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compute_msd.cpp
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Wed, Jul 3, 12:44
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Fri, Jul 5, 12:44 (2 d)
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rLAMMPS lammps
compute_msd.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_msd.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "modify.h"
#include "fix_store.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 3) error->all(FLERR,"Illegal compute msd command");
vector_flag = 1;
size_vector = 4;
extvector = 0;
create_attribute = 1;
// optional args
comflag = 0;
avflag = 0;
int iarg = 3;
while (iarg < narg) {
if (strcmp(arg[iarg],"com") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command");
if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
else error->all(FLERR,"Illegal compute msd command");
iarg += 2;
} else if (strcmp(arg[iarg],"average") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command");
if (strcmp(arg[iarg+1],"no") == 0) avflag = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) avflag = 1;
else error->all(FLERR,"Illegal compute msd command");
iarg += 2;
} else error->all(FLERR,"Illegal compute msd command");
}
// create a new fix STORE style for reference positions
// 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;
// calculate xu,yu,zu for fix store array
// skip if reset from restart file
if (fix->restart_reset) fix->restart_reset = 0;
else {
double **xoriginal = fix->astore;
double **x = atom->x;
int *mask = atom->mask;
imageint *image = atom->image;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
// adjust for COM if requested
if (comflag) {
double cm[3];
masstotal = group->mass(igroup);
group->xcm(igroup,masstotal,cm);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xoriginal[i][0] -= cm[0];
xoriginal[i][1] -= cm[1];
xoriginal[i][2] -= cm[2];
}
}
// initialize counter for average positions if requested
naverage = 0;
}
// displacement vector
vector = new double[4];
}
/* ---------------------------------------------------------------------- */
ComputeMSD::~ComputeMSD()
{
// check nfix in case all fixes have already been deleted
if (modify->nfix) modify->delete_fix(id_fix);
delete [] id_fix;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeMSD::init()
{
// set fix which stores reference atom coords
int ifix = modify->find_fix(id_fix);
if (ifix < 0) error->all(FLERR,"Could not find compute msd fix ID");
fix = (FixStore *) modify->fix[ifix];
// nmsd = # of atoms in group
nmsd = group->count(igroup);
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void ComputeMSD::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 reference position
// reference 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;
imageint *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[4];
msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
double xtmp, ytmp, ztmp;
// update number of averages if requested
double navfac;
if (avflag) {
naverage++;
navfac = 1.0/(naverage+1);
}
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;
xtmp = x[i][0] + xbox*xprd - cm[0];
ytmp = x[i][1] + ybox*yprd - cm[1];
ztmp = x[i][2] + zbox*zprd - cm[2];
// use running average position for reference if requested
if (avflag) {
xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac;
xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac;
}
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
dz = ztmp - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += 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;
xtmp = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0];
ytmp = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1];
ztmp = x[i][2] + h[2]*zbox - cm[2];
// use running average position for reference if requested
if (avflag) {
xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac;
xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac;
}
dx = xtmp - xoriginal[i][0];
dy = ytmp - xoriginal[i][1];
dz = ztmp - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
}
MPI_Allreduce(msd,vector,4,MPI_DOUBLE,MPI_SUM,world);
if (nmsd) {
vector[0] /= nmsd;
vector[1] /= nmsd;
vector[2] /= nmsd;
vector[3] /= nmsd;
}
}
/* ----------------------------------------------------------------------
initialize one atom's storage values, called when atom is created
------------------------------------------------------------------------- */
void ComputeMSD::set_arrays(int i)
{
double **xoriginal = fix->astore;
double **x = atom->x;
xoriginal[i][0] = x[i][0];
xoriginal[i][1] = x[i][1];
xoriginal[i][2] = x[i][2];
}
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