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lammps/src/compute_msd_nongauss.cpp
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compute_msd_nongauss.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 authors: Rob Hoy
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_msd_nongauss.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "fix_store.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSDNonGauss::ComputeMSDNonGauss(LAMMPS *lmp, int narg, char **arg) :
ComputeMSD(lmp, narg, arg)
{
size_vector = 3;
}
/* ---------------------------------------------------------------------- */
void ComputeMSDNonGauss::compute_vector()
{
invoked_vector = update->ntimestep;
// cm = current center of mass
double cm[3];
if (comflag) group->xcm(igroup,masstotal,cm);
else cm[0] = cm[1] = cm[2] = 0.0;
// dx,dy,dz = displacement of atom from original position
// original unwrapped position is stored by fix
// relative to center of mass if comflag is set
// for triclinic, need to unwrap current atom coord via h matrix
double **xoriginal = fix->astore;
double **x = atom->x;
int *mask = atom->mask;
tagint *image = atom->image;
int nlocal = atom->nlocal;
double *h = domain->h;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double dx,dy,dz;
int xbox,ybox,zbox;
double msd[2];
msd[0] = msd[1] = 0.0;
if (domain->triclinic == 0) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
msd[0] += dx*dx + dy*dy + dz*dz;
msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & IMGMASK) - IMGMAX;
ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
zbox = (image[i] >> IMG2BITS) - IMGMAX;
dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
cm[0] - xoriginal[i][0];
dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
msd[0] += dx*dx + dy*dy + dz*dz;
msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
}
}
MPI_Allreduce(msd,vector,2,MPI_DOUBLE,MPI_SUM,world);
if (nmsd) {
vector[0] /= nmsd;
vector[1] /= nmsd;
vector[2] = (3*vector[1])/(5*vector[0]*vector[0]) - 1;
}
}
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