forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6833 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
a572d7eb7e
commit
a108f5ddc6
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@ -18,7 +18,7 @@ PACKAGE = asphere class2 colloid dipole gpu granular \
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shock srd xtc
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PACKUSER = user-misc user-atc user-awpmd user-cg-cmm \
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user-cuda user-eff user-ewaldn user-omp user-reaxc
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user-cuda user-eff user-ewaldn user-omp user-reaxc user-sph
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PACKALL = $(PACKAGE) $(PACKUSER)
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@ -0,0 +1,59 @@
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# Install/unInstall package files in LAMMPS
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if (test $1 = 1) then
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cp -p atom_vec_meso.cpp ..
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cp -p pair_sph_heatconduction.cpp ..
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cp -p pair_sph_idealgas.cpp ..
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cp -p pair_sph_lj.cpp ..
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cp -p pair_sph_rhosum.cpp ..
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cp -p pair_sph_taitwater.cpp ..
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cp -p pair_sph_taitwater_morris.cpp ..
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cp -p compute_meso_e_atom.cpp ..
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cp -p compute_meso_rho_atom.cpp ..
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cp -p compute_meso_t_atom.cpp ..
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cp -p fix_meso.cpp ..
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cp -p fix_meso_stationary.cpp ..
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cp -p atom_vec_meso.h ..
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cp -p pair_sph_heatconduction.h ..
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cp -p pair_sph_idealgas.h ..
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cp -p pair_sph_lj.h ..
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cp -p pair_sph_rhosum.h ..
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cp -p pair_sph_taitwater.h ..
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cp -p pair_sph_taitwater_morris.h ..
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cp -p compute_meso_e_atom.h ..
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cp -p compute_meso_rho_atom.h ..
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cp -p compute_meso_t_atom.h ..
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cp -p fix_meso.h ..
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cp -p fix_meso_stationary.h ..
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elif (test $1 = 0) then
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rm -f ../atom_vec_meso.cpp
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rm -f ../pair_sph_heatconduction.cpp
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rm -f ../pair_sph_idealgas.cpp
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rm -f ../pair_sph_lj.cpp
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rm -f ../pair_sph_rhosum.cpp
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rm -f ../pair_sph_taitwater.cpp
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rm -f ../pair_sph_taitwater_morris.cpp
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rm -f ../compute_meso_e_atom.cpp
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rm -f ../compute_meso_rho_atom.cpp
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rm -f ../compute_meso_t_atom.cpp
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rm -f ../fix_meso.cpp
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rm -f ../fix_meso_stationary.cpp
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rm -f ../atom_vec_meso.h
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rm -f ../pair_sph_heatconduction.h
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rm -f ../pair_sph_idealgas.h
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rm -f ../pair_sph_lj.h
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rm -f ../pair_sph_rhosum.h
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rm -f ../pair_sph_taitwater.h
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rm -f ../pair_sph_taitwater_morris.h
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rm -f ../compute_meso_e_atom.h
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rm -f ../compute_meso_rho_atom.h
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rm -f ../compute_meso_t_atom.h
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rm -f ../fix_meso.h
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rm -f ../fix_meso_stationary.h
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fi
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@ -0,0 +1,868 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "atom_vec_meso.h"
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#include "atom.h"
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#include "domain.h"
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#include "modify.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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AtomVecMeso::AtomVecMeso(LAMMPS *lmp, int narg, char **arg) :
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AtomVec(lmp, narg, arg) {
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molecular = 0;
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mass_type = 1;
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comm_x_only = 0; // we communicate not only x forward but also vest ...
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comm_f_only = 0; // we also communicate de and drho in reverse direction
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size_forward = 8; // 3 + rho + e + vest[3], that means we may only communicate 5 in hybrid
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size_reverse = 5; // 3 + drho + de
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size_border = 12; // 6 + rho + e + vest[3] + cv
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size_velocity = 3;
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size_data_atom = 8;
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size_data_vel = 4;
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xcol_data = 6;
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atom->e_flag = 1;
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atom->rho_flag = 1;
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atom->cv_flag = 1;
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atom->vest_flag = 1;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by DELTA
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecMeso::grow(int n) {
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if (n == 0)
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nmax += DELTA;
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else
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nmax = n;
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atom->nmax = nmax;
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one("Per-processor system is too big");
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tag = memory->grow(atom->tag, nmax, "atom:tag");
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type = memory->grow(atom->type, nmax, "atom:type");
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mask = memory->grow(atom->mask, nmax, "atom:mask");
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image = memory->grow(atom->image, nmax, "atom:image");
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x = memory->grow(atom->x, nmax, 3, "atom:x");
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v = memory->grow(atom->v, nmax, 3, "atom:v");
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f = memory->grow(atom->f, nmax, 3, "atom:f");
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rho = memory->grow(atom->rho, nmax, "atom:rho");
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drho = memory->grow(atom->drho, nmax, "atom:drho");
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e = memory->grow(atom->e, nmax, "atom:e");
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de = memory->grow(atom->de, nmax, "atom:de");
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vest = memory->grow(atom->vest, nmax, 3, "atom:vest");
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cv = memory->grow(atom->cv, nmax, "atom:cv");
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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/* ----------------------------------------------------------------------
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reset local array ptrs
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------------------------------------------------------------------------- */
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void AtomVecMeso::grow_reset() {
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tag = atom->tag;
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type = atom->type;
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mask = atom->mask;
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image = atom->image;
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x = atom->x;
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v = atom->v;
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f = atom->f;
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rho = atom->rho;
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drho = atom->drho;
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e = atom->e;
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de = atom->de;
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vest = atom->vest;
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cv = atom->cv;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecMeso::copy(int i, int j, int delflag) {
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//printf("in AtomVecMeso::copy\n");
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tag[j] = tag[i];
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type[j] = type[i];
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mask[j] = mask[i];
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image[j] = image[i];
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x[j][0] = x[i][0];
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x[j][1] = x[i][1];
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x[j][2] = x[i][2];
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v[j][0] = v[i][0];
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v[j][1] = v[i][1];
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v[j][2] = v[i][2];
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rho[j] = rho[i];
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drho[j] = drho[i];
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e[j] = e[i];
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de[j] = de[i];
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cv[j] = cv[i];
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vest[j][0] = vest[i][0];
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vest[j][1] = vest[i][1];
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vest[j][2] = vest[i][2];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i, j);
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_comm_hybrid(int n, int *list, double *buf) {
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//printf("in AtomVecMeso::pack_comm_hybrid\n");
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int i, j, m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::unpack_comm_hybrid(int n, int first, double *buf) {
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//printf("in AtomVecMeso::unpack_comm_hybrid\n");
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int i, m, last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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rho[i] = buf[m++];
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e[i] = buf[m++];
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vest[i][0] = buf[m++];
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vest[i][1] = buf[m++];
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vest[i][2] = buf[m++];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_border_hybrid(int n, int *list, double *buf) {
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//printf("in AtomVecMeso::pack_border_hybrid\n");
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int i, j, m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::unpack_border_hybrid(int n, int first, double *buf) {
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//printf("in AtomVecMeso::unpack_border_hybrid\n");
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int i, m, last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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rho[i] = buf[m++];
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e[i] = buf[m++];
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vest[i][0] = buf[m++];
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vest[i][1] = buf[m++];
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vest[i][2] = buf[m++];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_reverse_hybrid(int n, int first, double *buf) {
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//printf("in AtomVecMeso::pack_reverse_hybrid\n");
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int i, m, last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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buf[m++] = drho[i];
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buf[m++] = de[i];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::unpack_reverse_hybrid(int n, int *list, double *buf) {
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//printf("in AtomVecMeso::unpack_reverse_hybrid\n");
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int i, j, m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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drho[j] += buf[m++];
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de[j] += buf[m++];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_comm(int n, int *list, double *buf, int pbc_flag,
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int *pbc) {
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//printf("in AtomVecMeso::pack_comm\n");
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int i, j, m;
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double dx, dy, dz;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0] * domain->xprd;
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dy = pbc[1] * domain->yprd;
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dz = pbc[2] * domain->zprd;
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} else {
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dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
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dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
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dz = pbc[2] * domain->zprd;
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}
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_comm_vel(int n, int *list, double *buf, int pbc_flag,
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int *pbc) {
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//printf("in AtomVecMeso::pack_comm_vel\n");
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int i, j, m;
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double dx, dy, dz;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0] * domain->xprd;
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dy = pbc[1] * domain->yprd;
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dz = pbc[2] * domain->zprd;
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} else {
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dx = pbc[0] * domain->xprd + pbc[5] * domain->xy + pbc[4] * domain->xz;
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dy = pbc[1] * domain->yprd + pbc[3] * domain->yz;
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dz = pbc[2] * domain->zprd;
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}
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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buf[m++] = rho[j];
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buf[m++] = e[j];
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buf[m++] = vest[j][0];
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buf[m++] = vest[j][1];
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buf[m++] = vest[j][2];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecMeso::unpack_comm(int n, int first, double *buf) {
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//printf("in AtomVecMeso::unpack_comm\n");
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int i, m, last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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rho[i] = buf[m++];
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e[i] = buf[m++];
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vest[i][0] = buf[m++];
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vest[i][1] = buf[m++];
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vest[i][2] = buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecMeso::unpack_comm_vel(int n, int first, double *buf) {
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//printf("in AtomVecMeso::unpack_comm_vel\n");
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int i, m, last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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v[i][0] = buf[m++];
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v[i][1] = buf[m++];
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v[i][2] = buf[m++];
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rho[i] = buf[m++];
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e[i] = buf[m++];
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vest[i][0] = buf[m++];
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vest[i][1] = buf[m++];
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vest[i][2] = buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecMeso::pack_reverse(int n, int first, double *buf) {
|
||||
//printf("in AtomVecMeso::pack_reverse\n");
|
||||
int i, m, last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
buf[m++] = f[i][0];
|
||||
buf[m++] = f[i][1];
|
||||
buf[m++] = f[i][2];
|
||||
buf[m++] = drho[i];
|
||||
buf[m++] = de[i];
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecMeso::unpack_reverse(int n, int *list, double *buf) {
|
||||
//printf("in AtomVecMeso::unpack_reverse\n");
|
||||
int i, j, m;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
f[j][0] += buf[m++];
|
||||
f[j][1] += buf[m++];
|
||||
f[j][2] += buf[m++];
|
||||
drho[j] += buf[m++];
|
||||
de[j] += buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecMeso::pack_border(int n, int *list, double *buf, int pbc_flag,
|
||||
int *pbc) {
|
||||
//printf("in AtomVecMeso::pack_border\n");
|
||||
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++] = x[j][0];
|
||||
buf[m++] = x[j][1];
|
||||
buf[m++] = x[j][2];
|
||||
buf[m++] = tag[j];
|
||||
buf[m++] = type[j];
|
||||
buf[m++] = mask[j];
|
||||
buf[m++] = rho[j];
|
||||
buf[m++] = e[j];
|
||||
buf[m++] = cv[j];
|
||||
buf[m++] = vest[j][0];
|
||||
buf[m++] = vest[j][1];
|
||||
buf[m++] = vest[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];
|
||||
}
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = x[j][0] + dx;
|
||||
buf[m++] = x[j][1] + dy;
|
||||
buf[m++] = x[j][2] + dz;
|
||||
buf[m++] = tag[j];
|
||||
buf[m++] = type[j];
|
||||
buf[m++] = mask[j];
|
||||
buf[m++] = rho[j];
|
||||
buf[m++] = e[j];
|
||||
buf[m++] = cv[j];
|
||||
buf[m++] = vest[j][0];
|
||||
buf[m++] = vest[j][1];
|
||||
buf[m++] = vest[j][2];
|
||||
}
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecMeso::pack_border_vel(int n, int *list, double *buf, int pbc_flag,
|
||||
int *pbc) {
|
||||
//printf("in AtomVecMeso::pack_border_vel\n");
|
||||
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++] = x[j][0];
|
||||
buf[m++] = x[j][1];
|
||||
buf[m++] = x[j][2];
|
||||
buf[m++] = tag[j];
|
||||
buf[m++] = type[j];
|
||||
buf[m++] = mask[j];
|
||||
buf[m++] = v[j][0];
|
||||
buf[m++] = v[j][1];
|
||||
buf[m++] = v[j][2];
|
||||
buf[m++] = rho[j];
|
||||
buf[m++] = e[j];
|
||||
buf[m++] = cv[j];
|
||||
buf[m++] = vest[j][0];
|
||||
buf[m++] = vest[j][1];
|
||||
buf[m++] = vest[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];
|
||||
}
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = x[j][0] + dx;
|
||||
buf[m++] = x[j][1] + dy;
|
||||
buf[m++] = x[j][2] + dz;
|
||||
buf[m++] = tag[j];
|
||||
buf[m++] = type[j];
|
||||
buf[m++] = mask[j];
|
||||
buf[m++] = v[j][0];
|
||||
buf[m++] = v[j][1];
|
||||
buf[m++] = v[j][2];
|
||||
buf[m++] = rho[j];
|
||||
buf[m++] = e[j];
|
||||
buf[m++] = cv[j];
|
||||
buf[m++] = vest[j][0];
|
||||
buf[m++] = vest[j][1];
|
||||
buf[m++] = vest[j][2];
|
||||
}
|
||||
}
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecMeso::unpack_border(int n, int first, double *buf) {
|
||||
//printf("in AtomVecMeso::unpack_border\n");
|
||||
int i, m, last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
if (i == nmax)
|
||||
grow(0);
|
||||
x[i][0] = buf[m++];
|
||||
x[i][1] = buf[m++];
|
||||
x[i][2] = buf[m++];
|
||||
tag[i] = static_cast<int> (buf[m++]);
|
||||
type[i] = static_cast<int> (buf[m++]);
|
||||
mask[i] = static_cast<int> (buf[m++]);
|
||||
rho[i] = buf[m++];
|
||||
e[i] = buf[m++];
|
||||
cv[i] = buf[m++];
|
||||
vest[i][0] = buf[m++];
|
||||
vest[i][1] = buf[m++];
|
||||
vest[i][2] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecMeso::unpack_border_vel(int n, int first, double *buf) {
|
||||
//printf("in AtomVecMeso::unpack_border_vel\n");
|
||||
int i, m, last;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
if (i == nmax)
|
||||
grow(0);
|
||||
x[i][0] = buf[m++];
|
||||
x[i][1] = buf[m++];
|
||||
x[i][2] = buf[m++];
|
||||
tag[i] = static_cast<int> (buf[m++]);
|
||||
type[i] = static_cast<int> (buf[m++]);
|
||||
mask[i] = static_cast<int> (buf[m++]);
|
||||
v[i][0] = buf[m++];
|
||||
v[i][1] = buf[m++];
|
||||
v[i][2] = buf[m++];
|
||||
rho[i] = buf[m++];
|
||||
e[i] = buf[m++];
|
||||
cv[i] = buf[m++];
|
||||
vest[i][0] = buf[m++];
|
||||
vest[i][1] = buf[m++];
|
||||
vest[i][2] = buf[m++];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack data for atom I for sending to another proc
|
||||
xyz must be 1st 3 values, so comm::exchange() can test on them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecMeso::pack_exchange(int i, double *buf) {
|
||||
//printf("in AtomVecMeso::pack_exchange\n");
|
||||
int m = 1;
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
buf[m++] = x[i][2];
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
buf[m++] = v[i][2];
|
||||
buf[m++] = tag[i];
|
||||
buf[m++] = type[i];
|
||||
buf[m++] = mask[i];
|
||||
buf[m++] = image[i];
|
||||
buf[m++] = rho[i];
|
||||
buf[m++] = e[i];
|
||||
buf[m++] = cv[i];
|
||||
buf[m++] = vest[i][0];
|
||||
buf[m++] = vest[i][1];
|
||||
buf[m++] = vest[i][2];
|
||||
|
||||
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;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecMeso::unpack_exchange(double *buf) {
|
||||
//printf("in AtomVecMeso::unpack_exchange\n");
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax)
|
||||
grow(0);
|
||||
|
||||
int m = 1;
|
||||
x[nlocal][0] = buf[m++];
|
||||
x[nlocal][1] = buf[m++];
|
||||
x[nlocal][2] = buf[m++];
|
||||
v[nlocal][0] = buf[m++];
|
||||
v[nlocal][1] = buf[m++];
|
||||
v[nlocal][2] = buf[m++];
|
||||
tag[nlocal] = static_cast<int> (buf[m++]);
|
||||
type[nlocal] = static_cast<int> (buf[m++]);
|
||||
mask[nlocal] = static_cast<int> (buf[m++]);
|
||||
image[nlocal] = static_cast<int> (buf[m++]);
|
||||
rho[nlocal] = buf[m++];
|
||||
e[nlocal] = buf[m++];
|
||||
cv[nlocal] = buf[m++];
|
||||
vest[nlocal][0] = buf[m++];
|
||||
vest[nlocal][1] = buf[m++];
|
||||
vest[nlocal][2] = 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 AtomVecMeso::size_restart() {
|
||||
int i;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int n = 17 * nlocal; // 11 + rho + e + cv + vest[3]
|
||||
|
||||
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 AtomVecMeso::pack_restart(int i, double *buf) {
|
||||
int m = 1;
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
buf[m++] = x[i][2];
|
||||
buf[m++] = tag[i];
|
||||
buf[m++] = type[i];
|
||||
buf[m++] = mask[i];
|
||||
buf[m++] = image[i];
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
buf[m++] = v[i][2];
|
||||
buf[m++] = rho[i];
|
||||
buf[m++] = e[i];
|
||||
buf[m++] = cv[i];
|
||||
buf[m++] = vest[i][0];
|
||||
buf[m++] = vest[i][1];
|
||||
buf[m++] = vest[i][2];
|
||||
|
||||
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 AtomVecMeso::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");
|
||||
}
|
||||
|
||||
int m = 1;
|
||||
x[nlocal][0] = buf[m++];
|
||||
x[nlocal][1] = buf[m++];
|
||||
x[nlocal][2] = buf[m++];
|
||||
tag[nlocal] = static_cast<int> (buf[m++]);
|
||||
type[nlocal] = static_cast<int> (buf[m++]);
|
||||
mask[nlocal] = static_cast<int> (buf[m++]);
|
||||
image[nlocal] = static_cast<int> (buf[m++]);
|
||||
v[nlocal][0] = buf[m++];
|
||||
v[nlocal][1] = buf[m++];
|
||||
v[nlocal][2] = buf[m++];
|
||||
rho[nlocal] = buf[m++];
|
||||
e[nlocal] = buf[m++];
|
||||
cv[nlocal] = buf[m++];
|
||||
vest[nlocal][0] = buf[m++];
|
||||
vest[nlocal][1] = buf[m++];
|
||||
vest[nlocal][2] = buf[m++];
|
||||
|
||||
double **extra = atom->extra;
|
||||
if (atom->nextra_store) {
|
||||
int size = static_cast<int> (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 AtomVecMeso::create_atom(int itype, double *coord) {
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax)
|
||||
grow(0);
|
||||
|
||||
tag[nlocal] = 0;
|
||||
type[nlocal] = itype;
|
||||
x[nlocal][0] = coord[0];
|
||||
x[nlocal][1] = coord[1];
|
||||
x[nlocal][2] = coord[2];
|
||||
mask[nlocal] = 1;
|
||||
image[nlocal] = (512 << 20) | (512 << 10) | 512;
|
||||
v[nlocal][0] = 0.0;
|
||||
v[nlocal][1] = 0.0;
|
||||
v[nlocal][2] = 0.0;
|
||||
rho[nlocal] = 0.0;
|
||||
e[nlocal] = 0.0;
|
||||
cv[nlocal] = 1.0;
|
||||
vest[nlocal][0] = 0.0;
|
||||
vest[nlocal][1] = 0.0;
|
||||
vest[nlocal][2] = 0.0;
|
||||
de[nlocal] = 0.0;
|
||||
drho[nlocal] = 0.0;
|
||||
|
||||
atom->nlocal++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack one line from Atoms section of data file
|
||||
initialize other atom quantities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecMeso::data_atom(double *coord, int imagetmp, char **values) {
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax)
|
||||
grow(0);
|
||||
|
||||
tag[nlocal] = atoi(values[0]);
|
||||
if (tag[nlocal] <= 0)
|
||||
error->one("Invalid atom ID in Atoms section of data file");
|
||||
|
||||
type[nlocal] = atoi(values[1]);
|
||||
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
|
||||
error->one("Invalid atom type in Atoms section of data file");
|
||||
|
||||
rho[nlocal] = atof(values[2]);
|
||||
e[nlocal] = atof(values[3]);
|
||||
cv[nlocal] = atof(values[4]);
|
||||
|
||||
x[nlocal][0] = coord[0];
|
||||
x[nlocal][1] = coord[1];
|
||||
x[nlocal][2] = coord[2];
|
||||
|
||||
//printf("rho=%f, e=%f, cv=%f, x=%f\n", rho[nlocal], e[nlocal], cv[nlocal], x[nlocal][0]);
|
||||
|
||||
image[nlocal] = imagetmp;
|
||||
|
||||
mask[nlocal] = 1;
|
||||
v[nlocal][0] = 0.0;
|
||||
v[nlocal][1] = 0.0;
|
||||
v[nlocal][2] = 0.0;
|
||||
|
||||
vest[nlocal][0] = 0.0;
|
||||
vest[nlocal][1] = 0.0;
|
||||
vest[nlocal][2] = 0.0;
|
||||
|
||||
de[nlocal] = 0.0;
|
||||
drho[nlocal] = 0.0;
|
||||
|
||||
atom->nlocal++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack hybrid quantities from one line in Atoms section of data file
|
||||
initialize other atom quantities for this sub-style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecMeso::data_atom_hybrid(int nlocal, char **values) {
|
||||
|
||||
rho[nlocal] = atof(values[0]);
|
||||
e[nlocal] = atof(values[1]);
|
||||
cv[nlocal] = atof(values[2]);
|
||||
|
||||
return 3;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return # of bytes of allocated memory
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
bigint AtomVecMeso::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);
|
||||
if (atom->memcheck("v"))
|
||||
bytes += memory->usage(v, nmax);
|
||||
if (atom->memcheck("f"))
|
||||
bytes += memory->usage(f, nmax);
|
||||
if (atom->memcheck("rho"))
|
||||
bytes += memory->usage(rho, nmax);
|
||||
if (atom->memcheck("drho"))
|
||||
bytes += memory->usage(drho, nmax);
|
||||
if (atom->memcheck("e"))
|
||||
bytes += memory->usage(e, nmax);
|
||||
if (atom->memcheck("de"))
|
||||
bytes += memory->usage(de, nmax);
|
||||
if (atom->memcheck("cv"))
|
||||
bytes += memory->usage(cv, nmax);
|
||||
if (atom->memcheck("vest"))
|
||||
bytes += memory->usage(vest, nmax);
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,74 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(meso,AtomVecMeso)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_ATOM_VEC_MESO_H
|
||||
#define LMP_ATOM_VEC_MESO_H
|
||||
|
||||
#include "atom_vec.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AtomVecMeso : public AtomVec {
|
||||
public:
|
||||
AtomVecMeso(class LAMMPS *, int, char **);
|
||||
~AtomVecMeso() {}
|
||||
void grow(int);
|
||||
void grow_reset();
|
||||
void copy(int, int, int);
|
||||
int pack_comm(int, int *, double *, int, int *);
|
||||
int pack_comm_vel(int, int *, double *, int, int *);
|
||||
void unpack_comm(int, int, double *);
|
||||
void unpack_comm_vel(int, int, double *);
|
||||
int pack_reverse(int, int, double *);
|
||||
void unpack_reverse(int, int *, double *);
|
||||
|
||||
int pack_comm_hybrid(int, int *, double *);
|
||||
int unpack_comm_hybrid(int, int, double *);
|
||||
|
||||
int pack_border_hybrid(int, int *, double *);
|
||||
int unpack_border_hybrid(int, int, double *);
|
||||
|
||||
int pack_reverse_hybrid(int, int, double *);
|
||||
int unpack_reverse_hybrid(int, int *, double *);
|
||||
|
||||
int pack_border(int, int *, double *, int, int *);
|
||||
int pack_border_vel(int, int *, double *, int, int *);
|
||||
void unpack_border(int, int, double *);
|
||||
void unpack_border_vel(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 *, int, char **);
|
||||
int data_atom_hybrid(int, char **);
|
||||
bigint memory_usage();
|
||||
|
||||
private:
|
||||
int *tag,*type,*mask,*image;
|
||||
double **x,**v,**f;
|
||||
double *rho, *drho, *e, *de, *cv;
|
||||
double **vest; // estimated velocity during force computation
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,97 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "compute_meso_e_atom.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoEAtom::ComputeMesoEAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all("Number of arguments for compute meso_e/atom command != 3");
|
||||
if (atom->e_flag != 1) error->all("compute meso_e/atom command requires atom_style with energy (e.g. meso)");
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 0;
|
||||
|
||||
nmax = 0;
|
||||
evector = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoEAtom::~ComputeMesoEAtom()
|
||||
{
|
||||
memory->sfree(evector);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoEAtom::init()
|
||||
{
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->ncompute; i++)
|
||||
if (strcmp(modify->compute[i]->style,"evector/atom") == 0) count++;
|
||||
if (count > 1 && comm->me == 0)
|
||||
error->warning("More than one compute evector/atom");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoEAtom::compute_peratom()
|
||||
{
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// grow evector array if necessary
|
||||
|
||||
if (atom->nlocal > nmax) {
|
||||
memory->sfree(evector);
|
||||
nmax = atom->nmax;
|
||||
evector = (double *) memory->smalloc(nmax*sizeof(double),"evector/atom:evector");
|
||||
vector_atom = evector;
|
||||
}
|
||||
|
||||
double *e = atom->e;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
evector[i] = e[i];
|
||||
}
|
||||
else {
|
||||
evector[i] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeMesoEAtom::memory_usage()
|
||||
{
|
||||
double bytes = nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(meso_e/atom,ComputeMesoEAtom)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_MESO_E_ATOM_H
|
||||
#define LMP_COMPUTE_MESO_E_ATOM_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeMesoEAtom : public Compute {
|
||||
public:
|
||||
ComputeMesoEAtom(class LAMMPS *, int, char **);
|
||||
~ComputeMesoEAtom();
|
||||
void init();
|
||||
void compute_peratom();
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nmax;
|
||||
double *evector;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "compute_meso_rho_atom.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoRhoAtom::ComputeMesoRhoAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all("Illegal compute meso_rho/atom command");
|
||||
if (atom->rho_flag != 1) error->all("compute meso_rho/atom command requires atom_style with density (e.g. meso)");
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 0;
|
||||
|
||||
nmax = 0;
|
||||
rhoVector = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoRhoAtom::~ComputeMesoRhoAtom()
|
||||
{
|
||||
memory->sfree(rhoVector);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoRhoAtom::init()
|
||||
{
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->ncompute; i++)
|
||||
if (strcmp(modify->compute[i]->style,"rhoVector/atom") == 0) count++;
|
||||
if (count > 1 && comm->me == 0)
|
||||
error->warning("More than one compute rhoVector/atom");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoRhoAtom::compute_peratom()
|
||||
{
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// grow rhoVector array if necessary
|
||||
|
||||
if (atom->nlocal > nmax) {
|
||||
memory->sfree(rhoVector);
|
||||
nmax = atom->nmax;
|
||||
rhoVector = (double *) memory->smalloc(nmax*sizeof(double),"atom:rhoVector");
|
||||
vector_atom = rhoVector;
|
||||
}
|
||||
|
||||
// compute kinetic energy for each atom in group
|
||||
|
||||
double *rho = atom->rho;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
rhoVector[i] = rho[i];
|
||||
}
|
||||
else {
|
||||
rhoVector[i] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeMesoRhoAtom::memory_usage()
|
||||
{
|
||||
double bytes = nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(meso_rho/atom,ComputeMesoRhoAtom)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_MESO_RHO_ATOM_H
|
||||
#define LMP_COMPUTE_MESO_RHO_ATOM_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeMesoRhoAtom : public Compute {
|
||||
public:
|
||||
ComputeMesoRhoAtom(class LAMMPS *, int, char **);
|
||||
~ComputeMesoRhoAtom();
|
||||
void init();
|
||||
void compute_peratom();
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nmax;
|
||||
double *rhoVector;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,101 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "string.h"
|
||||
#include "compute_meso_t_atom.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoTAtom::ComputeMesoTAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg)
|
||||
{
|
||||
if (narg != 3) error->all("Number of arguments for compute meso_t/atom command != 3");
|
||||
if ((atom->e_flag != 1) || (atom->cv_flag != 1))
|
||||
error->all("compute meso_e/atom command requires atom_style with both energy and heat capacity (e.g. meso)");
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 0;
|
||||
|
||||
nmax = 0;
|
||||
tvector = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ComputeMesoTAtom::~ComputeMesoTAtom()
|
||||
{
|
||||
memory->sfree(tvector);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoTAtom::init()
|
||||
{
|
||||
|
||||
int count = 0;
|
||||
for (int i = 0; i < modify->ncompute; i++)
|
||||
if (strcmp(modify->compute[i]->style,"meso_t/atom") == 0) count++;
|
||||
if (count > 1 && comm->me == 0)
|
||||
error->warning("More than one compute meso_t/atom");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ComputeMesoTAtom::compute_peratom()
|
||||
{
|
||||
invoked_peratom = update->ntimestep;
|
||||
|
||||
// grow tvector array if necessary
|
||||
|
||||
if (atom->nlocal > nmax) {
|
||||
memory->sfree(tvector);
|
||||
nmax = atom->nmax;
|
||||
tvector = (double *) memory->smalloc(nmax*sizeof(double),"tvector/atom:tvector");
|
||||
vector_atom = tvector;
|
||||
}
|
||||
|
||||
double *e = atom->e;
|
||||
double *cv = atom->cv;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (cv[i] > 0.0) {
|
||||
tvector[i] = e[i] / cv[i];
|
||||
}
|
||||
}
|
||||
else {
|
||||
tvector[i] = 0.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ComputeMesoTAtom::memory_usage()
|
||||
{
|
||||
double bytes = nmax * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,43 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 COMPUTE_CLASS
|
||||
|
||||
ComputeStyle(meso_t/atom,ComputeMesoTAtom)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_COMPUTE_MESO_T_ATOM_H
|
||||
#define LMP_COMPUTE_MESO_T_ATOM_H
|
||||
|
||||
#include "compute.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ComputeMesoTAtom : public Compute {
|
||||
public:
|
||||
ComputeMesoTAtom(class LAMMPS *, int, char **);
|
||||
~ComputeMesoTAtom();
|
||||
void init();
|
||||
void compute_peratom();
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int nmax;
|
||||
double *tvector;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,167 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdio.h"
|
||||
#include "string.h"
|
||||
#include "fix_meso.h"
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "respa.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "pair.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMeso::FixMeso(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg) {
|
||||
|
||||
if ((atom->e_flag != 1) || (atom->rho_flag != 1))
|
||||
error->all(
|
||||
"fix meso command requires atom_style with both energy and density");
|
||||
|
||||
if (narg != 3)
|
||||
error->all("Illegal number of arguments for fix meso command");
|
||||
|
||||
time_integrate = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixMeso::setmask() {
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMeso::init() {
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allow for both per-type and per-atom mass
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMeso::initial_integrate(int vflag) {
|
||||
// update v and x and rho and e of atoms in group
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **vest = atom->vest;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *mass = atom->mass;
|
||||
double *rmass = atom->rmass;
|
||||
int rmass_flag = atom->rmass_flag;
|
||||
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int i;
|
||||
double dtfm;
|
||||
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
if (rmass_flag) {
|
||||
dtfm = dtf / rmass[i];
|
||||
} else {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
}
|
||||
|
||||
e[i] += dtf * de[i]; // half-step update of particle internal energy
|
||||
rho[i] += dtf * drho[i]; // ... and density
|
||||
|
||||
// extrapolate velocity for use with velocity-dependent potentials, e.g. SPH
|
||||
vest[i][0] = v[i][0] + 2.0 * dtfm * f[i][0];
|
||||
vest[i][1] = v[i][1] + 2.0 * dtfm * f[i][1];
|
||||
vest[i][2] = v[i][2] + 2.0 * dtfm * f[i][2];
|
||||
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMeso::final_integrate() {
|
||||
|
||||
// update v, rho, and e of atoms in group
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
double *mass = atom->mass;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
double dtfm;
|
||||
double *rmass = atom->rmass;
|
||||
int rmass_flag = atom->rmass_flag;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
|
||||
if (rmass_flag) {
|
||||
dtfm = dtf / rmass[i];
|
||||
} else {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
}
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
e[i] += dtf * de[i];
|
||||
rho[i] += dtf * drho[i];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMeso::reset_dt() {
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 FIX_CLASS
|
||||
|
||||
FixStyle(meso,FixMeso)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MESO_H
|
||||
#define LMP_FIX_MESO_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixMeso : public Fix {
|
||||
public:
|
||||
FixMeso(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void reset_dt();
|
||||
|
||||
private:
|
||||
class NeighList *list;
|
||||
protected:
|
||||
double dtv,dtf;
|
||||
double *step_respa;
|
||||
int mass_require;
|
||||
|
||||
class Pair *pair;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,122 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "stdio.h"
|
||||
#include "string.h"
|
||||
#include "fix_meso_stationary.h"
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "respa.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "pair.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixMesoStationary::FixMesoStationary(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg) {
|
||||
|
||||
if ((atom->e_flag != 1) || (atom->rho_flag != 1))
|
||||
error->all(
|
||||
"fix meso/stationary command requires atom_style with both energy and density, e.g. meso");
|
||||
|
||||
if (narg != 3)
|
||||
error->all("Illegal number of arguments for fix meso/stationary command");
|
||||
|
||||
time_integrate = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixMesoStationary::setmask() {
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoStationary::init() {
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allow for both per-type and per-atom mass
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoStationary::initial_integrate(int vflag) {
|
||||
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int i;
|
||||
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
e[i] += dtf * de[i]; // half-step update of particle internal energy
|
||||
rho[i] += dtf * drho[i]; // ... and density
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoStationary::final_integrate() {
|
||||
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *rho = atom->rho;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
double *mass = atom->mass;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup)
|
||||
nlocal = atom->nfirst;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
e[i] += dtf * de[i];
|
||||
rho[i] += dtf * drho[i];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixMesoStationary::reset_dt() {
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,49 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 FIX_CLASS
|
||||
|
||||
FixStyle(meso/stationary,FixMesoStationary)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MESO_STATIONARY_H
|
||||
#define LMP_FIX_MESO_STATIONARY_H
|
||||
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixMesoStationary : public Fix {
|
||||
public:
|
||||
FixMesoStationary(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
virtual void init();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
void reset_dt();
|
||||
|
||||
private:
|
||||
class NeighList *list;
|
||||
protected:
|
||||
double dtv,dtf;
|
||||
double *step_respa;
|
||||
int mass_require;
|
||||
|
||||
class Pair *pair;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,221 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_heatconduction.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neigh_list.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHHeatConduction::PairSPHHeatConduction(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHHeatConduction::~PairSPHHeatConduction() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
memory->destroy(cut);
|
||||
memory->destroy(alpha);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHHeatConduction::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double imass, jmass, h, ih, ihsq;
|
||||
double rsq, wfd, D, deltaE;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double *e = atom->e;
|
||||
double *de = atom->de;
|
||||
double *mass = atom->mass;
|
||||
double *rho = atom->rho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms and do heat diffusion
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = type[i];
|
||||
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
// kernel function
|
||||
wfd = h - sqrt(rsq);
|
||||
if (domain->dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// deltaE, which is missing a factor of 1/r
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
jmass = mass[jtype];
|
||||
D = alpha[itype][jtype]; // diffusion coefficient
|
||||
|
||||
deltaE = 2.0 * imass * jmass / (imass+jmass);
|
||||
deltaE *= (rho[i] + rho[j]) / (rho[i] * rho[j]);
|
||||
deltaE *= D * (e[i] - e[j]) * wfd;
|
||||
|
||||
de[i] += deltaE;
|
||||
if (newton_pair || j < nlocal) {
|
||||
de[j] -= deltaE;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHHeatConduction::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
memory->create(alpha, n + 1, n + 1, "pair:alpha");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHHeatConduction::settings(int narg, char **arg) {
|
||||
if (narg != 0)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/heatconduction");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHHeatConduction::coeff(int narg, char **arg) {
|
||||
if (narg != 4)
|
||||
error->all("Incorrect number of args for pair_style sph/heatconduction coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double alpha_one = force->numeric(arg[2]);
|
||||
double cut_one = force->numeric(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
//printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
alpha[i][j] = alpha_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHHeatConduction::init_one(int i, int j) {
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("All pair sph/heatconduction coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
alpha[j][i] = alpha[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHHeatConduction::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
|
@ -0,0 +1,45 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/heatconduction,PairSPHHeatConduction)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_SPH_HEATCONDUCTION_H
|
||||
#define LMP_PAIR_SPH_HEATCONDUCTION_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHHeatConduction : public Pair {
|
||||
public:
|
||||
PairSPHHeatConduction(class LAMMPS *);
|
||||
virtual ~PairSPHHeatConduction();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double **cut, **alpha;
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,262 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_idealgas.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHIdealGas::PairSPHIdealGas(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHIdealGas::~PairSPHIdealGas() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(viscosity);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHIdealGas::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq;
|
||||
double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **v = atom->vest;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *de = atom->de;
|
||||
double *e = atom->e;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
fi = 0.4 * e[i] / imass / rho[i]; // ideal gas EOS; this expression is fi = pressure / rho^2
|
||||
ci = sqrt(0.4*e[i]/imass); // speed of sound with heat capacity ratio gamma=1.4
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1. / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
wfd = h - sqrt(rsq);
|
||||
if (domain->dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// (1) using delV . delX instead of delV . (delX/r) and
|
||||
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
fj = 0.4 * e[j] / jmass / rho[j];
|
||||
|
||||
// dot product of velocity delta and distance vector
|
||||
delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
|
||||
+ delz * (vztmp - v[j][2]);
|
||||
|
||||
// artificial viscosity (Monaghan 1992)
|
||||
if (delVdotDelR < 0.) {
|
||||
cj = sqrt(0.4*e[j]/jmass);
|
||||
mu = h * delVdotDelR / (rsq + 0.01 * h * h);
|
||||
fvisc = -viscosity[itype][jtype] * (ci + cj) * mu / (rho[i] + rho[j]);
|
||||
} else {
|
||||
fvisc = 0.;
|
||||
}
|
||||
|
||||
// total pair force & thermal energy increment
|
||||
fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
|
||||
deltaE = -0.5 * fpair * delVdotDelR;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
|
||||
// and change in density
|
||||
drho[i] += jmass * delVdotDelR * wfd;
|
||||
|
||||
// change in thermal energy
|
||||
de[i] += deltaE;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
de[j] += deltaE;
|
||||
drho[j] += imass * delVdotDelR * wfd;
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely,
|
||||
delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHIdealGas::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHIdealGas::settings(int narg, char **arg) {
|
||||
if (narg != 0)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/idealgas");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHIdealGas::coeff(int narg, char **arg) {
|
||||
if (narg != 4)
|
||||
error->all("Incorrect number of args for pair_style sph/idealgas coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double viscosity_one = force->numeric(arg[2]);
|
||||
double cut_one = force->numeric(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
viscosity[i][j] = viscosity_one;
|
||||
//printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair sph/idealgas coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHIdealGas::init_one(int i, int j) {
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("All pair sph/idealgas coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHIdealGas::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
|
@ -0,0 +1,46 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/idealgas,PairSPHIdealGas)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_IDEALGAS_H
|
||||
#define LMP_PAIR_IDEALGAS_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHIdealGas : public Pair {
|
||||
public:
|
||||
PairSPHIdealGas(class LAMMPS *);
|
||||
virtual ~PairSPHIdealGas();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double **cut,**viscosity;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,368 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_lj.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHLJ::PairSPHLJ(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHLJ::~PairSPHLJ() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(viscosity);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHLJ::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, ihcub;
|
||||
double rsq, wfd, delVdotDelR, mu, deltaE, ci, cj, lrc;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **v = atom->vest;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *de = atom->de;
|
||||
double *e = atom->e;
|
||||
double *cv = atom->cv;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
// compute pressure of particle i with LJ EOS
|
||||
LJEOS2(rho[i], e[i], cv[i], &fi, &ci);
|
||||
fi /= (rho[i] * rho[i]);
|
||||
//printf("fi = %f\n", fi);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
ihcub = ihsq * ih;
|
||||
|
||||
wfd = h - sqrt(rsq);
|
||||
if (domain->dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// (1) using delV . delX instead of delV . (delX/r) and
|
||||
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
// function call to LJ EOS
|
||||
LJEOS2(rho[j], e[j], cv[j], &fj, &cj);
|
||||
fj /= (rho[j] * rho[j]);
|
||||
|
||||
// apply long-range correction to model a LJ fluid with cutoff
|
||||
// this implies that the modelled LJ fluid has cutoff == SPH cutoff
|
||||
lrc = - 11.1701 * (ihcub * ihcub * ihcub - 1.5 * ihcub);
|
||||
fi += lrc;
|
||||
fj += lrc;
|
||||
|
||||
// dot product of velocity delta and distance vector
|
||||
delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
|
||||
+ delz * (vztmp - v[j][2]);
|
||||
|
||||
// artificial viscosity (Monaghan 1992)
|
||||
if (delVdotDelR < 0.) {
|
||||
mu = h * delVdotDelR / (rsq + 0.01 * h * h);
|
||||
fvisc = -viscosity[itype][jtype] * (ci + cj) * mu / (rho[i] + rho[j]);
|
||||
} else {
|
||||
fvisc = 0.;
|
||||
}
|
||||
|
||||
// total pair force & thermal energy increment
|
||||
fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
|
||||
deltaE = -0.5 * fpair * delVdotDelR;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
|
||||
// and change in density
|
||||
drho[i] += jmass * delVdotDelR * wfd;
|
||||
|
||||
// change in thermal energy
|
||||
de[i] += deltaE;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
de[j] += deltaE;
|
||||
drho[j] += imass * delVdotDelR * wfd;
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHLJ::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHLJ::settings(int narg, char **arg) {
|
||||
if (narg != 0)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/lj");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHLJ::coeff(int narg, char **arg) {
|
||||
if (narg != 4)
|
||||
error->all(
|
||||
"Incorrect args for pair_style sph/lj coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double viscosity_one = force->numeric(arg[2]);
|
||||
double cut_one = force->numeric(arg[3]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
viscosity[i][j] = viscosity_one;
|
||||
printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHLJ::init_one(int i, int j) {
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("All pair sph/lj coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
viscosity[j][i] = viscosity[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHLJ::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
|
||||
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
|
||||
|
||||
|
||||
double T = e / cv;
|
||||
if (T < 1.e-2) T = 1.e-2;
|
||||
//printf("%f %f\n", T, rho);
|
||||
double iT = 0.1e1 / T;
|
||||
//double itpow1_4 = exp(0.25 * log(iT)); //pow(iT, 0.1e1 / 0.4e1);
|
||||
double itpow1_4 = pow(iT, 0.1e1 / 0.4e1);
|
||||
double x = rho * itpow1_4;
|
||||
double xsq = x * x;
|
||||
double xpow3 = xsq * x;
|
||||
double xpow4 = xsq * xsq;
|
||||
double xpow9 = xpow3 * xpow3 * xpow3;
|
||||
|
||||
|
||||
return (0.1e1 + rho * (0.3629e1 + 0.7264e1 * x + 0.104925e2 * xsq + 0.11460e2
|
||||
* xpow3 + 0.21760e1 * xpow9 - itpow1_4 * itpow1_4 * (0.5369e1 + 0.13160e2
|
||||
* x + 0.18525e2 * xsq - 0.17076e2 * xpow3 + 0.9320e1 * xpow4) + iT
|
||||
* (-0.3492e1 + 0.18698e2 * x - 0.35505e2 * xsq + 0.31816e2 * xpow3
|
||||
- 0.11195e2 * xpow4)) * itpow1_4) * rho * T;
|
||||
}*/
|
||||
|
||||
|
||||
/* --------------------------------------------------------------------------------------------- */
|
||||
/* Lennard-Jones EOS,
|
||||
Francis H. Ree
|
||||
"Analytic representation of thermodynamic data for the Lennard‐Jones fluid",
|
||||
Journal of Chemical Physics 73 pp. 5401-5403 (1980)
|
||||
*/
|
||||
|
||||
void PairSPHLJ::LJEOS2(double rho, double e, double cv, double *p, double *c) {
|
||||
double T = e/cv;
|
||||
double beta = 1.0 / T;
|
||||
double beta_sqrt = sqrt(beta);
|
||||
double x = rho * sqrt(beta_sqrt);
|
||||
|
||||
double xsq = x * x;
|
||||
double xpow3 = xsq * x;
|
||||
double xpow4 = xsq * xsq;
|
||||
|
||||
/* differential of Helmholtz free energy w.r.t. x */
|
||||
double diff_A_NkT = 3.629 + 7.264*x - beta*(3.492 - 18.698*x + 35.505*xsq - 31.816*xpow3 + 11.195*xpow4)
|
||||
- beta_sqrt*(5.369 + 13.16*x + 18.525*xsq - 17.076*xpow3 + 9.32*xpow4)
|
||||
+ 10.4925*xsq + 11.46*xpow3 + 2.176*xpow4*xpow4*x;
|
||||
|
||||
/* differential of Helmholtz free energy w.r.t. x^2 */
|
||||
double d2A_dx2 = 7.264 + 20.985*x \
|
||||
+ beta*(18.698 - 71.01*x + 95.448*xsq - 44.78*xpow3)\
|
||||
- beta_sqrt*(13.16 + 37.05*x - 51.228*xsq + 37.28*xpow3)\
|
||||
+ 34.38*xsq + 19.584*xpow4*xpow4;
|
||||
|
||||
// p = rho k T * (1 + rho * d(A/(NkT))/drho)
|
||||
// dx/drho = rho/x
|
||||
*p = rho * T * (1.0 + diff_A_NkT * x); // pressure
|
||||
double csq = T * (1.0 + 2.0 * diff_A_NkT * x + d2A_dx2 * x * x); // soundspeed squared
|
||||
if (csq > 0.0) {
|
||||
*c = sqrt(csq); // soundspeed
|
||||
} else {
|
||||
*c = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
/* ------------------------------------------------------------------------------ */
|
||||
|
||||
/* Jirí Kolafa, Ivo Nezbeda
|
||||
* "The Lennard-Jones fluid: an accurate analytic and theoretically-based equation of state",
|
||||
* Fluid Phase Equilibria 100 pp. 1-34 (1994) */
|
||||
/*double PairSPHLJ::LJEOS2(double rho, double e, double cv) {
|
||||
double T = e / cv;
|
||||
|
||||
double sT = sqrt(T);
|
||||
double isT = 1.0 / sT;
|
||||
double dC = -0.063920968 * log(T) + 0.011117524 / T - 0.076383859 / sT
|
||||
+ 1.080142248 + 0.000693129 * sT;
|
||||
double eta = 3.141592654 / 6. * rho * (dC * dC * dC);
|
||||
double zHS = (1 + eta * (1 + eta * (1 - eta / 1.5 * (1 + eta))))
|
||||
/ ((1. - eta) * (1. - eta) * (1. - eta));
|
||||
double BC = (((((-0.58544978 * isT + 0.43102052) * isT + .87361369) * isT
|
||||
- 4.13749995) * isT + 2.90616279) * isT - 7.02181962) / T + 0.02459877;
|
||||
double gammaBH = 1.92907278;
|
||||
|
||||
double sum = ((2.01546797 * 2 + rho * ((-28.17881636) * 3 + rho
|
||||
* (28.28313847 * 4 + rho * (-10.42402873) * 5))) + (-19.58371655 * 2
|
||||
+ rho * (+75.62340289 * 3 + rho * ((-120.70586598) * 4 + rho
|
||||
* (+93.92740328 * 5 + rho * (-27.37737354) * 6)))) / sqrt(T)
|
||||
+ ((29.34470520 * 2 + rho * ((-112.35356937) * 3 + rho * (+170.64908980
|
||||
* 4 + rho * ((-123.06669187) * 5 + rho * 34.42288969 * 6))))
|
||||
+ ((-13.37031968) * 2 + rho * (65.38059570 * 3 + rho
|
||||
* ((-115.09233113) * 4 + rho * (88.91973082 * 5 + rho
|
||||
* (-25.62099890) * 6)))) / T) / T) * rho * rho;
|
||||
return ((zHS + BC / exp(gammaBH * rho * rho) * rho * (1 - 2 * gammaBH * rho
|
||||
* rho)) * T + sum) * rho;
|
||||
}
|
||||
*/
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/lj,PairSPHLJ)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LJ_H
|
||||
#define LMP_PAIR_LJ_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHLJ : public Pair {
|
||||
public:
|
||||
PairSPHLJ(class LAMMPS *);
|
||||
virtual ~PairSPHLJ();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
//double LJEOS(int);
|
||||
void LJEOS2(double, double, double, double *, double *);
|
||||
|
||||
protected:
|
||||
double **cut,**viscosity;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,316 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_rhosum.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHRhoSum::PairSPHRhoSum(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
|
||||
// set comm size needed by this Pair
|
||||
|
||||
comm_forward = 1;
|
||||
first = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHRhoSum::~PairSPHRhoSum() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::init_style() {
|
||||
// need a full neighbor list
|
||||
int irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->full = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz;
|
||||
double r, rsq, imass, h, ih, ihsq;
|
||||
int *jlist;
|
||||
double wf;
|
||||
// neighbor list variables
|
||||
int inum, *ilist, *numneigh, **firstneigh;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double *rho = atom->rho;
|
||||
int *type = atom->type;
|
||||
double *mass = atom->mass;
|
||||
|
||||
// check consistency of pair coefficients
|
||||
|
||||
if (first) {
|
||||
for (i = 1; i <= atom->ntypes; i++) {
|
||||
for (j = 1; i <= atom->ntypes; i++) {
|
||||
if (cutsq[i][j] > 0.0) {
|
||||
if (!setflag[i][i] || !setflag[j][j]) {
|
||||
if (comm->me == 0) {
|
||||
printf(
|
||||
"SPH particle types %d and %d interact, but not all of their single particle properties are set.\n",
|
||||
i, j);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
first = 0;
|
||||
}
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// recompute density
|
||||
// we use a full neighborlist here
|
||||
|
||||
if (nstep != 0) {
|
||||
if ((update->ntimestep % nstep) == 0) {
|
||||
|
||||
// initialize density with self-contribution,
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
itype = type[i];
|
||||
imass = mass[itype];
|
||||
|
||||
h = cut[itype][itype];
|
||||
if (domain->dimension == 3) {
|
||||
/*
|
||||
// Lucy kernel, 3d
|
||||
wf = 2.0889086280811262819e0 / (h * h * h);
|
||||
*/
|
||||
|
||||
// quadric kernel, 3d
|
||||
wf = 2.1541870227086614782 / (h * h * h);
|
||||
} else {
|
||||
/*
|
||||
// Lucy kernel, 2d
|
||||
wf = 1.5915494309189533576e0 / (h * h);
|
||||
*/
|
||||
|
||||
// quadric kernel, 2d
|
||||
wf = 1.5915494309189533576e0 / (h * h);
|
||||
}
|
||||
|
||||
rho[i] = imass * wf;
|
||||
}
|
||||
|
||||
// add density at each atom via kernel function overlap
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
jtype = type[j];
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
if (domain->dimension == 3) {
|
||||
/*
|
||||
// Lucy kernel, 3d
|
||||
r = sqrt(rsq);
|
||||
wf = (h - r) * ihsq;
|
||||
wf = 2.0889086280811262819e0 * (h + 3. * r) * wf * wf * wf * ih;
|
||||
*/
|
||||
|
||||
// quadric kernel, 3d
|
||||
wf = 1.0 - rsq * ihsq;
|
||||
wf = wf * wf;
|
||||
wf = wf * wf;
|
||||
wf = 2.1541870227086614782e0 * wf * ihsq * ih;
|
||||
} else {
|
||||
// Lucy kernel, 2d
|
||||
//r = sqrt(rsq);
|
||||
//wf = (h - r) * ihsq;
|
||||
//wf = 1.5915494309189533576e0 * (h + 3. * r) * wf * wf * wf;
|
||||
|
||||
// quadric kernel, 2d
|
||||
wf = 1.0 - rsq * ihsq;
|
||||
wf = wf * wf;
|
||||
wf = wf * wf;
|
||||
wf = 1.5915494309189533576e0 * wf * ihsq;
|
||||
}
|
||||
|
||||
rho[i] += mass[jtype] * wf;
|
||||
}
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// communicate densities
|
||||
comm->forward_comm_pair(this);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::settings(int narg, char **arg) {
|
||||
if (narg != 1)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/rhosum");
|
||||
nstep = force->inumeric(arg[0]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::coeff(int narg, char **arg) {
|
||||
if (narg != 3)
|
||||
error->all("Incorrect number of args for sph/rhosum coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double cut_one = force->numeric(arg[2]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
//printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHRhoSum::init_one(int i, int j) {
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("All pair sph/rhosum coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHRhoSum::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int PairSPHRhoSum::pack_comm(int n, int *list, double *buf, int pbc_flag,
|
||||
int *pbc) {
|
||||
int i, j, m;
|
||||
double *rho = atom->rho;
|
||||
|
||||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = rho[j];
|
||||
}
|
||||
return 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHRhoSum::unpack_comm(int n, int first, double *buf) {
|
||||
int i, m, last;
|
||||
double *rho = atom->rho;
|
||||
|
||||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
rho[i] = buf[m++];
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/rhosum,PairSPHRhoSum)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_SPH_RHOSUM_H
|
||||
#define LMP_PAIR_SPH_RHOSUM_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHRhoSum : public Pair {
|
||||
public:
|
||||
PairSPHRhoSum(class LAMMPS *);
|
||||
virtual ~PairSPHRhoSum();
|
||||
void init_style();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
int pack_comm(int, int *, double *, int, int *);
|
||||
void unpack_comm(int, int, double *);
|
||||
|
||||
protected:
|
||||
double **cut;
|
||||
int nstep, first;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,303 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_taitwater.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHTaitwater::PairSPHTaitwater(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
|
||||
first = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHTaitwater::~PairSPHTaitwater() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(rho0);
|
||||
memory->destroy(soundspeed);
|
||||
memory->destroy(B);
|
||||
memory->destroy(viscosity);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwater::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq;
|
||||
double rsq, tmp, wfd, delVdotDelR, mu, deltaE;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **v = atom->vest;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *de = atom->de;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
// check consistency of pair coefficients
|
||||
|
||||
if (first) {
|
||||
for (i = 1; i <= atom->ntypes; i++) {
|
||||
for (j = 1; i <= atom->ntypes; i++) {
|
||||
if (cutsq[i][j] > 1.e-32) {
|
||||
if (!setflag[i][i] || !setflag[j][j]) {
|
||||
if (comm->me == 0) {
|
||||
printf(
|
||||
"SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n",
|
||||
i, j, sqrt(cutsq[i][j]));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
first = 0;
|
||||
}
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
// compute pressure of atom i with Tait EOS
|
||||
tmp = rho[i] / rho0[itype];
|
||||
fi = tmp * tmp * tmp;
|
||||
fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
wfd = h - sqrt(rsq);
|
||||
if (domain->dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// (1) using delV . delX instead of delV . (delX/r) and
|
||||
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
// compute pressure of atom j with Tait EOS
|
||||
tmp = rho[j] / rho0[jtype];
|
||||
fj = tmp * tmp * tmp;
|
||||
fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]);
|
||||
|
||||
// dot product of velocity delta and distance vector
|
||||
delVdotDelR = delx * (vxtmp - v[j][0]) + dely * (vytmp - v[j][1])
|
||||
+ delz * (vztmp - v[j][2]);
|
||||
|
||||
// artificial viscosity (Monaghan 1992)
|
||||
if (delVdotDelR < 0.) {
|
||||
mu = h * delVdotDelR / (rsq + 0.01 * h * h);
|
||||
fvisc = -viscosity[itype][jtype] * (soundspeed[itype]
|
||||
+ soundspeed[jtype]) * mu / (rho[i] + rho[j]);
|
||||
} else {
|
||||
fvisc = 0.;
|
||||
}
|
||||
|
||||
// total pair force & thermal energy increment
|
||||
fpair = -imass * jmass * (fi + fj + fvisc) * wfd;
|
||||
deltaE = -0.5 * fpair * delVdotDelR;
|
||||
|
||||
f[i][0] += delx * fpair;
|
||||
f[i][1] += dely * fpair;
|
||||
f[i][2] += delz * fpair;
|
||||
|
||||
// and change in density
|
||||
drho[i] += jmass * delVdotDelR * wfd;
|
||||
|
||||
// change in thermal energy
|
||||
de[i] += deltaE;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair;
|
||||
f[j][1] -= dely * fpair;
|
||||
f[j][2] -= delz * fpair;
|
||||
de[j] += deltaE;
|
||||
drho[j] += imass * delVdotDelR * wfd;
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwater::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create(rho0, n + 1, "pair:rho0");
|
||||
memory->create(soundspeed, n + 1, "pair:soundspeed");
|
||||
memory->create(B, n + 1, "pair:B");
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwater::settings(int narg, char **arg) {
|
||||
if (narg != 0)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/taitwater");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwater::coeff(int narg, char **arg) {
|
||||
if (narg != 6)
|
||||
error->all(
|
||||
"Incorrect args for pair_style sph/taitwater coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double rho0_one = force->numeric(arg[2]);
|
||||
double soundspeed_one = force->numeric(arg[3]);
|
||||
double viscosity_one = force->numeric(arg[4]);
|
||||
double cut_one = force->numeric(arg[5]);
|
||||
double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
rho0[i] = rho0_one;
|
||||
soundspeed[i] = soundspeed_one;
|
||||
B[i] = B_one;
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
viscosity[i][j] = viscosity_one;
|
||||
//printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
|
||||
setflag[i][j] = 1;
|
||||
|
||||
//cut[j][i] = cut[i][j];
|
||||
//viscosity[j][i] = viscosity[i][j];
|
||||
//setflag[j][i] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHTaitwater::init_one(int i, int j) {
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("Not all pair sph/taitwater coeffs are set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
viscosity[j][i] = viscosity[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHTaitwater::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/taitwater,PairSPHTaitwater)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TAITWATER_H
|
||||
#define LMP_PAIR_TAITWATER_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHTaitwater : public Pair {
|
||||
public:
|
||||
PairSPHTaitwater(class LAMMPS *);
|
||||
virtual ~PairSPHTaitwater();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double *rho0, *soundspeed, *B;
|
||||
double **cut,**viscosity;
|
||||
int first;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,300 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "pair_sph_taitwater_morris.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "comm.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "domain.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHTaitwaterMorris::PairSPHTaitwaterMorris(LAMMPS *lmp) :
|
||||
Pair(lmp) {
|
||||
|
||||
first = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairSPHTaitwaterMorris::~PairSPHTaitwaterMorris() {
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(rho0);
|
||||
memory->destroy(soundspeed);
|
||||
memory->destroy(B);
|
||||
memory->destroy(viscosity);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwaterMorris::compute(int eflag, int vflag) {
|
||||
int i, j, ii, jj, inum, jnum, itype, jtype;
|
||||
double xtmp, ytmp, ztmp, delx, dely, delz, fpair;
|
||||
|
||||
int *ilist, *jlist, *numneigh, **firstneigh;
|
||||
double vxtmp, vytmp, vztmp, imass, jmass, fi, fj, fvisc, h, ih, ihsq, velx, vely, velz;
|
||||
double rsq, tmp, wfd, delVdotDelR, deltaE;
|
||||
|
||||
if (eflag || vflag)
|
||||
ev_setup(eflag, vflag);
|
||||
else
|
||||
evflag = vflag_fdotr = 0;
|
||||
|
||||
double **v = atom->vest;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *rho = atom->rho;
|
||||
double *mass = atom->mass;
|
||||
double *de = atom->de;
|
||||
double *drho = atom->drho;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
// check consistency of pair coefficients
|
||||
|
||||
if (first) {
|
||||
for (i = 1; i <= atom->ntypes; i++) {
|
||||
for (j = 1; i <= atom->ntypes; i++) {
|
||||
if (cutsq[i][j] > 1.e-32) {
|
||||
if (!setflag[i][i] || !setflag[j][j]) {
|
||||
if (comm->me == 0) {
|
||||
printf(
|
||||
"SPH particle types %d and %d interact with cutoff=%g, but not all of their single particle properties are set.\n",
|
||||
i, j, sqrt(cutsq[i][j]));
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
first = 0;
|
||||
}
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
vxtmp = v[i][0];
|
||||
vytmp = v[i][1];
|
||||
vztmp = v[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
imass = mass[itype];
|
||||
|
||||
// compute pressure of atom i with Tait EOS
|
||||
tmp = rho[i] / rho0[itype];
|
||||
fi = tmp * tmp * tmp;
|
||||
fi = B[itype] * (fi * fi * tmp - 1.0) / (rho[i] * rho[i]);
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx * delx + dely * dely + delz * delz;
|
||||
jtype = type[j];
|
||||
jmass = mass[jtype];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
h = cut[itype][jtype];
|
||||
ih = 1.0 / h;
|
||||
ihsq = ih * ih;
|
||||
|
||||
wfd = h - sqrt(rsq);
|
||||
if (domain->dimension == 3) {
|
||||
// Lucy Kernel, 3d
|
||||
// Note that wfd, the derivative of the weight function with respect to r,
|
||||
// is lacking a factor of r.
|
||||
// The missing factor of r is recovered by
|
||||
// (1) using delV . delX instead of delV . (delX/r) and
|
||||
// (2) using f[i][0] += delx * fpair instead of f[i][0] += (delx/r) * fpair
|
||||
wfd = -25.066903536973515383e0 * wfd * wfd * ihsq * ihsq * ihsq * ih;
|
||||
} else {
|
||||
// Lucy Kernel, 2d
|
||||
wfd = -19.098593171027440292e0 * wfd * wfd * ihsq * ihsq * ihsq;
|
||||
}
|
||||
|
||||
// compute pressure of atom j with Tait EOS
|
||||
tmp = rho[j] / rho0[jtype];
|
||||
fj = tmp * tmp * tmp;
|
||||
fj = B[jtype] * (fj * fj * tmp - 1.0) / (rho[j] * rho[j]);
|
||||
|
||||
velx=vxtmp - v[j][0];
|
||||
vely=vytmp - v[j][1];
|
||||
velz=vztmp - v[j][2];
|
||||
|
||||
// dot product of velocity delta and distance vector
|
||||
delVdotDelR = delx * velx + dely * vely + delz * velz;
|
||||
|
||||
// Morris Viscosity (Morris, 1996)
|
||||
|
||||
fvisc = 2 * viscosity[itype][jtype] / (rho[i] * rho[j]);
|
||||
|
||||
fvisc *= imass * jmass * wfd;
|
||||
|
||||
// total pair force & thermal energy increment
|
||||
fpair = -imass * jmass * (fi + fj) * wfd;
|
||||
deltaE = -0.5 *(fpair * delVdotDelR + fvisc * (velx*velx + vely*vely + velz*velz));
|
||||
|
||||
// printf("testvar= %f, %f \n", delx, dely);
|
||||
|
||||
f[i][0] += delx * fpair + velx * fvisc;
|
||||
f[i][1] += dely * fpair + vely * fvisc;
|
||||
f[i][2] += delz * fpair + velz * fvisc;
|
||||
|
||||
// and change in density
|
||||
drho[i] += jmass * delVdotDelR * wfd;
|
||||
|
||||
// change in thermal energy
|
||||
de[i] += deltaE;
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx * fpair + velx * fvisc;
|
||||
f[j][1] -= dely * fpair + vely * fvisc;
|
||||
f[j][2] -= delz * fpair + velz * fvisc;
|
||||
de[j] += deltaE;
|
||||
drho[j] += imass * delVdotDelR * wfd;
|
||||
}
|
||||
|
||||
if (evflag)
|
||||
ev_tally(i, j, nlocal, newton_pair, 0.0, 0.0, fpair, delx, dely, delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwaterMorris::allocate() {
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag, n + 1, n + 1, "pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq, n + 1, n + 1, "pair:cutsq");
|
||||
|
||||
memory->create(rho0, n + 1, "pair:rho0");
|
||||
memory->create(soundspeed, n + 1, "pair:soundspeed");
|
||||
memory->create(B, n + 1, "pair:B");
|
||||
memory->create(cut, n + 1, n + 1, "pair:cut");
|
||||
memory->create(viscosity, n + 1, n + 1, "pair:viscosity");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwaterMorris::settings(int narg, char **arg) {
|
||||
if (narg != 0)
|
||||
error->all(
|
||||
"Illegal number of setting arguments for pair_style sph/taitwater/morris");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairSPHTaitwaterMorris::coeff(int narg, char **arg) {
|
||||
if (narg != 6)
|
||||
error->all(
|
||||
"Incorrect args for pair_style sph/taitwater/morris coefficients");
|
||||
if (!allocated)
|
||||
allocate();
|
||||
|
||||
int ilo, ihi, jlo, jhi;
|
||||
force->bounds(arg[0], atom->ntypes, ilo, ihi);
|
||||
force->bounds(arg[1], atom->ntypes, jlo, jhi);
|
||||
|
||||
double rho0_one = force->numeric(arg[2]);
|
||||
double soundspeed_one = force->numeric(arg[3]);
|
||||
double viscosity_one = force->numeric(arg[4]);
|
||||
double cut_one = force->numeric(arg[5]);
|
||||
double B_one = soundspeed_one * soundspeed_one * rho0_one / 7.0;
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
rho0[i] = rho0_one;
|
||||
soundspeed[i] = soundspeed_one;
|
||||
B[i] = B_one;
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
viscosity[i][j] = viscosity_one;
|
||||
//printf("setting cut[%d][%d] = %f\n", i, j, cut_one);
|
||||
cut[i][j] = cut_one;
|
||||
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0)
|
||||
error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHTaitwaterMorris::init_one(int i, int j) {
|
||||
|
||||
if (setflag[i][j] == 0) {
|
||||
error->all("Not all pair sph/taitwater/morris coeffs are not set");
|
||||
}
|
||||
|
||||
cut[j][i] = cut[i][j];
|
||||
viscosity[j][i] = viscosity[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairSPHTaitwaterMorris::single(int i, int j, int itype, int jtype,
|
||||
double rsq, double factor_coul, double factor_lj, double &fforce) {
|
||||
fforce = 0.0;
|
||||
|
||||
return 0.0;
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 PAIR_CLASS
|
||||
|
||||
PairStyle(sph/taitwater/morris,PairSPHTaitwaterMorris)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TAITWATER_MORRIS_H
|
||||
#define LMP_PAIR_TAITWATER_MORRIS_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairSPHTaitwaterMorris : public Pair {
|
||||
public:
|
||||
PairSPHTaitwaterMorris(class LAMMPS *);
|
||||
virtual ~PairSPHTaitwaterMorris();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
virtual double init_one(int, int);
|
||||
virtual double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
protected:
|
||||
double *rho0, *soundspeed, *B;
|
||||
double **cut,**viscosity;
|
||||
int first;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue