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lammps/src/compute_gyration.cpp
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compute_gyration.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 "math.h"
#include "compute_gyration.h"
#include "update.h"
#include "atom.h"
#include "group.h"
#include "domain.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute gyration command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 0;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeGyration::~ComputeGyration()
{
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeGyration::init()
{
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
double ComputeGyration::compute_scalar()
{
invoked_scalar = update->ntimestep;
double xcm[3];
group->xcm(igroup,masstotal,xcm);
scalar = group->gyration(igroup,masstotal,xcm);
return scalar;
}
/* ----------------------------------------------------------------------
compute the radius-of-gyration tensor of group of atoms
around center-of-mass cm
must unwrap atoms to compute Rg tensor correctly
------------------------------------------------------------------------- */
void ComputeGyration::compute_vector()
{
invoked_vector = update->ntimestep;
double xcm[3];
group->xcm(igroup,masstotal,xcm);
double **x = atom->x;
int *mask = atom->mask;
int *type = atom->type;
tagint *image = atom->image;
double *mass = atom->mass;
double *rmass = atom->rmass;
int nlocal = atom->nlocal;
int xbox,ybox,zbox;
double dx,dy,dz,massone;
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double rg[6];
rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
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) - xcm[0];
dy = (x[i][1] + ybox*yprd) - xcm[1];
dz = (x[i][2] + zbox*zprd) - xcm[2];
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
rg[0] += dx*dx * massone;
rg[1] += dy*dy * massone;
rg[2] += dz*dz * massone;
rg[3] += dx*dy * massone;
rg[4] += dx*dz * massone;
rg[5] += dy*dz * massone;
}
MPI_Allreduce(rg,vector,6,MPI_DOUBLE,MPI_SUM,world);
if (masstotal == 0.0) return;
for (int i = 0; i < 6; i++) vector[i] /= masstotal;
}
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