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compute_epair_atom.cpp
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Wed, Jul 3, 13:41

compute_epair_atom.cpp
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/* ----------------------------------------------------------------------
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_epair_atom.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
ComputeEpairAtom::ComputeEpairAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute epair/atom command");
peratom_flag = 1;
size_peratom = 0;
comm_reverse = 1;
nmax = 0;
energy = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeEpairAtom::~ComputeEpairAtom()
{
memory->sfree(energy);
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::init()
{
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support computing per-atom energy");
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
if (force->pair_match("eam")) eamstyle = 1;
else eamstyle = 0;
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"epair/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute epair/atom");
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::compute_peratom()
{
int i,j,ii,jj,n,inum,jnum,itype,jtype,iflag,jflag;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double factor_coul,factor_lj,eng;
int *ilist,*jlist,*numneigh,**firstneigh;
Pair::One one;
// grow energy array if necessary
if (atom->nmax > nmax) {
memory->sfree(energy);
nmax = atom->nmax;
energy = (double *)
memory->smalloc(nmax*sizeof(double),"compute/epair/atom:energy");
scalar_atom = energy;
}
// clear energy array
// n includes ghosts only if newton_pair flag is set
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
if (newton_pair) n = nlocal + atom->nghost;
else n = nlocal;
for (i = 0; i < n; i++) energy[i] = 0.0;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// compute pairwise energy for atoms via pair->single()
// if neither atom is in compute group, skip that pair
// only add energy to atoms in group
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double **cutsq = force->pair->cutsq;
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
int nall = nlocal + atom->nghost;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
iflag = mask[i] & groupbit;
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jflag = mask[j] & groupbit;
if (iflag == 0 && jflag == 0) continue;
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
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];
if (rsq < cutsq[itype][jtype]) {
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,1,one);
eng = one.eng_coul + one.eng_vdwl;
if (iflag) energy[i] += eng;
if (jflag && (newton_pair || j < nlocal)) energy[j] += eng;
}
}
}
// communicate energy between neigchbor procs
if (newton_pair) comm->reverse_comm_compute(this);
// remove double counting of per-atom energy
for (i = 0; i < nlocal; i++) energy[i] *= 0.5;
// for EAM, include embedding function contribution to energy
// only for atoms in compute group
if (eamstyle) {
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
force->pair->single_embed(i,type[i],eng);
energy[i] += eng;
}
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeEpairAtom::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = energy[i];
return 1;
}
/* ---------------------------------------------------------------------- */
void ComputeEpairAtom::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
energy[j] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeEpairAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

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