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lammps/src/USER-DPD/compute_dpd_atom.cpp
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compute_dpd_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
#include "math.h"
#include <string.h>
#include <stdlib.h>
#include "compute_dpd_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
#include <vector>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute dpd/atom command");
peratom_flag = 1;
size_peratom_cols = 4;
nmax = 0;
dpdAtom = NULL;
if (atom->dpd_flag != 1) error->all(FLERR,"compute dpd requires atom_style with internal temperature and energies (e.g. dpd)");
}
/* ---------------------------------------------------------------------- */
ComputeDpdAtom::~ComputeDpdAtom()
{
memory->destroy(dpdAtom);
}
/* ---------------------------------------------------------------------- */
void ComputeDpdAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"dpd/atom") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute dpd/atom command");
}
/* ----------------------------------------------------------------------
gather compute vector data from other nodes
------------------------------------------------------------------------- */
void ComputeDpdAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *uChem = atom->uChem;
double *dpdTheta = atom->dpdTheta;
int nlocal = atom->nlocal;
int *mask = atom->mask;
if (nlocal > nmax) {
memory->destroy(dpdAtom);
nmax = atom->nmax;
memory->create(dpdAtom,nmax,size_peratom_cols,"dpd/atom:dpdAtom");
array_atom = dpdAtom;
}
for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit){
dpdAtom[i][0] = uCond[i];
dpdAtom[i][1] = uMech[i];
dpdAtom[i][2] = uChem[i];
dpdAtom[i][3] = dpdTheta[i];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeDpdAtom::memory_usage()
{
double bytes = size_peratom_cols * nmax * sizeof(double);
return bytes;
}
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