117 lines
3.1 KiB
C++
117 lines
3.1 KiB
C++
// clang-format off
|
|
/* ----------------------------------------------------------------------
|
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
https://www.lammps.org/, 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_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[size_vector];
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeGyration::~ComputeGyration()
|
|
{
|
|
delete [] vector;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeGyration::init()
|
|
{
|
|
masstotal = group->mass(igroup);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double ComputeGyration::compute_scalar()
|
|
{
|
|
invoked_scalar = update->ntimestep;
|
|
|
|
double xcm[3];
|
|
if (group->dynamic[igroup]) masstotal = group->mass(igroup);
|
|
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;
|
|
imageint *image = atom->image;
|
|
double *mass = atom->mass;
|
|
double *rmass = atom->rmass;
|
|
int nlocal = atom->nlocal;
|
|
|
|
double dx,dy,dz,massone;
|
|
double unwrap[3];
|
|
|
|
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) {
|
|
if (rmass) massone = rmass[i];
|
|
else massone = mass[type[i]];
|
|
|
|
domain->unmap(x[i],image[i],unwrap);
|
|
dx = unwrap[0] - xcm[0];
|
|
dy = unwrap[1] - xcm[1];
|
|
dz = unwrap[2] - xcm[2];
|
|
|
|
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)
|
|
for (int i = 0; i < 6; i++)
|
|
vector[i] /= masstotal;
|
|
}
|