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lammps/src/compute_msd_molecule.cpp
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compute_msd_molecule.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 "compute_msd_molecule.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeMSDMolecule::ComputeMSDMolecule(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute msd/molecule command");
if (atom->molecular == 0)
error->all("Compute msd/molecule requires molecular atom style");
array_flag = 1;
size_array_cols = 4;
extarray = 0;
// setup molecule-based data and initial COM positions
nmolecules = molecules_in_group(idlo,idhi);
size_array_rows = nmolecules;
massproc = (double *) memory->smalloc(nmolecules*sizeof(double),
"msd/molecule:massproc");
masstotal = (double *) memory->smalloc(nmolecules*sizeof(double),
"msd/molecule:masstotal");
com = memory->create_2d_double_array(nmolecules,3,"msd/molecule:com");
comall = memory->create_2d_double_array(nmolecules,3,"msd/molecule:comall");
cominit = memory->create_2d_double_array(nmolecules,3,
"msd/molecule:cominit");
msd = memory->create_2d_double_array(nmolecules,4,"msd/molecule:msd");
array = msd;
// compute masstotal for each molecule
int *mask = atom->mask;
int *molecule = atom->molecule;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int i,imol;
double massone;
for (i = 0; i < nmolecules; i++) massproc[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
massproc[imol] += massone;
}
MPI_Allreduce(massproc,masstotal,nmolecules,MPI_DOUBLE,MPI_SUM,world);
// compute initial COM for each molecule
firstflag = 1;
compute_array();
for (i = 0; i < nmolecules; i++) {
cominit[i][0] = comall[i][0];
cominit[i][1] = comall[i][1];
cominit[i][2] = comall[i][2];
}
firstflag = 0;
}
/* ---------------------------------------------------------------------- */
ComputeMSDMolecule::~ComputeMSDMolecule()
{
memory->sfree(massproc);
memory->sfree(masstotal);
memory->destroy_2d_double_array(com);
memory->destroy_2d_double_array(comall);
memory->destroy_2d_double_array(cominit);
memory->destroy_2d_double_array(msd);
}
/* ---------------------------------------------------------------------- */
void ComputeMSDMolecule::init()
{
int ntmp = molecules_in_group(idlo,idhi);
if (ntmp != nmolecules)
error->all("Molecule count changed in compute msd/molecule");
}
/* ---------------------------------------------------------------------- */
void ComputeMSDMolecule::compute_array()
{
int i,imol;
double xbox,ybox,zbox,dx,dy,dz;
double massone;
invoked_array = update->ntimestep;
// compute current COM positions
for (i = 0; i < nmolecules; i++)
com[i][0] = com[i][1] = com[i][2] = 0.0;
double **x = atom->x;
int *mask = atom->mask;
int *molecule = atom->molecule;
int *type = atom->type;
int *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
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;
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
com[imol][0] += (x[i][0] + xbox*xprd) * massone;
com[imol][1] += (x[i][1] + ybox*yprd) * massone;
com[imol][2] += (x[i][2] + zbox*zprd) * massone;
}
MPI_Allreduce(&com[0][0],&comall[0][0],3*nmolecules,
MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < nmolecules; i++) {
comall[i][0] /= masstotal[i];
comall[i][1] /= masstotal[i];
comall[i][2] /= masstotal[i];
}
// MSD is difference between current and initial COM
// cominit does not yet exist when called from constructor
if (firstflag) return;
for (i = 0; i < nmolecules; i++) {
dx = comall[i][0] - cominit[i][0];
dy = comall[i][1] - cominit[i][1];
dz = comall[i][2] - cominit[i][2];
msd[i][0] = dx*dx;
msd[i][1] = dy*dy;
msd[i][2] = dz*dz;
msd[i][3] = dx*dx + dy*dy + dz*dz;
}
}
/* ----------------------------------------------------------------------
memory usage of local data
------------------------------------------------------------------------- */
double ComputeMSDMolecule::memory_usage()
{
double bytes = 2*nmolecules * sizeof(double);
if (molmap) bytes += (idhi-idlo+1) * sizeof(int);
bytes += 2*nmolecules*3 * sizeof(double);
bytes += nmolecules*4 * sizeof(double);
return bytes;
}
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