include "memory.h" -#include "error.h" +#include "neigh_list.h" +#include "neigh_request.h" +#include "neighbor.h" +#include "respa.h" +#include "update.h" +#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/pair_lj_relres.cpp b/src/pair_lj_relres.cpp index 1f40d03aa9..306b68684e 100644 --- a/src/pair_lj_relres.cpp +++ b/src/pair_lj_relres.cpp @@ -26,7 +26,6 @@ #include "memory.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/reader.cpp b/src/reader.cpp index c22a9f7e5d..ba172f58ee 100644 --- a/src/reader.cpp +++ b/src/reader.cpp @@ -15,8 +15,6 @@ #include "error.h" -#include - using namespace LAMMPS_NS; // only proc 0 calls methods of this class, except for constructor/destructor diff --git a/src/region_sphere.cpp b/src/region_sphere.cpp index 8921cbd456..3a5a51834b 100644 --- a/src/region_sphere.cpp +++ b/src/region_sphere.cpp @@ -19,7 +19,6 @@ #include "variable.h" #include -#include using namespace LAMMPS_NS; diff --git a/src/tokenizer.cpp b/src/tokenizer.cpp index d26a5199f9..ea8ff2ce43 100644 --- a/src/tokenizer.cpp +++ b/src/tokenizer.cpp @@ -19,7 +19,6 @@ #include "utils.h" #include "fmt/format.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/universe.cpp b/src/universe.cpp index a7fa8fc2e2..79de6948df 100644 --- a/src/universe.cpp +++ b/src/universe.cpp @@ -15,9 +15,7 @@ #include "error.h" #include "memory.h" -#include "version.h" -#include #include using namespace LAMMPS_NS; diff --git a/src/variable.cpp b/src/variable.cpp index d903490219..f66b99d6e5 100644 --- a/src/variable.cpp +++ b/src/variable.cpp @@ -40,7 +40,6 @@ #include #include #include -#include using namespace LAMMPS_NS; using namespace MathConst; diff --git a/src/write_coeff.cpp b/src/write_coeff.cpp index 485bc3b29b..79a99502a6 100644 --- a/src/write_coeff.cpp +++ b/src/write_coeff.cpp @@ -22,7 +22,6 @@ #include "force.h" #include "improper.h" #include "pair.h" -#include "universe.h" #include #include diff --git a/src/write_data.cpp b/src/write_data.cpp index 6d10359e8b..8ec24bb4cf 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -29,7 +29,6 @@ #include "output.h" #include "pair.h" #include "thermo.h" -#include "universe.h" #include "update.h" #include diff --git a/src/write_restart.cpp b/src/write_restart.cpp index afe1d2d528..795e93b05e 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -32,7 +32,6 @@ #include "output.h" #include "pair.h" #include "thermo.h" -#include "universe.h" #include "update.h" #include From b9cb63ae56832ae2c10e102280032bee7f71cbea Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 00:47:58 -0400 Subject: [PATCH 081/100] remove redundant check --- src/pair_hybrid_scaled.cpp | 2 -- 1 file changed, 2 deletions(-) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index 7a30c9a3ee..cdbccbf7c7 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -457,8 +457,6 @@ void PairHybridScaled::coeff(int narg, char **arg) if (multiple[m]) { multflag = 1; if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients"); - if (!isdigit(arg[3][0])) - error->all(FLERR,"Incorrect args for pair coefficients"); int index = utils::inumeric(FLERR,arg[3],false,lmp); if (index == multiple[m]) break; else continue; From bddc6d58201b3ef4618de87732118341a8a34a05 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:58:19 -0400 Subject: [PATCH 082/100] make installation procedure consistent with install.py --- python/setup.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/python/setup.py b/python/setup.py index aff0b14671..2f2b67b6f1 100644 --- a/python/setup.py +++ b/python/setup.py @@ -1,7 +1,8 @@ # this only installs the LAMMPS python package # it assumes the LAMMPS shared library is already installed from distutils.core import setup -import os +from sys import version_info +import os,time LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__)) LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR) @@ -12,7 +13,13 @@ def get_lammps_version(): line = f.readline() start_pos = line.find('"')+1 end_pos = line.find('"', start_pos) - return "".join(line[start_pos:end_pos].split()) + t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y") + return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday) + +if version_info.major >= 3: + pkgs = ['lammps', 'lammps.mliap'] +else: + pkgs = ['lammps'] setup( name = "lammps", @@ -22,5 +29,5 @@ setup( url = "https://lammps.sandia.gov", description = "LAMMPS Molecular Dynamics Python package", license = "GPL", - packages=["lammps","lammps.mliap"], + packages=pkgs, ) From 82337c8cc574bc454a5ceb4618151fdaf04e24b9 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:58:41 -0400 Subject: [PATCH 083/100] silence compiler warnings when compiling with python 2 --- src/PYTHON/fix_python_invoke.cpp | 6 ++++-- src/PYTHON/fix_python_move.cpp | 14 +++++++------- src/PYTHON/pair_python.cpp | 4 ++-- 3 files changed, 13 insertions(+), 11 deletions(-) diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 6483e21f91..7d981a749e 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -92,8 +92,9 @@ int FixPythonInvoke::setmask() void FixPythonInvoke::end_of_step() { PyUtils::GIL lock; + char fmt[] = "O"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr); if (!result) { PyUtils::Print_Errors(); @@ -110,8 +111,9 @@ void FixPythonInvoke::post_force(int vflag) if (update->ntimestep % nevery != 0) return; PyUtils::GIL lock; + char fmt[] = "Oi"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr, vflag); if (!result) { PyUtils::Print_Errors(); diff --git a/src/PYTHON/fix_python_move.cpp b/src/PYTHON/fix_python_move.cpp index e04a32afe4..8ec2e1b74d 100644 --- a/src/PYTHON/fix_python_move.cpp +++ b/src/PYTHON/fix_python_move.cpp @@ -75,7 +75,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) : } PyObject *ptr = PY_VOID_POINTER(lmp); - PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr); + PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr); Py_CLEAR(ptr); if (!py_move_obj) { @@ -112,7 +112,7 @@ int FixPythonMove::setmask() void FixPythonMove::init() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr); + PyObject * result = PyObject_CallMethod((PyObject *)py_move, (char *)"init", nullptr); if (!result) { PyUtils::Print_Errors(); @@ -126,7 +126,7 @@ void FixPythonMove::init() void FixPythonMove::initial_integrate(int vflag) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate", (char *)"i", vflag); if (!result) { PyUtils::Print_Errors(); @@ -140,7 +140,7 @@ void FixPythonMove::initial_integrate(int vflag) void FixPythonMove::final_integrate() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate", nullptr); if (!result) { PyUtils::Print_Errors(); @@ -154,7 +154,7 @@ void FixPythonMove::final_integrate() void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate_respa", (char *)"iii", vflag, ilevel, iloop); if (!result) { PyUtils::Print_Errors(); @@ -168,7 +168,7 @@ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop) void FixPythonMove::final_integrate_respa(int ilevel, int iloop) { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate_respa", (char *)"ii", ilevel, iloop); if (!result) { PyUtils::Print_Errors(); @@ -182,7 +182,7 @@ void FixPythonMove::final_integrate_respa(int ilevel, int iloop) void FixPythonMove::reset_dt() { PyUtils::GIL lock; - PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr); + PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"reset_dt", nullptr); if (!result) { PyUtils::Print_Errors(); diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp index b147c9cb79..5020119e0d 100644 --- a/src/PYTHON/pair_python.cpp +++ b/src/PYTHON/pair_python.cpp @@ -288,7 +288,7 @@ void PairPython::coeff(int narg, char **arg) py_potential = (void *) py_pair_instance; - PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style); + PyObject *py_value = PyObject_CallMethod(py_pair_instance, (char *)"check_units", (char *)"s", update->unit_style); if (!py_value) { PyUtils::Print_Errors(); error->all(FLERR,"Calling 'check_units' function failed"); @@ -306,7 +306,7 @@ void PairPython::coeff(int narg, char **arg) } else skip_types[i] = 0; const int type = i; const char * name = arg[2+i]; - py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type); + py_value = PyObject_CallMethod(py_pair_instance, (char *)"map_coeff", (char *)"si", name, type); if (!py_value) { PyUtils::Print_Errors(); error->all(FLERR,"Calling 'map_coeff' function failed"); From 208d9f1fce3b8cb7c2f3bca4dc93d746c38982ef Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 09:59:15 -0400 Subject: [PATCH 084/100] use safe fread function to silence compiler warnings --- src/pair_lj_relres.cpp | 30 +++++++++++++++--------------- src/pair_morse.cpp | 11 ++++++----- 2 files changed, 21 insertions(+), 20 deletions(-) diff --git a/src/pair_lj_relres.cpp b/src/pair_lj_relres.cpp index 306b68684e..2131907f3a 100644 --- a/src/pair_lj_relres.cpp +++ b/src/pair_lj_relres.cpp @@ -607,18 +607,18 @@ void PairLJRelRes::read_restart(FILE *fp) int me = comm->me; for (i = 1; i <= atom->ntypes; i++) for (j = i; j <= atom->ntypes; j++) { - if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp); + if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error); MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world); if (setflag[i][j]) { if (me == 0) { - fread(&epsilonf[i][j],sizeof(double),1,fp); - fread(&sigmaf[i][j],sizeof(double),1,fp); - fread(&epsilon[i][j],sizeof(double),1,fp); - fread(&sigma[i][j],sizeof(double),1,fp); - fread(&cutf_inner[i][j],sizeof(double),1,fp); - fread(&cutf[i][j],sizeof(double),1,fp); - fread(&cut_inner[i][j],sizeof(double),1,fp); - fread(&cut[i][j],sizeof(double),1,fp); + utils::sfread(FLERR,&epsilonf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&sigmaf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf_inner[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error); } MPI_Bcast(&epsilonf[i][j],1,MPI_DOUBLE,0,world); MPI_Bcast(&sigmaf[i][j],1,MPI_DOUBLE,0,world); @@ -654,12 +654,12 @@ void PairLJRelRes::read_restart_settings(FILE *fp) { int me = comm->me; if (me == 0) { - fread(&cutf_inner_global,sizeof(double),1,fp); - fread(&cutf_global,sizeof(double),1,fp); - fread(&cut_inner_global,sizeof(double),1,fp); - fread(&cut_global,sizeof(double),1,fp); - fread(&offset_flag,sizeof(int),1,fp); - fread(&mix_flag,sizeof(int),1,fp); + utils::sfread(FLERR,&cutf_inner_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cutf_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error); + utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error); + utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error); } MPI_Bcast(&cutf_inner_global,1,MPI_DOUBLE,0,world); MPI_Bcast(&cutf_global,1,MPI_DOUBLE,0,world); diff --git a/src/pair_morse.cpp b/src/pair_morse.cpp index 6c67a8ef55..e6d924dab6 100644 --- a/src/pair_morse.cpp +++ b/src/pair_morse.cpp @@ -13,14 +13,15 @@ #include "pair_morse.h" -#include -#include #include "atom.h" #include "comm.h" -#include "force.h" -#include "neigh_list.h" -#include "memory.h" #include "error.h" +#include "force.h" +#include "memory.h" +#include "neigh_list.h" + +#include +#include using namespace LAMMPS_NS; From 3b2c0871ccc766a4e66174880f4524c86079d435 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:53:03 -0400 Subject: [PATCH 085/100] add and use Neighbor::modify_params() convenience function --- src/MC/fix_charge_regulation.cpp | 9 +-------- src/MC/fix_gcmc.cpp | 9 +-------- src/MC/fix_widom.cpp | 9 +-------- src/USER-MISC/fix_srp.cpp | 12 +----------- src/neighbor.cpp | 16 ++++++++++++++++ src/neighbor.h | 1 + 6 files changed, 21 insertions(+), 35 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 6775b4e4ca..17d3af3e34 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -187,14 +187,7 @@ void FixChargeRegulation::init() { // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // check that no deletable atoms are in atom->firstgroup diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index b946615b04..ff894d976b 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -580,14 +580,7 @@ void FixGCMC::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id); } // create a new group for temporary use with selected molecules diff --git a/src/MC/fix_widom.cpp b/src/MC/fix_widom.cpp index e898196e14..65f00811c1 100644 --- a/src/MC/fix_widom.cpp +++ b/src/MC/fix_widom.cpp @@ -342,14 +342,7 @@ void FixWidom::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - int narg = 4; - char **arg = new char*[narg];; - arg[0] = (char *) "exclude"; - arg[1] = (char *) "group"; - arg[2] = (char *) group_id.c_str(); - arg[3] = (char *) "all"; - neighbor->modify_params(narg,arg); - delete [] arg; + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // create a new group for temporary use with selected molecules diff --git a/src/USER-MISC/fix_srp.cpp b/src/USER-MISC/fix_srp.cpp index eb57da30e9..51047dfaa6 100644 --- a/src/USER-MISC/fix_srp.cpp +++ b/src/USER-MISC/fix_srp.cpp @@ -128,20 +128,10 @@ void FixSRP::init() // bond particles do not interact with other types // type bptype only interacts with itself - char* arg1[4]; - arg1[0] = (char *) "exclude"; - arg1[1] = (char *) "type"; - char c0[20]; - char c1[20]; - for (int z = 1; z < atom->ntypes; z++) { if (z == bptype) continue; - sprintf(c0, "%d", z); - arg1[2] = c0; - sprintf(c1, "%d", bptype); - arg1[3] = c1; - neighbor->modify_params(4, arg1); + neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype)); } } diff --git a/src/neighbor.cpp b/src/neighbor.cpp index 704d94c77c..ee4226f43e 100644 --- a/src/neighbor.cpp +++ b/src/neighbor.cpp @@ -2356,6 +2356,22 @@ void Neighbor::modify_params(int narg, char **arg) } } +/* ---------------------------------------------------------------------- + convenience function to allow modifying parameters from a single string +------------------------------------------------------------------------- */ + +void Neighbor::modify_params(const std::string &modcmd) +{ + auto args = utils::split_words(modcmd); + char **newarg = new char*[args.size()]; + int i=0; + for (const auto &arg : args) { + newarg[i++] = (char *)arg.c_str(); + } + modify_params(args.size(),newarg); + delete[] newarg; +} + /* ---------------------------------------------------------------------- remove the first group-group exclusion matching group1, group2 ------------------------------------------------------------------------- */ diff --git a/src/neighbor.h b/src/neighbor.h index b9b40bcf1a..0babfae9ef 100644 --- a/src/neighbor.h +++ b/src/neighbor.h @@ -118,6 +118,7 @@ class Neighbor : protected Pointers { void set(int, char **); // set neighbor style and skin distance void reset_timestep(bigint); // reset of timestep counter void modify_params(int, char**); // modify params that control builds + void modify_params(const std::string &); // convenience overload void exclusion_group_group_delete(int, int); // rm a group-group exclusion int exclude_setting(); // return exclude value to accelerator pkg From 533739b1287e04e431ddca4966a6d547763b80e8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:53:51 -0400 Subject: [PATCH 086/100] avoid NULL pointer dereference / slience warnings issued by static code analysis --- src/MC/fix_charge_regulation.cpp | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/src/MC/fix_charge_regulation.cpp b/src/MC/fix_charge_regulation.cpp index 17d3af3e34..4e7e5ab5a0 100644 --- a/src/MC/fix_charge_regulation.cpp +++ b/src/MC/fix_charge_regulation.cpp @@ -349,7 +349,7 @@ void FixChargeRegulation::forward_acid() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -408,7 +408,7 @@ void FixChargeRegulation::backward_acid() { double energy_before = energy_stored; double factor; int mask_tmp; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -481,7 +481,7 @@ void FixChargeRegulation::forward_base() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; double pos[3]; pos[0] = 0; pos[1] = 0; @@ -539,7 +539,7 @@ void FixChargeRegulation::backward_base() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; int mask_tmp; double pos[3]; pos[0] = 0; @@ -612,7 +612,7 @@ void FixChargeRegulation::forward_ions() { double energy_before = energy_stored; double factor; - double *dummyp = nullptr; + double dummyp[3]; int m1 = -1, m2 = -1; factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus / ((1 + ncation) * (1 + nanion)); @@ -647,7 +647,7 @@ void FixChargeRegulation::backward_ions() { double energy_before = energy_stored; double factor; int mask1_tmp = 0, mask2_tmp = 0; - double *dummyp = nullptr; + double dummyp[3]; int m1 = -1, m2 = -1; m1 = get_random_particle(cation_type, +1, 0, dummyp); @@ -726,7 +726,7 @@ void FixChargeRegulation::forward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp = nullptr; + double dummyp[3]; int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted if (salt_charge[0] <= -salt_charge[1]) { @@ -780,7 +780,7 @@ void FixChargeRegulation::backward_ions_multival() { double energy_before = energy_stored; double factor = 1; - double *dummyp = nullptr; // dummy pointer + double dummyp[3]; // dummy particle int mm[salt_charge_ratio + 1]; // particle ID array for all deleted ions double qq[salt_charge_ratio + 1]; // charge array for all deleted ions int mask_tmp[salt_charge_ratio + 1]; // temporary mask array From 680e6a389dac748000bf9a8e53a20b4e14cae26a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:54:04 -0400 Subject: [PATCH 087/100] use type cast consistently --- src/PYTHON/fix_python_invoke.cpp | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/PYTHON/fix_python_invoke.cpp b/src/PYTHON/fix_python_invoke.cpp index 7d981a749e..82baef909b 100644 --- a/src/PYTHON/fix_python_invoke.cpp +++ b/src/PYTHON/fix_python_invoke.cpp @@ -92,9 +92,8 @@ int FixPythonInvoke::setmask() void FixPythonInvoke::end_of_step() { PyUtils::GIL lock; - char fmt[] = "O"; - PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr); + PyObject * result = PyObject_CallFunction((PyObject*)pFunc, (char *)"O", (PyObject*)lmpPtr); if (!result) { PyUtils::Print_Errors(); From 9dbdb4386b6e74f020c594218fa4a175e056dd54 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:54:47 -0400 Subject: [PATCH 088/100] fix typo --- src/MC/fix_gcmc.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/MC/fix_gcmc.cpp b/src/MC/fix_gcmc.cpp index ff894d976b..3ab6327404 100644 --- a/src/MC/fix_gcmc.cpp +++ b/src/MC/fix_gcmc.cpp @@ -580,7 +580,7 @@ void FixGCMC::init() // neighbor list exclusion setup // turn off interactions between group all and the exclusion group - neighbor->modify_params(fmt::format("exclude group {} all",group_id); + neighbor->modify_params(fmt::format("exclude group {} all",group_id)); } // create a new group for temporary use with selected molecules From 8aed7e55b37752e574116e40d7210d63a99b4d32 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 14:59:37 -0400 Subject: [PATCH 089/100] add error check when updating variables in ::single() function --- src/pair_hybrid_scaled.cpp | 3 +++ 1 file changed, 3 insertions(+) diff --git a/src/pair_hybrid_scaled.cpp b/src/pair_hybrid_scaled.cpp index cdbccbf7c7..de8801fe24 100644 --- a/src/pair_hybrid_scaled.cpp +++ b/src/pair_hybrid_scaled.cpp @@ -396,6 +396,9 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq, double *vals = new double[nvars]; for (i = 0; i < nvars; ++i) { j = input->variable->find(scalevars[i].c_str()); + if (j < 0) + error->all(FLERR,fmt::format("Variable '{}' not found when updating " + "scale factors",scalevars[i])); vals[i] = input->variable->compute_equal(j); } for (i = 0; i < nstyles; ++i) { From b53822da467caed956bb205562abe74bd407374b Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 17:47:00 -0400 Subject: [PATCH 090/100] provide Command base class in command.h for deriving command styles from --- examples/plugins/helloplugin.cpp | 6 +- src/KIM/kim_command.h | 6 +- src/MESSAGE/message.h | 6 +- src/MESSAGE/server.h | 6 +- src/PLUGIN/plugin.cpp | 2 +- src/PLUGIN/plugin.h | 4 +- src/REPLICA/hyper.cpp | 2 +- src/REPLICA/hyper.h | 4 +- src/REPLICA/neb.cpp | 4 +- src/REPLICA/neb.h | 4 +- src/REPLICA/prd.cpp | 2 +- src/REPLICA/prd.h | 4 +- src/REPLICA/tad.cpp | 2 +- src/REPLICA/tad.h | 4 +- src/REPLICA/temper.cpp | 2 +- src/REPLICA/temper.h | 4 +- src/SPIN/neb_spin.cpp | 2 +- src/SPIN/neb_spin.h | 4 +- src/USER-COLVARS/group_ndx.h | 6 +- src/USER-COLVARS/ndx_group.h | 6 +- src/USER-MISC/temper_grem.cpp | 2 +- src/USER-MISC/temper_grem.h | 4 +- src/USER-MISC/temper_npt.cpp | 2 +- src/USER-MISC/temper_npt.h | 4 +- src/USER-PHONON/dynamical_matrix.cpp | 2 +- src/USER-PHONON/dynamical_matrix.h | 86 ++++++++++++++-------------- src/USER-PHONON/third_order.cpp | 2 +- src/USER-PHONON/third_order.h | 4 +- src/balance.cpp | 2 +- src/balance.h | 4 +- src/change_box.cpp | 2 +- src/change_box.h | 4 +- src/command.h | 29 ++++++++++ src/create_atoms.cpp | 2 +- src/create_atoms.h | 4 +- src/create_bonds.cpp | 2 +- src/create_bonds.h | 4 +- src/create_box.cpp | 12 ++-- src/create_box.h | 4 +- src/delete_atoms.cpp | 2 +- src/delete_atoms.h | 4 +- src/delete_bonds.cpp | 2 +- src/delete_bonds.h | 4 +- src/deprecated.h | 6 +- src/displace_atoms.cpp | 2 +- src/displace_atoms.h | 4 +- src/info.h | 6 +- src/minimize.cpp | 2 +- src/minimize.h | 4 +- src/read_data.cpp | 6 +- src/read_data.h | 4 +- src/read_dump.cpp | 6 +- src/read_dump.h | 4 +- src/read_restart.cpp | 2 +- src/read_restart.h | 4 +- src/replicate.cpp | 2 +- src/replicate.h | 4 +- src/rerun.cpp | 2 +- src/rerun.h | 4 +- src/reset_atom_ids.cpp | 2 +- src/reset_atom_ids.h | 4 +- src/reset_mol_ids.cpp | 2 +- src/reset_mol_ids.h | 4 +- src/run.cpp | 2 +- src/run.h | 4 +- src/set.h | 6 +- src/velocity.cpp | 2 +- src/velocity.h | 4 +- src/write_coeff.h | 6 +- src/write_data.cpp | 2 +- src/write_data.h | 4 +- src/write_dump.h | 6 +- src/write_restart.cpp | 2 +- src/write_restart.h | 4 +- 74 files changed, 203 insertions(+), 180 deletions(-) create mode 100644 src/command.h diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp index 11f2cfb891..f453add374 100644 --- a/examples/plugins/helloplugin.cpp +++ b/examples/plugins/helloplugin.cpp @@ -2,16 +2,16 @@ #include "lammpsplugin.h" #include "comm.h" +#include "command.h" #include "error.h" -#include "pointers.h" #include "version.h" #include namespace LAMMPS_NS { - class Hello : protected Pointers { + class Hello : protected Command { public: - Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; } diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index f327e4f2f3..64abeed9e0 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -62,13 +62,13 @@ CommandStyle(kim,KimCommand) #ifndef LMP_KIM_COMMAND_H #define LMP_KIM_COMMAND_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class KimCommand : protected Pointers { +class KimCommand : protected Command { public: - KimCommand(class LAMMPS *lmp) : Pointers(lmp) {}; + KimCommand(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h index f8b2d47a21..c499ff6537 100644 --- a/src/MESSAGE/message.h +++ b/src/MESSAGE/message.h @@ -20,13 +20,13 @@ CommandStyle(message,Message) #ifndef LMP_MESSAGE_H #define LMP_MESSAGE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Message : protected Pointers { +class Message : protected Command { public: - Message(class LAMMPS *lmp) : Pointers(lmp) {}; + Message(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h index 579f6ab6f1..63191ccf33 100644 --- a/src/MESSAGE/server.h +++ b/src/MESSAGE/server.h @@ -20,13 +20,13 @@ CommandStyle(server,Server) #ifndef LMP_SERVER_H #define LMP_SERVER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Server : protected Pointers { +class Server : protected Command { public: - Server(class LAMMPS *lmp) : Pointers(lmp) {}; + Server(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index b52e1a1959..a2f74060f1 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -41,7 +41,7 @@ namespace LAMMPS_NS /* ---------------------------------------------------------------------- */ - Plugin::Plugin(LAMMPS *lmp) : Pointers(lmp) {} + Plugin::Plugin(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 946b08db1a..61355f4113 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -21,12 +21,12 @@ CommandStyle(plugin,Plugin) #define LMP_PLUGIN_H #include "lammpsplugin.h" -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class Plugin : protected Pointers { + class Plugin : protected Command { public: Plugin(class LAMMPS *); void command(int, char **); diff --git a/src/REPLICA/hyper.cpp b/src/REPLICA/hyper.cpp index 5a9cf8520e..8eb1c143e9 100644 --- a/src/REPLICA/hyper.cpp +++ b/src/REPLICA/hyper.cpp @@ -38,7 +38,7 @@ enum{NOHYPER,GLOBAL,LOCAL}; /* ---------------------------------------------------------------------- */ -Hyper::Hyper(LAMMPS *lmp) : Pointers(lmp), dumplist(nullptr) {} +Hyper::Hyper(LAMMPS *lmp) : Command(lmp), dumplist(nullptr) {} /* ---------------------------------------------------------------------- perform hyperdynamics simulation diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index 1b05172bcf..faad58994b 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -20,11 +20,11 @@ CommandStyle(hyper,Hyper) #ifndef LMP_HYPER_H #define LMP_HYPER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Hyper : protected Pointers { +class Hyper : protected Command { public: Hyper(class LAMMPS *); ~Hyper() {} diff --git a/src/REPLICA/neb.cpp b/src/REPLICA/neb.cpp index a6a70fde38..7183bdd168 100644 --- a/src/REPLICA/neb.cpp +++ b/src/REPLICA/neb.cpp @@ -42,7 +42,7 @@ using namespace MathConst; /* ---------------------------------------------------------------------- */ -NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {} +NEB::NEB(LAMMPS *lmp) : Command(lmp), all(nullptr), rdist(nullptr) {} /* ---------------------------------------------------------------------- internal NEB constructor, called from TAD @@ -50,7 +50,7 @@ NEB::NEB(LAMMPS *lmp) : Pointers(lmp), all(nullptr), rdist(nullptr) {} NEB::NEB(LAMMPS *lmp, double etol_in, double ftol_in, int n1steps_in, int n2steps_in, int nevery_in, double *buf_init, double *buf_final) - : Pointers(lmp), all(nullptr), rdist(nullptr) + : Command(lmp), all(nullptr), rdist(nullptr) { double delx,dely,delz; diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index b53992711c..d8a9d5d3e4 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -20,11 +20,11 @@ CommandStyle(neb,NEB) #ifndef LMP_NEB_H #define LMP_NEB_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class NEB : protected Pointers { +class NEB : protected Command { public: NEB(class LAMMPS *); NEB(class LAMMPS *, double, double, int, int, int, double *, double *); diff --git a/src/REPLICA/prd.cpp b/src/REPLICA/prd.cpp index 40e5fc8833..2ba0340109 100644 --- a/src/REPLICA/prd.cpp +++ b/src/REPLICA/prd.cpp @@ -46,7 +46,7 @@ enum{SINGLE_PROC_DIRECT,SINGLE_PROC_MAP,MULTI_PROC}; /* ---------------------------------------------------------------------- */ -PRD::PRD(LAMMPS *lmp) : Pointers(lmp) {} +PRD::PRD(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- perform PRD simulation on one or more replicas diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index 3539987093..b331f7dc02 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -20,11 +20,11 @@ CommandStyle(prd,PRD) #ifndef LMP_PRD_H #define LMP_PRD_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class PRD : protected Pointers { +class PRD : protected Command { public: PRD(class LAMMPS *); ~PRD() {} diff --git a/src/REPLICA/tad.cpp b/src/REPLICA/tad.cpp index 0bab7a31c8..a849e7a242 100644 --- a/src/REPLICA/tad.cpp +++ b/src/REPLICA/tad.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TAD::TAD(LAMMPS *lmp) : Pointers(lmp) {} +TAD::TAD(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index d44b226643..3a525146a6 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -20,11 +20,11 @@ CommandStyle(tad,TAD) #ifndef LMP_TAD_H #define LMP_TAD_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TAD : protected Pointers { +class TAD : protected Command { public: TAD(class LAMMPS *); ~TAD(); diff --git a/src/REPLICA/temper.cpp b/src/REPLICA/temper.cpp index 63b34b9b1d..d3894060a3 100644 --- a/src/REPLICA/temper.cpp +++ b/src/REPLICA/temper.cpp @@ -40,7 +40,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Temper::Temper(LAMMPS *lmp) : Pointers(lmp) {} +Temper::Temper(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index 883ec30b94..ce7944da95 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -20,11 +20,11 @@ CommandStyle(temper,Temper) #ifndef LMP_TEMPER_H #define LMP_TEMPER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Temper : protected Pointers { +class Temper : protected Command { public: Temper(class LAMMPS *); ~Temper(); diff --git a/src/SPIN/neb_spin.cpp b/src/SPIN/neb_spin.cpp index cbb495db8e..88a0ffc402 100644 --- a/src/SPIN/neb_spin.cpp +++ b/src/SPIN/neb_spin.cpp @@ -67,7 +67,7 @@ static const char cite_neb_spin[] = /* ---------------------------------------------------------------------- */ -NEBSpin::NEBSpin(LAMMPS *lmp) : Pointers(lmp) { +NEBSpin::NEBSpin(LAMMPS *lmp) : Command(lmp) { if (lmp->citeme) lmp->citeme->add(cite_neb_spin); } diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 568eca0957..3dbae09297 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -20,11 +20,11 @@ CommandStyle(neb/spin,NEBSpin) #ifndef LMP_NEB_SPIN_H #define LMP_NEB_SPIN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class NEBSpin : protected Pointers { +class NEBSpin : protected Command { public: NEBSpin(class LAMMPS *); ~NEBSpin(); diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index fa15f0e82e..46ba86c860 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -22,13 +22,13 @@ CommandStyle(group2ndx,Group2Ndx) #ifndef LMP_GROUP_NDX_H #define LMP_GROUP_NDX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Group2Ndx : protected Pointers { +class Group2Ndx : protected Command { public: - Group2Ndx(class LAMMPS *lmp) : Pointers(lmp) {}; + Group2Ndx(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: void write_group(FILE *, int); diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index ceca1f9570..1c881a65bf 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -22,14 +22,14 @@ CommandStyle(ndx2group,Ndx2Group) #ifndef LMP_NDX_GROUP_H #define LMP_NDX_GROUP_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class Ndx2Group : protected Pointers { +class Ndx2Group : protected Command { public: - Ndx2Group(class LAMMPS *lmp) : Pointers(lmp) {}; + Ndx2Group(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); void create(const std::string &, const std::vector &); }; diff --git a/src/USER-MISC/temper_grem.cpp b/src/USER-MISC/temper_grem.cpp index 3b987aaad2..ee60ab375d 100644 --- a/src/USER-MISC/temper_grem.cpp +++ b/src/USER-MISC/temper_grem.cpp @@ -40,7 +40,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TemperGrem::TemperGrem(LAMMPS *lmp) : Pointers(lmp) {} +TemperGrem::TemperGrem(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index f379814c61..b720aeb45c 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -20,11 +20,11 @@ CommandStyle(temper/grem,TemperGrem) #ifndef LMP_TEMPER_GREM_H #define LMP_TEMPER_GREM_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TemperGrem : protected Pointers { +class TemperGrem : protected Command { public: TemperGrem(class LAMMPS *); ~TemperGrem(); diff --git a/src/USER-MISC/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp index 08fa2246c3..1ed55a9cf3 100644 --- a/src/USER-MISC/temper_npt.cpp +++ b/src/USER-MISC/temper_npt.cpp @@ -42,7 +42,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {} +TemperNPT::TemperNPT(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h index 6beae68c6a..5c285f083c 100644 --- a/src/USER-MISC/temper_npt.h +++ b/src/USER-MISC/temper_npt.h @@ -21,11 +21,11 @@ CommandStyle(temper/npt,TemperNPT) #ifndef LMP_TEMPERNPT_H #define LMP_TEMPERNPT_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class TemperNPT : protected Pointers { +class TemperNPT : protected Command { public: TemperNPT(class LAMMPS *); ~TemperNPT(); diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp index 798b50fdf7..0476c734a5 100644 --- a/src/USER-PHONON/dynamical_matrix.cpp +++ b/src/USER-PHONON/dynamical_matrix.cpp @@ -32,7 +32,7 @@ enum{REGULAR,ESKM}; /* ---------------------------------------------------------------------- */ -DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(nullptr) +DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Command(lmp), fp(nullptr) { external_force_clear = 1; } diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/USER-PHONON/dynamical_matrix.h index 8ff11044ea..30baeda27f 100644 --- a/src/USER-PHONON/dynamical_matrix.h +++ b/src/USER-PHONON/dynamical_matrix.h @@ -11,62 +11,62 @@ CommandStyle(dynamical_matrix,DynamicalMatrix) #ifndef LMP_DYNAMICAL_MATRIX_H #define LMP_DYNAMICAL_MATRIX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class DynamicalMatrix : protected Pointers { - public: - DynamicalMatrix(class LAMMPS *); - virtual ~DynamicalMatrix(); - void command(int, char **); - void setup(); +class DynamicalMatrix : protected Command { + public: + DynamicalMatrix(class LAMMPS *); + virtual ~DynamicalMatrix(); + void command(int, char **); + void setup(); - protected: - int eflag,vflag; // flags for energy/virial computation - int external_force_clear; // clear forces locally or externally + protected: + int eflag,vflag; // flags for energy/virial computation + int external_force_clear; // clear forces locally or externally - int triclinic; // 0 if domain is orthog, 1 if triclinic - int pairflag; + int triclinic; // 0 if domain is orthog, 1 if triclinic + int pairflag; - int pair_compute_flag; // 0 if pair->compute is skipped - int kspace_compute_flag; // 0 if kspace->compute is skipped + int pair_compute_flag; // 0 if pair->compute is skipped + int kspace_compute_flag; // 0 if kspace->compute is skipped - int nvec; // local atomic dof = length of xvec + int nvec; // local atomic dof = length of xvec - void update_force(); - void force_clear(); - virtual void openfile(const char* filename); + void update_force(); + void force_clear(); + virtual void openfile(const char* filename); - private: - void options(int, char **); - void calculateMatrix(); - void dynmat_clear(double **dynmat); - void create_groupmap(); - void writeMatrix(double **dynmat); - void convert_units(const char *style); - void displace_atom(int local_idx, int direction, int magnitude); + private: + void options(int, char **); + void calculateMatrix(); + void dynmat_clear(double **dynmat); + void create_groupmap(); + void writeMatrix(double **dynmat); + void convert_units(const char *style); + void displace_atom(int local_idx, int direction, int magnitude); - double conversion; - double conv_energy; - double conv_distance; - double conv_mass; - double del; - int igroup,groupbit; - bigint gcount; // number of atoms in group - bigint dynlen; // rank of dynamical matrix - int scaleflag; - int me; - bigint *groupmap; + double conversion; + double conv_energy; + double conv_distance; + double conv_mass; + double del; + int igroup,groupbit; + bigint gcount; // number of atoms in group + bigint dynlen; // rank of dynamical matrix + int scaleflag; + int me; + bigint *groupmap; - int compressed; // 1 if dump file is written compressed, 0 no - int binaryflag; // 1 if dump file is written binary, 0 no - int file_opened; // 1 if openfile method has been called, 0 no - int file_flag; // 1 custom file name, 0 dynmat.dat + int compressed; // 1 if dump file is written compressed, 0 no + int binaryflag; // 1 if dump file is written binary, 0 no + int file_opened; // 1 if openfile method has been called, 0 no + int file_flag; // 1 custom file name, 0 dynmat.dat - FILE *fp; - }; + FILE *fp; +}; } diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp index 875490d643..ebcc682d7a 100644 --- a/src/USER-PHONON/third_order.cpp +++ b/src/USER-PHONON/third_order.cpp @@ -32,7 +32,7 @@ enum{REGULAR,BALLISTICO}; /* ---------------------------------------------------------------------- */ -ThirdOrder::ThirdOrder(LAMMPS *lmp) : Pointers(lmp), fp(nullptr) +ThirdOrder::ThirdOrder(LAMMPS *lmp) : Command(lmp), fp(nullptr) { external_force_clear = 1; } diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h index 83062b6b1f..87b0c695f6 100644 --- a/src/USER-PHONON/third_order.h +++ b/src/USER-PHONON/third_order.h @@ -12,11 +12,11 @@ CommandStyle(third_order,ThirdOrder) #ifndef LMP_THIRD_ORDER_H #define LMP_THIRD_ORDER_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { - class ThirdOrder : protected Pointers { + class ThirdOrder : protected Command { public: ThirdOrder(class LAMMPS *); virtual ~ThirdOrder(); diff --git a/src/balance.cpp b/src/balance.cpp index 6294e023b3..bf037e8f8f 100644 --- a/src/balance.cpp +++ b/src/balance.cpp @@ -51,7 +51,7 @@ enum{X,Y,Z}; /* ---------------------------------------------------------------------- */ -Balance::Balance(LAMMPS *lmp) : Pointers(lmp) +Balance::Balance(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/balance.h b/src/balance.h index 424da33757..25ccac85ae 100644 --- a/src/balance.h +++ b/src/balance.h @@ -20,11 +20,11 @@ CommandStyle(balance,Balance) #ifndef LMP_BALANCE_H #define LMP_BALANCE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Balance : protected Pointers { +class Balance : protected Command { public: class RCB *rcb; class FixStore *fixstore; // per-atom weights stored in FixStore diff --git a/src/change_box.cpp b/src/change_box.cpp index ba99e1b6e1..4471d85132 100644 --- a/src/change_box.cpp +++ b/src/change_box.cpp @@ -35,7 +35,7 @@ enum{X=0,Y,Z,YZ,XZ,XY}; /* ---------------------------------------------------------------------- */ -ChangeBox::ChangeBox(LAMMPS *lmp) : Pointers(lmp) {} +ChangeBox::ChangeBox(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/change_box.h b/src/change_box.h index d8a057f9a6..2f6802194b 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -20,11 +20,11 @@ CommandStyle(change_box,ChangeBox) #ifndef LMP_CHANGE_BOX_H #define LMP_CHANGE_BOX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ChangeBox : protected Pointers { +class ChangeBox : protected Command { public: ChangeBox(class LAMMPS *); void command(int, char **); diff --git a/src/command.h b/src/command.h new file mode 100644 index 0000000000..6abbc167ac --- /dev/null +++ b/src/command.h @@ -0,0 +1,29 @@ +/* -*- c++ -*- ---------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +#ifndef LMP_COMMAND_H +#define LMP_COMMAND_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class Command : protected Pointers { + public: + Command(class LAMMPS *lmp) : Pointers(lmp) {}; + virtual void command(int, char **) = 0; +}; + +} + +#endif diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp index 46aff081d9..7591ae7587 100644 --- a/src/create_atoms.cpp +++ b/src/create_atoms.cpp @@ -52,7 +52,7 @@ enum{NONE,RATIO,SUBSET}; /* ---------------------------------------------------------------------- */ -CreateAtoms::CreateAtoms(LAMMPS *lmp) : Pointers(lmp), basistype(nullptr) {} +CreateAtoms::CreateAtoms(LAMMPS *lmp) : Command(lmp), basistype(nullptr) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_atoms.h b/src/create_atoms.h index 5508752f00..8f0e016192 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -20,11 +20,11 @@ CommandStyle(create_atoms,CreateAtoms) #ifndef LMP_CREATE_ATOMS_H #define LMP_CREATE_ATOMS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateAtoms : protected Pointers { +class CreateAtoms : protected Command { public: CreateAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp index 494e743c05..bedbe4b436 100644 --- a/src/create_bonds.cpp +++ b/src/create_bonds.cpp @@ -38,7 +38,7 @@ enum{MANY,SBOND,SANGLE,SDIHEDRAL,SIMPROPER}; /* ---------------------------------------------------------------------- */ -CreateBonds::CreateBonds(LAMMPS *lmp) : Pointers(lmp) {} +CreateBonds::CreateBonds(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_bonds.h b/src/create_bonds.h index eea99b0113..f25cb6d1bc 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -20,11 +20,11 @@ CommandStyle(create_bonds,CreateBonds) #ifndef LMP_CREATE_BONDS_H #define LMP_CREATE_BONDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateBonds : protected Pointers { +class CreateBonds : protected Command { public: CreateBonds(class LAMMPS *); void command(int, char **); diff --git a/src/create_box.cpp b/src/create_box.cpp index 000fb42495..1350b6f392 100644 --- a/src/create_box.cpp +++ b/src/create_box.cpp @@ -12,22 +12,24 @@ ------------------------------------------------------------------------- */ #include "create_box.h" -#include + #include "atom.h" #include "atom_vec.h" +#include "comm.h" #include "domain.h" +#include "error.h" +#include "force.h" #include "region.h" #include "region_prism.h" -#include "force.h" -#include "comm.h" #include "update.h" -#include "error.h" + +#include using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -CreateBox::CreateBox(LAMMPS *lmp) : Pointers(lmp) {} +CreateBox::CreateBox(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/create_box.h b/src/create_box.h index 740769b4de..846af6bcee 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -20,11 +20,11 @@ CommandStyle(create_box,CreateBox) #ifndef LMP_CREATE_BOX_H #define LMP_CREATE_BOX_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class CreateBox : protected Pointers { +class CreateBox : protected Command { public: CreateBox(class LAMMPS *); void command(int, char **); diff --git a/src/delete_atoms.cpp b/src/delete_atoms.cpp index 3dbf21ae59..326201c9a2 100644 --- a/src/delete_atoms.cpp +++ b/src/delete_atoms.cpp @@ -41,7 +41,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Pointers(lmp) {} +DeleteAtoms::DeleteAtoms(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/delete_atoms.h b/src/delete_atoms.h index 5eab7f6ba7..e43bebfa54 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -20,12 +20,12 @@ CommandStyle(delete_atoms,DeleteAtoms) #ifndef LMP_DELETE_ATOMS_H #define LMP_DELETE_ATOMS_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class DeleteAtoms : protected Pointers { +class DeleteAtoms : protected Command { public: DeleteAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/delete_bonds.cpp b/src/delete_bonds.cpp index 5a487743e1..2bb46e7564 100644 --- a/src/delete_bonds.cpp +++ b/src/delete_bonds.cpp @@ -30,7 +30,7 @@ enum{MULTI,ATOM,BOND,ANGLE,DIHEDRAL,IMPROPER,STATS}; /* ---------------------------------------------------------------------- */ -DeleteBonds::DeleteBonds(LAMMPS *lmp) : Pointers(lmp) {} +DeleteBonds::DeleteBonds(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 60d76b9086..2f255e12d6 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -20,11 +20,11 @@ CommandStyle(delete_bonds,DeleteBonds) #ifndef LMP_DELETE_BONDS_H #define LMP_DELETE_BONDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class DeleteBonds : protected Pointers { +class DeleteBonds : protected Command { public: DeleteBonds(class LAMMPS *); void command(int, char **); diff --git a/src/deprecated.h b/src/deprecated.h index aceb1181c1..4b6cba7f30 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -26,13 +26,13 @@ CommandStyle(kim_query,Deprecated) #ifndef LMP_DEPRECATED_H #define LMP_DEPRECATED_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Deprecated : protected Pointers { +class Deprecated : protected Command { public: - Deprecated(class LAMMPS *lmp) : Pointers(lmp) {}; + Deprecated(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp index dd71e944ef..6bc3b0ab35 100644 --- a/src/displace_atoms.cpp +++ b/src/displace_atoms.cpp @@ -42,7 +42,7 @@ enum{MOVE,RAMP,RANDOM,ROTATE}; /* ---------------------------------------------------------------------- */ -DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Pointers(lmp) +DisplaceAtoms::DisplaceAtoms(LAMMPS *lmp) : Command(lmp) { mvec = nullptr; } diff --git a/src/displace_atoms.h b/src/displace_atoms.h index 737d55dbdd..98247b7244 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -20,11 +20,11 @@ CommandStyle(displace_atoms,DisplaceAtoms) #ifndef LMP_DISPLACE_ATOMS_H #define LMP_DISPLACE_ATOMS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class DisplaceAtoms : protected Pointers { +class DisplaceAtoms : protected Command { public: DisplaceAtoms(class LAMMPS *); ~DisplaceAtoms(); diff --git a/src/info.h b/src/info.h index d8fa23489e..536a93c559 100644 --- a/src/info.h +++ b/src/info.h @@ -20,15 +20,15 @@ CommandStyle(info,Info) #ifndef LMP_INFO_H #define LMP_INFO_H -#include "pointers.h" +#include "command.h" #include namespace LAMMPS_NS { -class Info : protected Pointers { +class Info : protected Command { public: - Info(class LAMMPS *lmp) : Pointers(lmp) {}; + Info(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); bool is_active(const char *, const char *); diff --git a/src/minimize.cpp b/src/minimize.cpp index 8e55d6e0ea..1fb0d219cd 100644 --- a/src/minimize.cpp +++ b/src/minimize.cpp @@ -25,7 +25,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Minimize::Minimize(LAMMPS *lmp) : Pointers(lmp) {} +Minimize::Minimize(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/minimize.h b/src/minimize.h index 42a2fcaf02..10b244130a 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -20,11 +20,11 @@ CommandStyle(minimize,Minimize) #ifndef LMP_MINIMIZE_H #define LMP_MINIMIZE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Minimize : protected Pointers { +class Minimize : protected Command { public: Minimize(class LAMMPS *); void command(int, char **); diff --git a/src/read_data.cpp b/src/read_data.cpp index cc3b2e5965..c0085f19d1 100644 --- a/src/read_data.cpp +++ b/src/read_data.cpp @@ -11,10 +11,6 @@ See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "read_data.h" #include "angle.h" @@ -66,7 +62,7 @@ const char *suffixes[] = {"/cuda","/gpu","/opt","/omp","/kk", /* ---------------------------------------------------------------------- */ -ReadData::ReadData(LAMMPS *lmp) : Pointers(lmp) +ReadData::ReadData(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); line = new char[MAXLINE]; diff --git a/src/read_data.h b/src/read_data.h index 68b40fc529..d251259a08 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -20,11 +20,11 @@ CommandStyle(read_data,ReadData) #ifndef LMP_READ_DATA_H #define LMP_READ_DATA_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadData : protected Pointers { +class ReadData : protected Command { public: ReadData(class LAMMPS *); ~ReadData(); diff --git a/src/read_dump.cpp b/src/read_dump.cpp index 0282e2d039..ddb793c629 100644 --- a/src/read_dump.cpp +++ b/src/read_dump.cpp @@ -15,10 +15,6 @@ Contributing author: Timothy Sirk (ARL) ------------------------------------------------------------------------- */ -// lmptype.h must be first b/c this file uses MAXBIGINT and includes mpi.h -// due to OpenMPI bug which sets INT64_MAX via its mpi.h -// before lmptype.h can set flags to insure it is done correctly - #include "read_dump.h" #include "atom.h" @@ -46,7 +42,7 @@ enum{NOADD,YESADD,KEEPADD}; /* ---------------------------------------------------------------------- */ -ReadDump::ReadDump(LAMMPS *lmp) : Pointers(lmp) +ReadDump::ReadDump(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/read_dump.h b/src/read_dump.h index 93fb4bc713..ba59cc9224 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -22,11 +22,11 @@ CommandStyle(read_dump,ReadDump) #ifndef LMP_READ_DUMP_H #define LMP_READ_DUMP_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadDump : protected Pointers { +class ReadDump : protected Command { public: ReadDump(class LAMMPS *); ~ReadDump(); diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 9e8fbce91c..7983a25ae9 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ReadRestart::ReadRestart(LAMMPS *lmp) : Pointers(lmp) {} +ReadRestart::ReadRestart(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/read_restart.h b/src/read_restart.h index 99b37cfa45..3a2c7965b3 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -20,11 +20,11 @@ CommandStyle(read_restart,ReadRestart) #ifndef LMP_READ_RESTART_H #define LMP_READ_RESTART_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ReadRestart : protected Pointers { +class ReadRestart : protected Command { public: ReadRestart(class LAMMPS *); void command(int, char **); diff --git a/src/replicate.cpp b/src/replicate.cpp index 6877ec091c..95bf615d04 100644 --- a/src/replicate.cpp +++ b/src/replicate.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Replicate::Replicate(LAMMPS *lmp) : Pointers(lmp) {} +Replicate::Replicate(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/replicate.h b/src/replicate.h index 58c0010aa3..fd865a9c71 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -20,11 +20,11 @@ CommandStyle(replicate,Replicate) #ifndef LMP_REPLICATE_H #define LMP_REPLICATE_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Replicate : protected Pointers { +class Replicate : protected Command { public: Replicate(class LAMMPS *); void command(int, char **); diff --git a/src/rerun.cpp b/src/rerun.cpp index 8615b02d95..9571724e2d 100644 --- a/src/rerun.cpp +++ b/src/rerun.cpp @@ -29,7 +29,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Rerun::Rerun(LAMMPS *lmp) : Pointers(lmp) {} +Rerun::Rerun(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/rerun.h b/src/rerun.h index ea1d0221c3..57aa32227f 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -20,11 +20,11 @@ CommandStyle(rerun,Rerun) #ifndef LMP_RERUN_H #define LMP_RERUN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Rerun : protected Pointers { +class Rerun : protected Command { public: Rerun(class LAMMPS *); void command(int, char **); diff --git a/src/reset_atom_ids.cpp b/src/reset_atom_ids.cpp index 7298103b80..47dae3cb56 100644 --- a/src/reset_atom_ids.cpp +++ b/src/reset_atom_ids.cpp @@ -43,7 +43,7 @@ static int compare_coords(const int, const int, void *); /* ---------------------------------------------------------------------- */ -ResetIDs::ResetIDs(LAMMPS *lmp) : Pointers(lmp) {} +ResetIDs::ResetIDs(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/reset_atom_ids.h b/src/reset_atom_ids.h index 02a7f77e8d..a017abbbc8 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atom_ids.h @@ -20,11 +20,11 @@ CommandStyle(reset_atom_ids,ResetIDs) #ifndef LMP_RESET_IDS_H #define LMP_RESET_IDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ResetIDs : protected Pointers { +class ResetIDs : protected Command { public: struct AtomRvous { bigint ibin; diff --git a/src/reset_mol_ids.cpp b/src/reset_mol_ids.cpp index aed26b4568..39f7307ca1 100644 --- a/src/reset_mol_ids.cpp +++ b/src/reset_mol_ids.cpp @@ -32,7 +32,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Pointers(lmp) { +ResetMolIDs::ResetMolIDs(LAMMPS *lmp) : Command(lmp) { cfa = nullptr; cca = nullptr; diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index fbb6fceb03..c25f64fe43 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -20,11 +20,11 @@ CommandStyle(reset_mol_ids,ResetMolIDs) #ifndef LMP_RESET_MOL_IDS_H #define LMP_RESET_MOL_IDS_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class ResetMolIDs : protected Pointers { +class ResetMolIDs : protected Command { public: ResetMolIDs(class LAMMPS *); ~ResetMolIDs(); diff --git a/src/run.cpp b/src/run.cpp index c503e174ff..379cf8015a 100644 --- a/src/run.cpp +++ b/src/run.cpp @@ -31,7 +31,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -Run::Run(LAMMPS *lmp) : Pointers(lmp) {} +Run::Run(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/run.h b/src/run.h index 5578ea9598..a9a4a556f0 100644 --- a/src/run.h +++ b/src/run.h @@ -20,11 +20,11 @@ CommandStyle(run,Run) #ifndef LMP_RUN_H #define LMP_RUN_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Run : protected Pointers { +class Run : protected Command { public: Run(class LAMMPS *); void command(int, char **); diff --git a/src/set.h b/src/set.h index 29f1ea526e..02e81b057a 100644 --- a/src/set.h +++ b/src/set.h @@ -20,13 +20,13 @@ CommandStyle(set,Set) #ifndef LMP_SET_H #define LMP_SET_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Set : protected Pointers { +class Set : protected Command { public: - Set(class LAMMPS *lmp) : Pointers(lmp) {}; + Set(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); private: diff --git a/src/velocity.cpp b/src/velocity.cpp index f4483074aa..e0c80baa91 100644 --- a/src/velocity.cpp +++ b/src/velocity.cpp @@ -42,7 +42,7 @@ enum{NONE,CONSTANT,EQUAL,ATOM}; /* ---------------------------------------------------------------------- */ -Velocity::Velocity(LAMMPS *lmp) : Pointers(lmp) {} +Velocity::Velocity(LAMMPS *lmp) : Command(lmp) {} /* ---------------------------------------------------------------------- */ diff --git a/src/velocity.h b/src/velocity.h index e14c0d0d1c..5c54302a1e 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -20,11 +20,11 @@ CommandStyle(velocity,Velocity) #ifndef LMP_VELOCITY_H #define LMP_VELOCITY_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class Velocity : protected Pointers { +class Velocity : protected Command { public: Velocity(class LAMMPS *); void command(int, char **); diff --git a/src/write_coeff.h b/src/write_coeff.h index b995e60d63..2555454db0 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -20,13 +20,13 @@ CommandStyle(write_coeff,WriteCoeff) #ifndef LMP_WRITE_COEFF_H #define LMP_WRITE_COEFF_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteCoeff : protected Pointers { +class WriteCoeff : protected Command { public: - WriteCoeff(class LAMMPS *lmp) : Pointers(lmp) {}; + WriteCoeff(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/write_data.cpp b/src/write_data.cpp index 6d10359e8b..d8b37ca265 100644 --- a/src/write_data.cpp +++ b/src/write_data.cpp @@ -41,7 +41,7 @@ enum{ELLIPSOID,LINE,TRIANGLE,BODY}; // also in AtomVecHybrid /* ---------------------------------------------------------------------- */ -WriteData::WriteData(LAMMPS *lmp) : Pointers(lmp) +WriteData::WriteData(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/write_data.h b/src/write_data.h index a4e71c9cda..c9ba5a4a52 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -20,11 +20,11 @@ CommandStyle(write_data,WriteData) #ifndef LMP_WRITE_DATA_H #define LMP_WRITE_DATA_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteData : protected Pointers { +class WriteData : protected Command { public: WriteData(class LAMMPS *); void command(int, char **); diff --git a/src/write_dump.h b/src/write_dump.h index db39a75d4b..5d1499934a 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -20,13 +20,13 @@ CommandStyle(write_dump,WriteDump) #ifndef LMP_WRITE_DUMP_H #define LMP_WRITE_DUMP_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteDump : protected Pointers { +class WriteDump : protected Command { public: - WriteDump(class LAMMPS *lmp) : Pointers(lmp) {}; + WriteDump(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; diff --git a/src/write_restart.cpp b/src/write_restart.cpp index afe1d2d528..ce0eddcd73 100644 --- a/src/write_restart.cpp +++ b/src/write_restart.cpp @@ -43,7 +43,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -WriteRestart::WriteRestart(LAMMPS *lmp) : Pointers(lmp) +WriteRestart::WriteRestart(LAMMPS *lmp) : Command(lmp) { MPI_Comm_rank(world,&me); MPI_Comm_size(world,&nprocs); diff --git a/src/write_restart.h b/src/write_restart.h index a4a606482e..0b8826f10b 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -20,11 +20,11 @@ CommandStyle(write_restart,WriteRestart) #ifndef LMP_WRITE_RESTART_H #define LMP_WRITE_RESTART_H -#include "pointers.h" +#include "command.h" namespace LAMMPS_NS { -class WriteRestart : protected Pointers { +class WriteRestart : protected Command { public: WriteRestart(class LAMMPS *); void command(int, char **); From 81578d99343f1b53bec4ec5e6c65651de1fbac19 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Tue, 13 Apr 2021 17:47:21 -0400 Subject: [PATCH 091/100] update docs for change in class topology --- doc/graphviz/lammps-classes.dot | 10 +++++++--- doc/src/Developer_org.rst | 16 ++++++++-------- doc/src/JPG/lammps-classes.png | Bin 260274 -> 293226 bytes doc/src/Modify_command.rst | 17 +++++++++-------- 4 files changed, 24 insertions(+), 19 deletions(-) diff --git a/doc/graphviz/lammps-classes.dot b/doc/graphviz/lammps-classes.dot index 3c2d2f418d..390dd2cc4b 100644 --- a/doc/graphviz/lammps-classes.dot +++ b/doc/graphviz/lammps-classes.dot @@ -18,8 +18,8 @@ digraph lammps { Up [shape=box label="Update" color=blue] Un [shape=box label="Universe" color=blue] Ti [shape=box label="Timer" color=blue] - Lt [label="Lattice"] Rg [label="Region" color=red] + Lt [label="Lattice"] Rb [shape=box label="RegionBlock"] Rs [shape=box label="RegionSphere"] Av [label="AtomVec" color=red] @@ -34,6 +34,7 @@ digraph lammps { Du [label="Dump" color=red] Fi [label="Fix" color=red] Cp [label="Compute" color=red] + Cm [label="Command" color=red] Th [label="Thermo"] Va [label="Variable"] Ew [shape=box label="Ewald"] @@ -71,16 +72,19 @@ digraph lammps { Dg [shape=box label="DumpCFG"] Ve [shape=box label="Verlet"] Rr [shape=box label="Respa"] + Ru [shape=box label="Run"] + Se [shape=box label="Set"] Pt [shape=box label="PPPMTIP4P"] Vs [shape=box label="VerletSplit"] Ro [shape=box label="RespaOMP"] Mc [shape=box label="MinCG"] Mf [shape=box label="MinFire"] La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2] - Do -> {Lt Rg} [penwidth=2] + Do -> {Rg Lt} [penwidth=2] Rg -> {Rb Rs} [style=dashed penwidth=2] Co -> {Cb Ct} [style=dashed penwidth=2] - In -> Va [penwidth=2] + In -> {Va Cm} [penwidth=2] + Cm -> {Ru Se} [style=dashed penwidth=2] Mo -> {Fi Cp} [penwidth=2] Fo -> {Pa Bo An Di Im Ks} [penwidth=2] Ks -> {Ew Pp} [style=dashed penwidth=2] diff --git a/doc/src/Developer_org.rst b/doc/src/Developer_org.rst index 6ecccf084d..133d567cb3 100644 --- a/doc/src/Developer_org.rst +++ b/doc/src/Developer_org.rst @@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries which may have different conventions, all C and C++ header files have a ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a ``.c`` extension. A small number of C++ classes and utility functions -are implemented with only a ``.h`` file. Examples are the Pointer class -or the MathVec functions. +are implemented with only a ``.h`` file. Examples are the Pointers and +Commands classes or the MathVec functions. Class topology -------------- @@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in between runs. For these an instance of the class is created, its command() method called and then, after completion, the class instance deleted. Examples for this are the create_box, create_atoms, minimize, -run, or velocity command styles. +run, set, or velocity command styles. For all those ``styles`` certain naming conventions are employed: for the fix nve command the class is called FixNVE and the source files are @@ -175,11 +175,11 @@ follows: - The Input class reads and processes input input strings and files, stores variables, and invokes :doc:`commands `. -- As discussed above, command style classes are directly derived from - the Pointers class. They provide input script commands that perform - one-time operations before/after/between simulations or which invoke a - simulation. They are instantiated from within the Input class, - invoked, then immediately destructed. +- Command style classes are derived from the Command class. They provide + input script commands that perform one-time operations + before/after/between simulations or which invoke a simulation. 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znBfGTuritiZNF+w4%sYB9=sbzkhq`oUxaW;&5K2z^27qz_Um!mP`9x#rcpA{F*iq;}mEeG}#b75ns+D04C(|=t_0{q^9B_Nu^Gn zUS4VTK}Vg@xbkc0k{YObQyb{5T9k{Nd^Nzm;#N*G`*3&8qX|CGQQuv=Ii-T?phOE5 z1IFwBOvst^c5nw091{pLRk5)Nj{^% zvYURQwgb)}N-lN^qULz5=09BS3j``&{{eW=ydT!58O)F+!}9>zrzbSlf(aG1id_@9 zEJJmHyTHMy{6l0JSy>A4R;R;%!K~sU%FMaIWt!JNOG5llmUx!G{@4(dar4Ho%wv9e Q;t#eHCXYWR_xS0*0HRiBzW@LL diff --git a/doc/src/Modify_command.rst b/doc/src/Modify_command.rst index 2d0a1d99d9..e0e3ecbb8d 100644 --- a/doc/src/Modify_command.rst +++ b/doc/src/Modify_command.rst @@ -1,14 +1,15 @@ Input script command style ========================== -New commands can be added to LAMMPS input scripts by adding new -classes that have a "command" method. For example, the create_atoms, -read_data, velocity, and run commands are all implemented in this -fashion. When such a command is encountered in the LAMMPS input -script, LAMMPS simply creates a class with the corresponding name, -invokes the "command" method of the class, and passes it the arguments -from the input script. The command method can perform whatever -operations it wishes on LAMMPS data structures. +New commands can be added to LAMMPS input scripts by adding new classes +that are derived from the Command class and thus must have a "command" +method. For example, the create_atoms, read_data, velocity, and run +commands are all implemented in this fashion. When such a command is +encountered in the LAMMPS input script, LAMMPS simply creates a class +instance with the corresponding name, invokes the "command" method of +the class, and passes it the arguments from the input script. The +command method can perform whatever operations it wishes on LAMMPS data +structures. The single method your new class must define is as follows: From 75579fc1003b815bdecd8e62f2e0d0de0daa13c8 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 07:05:00 -0400 Subject: [PATCH 092/100] take advantage of having the common Command base class to unify code paths --- doc/src/Developer_plugins.rst | 61 +++++++++++++----------------- examples/plugins/helloplugin.cpp | 11 +++--- src/KIM/kim_command.h | 2 +- src/MESSAGE/message.h | 2 +- src/MESSAGE/server.h | 2 +- src/PLUGIN/plugin.cpp | 2 +- src/PLUGIN/plugin.h | 2 +- src/REPLICA/hyper.h | 2 +- src/REPLICA/neb.h | 2 +- src/REPLICA/prd.h | 2 +- src/REPLICA/tad.h | 2 +- src/REPLICA/temper.h | 2 +- src/SPIN/neb_spin.h | 2 +- src/USER-COLVARS/group_ndx.h | 2 +- src/USER-COLVARS/ndx_group.h | 2 +- src/USER-MISC/temper_grem.h | 2 +- src/USER-MISC/temper_npt.h | 2 +- src/USER-PHONON/dynamical_matrix.h | 2 +- src/USER-PHONON/third_order.h | 2 +- src/balance.h | 2 +- src/change_box.h | 2 +- src/create_atoms.h | 2 +- src/create_bonds.h | 2 +- src/create_box.h | 2 +- src/delete_atoms.h | 2 +- src/delete_bonds.h | 2 +- src/deprecated.h | 2 +- src/displace_atoms.h | 2 +- src/info.h | 2 +- src/input.cpp | 11 +++--- src/input.h | 5 ++- src/lammpsplugin.h | 2 - src/minimize.h | 2 +- src/read_data.h | 2 +- src/read_dump.h | 2 +- src/read_restart.h | 2 +- src/replicate.h | 2 +- src/rerun.h | 2 +- src/reset_atom_ids.h | 2 +- src/reset_mol_ids.h | 2 +- src/run.h | 2 +- src/set.h | 2 +- src/velocity.h | 2 +- src/write_coeff.h | 2 +- src/write_data.h | 2 +- src/write_dump.h | 2 +- src/write_restart.h | 2 +- 47 files changed, 83 insertions(+), 91 deletions(-) diff --git a/doc/src/Developer_plugins.rst b/doc/src/Developer_plugins.rst index 68f1f1387c..1beedcf213 100644 --- a/doc/src/Developer_plugins.rst +++ b/doc/src/Developer_plugins.rst @@ -59,31 +59,25 @@ Members of ``lammpsplugin_t`` * - author - String with the name and email of the author * - creator.v1 - - Pointer to factory function for pair, bond, angle, dihedral, or improper styles + - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles * - creator.v2 - Pointer to factory function for compute, fix, or region styles - * - creator.v3 - - Pointer to factory function for command styles * - handle - Pointer to the open DSO file handle Only one of the three alternate creator entries can be used at a time -and which of those is determined by the style of plugin. The "creator.v1" -element is for factory functions of supported styles computing forces (i.e. -pair, bond, angle, dihedral, or improper styles) and the function takes -as single argument the pointer to the LAMMPS instance. The factory function -is cast to the ``lammpsplugin_factory1`` type before assignment. The -"creator.v2" element is for factory functions creating an instance of -a fix, compute, or region style and takes three arguments: a pointer to -the LAMMPS instance, an integer with the length of the argument list and -a ``char **`` pointer to the list of arguments. The factory function pointer -needs to be cast to the ``lammpsplugin_factory2`` type before assignment. -The "creator.v3" element takes the same arguments as "creator.v3" but is -specific to creating command styles: the factory function has to instantiate -the command style locally passing the LAMMPS pointer as argument and then -call its "command" member function with the number and list of arguments. -The factory function pointer needs to be cast to the -``lammpsplugin_factory3`` type before assignment. +and which of those is determined by the style of plugin. The +"creator.v1" element is for factory functions of supported styles +computing forces (i.e. command, pair, bond, angle, dihedral, or +improper styles) and the function takes as single argument the pointer +to the LAMMPS instance. The factory function is cast to the +``lammpsplugin_factory1`` type before assignment. The "creator.v2" +element is for factory functions creating an instance of a fix, compute, +or region style and takes three arguments: a pointer to the LAMMPS +instance, an integer with the length of the argument list and a ``char +**`` pointer to the list of arguments. The factory function pointer +needs to be cast to the ``lammpsplugin_factory2`` type before +assignment. Pair style example ^^^^^^^^^^^^^^^^^^ @@ -123,12 +117,12 @@ function would look like this: The factory function in this example is called ``morse2creator()``. It receives a pointer to the LAMMPS class as only argument and thus has to -be assigned to the *creator.v1* member of the plugin struct and cast to the -``lammpsplugin_factory1`` pointer type. It returns a +be assigned to the *creator.v1* member of the plugin struct and cast to +the ``lammpsplugin_factory1`` function pointer type. It returns a pointer to the allocated class instance derived from the ``Pair`` class. -This function may be declared static to avoid clashes with other plugins. -The name of the derived class, ``PairMorse2``, must be unique inside -the entire LAMMPS executable. +This function may be declared static to avoid clashes with other +plugins. The name of the derived class, ``PairMorse2``, however must be +unique inside the entire LAMMPS executable. Fix style example ^^^^^^^^^^^^^^^^^ @@ -169,9 +163,9 @@ Below is an example for that: Command style example ^^^^^^^^^^^^^^^^^^^^^ -For command styles there is a third variant of factory function as +Command styles also use the first variant of factory function as demonstrated in the following example, which also shows that the -implementation of the plugin class may also be within the same +implementation of the plugin class may be within the same source file as the plugin interface code: .. code-block:: C++ @@ -180,15 +174,15 @@ file as the plugin interface code: #include "comm.h" #include "error.h" - #include "pointers.h" + #include "command.h" #include "version.h" #include namespace LAMMPS_NS { - class Hello : protected Pointers { + class Hello : public Command { public: - Hello(class LAMMPS *lmp) : Pointers(lmp) {}; + Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); }; } @@ -202,10 +196,9 @@ file as the plugin interface code: utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); } - static void hellocreator(LAMMPS *lmp, int argc, char **argv) + static void hellocreator(LAMMPS *lmp) { - Hello hello(lmp); - hello.command(argc,argv); + return new Hello(lmp); } extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) @@ -216,9 +209,9 @@ file as the plugin interface code: plugin.version = LAMMPS_VERSION; plugin.style = "command"; plugin.name = "hello"; - plugin.info = "Hello world command v1.0"; + plugin.info = "Hello world command v1.1"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/examples/plugins/helloplugin.cpp b/examples/plugins/helloplugin.cpp index f453add374..f4a49c1a5a 100644 --- a/examples/plugins/helloplugin.cpp +++ b/examples/plugins/helloplugin.cpp @@ -9,7 +9,7 @@ #include namespace LAMMPS_NS { - class Hello : protected Command { + class Hello : public Command { public: Hello(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); @@ -25,10 +25,9 @@ void Hello::command(int argc, char **argv) utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0])); } -static void hellocreator(LAMMPS *lmp, int argc, char **argv) +static Command *hellocreator(LAMMPS *lmp) { - Hello hello(lmp); - hello.command(argc,argv); + return new Hello(lmp); } extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) @@ -39,9 +38,9 @@ extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc) plugin.version = LAMMPS_VERSION; plugin.style = "command"; plugin.name = "hello"; - plugin.info = "Hello world command v1.0"; + plugin.info = "Hello world command v1.1"; plugin.author = "Axel Kohlmeyer (akohlmey@gmail.com)"; - plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator; + plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator; plugin.handle = handle; (*register_plugin)(&plugin,lmp); } diff --git a/src/KIM/kim_command.h b/src/KIM/kim_command.h index 64abeed9e0..b27b0e0873 100644 --- a/src/KIM/kim_command.h +++ b/src/KIM/kim_command.h @@ -66,7 +66,7 @@ CommandStyle(kim,KimCommand) namespace LAMMPS_NS { -class KimCommand : protected Command { +class KimCommand : public Command { public: KimCommand(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/MESSAGE/message.h b/src/MESSAGE/message.h index c499ff6537..88c658e44b 100644 --- a/src/MESSAGE/message.h +++ b/src/MESSAGE/message.h @@ -24,7 +24,7 @@ CommandStyle(message,Message) namespace LAMMPS_NS { -class Message : protected Command { +class Message : public Command { public: Message(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/MESSAGE/server.h b/src/MESSAGE/server.h index 63191ccf33..7c93db8c64 100644 --- a/src/MESSAGE/server.h +++ b/src/MESSAGE/server.h @@ -24,7 +24,7 @@ CommandStyle(server,Server) namespace LAMMPS_NS { -class Server : protected Command { +class Server : public Command { public: Server(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/PLUGIN/plugin.cpp b/src/PLUGIN/plugin.cpp index a2f74060f1..d311b64520 100644 --- a/src/PLUGIN/plugin.cpp +++ b/src/PLUGIN/plugin.cpp @@ -257,7 +257,7 @@ namespace LAMMPS_NS "style {} from plugin", plugin->name)); } - (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v3; + (*command_map)[plugin->name] = (Input::CommandCreator)plugin->creator.v1; } else { utils::logmesg(lmp,fmt::format("Loading plugin for {} styles not " diff --git a/src/PLUGIN/plugin.h b/src/PLUGIN/plugin.h index 61355f4113..4b4bca9878 100644 --- a/src/PLUGIN/plugin.h +++ b/src/PLUGIN/plugin.h @@ -26,7 +26,7 @@ CommandStyle(plugin,Plugin) namespace LAMMPS_NS { - class Plugin : protected Command { + class Plugin : public Command { public: Plugin(class LAMMPS *); void command(int, char **); diff --git a/src/REPLICA/hyper.h b/src/REPLICA/hyper.h index faad58994b..a96ccf3727 100644 --- a/src/REPLICA/hyper.h +++ b/src/REPLICA/hyper.h @@ -24,7 +24,7 @@ CommandStyle(hyper,Hyper) namespace LAMMPS_NS { -class Hyper : protected Command { +class Hyper : public Command { public: Hyper(class LAMMPS *); ~Hyper() {} diff --git a/src/REPLICA/neb.h b/src/REPLICA/neb.h index d8a9d5d3e4..8298766ccf 100644 --- a/src/REPLICA/neb.h +++ b/src/REPLICA/neb.h @@ -24,7 +24,7 @@ CommandStyle(neb,NEB) namespace LAMMPS_NS { -class NEB : protected Command { +class NEB : public Command { public: NEB(class LAMMPS *); NEB(class LAMMPS *, double, double, int, int, int, double *, double *); diff --git a/src/REPLICA/prd.h b/src/REPLICA/prd.h index b331f7dc02..0d8fde1bfe 100644 --- a/src/REPLICA/prd.h +++ b/src/REPLICA/prd.h @@ -24,7 +24,7 @@ CommandStyle(prd,PRD) namespace LAMMPS_NS { -class PRD : protected Command { +class PRD : public Command { public: PRD(class LAMMPS *); ~PRD() {} diff --git a/src/REPLICA/tad.h b/src/REPLICA/tad.h index 3a525146a6..91e570c707 100644 --- a/src/REPLICA/tad.h +++ b/src/REPLICA/tad.h @@ -24,7 +24,7 @@ CommandStyle(tad,TAD) namespace LAMMPS_NS { -class TAD : protected Command { +class TAD : public Command { public: TAD(class LAMMPS *); ~TAD(); diff --git a/src/REPLICA/temper.h b/src/REPLICA/temper.h index ce7944da95..3f7d813f2a 100644 --- a/src/REPLICA/temper.h +++ b/src/REPLICA/temper.h @@ -24,7 +24,7 @@ CommandStyle(temper,Temper) namespace LAMMPS_NS { -class Temper : protected Command { +class Temper : public Command { public: Temper(class LAMMPS *); ~Temper(); diff --git a/src/SPIN/neb_spin.h b/src/SPIN/neb_spin.h index 3dbae09297..54d85093a5 100644 --- a/src/SPIN/neb_spin.h +++ b/src/SPIN/neb_spin.h @@ -24,7 +24,7 @@ CommandStyle(neb/spin,NEBSpin) namespace LAMMPS_NS { -class NEBSpin : protected Command { +class NEBSpin : public Command { public: NEBSpin(class LAMMPS *); ~NEBSpin(); diff --git a/src/USER-COLVARS/group_ndx.h b/src/USER-COLVARS/group_ndx.h index 46ba86c860..58b210937a 100644 --- a/src/USER-COLVARS/group_ndx.h +++ b/src/USER-COLVARS/group_ndx.h @@ -26,7 +26,7 @@ CommandStyle(group2ndx,Group2Ndx) namespace LAMMPS_NS { -class Group2Ndx : protected Command { +class Group2Ndx : public Command { public: Group2Ndx(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/USER-COLVARS/ndx_group.h b/src/USER-COLVARS/ndx_group.h index 1c881a65bf..e0fc6cf527 100644 --- a/src/USER-COLVARS/ndx_group.h +++ b/src/USER-COLVARS/ndx_group.h @@ -27,7 +27,7 @@ CommandStyle(ndx2group,Ndx2Group) namespace LAMMPS_NS { -class Ndx2Group : protected Command { +class Ndx2Group : public Command { public: Ndx2Group(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/USER-MISC/temper_grem.h b/src/USER-MISC/temper_grem.h index b720aeb45c..3c1891f22d 100644 --- a/src/USER-MISC/temper_grem.h +++ b/src/USER-MISC/temper_grem.h @@ -24,7 +24,7 @@ CommandStyle(temper/grem,TemperGrem) namespace LAMMPS_NS { -class TemperGrem : protected Command { +class TemperGrem : public Command { public: TemperGrem(class LAMMPS *); ~TemperGrem(); diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h index 5c285f083c..a0eb1c1e9b 100644 --- a/src/USER-MISC/temper_npt.h +++ b/src/USER-MISC/temper_npt.h @@ -25,7 +25,7 @@ CommandStyle(temper/npt,TemperNPT) namespace LAMMPS_NS { -class TemperNPT : protected Command { +class TemperNPT : public Command { public: TemperNPT(class LAMMPS *); ~TemperNPT(); diff --git a/src/USER-PHONON/dynamical_matrix.h b/src/USER-PHONON/dynamical_matrix.h index 30baeda27f..d8c3ad411b 100644 --- a/src/USER-PHONON/dynamical_matrix.h +++ b/src/USER-PHONON/dynamical_matrix.h @@ -15,7 +15,7 @@ CommandStyle(dynamical_matrix,DynamicalMatrix) namespace LAMMPS_NS { -class DynamicalMatrix : protected Command { +class DynamicalMatrix : public Command { public: DynamicalMatrix(class LAMMPS *); virtual ~DynamicalMatrix(); diff --git a/src/USER-PHONON/third_order.h b/src/USER-PHONON/third_order.h index 87b0c695f6..56a0266937 100644 --- a/src/USER-PHONON/third_order.h +++ b/src/USER-PHONON/third_order.h @@ -16,7 +16,7 @@ CommandStyle(third_order,ThirdOrder) namespace LAMMPS_NS { - class ThirdOrder : protected Command { + class ThirdOrder : public Command { public: ThirdOrder(class LAMMPS *); virtual ~ThirdOrder(); diff --git a/src/balance.h b/src/balance.h index 25ccac85ae..0642fe04f6 100644 --- a/src/balance.h +++ b/src/balance.h @@ -24,7 +24,7 @@ CommandStyle(balance,Balance) namespace LAMMPS_NS { -class Balance : protected Command { +class Balance : public Command { public: class RCB *rcb; class FixStore *fixstore; // per-atom weights stored in FixStore diff --git a/src/change_box.h b/src/change_box.h index 2f6802194b..f48edb2d9f 100644 --- a/src/change_box.h +++ b/src/change_box.h @@ -24,7 +24,7 @@ CommandStyle(change_box,ChangeBox) namespace LAMMPS_NS { -class ChangeBox : protected Command { +class ChangeBox : public Command { public: ChangeBox(class LAMMPS *); void command(int, char **); diff --git a/src/create_atoms.h b/src/create_atoms.h index 8f0e016192..deb155b96a 100644 --- a/src/create_atoms.h +++ b/src/create_atoms.h @@ -24,7 +24,7 @@ CommandStyle(create_atoms,CreateAtoms) namespace LAMMPS_NS { -class CreateAtoms : protected Command { +class CreateAtoms : public Command { public: CreateAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/create_bonds.h b/src/create_bonds.h index f25cb6d1bc..d2d50c86c6 100644 --- a/src/create_bonds.h +++ b/src/create_bonds.h @@ -24,7 +24,7 @@ CommandStyle(create_bonds,CreateBonds) namespace LAMMPS_NS { -class CreateBonds : protected Command { +class CreateBonds : public Command { public: CreateBonds(class LAMMPS *); void command(int, char **); diff --git a/src/create_box.h b/src/create_box.h index 846af6bcee..26a2be6fe1 100644 --- a/src/create_box.h +++ b/src/create_box.h @@ -24,7 +24,7 @@ CommandStyle(create_box,CreateBox) namespace LAMMPS_NS { -class CreateBox : protected Command { +class CreateBox : public Command { public: CreateBox(class LAMMPS *); void command(int, char **); diff --git a/src/delete_atoms.h b/src/delete_atoms.h index e43bebfa54..5ff1d12f65 100644 --- a/src/delete_atoms.h +++ b/src/delete_atoms.h @@ -25,7 +25,7 @@ CommandStyle(delete_atoms,DeleteAtoms) namespace LAMMPS_NS { -class DeleteAtoms : protected Command { +class DeleteAtoms : public Command { public: DeleteAtoms(class LAMMPS *); void command(int, char **); diff --git a/src/delete_bonds.h b/src/delete_bonds.h index 2f255e12d6..5c56a67f68 100644 --- a/src/delete_bonds.h +++ b/src/delete_bonds.h @@ -24,7 +24,7 @@ CommandStyle(delete_bonds,DeleteBonds) namespace LAMMPS_NS { -class DeleteBonds : protected Command { +class DeleteBonds : public Command { public: DeleteBonds(class LAMMPS *); void command(int, char **); diff --git a/src/deprecated.h b/src/deprecated.h index 4b6cba7f30..d5997d7199 100644 --- a/src/deprecated.h +++ b/src/deprecated.h @@ -30,7 +30,7 @@ CommandStyle(kim_query,Deprecated) namespace LAMMPS_NS { -class Deprecated : protected Command { +class Deprecated : public Command { public: Deprecated(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/displace_atoms.h b/src/displace_atoms.h index 98247b7244..c2c2e8306f 100644 --- a/src/displace_atoms.h +++ b/src/displace_atoms.h @@ -24,7 +24,7 @@ CommandStyle(displace_atoms,DisplaceAtoms) namespace LAMMPS_NS { -class DisplaceAtoms : protected Command { +class DisplaceAtoms : public Command { public: DisplaceAtoms(class LAMMPS *); ~DisplaceAtoms(); diff --git a/src/info.h b/src/info.h index 536a93c559..386d38c39f 100644 --- a/src/info.h +++ b/src/info.h @@ -26,7 +26,7 @@ CommandStyle(info,Info) namespace LAMMPS_NS { -class Info : protected Command { +class Info : public Command { public: Info(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/input.cpp b/src/input.cpp index 9079cdd76c..16cef08c36 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -21,6 +21,7 @@ #include "comm.h" #include "comm_brick.h" #include "comm_tiled.h" +#include "command.h" #include "compute.h" #include "dihedral.h" #include "domain.h" @@ -82,7 +83,7 @@ command line flags, holds the factory of commands and creates and initializes an instance of the Variable class. To execute a command, a specific class instance, derived from -:cpp:class:`Pointers`, is created, then its ``command()`` member +:cpp:class:`Command`, is created, then its ``command()`` member function executed, and finally the class instance is deleted. \endverbatim @@ -789,7 +790,8 @@ int Input::execute_command() if (command_map->find(command) != command_map->end()) { CommandCreator &command_creator = (*command_map)[command]; - command_creator(lmp,narg,arg); + Command *cmd = command_creator(lmp); + cmd->command(narg,arg); return 0; } @@ -803,10 +805,9 @@ int Input::execute_command() ------------------------------------------------------------------------- */ template -void Input::command_creator(LAMMPS *lmp, int narg, char **arg) +Command *Input::command_creator(LAMMPS *lmp) { - T cmd(lmp); - cmd.command(narg,arg); + return new T(lmp); } /* ---------------------------------------------------------------------- */ diff --git a/src/input.h b/src/input.h index 809a7a5f94..59be026640 100644 --- a/src/input.h +++ b/src/input.h @@ -19,6 +19,7 @@ #include namespace LAMMPS_NS { + class Command; class Input : protected Pointers { friend class Info; @@ -59,12 +60,12 @@ class Input : protected Pointers { FILE **infiles; // list of open input files public: - typedef void (*CommandCreator)(LAMMPS *, int, char **); + typedef Command * (*CommandCreator)(LAMMPS *); typedef std::map CommandCreatorMap; CommandCreatorMap *command_map; protected: - template static void command_creator(LAMMPS *, int, char **); + template static Command *command_creator(LAMMPS *); private: void parse(); // parse an input text line diff --git a/src/lammpsplugin.h b/src/lammpsplugin.h index 1baed9799d..e544e8bffe 100644 --- a/src/lammpsplugin.h +++ b/src/lammpsplugin.h @@ -20,7 +20,6 @@ extern "C" { typedef void *(lammpsplugin_factory1)(void *); typedef void *(lammpsplugin_factory2)(void *, int, char **); - typedef void (lammpsplugin_factory3)(void *, int, char **); typedef struct { const char *version; @@ -31,7 +30,6 @@ extern "C" { union { lammpsplugin_factory1 *v1; lammpsplugin_factory2 *v2; - lammpsplugin_factory3 *v3; } creator; void *handle; } lammpsplugin_t; diff --git a/src/minimize.h b/src/minimize.h index 10b244130a..32d08c5f52 100644 --- a/src/minimize.h +++ b/src/minimize.h @@ -24,7 +24,7 @@ CommandStyle(minimize,Minimize) namespace LAMMPS_NS { -class Minimize : protected Command { +class Minimize : public Command { public: Minimize(class LAMMPS *); void command(int, char **); diff --git a/src/read_data.h b/src/read_data.h index d251259a08..7ccbeebd58 100644 --- a/src/read_data.h +++ b/src/read_data.h @@ -24,7 +24,7 @@ CommandStyle(read_data,ReadData) namespace LAMMPS_NS { -class ReadData : protected Command { +class ReadData : public Command { public: ReadData(class LAMMPS *); ~ReadData(); diff --git a/src/read_dump.h b/src/read_dump.h index ba59cc9224..842b629fa4 100644 --- a/src/read_dump.h +++ b/src/read_dump.h @@ -26,7 +26,7 @@ CommandStyle(read_dump,ReadDump) namespace LAMMPS_NS { -class ReadDump : protected Command { +class ReadDump : public Command { public: ReadDump(class LAMMPS *); ~ReadDump(); diff --git a/src/read_restart.h b/src/read_restart.h index 3a2c7965b3..fc2a27fa67 100644 --- a/src/read_restart.h +++ b/src/read_restart.h @@ -24,7 +24,7 @@ CommandStyle(read_restart,ReadRestart) namespace LAMMPS_NS { -class ReadRestart : protected Command { +class ReadRestart : public Command { public: ReadRestart(class LAMMPS *); void command(int, char **); diff --git a/src/replicate.h b/src/replicate.h index fd865a9c71..b4be578b23 100644 --- a/src/replicate.h +++ b/src/replicate.h @@ -24,7 +24,7 @@ CommandStyle(replicate,Replicate) namespace LAMMPS_NS { -class Replicate : protected Command { +class Replicate : public Command { public: Replicate(class LAMMPS *); void command(int, char **); diff --git a/src/rerun.h b/src/rerun.h index 57aa32227f..c10ca8780e 100644 --- a/src/rerun.h +++ b/src/rerun.h @@ -24,7 +24,7 @@ CommandStyle(rerun,Rerun) namespace LAMMPS_NS { -class Rerun : protected Command { +class Rerun : public Command { public: Rerun(class LAMMPS *); void command(int, char **); diff --git a/src/reset_atom_ids.h b/src/reset_atom_ids.h index a017abbbc8..6c262f2bd8 100644 --- a/src/reset_atom_ids.h +++ b/src/reset_atom_ids.h @@ -24,7 +24,7 @@ CommandStyle(reset_atom_ids,ResetIDs) namespace LAMMPS_NS { -class ResetIDs : protected Command { +class ResetIDs : public Command { public: struct AtomRvous { bigint ibin; diff --git a/src/reset_mol_ids.h b/src/reset_mol_ids.h index c25f64fe43..5759cf8b4e 100644 --- a/src/reset_mol_ids.h +++ b/src/reset_mol_ids.h @@ -24,7 +24,7 @@ CommandStyle(reset_mol_ids,ResetMolIDs) namespace LAMMPS_NS { -class ResetMolIDs : protected Command { +class ResetMolIDs : public Command { public: ResetMolIDs(class LAMMPS *); ~ResetMolIDs(); diff --git a/src/run.h b/src/run.h index a9a4a556f0..747af6a61c 100644 --- a/src/run.h +++ b/src/run.h @@ -24,7 +24,7 @@ CommandStyle(run,Run) namespace LAMMPS_NS { -class Run : protected Command { +class Run : public Command { public: Run(class LAMMPS *); void command(int, char **); diff --git a/src/set.h b/src/set.h index 02e81b057a..330bd484a3 100644 --- a/src/set.h +++ b/src/set.h @@ -24,7 +24,7 @@ CommandStyle(set,Set) namespace LAMMPS_NS { -class Set : protected Command { +class Set : public Command { public: Set(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/velocity.h b/src/velocity.h index 5c54302a1e..d7405f87fd 100644 --- a/src/velocity.h +++ b/src/velocity.h @@ -24,7 +24,7 @@ CommandStyle(velocity,Velocity) namespace LAMMPS_NS { -class Velocity : protected Command { +class Velocity : public Command { public: Velocity(class LAMMPS *); void command(int, char **); diff --git a/src/write_coeff.h b/src/write_coeff.h index 2555454db0..8815162c48 100644 --- a/src/write_coeff.h +++ b/src/write_coeff.h @@ -24,7 +24,7 @@ CommandStyle(write_coeff,WriteCoeff) namespace LAMMPS_NS { -class WriteCoeff : protected Command { +class WriteCoeff : public Command { public: WriteCoeff(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/write_data.h b/src/write_data.h index c9ba5a4a52..cecfaa4800 100644 --- a/src/write_data.h +++ b/src/write_data.h @@ -24,7 +24,7 @@ CommandStyle(write_data,WriteData) namespace LAMMPS_NS { -class WriteData : protected Command { +class WriteData : public Command { public: WriteData(class LAMMPS *); void command(int, char **); diff --git a/src/write_dump.h b/src/write_dump.h index 5d1499934a..763fd12f60 100644 --- a/src/write_dump.h +++ b/src/write_dump.h @@ -24,7 +24,7 @@ CommandStyle(write_dump,WriteDump) namespace LAMMPS_NS { -class WriteDump : protected Command { +class WriteDump : public Command { public: WriteDump(class LAMMPS *lmp) : Command(lmp) {}; void command(int, char **); diff --git a/src/write_restart.h b/src/write_restart.h index 0b8826f10b..05f5c45ec6 100644 --- a/src/write_restart.h +++ b/src/write_restart.h @@ -24,7 +24,7 @@ CommandStyle(write_restart,WriteRestart) namespace LAMMPS_NS { -class WriteRestart : protected Command { +class WriteRestart : public Command { public: WriteRestart(class LAMMPS *); void command(int, char **); From 2e5079371ad9f5e2edb3eaf093167451605a9b38 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 07:26:34 -0400 Subject: [PATCH 093/100] must delete command explicitly now --- src/input.cpp | 1 + 1 file changed, 1 insertion(+) diff --git a/src/input.cpp b/src/input.cpp index 16cef08c36..d3352b380a 100644 --- a/src/input.cpp +++ b/src/input.cpp @@ -792,6 +792,7 @@ int Input::execute_command() CommandCreator &command_creator = (*command_map)[command]; Command *cmd = command_creator(lmp); cmd->command(narg,arg); + delete cmd; return 0; } From d5661e06ae266dee138e432f732922ab91b1b37e Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:00:38 -0400 Subject: [PATCH 094/100] Detect linux distribution and version --- cmake/Modules/LAMMPSUtils.cmake | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index acaef19498..41dcfc5b2f 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -104,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder) endforeach() endif() endfunction(FetchPotentials) + +# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux +if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release)) + file(STRINGS /etc/os-release distro REGEX "^NAME=") + string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}") + file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=") + string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}") + set(CMAKE_LINUX_DISTRO ${distro}) + set(CMAKE_DISTRO_VERSION ${disversion}) +endif() From 2a81411029c6410d4e979c9f3ac5b27d6f795d70 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:01:46 -0400 Subject: [PATCH 095/100] use linux distro and version info to decide when to look for faster linkers --- cmake/CMakeLists.txt | 2 +- cmake/Modules/Testing.cmake | 13 ++++++++----- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index a11c7575d2..263b5a566d 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -731,7 +731,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS) include(FeatureSummary) feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND) message(STATUS "<<< Build configuration >>> - Operating System: ${CMAKE_SYSTEM_NAME} + Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION} Build type: ${CMAKE_BUILD_TYPE} Install path: ${CMAKE_INSTALL_PREFIX} Generator: ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}") diff --git a/cmake/Modules/Testing.cmake b/cmake/Modules/Testing.cmake index 6d2f39b0f3..7fbd8212de 100644 --- a/cmake/Modules/Testing.cmake +++ b/cmake/Modules/Testing.cmake @@ -16,11 +16,14 @@ if(ENABLE_TESTING) set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command") set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options") - # check if a faster linker is available. - # only verified with GNU and Clang compilers and new CMake - if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) - if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") - OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")) + # we need to build and link a LOT of tester executables, so it is worth checking if + # a faster linker is available. requires GNU or Clang compiler, newer CMake. + # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails) + if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13) + AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") + OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))) + if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04)) + OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30))) include(CheckCXXCompilerFlag) set(CMAKE_CUSTOM_LINKER_DEFAULT default) check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG) From 6e739c04e43951596a6a13a4b8db374e03026e96 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 14 Apr 2021 20:02:05 -0400 Subject: [PATCH 096/100] use safe fread() call --- src/read_restart.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/read_restart.cpp b/src/read_restart.cpp index 9e8fbce91c..d3fecd9d80 100644 --- a/src/read_restart.cpp +++ b/src/read_restart.cpp @@ -1195,7 +1195,7 @@ void ReadRestart::check_eof_magic() if (me == 0) { long curpos = ftell(fp); fseek(fp,(long)-n,SEEK_END); - fread(str,sizeof(char),n,fp); + utils::sfread(FLERR,str,sizeof(char),n,fp,nullptr,error); fseek(fp,curpos,SEEK_SET); } From 0870a560939079644892c9ff2e650e2a45339243 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Thu, 15 Apr 2021 11:57:48 -0400 Subject: [PATCH 097/100] expand exception message to include cause of file open failure --- src/potential_file_reader.cpp | 3 ++- src/text_file_reader.cpp | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/src/potential_file_reader.cpp b/src/potential_file_reader.cpp index 2730a3d109..bddfca9bce 100644 --- a/src/potential_file_reader.cpp +++ b/src/potential_file_reader.cpp @@ -62,7 +62,8 @@ PotentialFileReader::PotentialFileReader(LAMMPS *lmp, try { reader = open_potential(filename); if (!reader) { - error->one(FLERR, fmt::format("cannot open {} potential file {}", potential_name, filename)); + error->one(FLERR, fmt::format("cannot open {} potential file {}: {}", + potential_name, filename, utils::getsyserror())); } } catch (FileReaderException &e) { error->one(FLERR, e.what()); diff --git a/src/text_file_reader.cpp b/src/text_file_reader.cpp index af27bfb16d..7a6e914639 100644 --- a/src/text_file_reader.cpp +++ b/src/text_file_reader.cpp @@ -46,7 +46,8 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f fp = fopen(filename.c_str(), "r"); if (fp == nullptr) { - throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename)); + throw FileReaderException(fmt::format("cannot open {} file {}: {}", + filetype, filename, utils::getsyserror())); } } From 7a97331e510aa53635a5b469deceb445e785c99a Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 16 Apr 2021 12:38:00 -0400 Subject: [PATCH 098/100] add support for Plumed2 version 2.5.7, 2.6.3, 2.7.1 --- cmake/Modules/Packages/USER-PLUMED.cmake | 5 +++-- lib/plumed/Install.py | 5 ++++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/cmake/Modules/Packages/USER-PLUMED.cmake b/cmake/Modules/Packages/USER-PLUMED.cmake index 8719e8179d..e71542cfc5 100644 --- a/cmake/Modules/Packages/USER-PLUMED.cmake +++ b/cmake/Modules/Packages/USER-PLUMED.cmake @@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED) set(PLUMED_BUILD_BYPRODUCTS "/lib/libplumedWrapper.a") endif() - set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball") - set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball") + set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball") + set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball") + mark_as_advanced(PLUMED_URL) mark_as_advanced(PLUMED_MD5) diff --git a/lib/plumed/Install.py b/lib/plumed/Install.py index c11d5bfee9..e3858b39d3 100644 --- a/lib/plumed/Install.py +++ b/lib/plumed/Install.py @@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py', # settings -version = "2.7.0" +version = "2.7.1" mode = "static" # help message @@ -47,9 +47,12 @@ checksums = { \ '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \ '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \ '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \ + '2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \ '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \ '2.6.1' : '89a9a450fc6025299fe16af235957163', \ + '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \ '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \ + '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \ } # parse and process arguments From 99035dc68096170e570f0213d6a388b6f06925a8 Mon Sep 17 00:00:00 2001 From: julient31 Date: Fri, 16 Apr 2021 11:59:37 -0600 Subject: [PATCH 099/100] removing all commented lines --- src/KOKKOS/atom_kokkos.h | 3 --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 14 ----------- src/KOKKOS/kokkos_type.h | 37 ----------------------------- 3 files changed, 54 deletions(-) diff --git a/src/KOKKOS/atom_kokkos.h b/src/KOKKOS/atom_kokkos.h index f5649f927e..f5cf4916cf 100644 --- a/src/KOKKOS/atom_kokkos.h +++ b/src/KOKKOS/atom_kokkos.h @@ -56,9 +56,6 @@ class AtomKokkos : public Atom { // SPIN package - // DAT::tdual_sp_array k_sp; - // DAT::tdual_fm_array k_fm; - // DAT::tdual_fm_long_array k_fm_long; DAT::tdual_float_1d_4 k_sp; DAT::tdual_f_array k_fm; DAT::tdual_f_array k_fm_long; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index 5e3ff19831..e9bbeebe28 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -189,7 +189,6 @@ struct AtomVecSpinKokkos_PackComm { AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, - // const typename DAT::tdual_sp_array &sp, const typename DAT::tdual_float_1d_4 &sp, const typename DAT::tdual_xfloat_2d &buf, const typename DAT::tdual_int_2d &list, @@ -201,7 +200,6 @@ struct AtomVecSpinKokkos_PackComm { _xprd(xprd),_yprd(yprd),_zprd(zprd), _xy(xy),_xz(xz),_yz(yz) { const size_t maxsend = (buf.view().extent(0)*buf.view().extent(1))/3; - // const size_t elements = 3; const size_t elements = 7; buffer_view(_buf,buf,maxsend,elements); _pbc[0] = pbc[0]; _pbc[1] = pbc[1]; _pbc[2] = pbc[2]; @@ -1270,16 +1268,10 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); - // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_sp,space); - // if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_fm,space); - // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) perform_async_copy(atomKK->k_fm_long,space); } else { @@ -1297,16 +1289,10 @@ void AtomVecSpinKokkos::sync_overlapping_device(ExecutionSpace space, unsigned i perform_async_copy(atomKK->k_mask,space); if ((mask & IMAGE_MASK) && atomKK->k_image.need_sync()) perform_async_copy(atomKK->k_image,space); - // if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) - // perform_async_copy(atomKK->k_sp,space); if ((mask & SP_MASK) && atomKK->k_sp.need_sync()) perform_async_copy(atomKK->k_sp,space); - // if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) - // perform_async_copy(atomKK->k_fm,space); if ((mask & FM_MASK) && atomKK->k_fm.need_sync()) perform_async_copy(atomKK->k_fm,space); - // if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) - // perform_async_copy(atomKK->k_fm_long,space); if ((mask & FML_MASK) && atomKK->k_fm_long.need_sync()) perform_async_copy(atomKK->k_fm_long,space); } diff --git a/src/KOKKOS/kokkos_type.h b/src/KOKKOS/kokkos_type.h index b0fbdf1f9f..af5adeee73 100644 --- a/src/KOKKOS/kokkos_type.h +++ b/src/KOKKOS/kokkos_type.h @@ -773,17 +773,10 @@ typedef tdual_virial_array::t_dev_const_randomread t_virial_array_randomread; //3d SP_FLOAT array n*4 #ifdef LMP_KOKKOS_NO_LEGACY -// typedef Kokkos::DualView tdual_sp_array; typedef Kokkos::DualView tdual_float_1d_4; #else -// typedef Kokkos::DualView tdual_sp_array; typedef Kokkos::DualView tdual_float_1d_4; #endif -// typedef tdual_sp_array::t_dev t_sp_array; -// typedef tdual_sp_array::t_dev_const t_sp_array_const; -// typedef tdual_sp_array::t_dev_um t_sp_array_um; -// typedef tdual_sp_array::t_dev_const_um t_sp_array_const_um; -// typedef tdual_sp_array::t_dev_const_randomread t_sp_array_randomread; typedef tdual_float_1d_4::t_dev t_sp_array; typedef tdual_float_1d_4::t_dev_const t_sp_array_const; typedef tdual_float_1d_4::t_dev_um t_sp_array_um; @@ -792,12 +785,6 @@ typedef tdual_float_1d_4::t_dev_const_randomread t_sp_array_randomread; //3d FM_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_array; -// typedef tdual_fm_array::t_dev t_fm_array; -// typedef tdual_fm_array::t_dev_const t_fm_array_const; -// typedef tdual_fm_array::t_dev_um t_fm_array_um; -// typedef tdual_fm_array::t_dev_const_um t_fm_array_const_um; -// typedef tdual_fm_array::t_dev_const_randomread t_fm_array_randomread; typedef tdual_f_array::t_dev t_fm_array; typedef tdual_f_array::t_dev_const t_fm_array_const; typedef tdual_f_array::t_dev_um t_fm_array_um; @@ -806,12 +793,6 @@ typedef tdual_f_array::t_dev_const_randomread t_fm_array_randomread; //3d FML_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_long_array; -// typedef tdual_fm_long_array::t_dev t_fm_long_array; -// typedef tdual_fm_long_array::t_dev_const t_fm_long_array_const; -// typedef tdual_fm_long_array::t_dev_um t_fm_long_array_um; -// typedef tdual_fm_long_array::t_dev_const_um t_fm_long_array_const_um; -// typedef tdual_fm_long_array::t_dev_const_randomread t_fm_long_array_randomread; typedef tdual_f_array::t_dev t_fm_long_array; typedef tdual_f_array::t_dev_const t_fm_long_array_const; typedef tdual_f_array::t_dev_um t_fm_long_array_um; @@ -1057,12 +1038,6 @@ typedef tdual_virial_array::t_host_const_randomread t_virial_array_randomread; // Spin types //2d X_FLOAT array n*4 -// typedef Kokkos::DualView tdual_sp_array; -// typedef tdual_sp_array::t_host t_sp_array; -// typedef tdual_sp_array::t_host_const t_sp_array_const; -// typedef tdual_sp_array::t_host_um t_sp_array_um; -// typedef tdual_sp_array::t_host_const_um t_sp_array_const_um; -// typedef tdual_sp_array::t_host_const_randomread t_sp_array_randomread; typedef tdual_float_1d_4::t_host t_sp_array; typedef tdual_float_1d_4::t_host_const t_sp_array_const; typedef tdual_float_1d_4::t_host_um t_sp_array_um; @@ -1070,12 +1045,6 @@ typedef tdual_float_1d_4::t_host_const_um t_sp_array_const_um; typedef tdual_float_1d_4::t_host_const_randomread t_sp_array_randomread; //2d F_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_array; -// typedef tdual_fm_array::t_host t_fm_array; -// typedef tdual_fm_array::t_host_const t_fm_array_const; -// typedef tdual_fm_array::t_host_um t_fm_array_um; -// typedef tdual_fm_array::t_host_const_um t_fm_array_const_um; -// typedef tdual_fm_array::t_host_const_randomread t_fm_array_randomread; typedef tdual_f_array::t_host t_fm_array; typedef tdual_f_array::t_host_const t_fm_array_const; typedef tdual_f_array::t_host_um t_fm_array_um; @@ -1083,12 +1052,6 @@ typedef tdual_f_array::t_host_const_um t_fm_array_const_um; typedef tdual_f_array::t_host_const_randomread t_fm_array_randomread; //2d F_FLOAT array n*3 -// typedef Kokkos::DualView tdual_fm_long_array; -// typedef tdual_fm_long_array::t_host t_fm_long_array; -// typedef tdual_fm_long_array::t_host_const t_fm_long_array_const; -// typedef tdual_fm_long_array::t_host_um t_fm_long_array_um; -// typedef tdual_fm_long_array::t_host_const_um t_fm_long_array_const_um; -// typedef tdual_fm_long_array::t_host_const_randomread t_fm_long_array_randomread; typedef tdual_f_array::t_host t_fm_long_array; typedef tdual_f_array::t_host_const t_fm_long_array_const; typedef tdual_f_array::t_host_um t_fm_long_array_um; From e906fae88ce7c7421858ec05a3dfa40678ea62e0 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Fri, 16 Apr 2021 17:10:07 -0400 Subject: [PATCH 100/100] whitespace fixes --- src/KOKKOS/atom_vec_spin_kokkos.cpp | 24 ++++++++++++------------ src/KOKKOS/atom_vec_spin_kokkos.h | 2 +- src/KOKKOS/verlet_kokkos.cpp | 6 +++--- src/SPIN/fix_nve_spin.cpp | 2 +- 4 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/KOKKOS/atom_vec_spin_kokkos.cpp b/src/KOKKOS/atom_vec_spin_kokkos.cpp index e9bbeebe28..399ab23a5f 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.cpp +++ b/src/KOKKOS/atom_vec_spin_kokkos.cpp @@ -56,7 +56,7 @@ AtomVecSpinKokkos::AtomVecSpinKokkos(LAMMPS *lmp) : AtomVecKokkos(lmp) xcol_data = 4; atom->sp_flag = 1; - + k_count = DAT::tdual_int_1d("atom::k_count",1); atomKK = (AtomKokkos *) atom; commKK = (CommKokkos *) comm; @@ -84,13 +84,13 @@ void AtomVecSpinKokkos::grow(int n) memoryKK->grow_kokkos(atomKK->k_type,atomKK->type,nmax,"atom:type"); memoryKK->grow_kokkos(atomKK->k_mask,atomKK->mask,nmax,"atom:mask"); memoryKK->grow_kokkos(atomKK->k_image,atomKK->image,nmax,"atom:image"); - + // allocating mech. quantities memoryKK->grow_kokkos(atomKK->k_x,atomKK->x,nmax,"atom:x"); memoryKK->grow_kokkos(atomKK->k_v,atomKK->v,nmax,"atom:v"); memoryKK->grow_kokkos(atomKK->k_f,atomKK->f,nmax,"atom:f"); - + // allocating mag. quantities memoryKK->grow_kokkos(atomKK->k_sp,atomKK->sp,nmax,"atom:sp"); @@ -134,11 +134,11 @@ void AtomVecSpinKokkos::grow_pointers() f = atomKK->f; d_f = atomKK->k_f.d_view; h_f = atomKK->k_f.h_view; - - sp = atomKK->sp; + + sp = atomKK->sp; d_sp = atomKK->k_sp.d_view; h_sp = atomKK->k_sp.h_view; - fm = atomKK->fm; + fm = atomKK->fm; d_fm = atomKK->k_fm.d_view; h_fm = atomKK->k_fm.h_view; fm_long = atomKK->fm_long; @@ -163,7 +163,7 @@ void AtomVecSpinKokkos::copy(int i, int j, int delflag) h_v(j,1) = h_v(i,1); h_v(j,2) = h_v(i,2); - h_sp(j,0) = h_sp(i,0); + h_sp(j,0) = h_sp(i,0); h_sp(j,1) = h_sp(i,1); h_sp(j,2) = h_sp(i,2); h_sp(j,3) = h_sp(i,3); @@ -186,7 +186,7 @@ struct AtomVecSpinKokkos_PackComm { const int _iswap; X_FLOAT _xprd,_yprd,_zprd,_xy,_xz,_yz; X_FLOAT _pbc[6]; - + AtomVecSpinKokkos_PackComm( const typename DAT::tdual_x_array &x, const typename DAT::tdual_float_1d_4 &sp, @@ -268,7 +268,7 @@ struct AtomVecSpinKokkos_PackBorder { _buf(buf),_list(list),_iswap(iswap), _x(x),_tag(tag),_type(type),_mask(mask),_sp(sp), _dx(dx),_dy(dy),_dz(dz) {} - + KOKKOS_INLINE_FUNCTION void operator() (const int& i) const { const int j = _list(_iswap,i); @@ -741,9 +741,9 @@ struct AtomVecSpinKokkos_PackExchangeFunctor { } } }; - + /* ---------------------------------------------------------------------- */ - + int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2d &k_buf, DAT::tdual_int_1d k_sendlist, DAT::tdual_int_1d k_copylist, @@ -768,7 +768,7 @@ int AtomVecSpinKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat_2 } /* ---------------------------------------------------------------------- */ - + int AtomVecSpinKokkos::pack_exchange(int i, double *buf) { int m = 1; diff --git a/src/KOKKOS/atom_vec_spin_kokkos.h b/src/KOKKOS/atom_vec_spin_kokkos.h index 5dca7b4e13..bcb5ea3b45 100644 --- a/src/KOKKOS/atom_vec_spin_kokkos.h +++ b/src/KOKKOS/atom_vec_spin_kokkos.h @@ -51,7 +51,7 @@ class AtomVecSpinKokkos : public AtomVecKokkos { void write_data(FILE *, int, double **); int write_data_hybrid(FILE *, double *); double memory_usage(); - + // clear magnetic and mechanic forces void force_clear(int, size_t); diff --git a/src/KOKKOS/verlet_kokkos.cpp b/src/KOKKOS/verlet_kokkos.cpp index 27f4646366..254e269671 100644 --- a/src/KOKKOS/verlet_kokkos.cpp +++ b/src/KOKKOS/verlet_kokkos.cpp @@ -594,7 +594,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(nall, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { @@ -616,7 +616,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(atomKK->nfirst, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { @@ -635,7 +635,7 @@ void VerletKokkos::force_clear() Kokkos::parallel_for(range, Zero::t_f_array>(atomKK->k_torque.view())); atomKK->modified(Device,TORQUE_MASK); } - + // reset SPIN forces if (extraflag) { diff --git a/src/SPIN/fix_nve_spin.cpp b/src/SPIN/fix_nve_spin.cpp index faf9e5c1db..eb6d918ab0 100644 --- a/src/SPIN/fix_nve_spin.cpp +++ b/src/SPIN/fix_nve_spin.cpp @@ -524,7 +524,7 @@ void FixNVESpin::sectoring() sublo[dim]=sublotmp[dim]; subhi[dim]=subhitmp[dim]; } - } + } const double rsx = subhi[0] - sublo[0]; const double rsy = subhi[1] - sublo[1];

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