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lammps/src/fix_msd.cpp
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fix_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 "stdlib.h"
#include "string.h"
#include "fix_msd.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixMSD::FixMSD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 5) error->all("Illegal fix msd command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix msd command");
first = 1;
restart_peratom = 1;
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix msd file %s",arg[4]);
error->one(str);
}
}
if (me == 0) {
fprintf(fp,"Mean-squared Displacement for group %s\n",
group->names[igroup]);
fprintf(fp,"TimeStep x y z total\n");
}
// perform initial allocation of atom-based array
// register with Atom class
xoriginal = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// xoriginal = initial unwrapped positions of atoms
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
xoriginal[i][0] = x[i][0] + xbox*xprd;
xoriginal[i][1] = x[i][1] + ybox*yprd;
xoriginal[i][2] = x[i][2] + zbox*zprd;
} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
}
// nmsd = # of atoms in group
nmsd = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) nmsd++;
int nmsd_all;
MPI_Allreduce(&nmsd,&nmsd_all,1,MPI_INT,MPI_SUM,world);
nmsd = nmsd_all;
if (nmsd == 0) error->all("Fix msd group has no atoms");
}
/* ---------------------------------------------------------------------- */
FixMSD::~FixMSD()
{
if (me == 0) fclose(fp);
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored array
memory->destroy_2d_double_array(xoriginal);
}
/* ---------------------------------------------------------------------- */
int FixMSD::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixMSD::init()
{
// warn if more than one msd fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"msd") == 0) count++;
if (count > 1 && me == 0) error->warning("More than one msd fix");
}
/* ---------------------------------------------------------------------- */
void FixMSD::setup()
{
if (first) end_of_step();
first = 0;
}
/* ---------------------------------------------------------------------- */
void FixMSD::end_of_step()
{
double **x = atom->x;
int *mask = atom->mask;
int *image = atom->image;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
int xbox,ybox,zbox;
double dx,dy,dz;
double msd[4];
msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
xbox = (image[i] & 1023) - 512;
ybox = (image[i] >> 10 & 1023) - 512;
zbox = (image[i] >> 20) - 512;
dx = x[i][0] + xbox*xprd - xoriginal[i][0];
dy = x[i][1] + ybox*yprd - xoriginal[i][1];
dz = x[i][2] + zbox*zprd - xoriginal[i][2];
msd[0] += dx*dx;
msd[1] += dy*dy;
msd[2] += dz*dz;
msd[3] += dx*dx + dy*dy + dz*dz;
}
double msd_all[4];
MPI_Allreduce(msd,msd_all,4,MPI_DOUBLE,MPI_SUM,world);
msd_all[0] /= nmsd;
msd_all[1] /= nmsd;
msd_all[2] /= nmsd;
msd_all[3] /= nmsd;
if (me == 0) fprintf(fp,"%d %g %g %g %g\n",update->ntimestep,
msd_all[0],msd_all[1],msd_all[2],msd_all[3]);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int FixMSD::memory_usage()
{
int bytes = atom->nmax*3 * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixMSD::grow_arrays(int nmax)
{
xoriginal =
memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixMSD::copy_arrays(int i, int j)
{
xoriginal[j][0] = xoriginal[i][0];
xoriginal[j][1] = xoriginal[i][1];
xoriginal[j][2] = xoriginal[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixMSD::pack_exchange(int i, double *buf)
{
buf[0] = xoriginal[i][0];
buf[1] = xoriginal[i][1];
buf[2] = xoriginal[i][2];
return 3;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixMSD::unpack_exchange(int nlocal, double *buf)
{
xoriginal[nlocal][0] = buf[0];
xoriginal[nlocal][1] = buf[1];
xoriginal[nlocal][2] = buf[2];
return 3;
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixMSD::pack_restart(int i, double *buf)
{
buf[0] = 4;
buf[1] = xoriginal[i][0];
buf[2] = xoriginal[i][1];
buf[3] = xoriginal[i][2];
return 4;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixMSD::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
xoriginal[nlocal][0] = extra[nlocal][m++];
xoriginal[nlocal][1] = extra[nlocal][m++];
xoriginal[nlocal][2] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixMSD::maxsize_restart()
{
return 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixMSD::size_restart(int nlocal)
{
return 4;
}
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