116 lines
3.1 KiB
C++
116 lines
3.1 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "compute_gyration.h"
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "group.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeGyration::ComputeGyration(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all(FLERR, "Illegal compute gyration command");
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scalar_flag = vector_flag = 1;
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size_vector = 6;
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extscalar = 0;
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extvector = 0;
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vector = new double[size_vector];
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}
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/* ---------------------------------------------------------------------- */
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ComputeGyration::~ComputeGyration()
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{
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delete[] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeGyration::init()
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{
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masstotal = group->mass(igroup);
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}
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/* ---------------------------------------------------------------------- */
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double ComputeGyration::compute_scalar()
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{
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invoked_scalar = update->ntimestep;
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double xcm[3];
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if (group->dynamic[igroup]) masstotal = group->mass(igroup);
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group->xcm(igroup, masstotal, xcm);
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scalar = group->gyration(igroup, masstotal, xcm);
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return scalar;
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}
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/* ----------------------------------------------------------------------
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compute the radius-of-gyration tensor of group of atoms
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around center-of-mass cm
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must unwrap atoms to compute Rg tensor correctly
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------------------------------------------------------------------------- */
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void ComputeGyration::compute_vector()
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{
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invoked_vector = update->ntimestep;
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double xcm[3];
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group->xcm(igroup, masstotal, xcm);
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double **x = atom->x;
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int *mask = atom->mask;
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int *type = atom->type;
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imageint *image = atom->image;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int nlocal = atom->nlocal;
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double dx, dy, dz, massone;
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double unwrap[3];
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double rg[6];
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rg[0] = rg[1] = rg[2] = rg[3] = rg[4] = rg[5] = 0.0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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if (rmass)
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massone = rmass[i];
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else
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massone = mass[type[i]];
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domain->unmap(x[i], image[i], unwrap);
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dx = unwrap[0] - xcm[0];
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dy = unwrap[1] - xcm[1];
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dz = unwrap[2] - xcm[2];
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rg[0] += dx * dx * massone;
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rg[1] += dy * dy * massone;
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rg[2] += dz * dz * massone;
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rg[3] += dx * dy * massone;
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rg[4] += dx * dz * massone;
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rg[5] += dy * dz * massone;
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}
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MPI_Allreduce(rg, vector, 6, MPI_DOUBLE, MPI_SUM, world);
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if (masstotal > 0.0)
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for (int i = 0; i < 6; i++) vector[i] /= masstotal;
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}
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