forked from lijiext/lammps
684 lines
18 KiB
C++
684 lines
18 KiB
C++
/* ----------------------------------------------------------------------
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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_atomic.h"
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#include "atom.h"
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#include "comm.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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/* ---------------------------------------------------------------------- */
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AtomVecAtomic::AtomVecAtomic(LAMMPS *lmp) : AtomVec(lmp)
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{
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molecular = 0;
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mass_type = 1;
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comm_x_only = comm_f_only = 1;
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size_forward = 3;
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size_reverse = 3;
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size_border = 6;
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size_velocity = 3;
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size_data_atom = 5;
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size_data_vel = 4;
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xcol_data = 3;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by a chunk
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecAtomic::grow(int n)
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{
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"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*comm->nthreads,3,"atom:f");
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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 AtomVecAtomic::grow_reset()
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{
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tag = atom->tag; type = atom->type;
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mask = atom->mask; image = atom->image;
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x = atom->x; v = atom->v; f = atom->f;
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}
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/* ----------------------------------------------------------------------
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copy atom I info to atom J
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------------------------------------------------------------------------- */
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void AtomVecAtomic::copy(int i, int j, int delflag)
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{
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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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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,delflag);
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_comm(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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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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}
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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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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_comm_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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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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}
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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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if (!deform_vremap) {
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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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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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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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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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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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}
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}
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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 AtomVecAtomic::unpack_comm(int n, int first, double *buf)
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{
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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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}
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_comm_vel(int n, int first, double *buf)
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{
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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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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_reverse(int n, int first, double *buf)
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{
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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++] = f[i][0];
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buf[m++] = f[i][1];
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buf[m++] = f[i][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_reverse(int n, int *list, double *buf)
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{
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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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f[j][0] += buf[m++];
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f[j][1] += buf[m++];
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f[j][2] += buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_border(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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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++] = ubuf(tag[j]).d;
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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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];
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dy = pbc[1];
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dz = pbc[2];
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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++] = ubuf(tag[j]).d;
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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}
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::pack_border_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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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++] = ubuf(tag[j]).d;
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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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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}
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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];
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dy = pbc[1];
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dz = pbc[2];
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}
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if (!deform_vremap) {
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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++] = ubuf(tag[j]).d;
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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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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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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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++] = ubuf(tag[j]).d;
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buf[m++] = ubuf(type[j]).d;
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buf[m++] = ubuf(mask[j]).d;
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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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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}
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}
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}
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_border(int n, int first, double *buf)
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{
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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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if (i == nmax) grow(0);
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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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tag[i] = (tagint) ubuf(buf[m++]).i;
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type[i] = (int) ubuf(buf[m++]).i;
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mask[i] = (int) ubuf(buf[m++]).i;
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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->
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unpack_border(n,first,&buf[m]);
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecAtomic::unpack_border_vel(int n, int first, double *buf)
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{
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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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if (i == nmax) grow(0);
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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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tag[i] = (tagint) ubuf(buf[m++]).i;
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type[i] = (int) ubuf(buf[m++]).i;
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mask[i] = (int) ubuf(buf[m++]).i;
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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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}
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if (atom->nextra_border)
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for (int iextra = 0; iextra < atom->nextra_border; iextra++)
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m += modify->fix[atom->extra_border[iextra]]->
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unpack_border(n,first,&buf[m]);
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}
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/* ----------------------------------------------------------------------
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pack data for atom I for sending to another proc
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xyz must be 1st 3 values, so comm::exchange() can test on them
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------------------------------------------------------------------------- */
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int AtomVecAtomic::pack_exchange(int i, double *buf)
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{
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int m = 1;
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buf[m++] = x[i][0];
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buf[m++] = x[i][1];
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buf[m++] = x[i][2];
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buf[m++] = v[i][0];
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buf[m++] = v[i][1];
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buf[m++] = v[i][2];
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buf[m++] = ubuf(tag[i]).d;
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buf[m++] = ubuf(type[i]).d;
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buf[m++] = ubuf(mask[i]).d;
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buf[m++] = ubuf(image[i]).d;
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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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m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
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buf[0] = m;
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecAtomic::unpack_exchange(double *buf)
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{
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int nlocal = atom->nlocal;
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if (nlocal == nmax) grow(0);
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int m = 1;
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x[nlocal][0] = buf[m++];
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x[nlocal][1] = buf[m++];
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x[nlocal][2] = buf[m++];
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v[nlocal][0] = buf[m++];
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v[nlocal][1] = buf[m++];
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v[nlocal][2] = buf[m++];
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tag[nlocal] = (tagint) ubuf(buf[m++]).i;
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type[nlocal] = (int) ubuf(buf[m++]).i;
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mask[nlocal] = (int) ubuf(buf[m++]).i;
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image[nlocal] = (imageint) ubuf(buf[m++]).i;
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if (atom->nextra_grow)
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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 AtomVecAtomic::size_restart()
|
|
{
|
|
int i;
|
|
|
|
int nlocal = atom->nlocal;
|
|
int n = 11 * nlocal;
|
|
|
|
if (atom->nextra_restart)
|
|
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
|
for (i = 0; i < nlocal; i++)
|
|
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
|
|
|
|
return n;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom I's data for restart file including extra quantities
|
|
xyz must be 1st 3 values, so that read_restart can test on them
|
|
molecular types may be negative, but write as positive
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecAtomic::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++] = ubuf(tag[i]).d;
|
|
buf[m++] = ubuf(type[i]).d;
|
|
buf[m++] = ubuf(mask[i]).d;
|
|
buf[m++] = ubuf(image[i]).d;
|
|
buf[m++] = v[i][0];
|
|
buf[m++] = v[i][1];
|
|
buf[m++] = v[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 AtomVecAtomic::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] = (tagint) ubuf(buf[m++]).i;
|
|
type[nlocal] = (int) ubuf(buf[m++]).i;
|
|
mask[nlocal] = (int) ubuf(buf[m++]).i;
|
|
image[nlocal] = (imageint) ubuf(buf[m++]).i;
|
|
v[nlocal][0] = buf[m++];
|
|
v[nlocal][1] = buf[m++];
|
|
v[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 AtomVecAtomic::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] = ((imageint) IMGMAX << IMG2BITS) |
|
|
((imageint) IMGMAX << IMGBITS) | IMGMAX;
|
|
v[nlocal][0] = 0.0;
|
|
v[nlocal][1] = 0.0;
|
|
v[nlocal][2] = 0.0;
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one line from Atoms section of data file
|
|
initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomic::data_atom(double *coord, imageint imagetmp, char **values)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
|
|
tag[nlocal] = ATOTAGINT(values[0]);
|
|
type[nlocal] = atoi(values[1]);
|
|
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
|
|
error->one(FLERR,"Invalid atom type in Atoms section of data file");
|
|
|
|
x[nlocal][0] = coord[0];
|
|
x[nlocal][1] = coord[1];
|
|
x[nlocal][2] = coord[2];
|
|
|
|
image[nlocal] = imagetmp;
|
|
|
|
mask[nlocal] = 1;
|
|
v[nlocal][0] = 0.0;
|
|
v[nlocal][1] = 0.0;
|
|
v[nlocal][2] = 0.0;
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom info for data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomic::pack_data(double **buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
buf[i][0] = ubuf(tag[i]).d;
|
|
buf[i][1] = ubuf(type[i]).d;
|
|
buf[i][2] = x[i][0];
|
|
buf[i][3] = x[i][1];
|
|
buf[i][4] = x[i][2];
|
|
buf[i][5] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
|
|
buf[i][6] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
|
|
buf[i][7] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write atom info to data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecAtomic::write_data(FILE *fp, int n, double **buf)
|
|
{
|
|
for (int i = 0; i < n; i++)
|
|
fprintf(fp,TAGINT_FORMAT " %d %-1.16e %-1.16e %-1.16e %d %d %d\n",
|
|
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
|
|
buf[i][2],buf[i][3],buf[i][4],
|
|
(int) ubuf(buf[i][5]).i,(int) ubuf(buf[i][6]).i,
|
|
(int) ubuf(buf[i][7]).i);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return # of bytes of allocated memory
|
|
------------------------------------------------------------------------- */
|
|
|
|
bigint AtomVecAtomic::memory_usage()
|
|
{
|
|
bigint bytes = 0;
|
|
|
|
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
|
|
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
|
|
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
|
|
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
|
|
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
|
|
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
|
|
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
|
|
|
|
return bytes;
|
|
}
|