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lammps/src/compute_vacf.cpp
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compute_vacf.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 ret
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_vacf.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "modify.h"
#include "fix_store.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeVACF::ComputeVACF(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
id_fix(NULL)
{
if (narg < 3) error->all(FLERR,"Illegal compute vacf command");
vector_flag = 1;
size_vector = 4;
extvector = 0;
create_attribute = 1;
// create a new fix STORE style
// id = compute-ID + COMPUTE_STORE, fix group = compute group
int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
id_fix = new char[n];
strcpy(id_fix,id);
strcat(id_fix,"_COMPUTE_STORE");
char **newarg = new char*[6];
newarg[0] = id_fix;
newarg[1] = group->names[igroup];
newarg[2] = (char *) "STORE";
newarg[3] = (char *) "peratom";
newarg[4] = (char *) "1";
newarg[5] = (char *) "3";
modify->add_fix(6,newarg);
fix = (FixStore *) modify->fix[modify->nfix-1];
delete [] newarg;
// store current velocities in fix store array
// skip if reset from restart file
if (fix->restart_reset) fix->restart_reset = 0;
else {
double **voriginal = fix->astore;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
voriginal[i][0] = v[i][0];
voriginal[i][1] = v[i][1];
voriginal[i][2] = v[i][2];
} else voriginal[i][0] = voriginal[i][1] = voriginal[i][2] = 0.0;
}
// displacement vector
vector = new double[4];
}
/* ---------------------------------------------------------------------- */
ComputeVACF::~ComputeVACF()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeVACF::init()
{
// set fix which stores original atom velocities
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find compute vacf fix ID");
fix = (FixStore *) modify->fix[ifix];
// nvacf = # of atoms in group
nvacf = group->count(igroup);
}
/* ---------------------------------------------------------------------- */
void ComputeVACF::compute_vector()
{
invoked_vector = update->ntimestep;
double **voriginal = fix->astore;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double vxsq,vysq,vzsq;
double vacf[4];
vacf[0] = vacf[1] = vacf[2] = vacf[3] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vxsq = v[i][0] * voriginal[i][0];
vysq = v[i][1] * voriginal[i][1];
vzsq = v[i][2] * voriginal[i][2];
vacf[0] += vxsq;
vacf[1] += vysq;
vacf[2] += vzsq;
vacf[3] += vxsq + vysq + vzsq;
}
MPI_Allreduce(vacf,vector,4,MPI_DOUBLE,MPI_SUM,world);
if (nvacf) {
vector[0] /= nvacf;
vector[1] /= nvacf;
vector[2] /= nvacf;
vector[3] /= nvacf;
}
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void ComputeVACF::set_arrays(int i)
{
double **voriginal = fix->astore;
double **v = atom->v;
voriginal[i][0] = v[i][0];
voriginal[i][1] = v[i][1];
voriginal[i][2] = v[i][2];
}
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