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compute_pe_atom.cpp
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Sun, Nov 10, 13:55

compute_pe_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_pe_atom.h"
#include "atom.h"
#include "update.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputePEAtom::ComputePEAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
energy(NULL)
{
if (narg < 3) error->all(FLERR,"Illegal compute pe/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
peatomflag = 1;
timeflag = 1;
comm_reverse = 1;
if (narg == 3) {
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = 1;
fixflag = 1;
} else {
pairflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
kspaceflag = 0;
fixflag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else error->all(FLERR,"Illegal compute pe/atom command");
iarg++;
}
}
nmax = 0;
}
/* ---------------------------------------------------------------------- */
ComputePEAtom::~ComputePEAtom()
{
memory->destroy(energy);
}
/* ---------------------------------------------------------------------- */
void ComputePEAtom::compute_peratom()
{
int i;
invoked_peratom = update->ntimestep;
if (update->eflag_atom != invoked_peratom)
error->all(FLERR,"Per-atom energy was not tallied on needed timestep");
// grow local energy array if necessary
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(energy);
nmax = atom->nmax;
memory->create(energy,nmax,"pe/atom:energy");
vector_atom = energy;
}
// npair includes ghosts if either newton flag is set
// b/c some bonds/dihedrals call pair::ev_tally with pairwise info
// nbond includes ghosts if newton_bond is set
// ntotal includes ghosts if either newton flag is set
// KSpace includes ghosts if tip4pflag is set
int nlocal = atom->nlocal;
int npair = nlocal;
int nbond = nlocal;
int ntotal = nlocal;
int nkspace = nlocal;
if (force->newton) npair += atom->nghost;
if (force->newton_bond) nbond += atom->nghost;
if (force->newton) ntotal += atom->nghost;
if (force->kspace && force->kspace->tip4pflag) nkspace += atom->nghost;
// clear local energy array
for (i = 0; i < ntotal; i++) energy[i] = 0.0;
// add in per-atom contributions from each force
if (pairflag && force->pair) {
double *eatom = force->pair->eatom;
for (i = 0; i < npair; i++) energy[i] += eatom[i];
}
if (bondflag && force->bond) {
double *eatom = force->bond->eatom;
for (i = 0; i < nbond; i++) energy[i] += eatom[i];
}
if (angleflag && force->angle) {
double *eatom = force->angle->eatom;
for (i = 0; i < nbond; i++) energy[i] += eatom[i];
}
if (dihedralflag && force->dihedral) {
double *eatom = force->dihedral->eatom;
for (i = 0; i < nbond; i++) energy[i] += eatom[i];
}
if (improperflag && force->improper) {
double *eatom = force->improper->eatom;
for (i = 0; i < nbond; i++) energy[i] += eatom[i];
}
if (kspaceflag && force->kspace) {
double *eatom = force->kspace->eatom;
for (i = 0; i < nkspace; i++) energy[i] += eatom[i];
}
// add in per-atom contributions from relevant fixes
// always only for owned atoms, not ghost
if (fixflag && modify->n_thermo_energy_atom)
modify->thermo_energy_atom(nlocal,energy);
// communicate ghost energy between neighbor procs
if (force->newton || (force->kspace && force->kspace->tip4pflag))
comm->reverse_comm_compute(this);
// zero energy of atoms not in group
// only do this after comm since ghost contributions must be included
int *mask = atom->mask;
for (i = 0; i < nlocal; i++)
if (!(mask[i] & groupbit)) energy[i] = 0.0;
}
/* ---------------------------------------------------------------------- */
int ComputePEAtom::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 m;
}
/* ---------------------------------------------------------------------- */
void ComputePEAtom::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 ComputePEAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}

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