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compute_etotal_atom.cpp
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Thu, Nov 14, 11:27

compute_etotal_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_etotal_atom.h"
#include "atom.h"
#include "modify.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeEtotalAtom::ComputeEtotalAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute etotal/atom command");
// store epair ID used by energy computation
int n = strlen(arg[3]) + 1;
id_pre = new char[n];
strcpy(id_pre,arg[3]);
peratom_flag = 1;
size_peratom = 0;
nmax = 0;
etotal = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeEtotalAtom::~ComputeEtotalAtom()
{
delete [] id_pre;
memory->sfree(etotal);
}
/* ---------------------------------------------------------------------- */
void ComputeEtotalAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"etotal/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one compute etotal/atom");
// set epair Compute used by this compute
int icompute = modify->find_compute(id_pre);
if (icompute < 0)
error->all("Could not find compute etotal/atom pre-compute ID");
compute_epair = modify->compute[icompute];
}
/* ---------------------------------------------------------------------- */
void ComputeEtotalAtom::compute_peratom()
{
// grow etotal array if necessary
if (atom->nlocal > nmax) {
memory->sfree(etotal);
nmax = atom->nmax;
etotal = (double *)
memory->smalloc(nmax*sizeof(double),"compute/etotal/atom:etotal");
scalar_atom = etotal;
}
// compute total energy for each atom in group
double *epair = compute_epair->scalar_atom;
double mvv2e = force->mvv2e;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
double ke;
if (mass)
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ke = 0.5 * mvv2e * mass[type[i]] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
etotal[i] = ke + epair[i];
}
}
else
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
ke = 0.5 * mvv2e * rmass[i] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
etotal[i] = ke + epair[i];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int ComputeEtotalAtom::memory_usage()
{
int bytes = nmax * sizeof(double);
return bytes;
}

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