106 lines
3.3 KiB
C++
106 lines
3.3 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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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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/* ----------------------------------------------------------------------
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Contributing authors: Rob Hoy
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------------------------------------------------------------------------- */
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#include "compute_msd_nongauss.h"
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#include "atom.h"
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#include "update.h"
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#include "group.h"
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#include "domain.h"
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#include "fix_store.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeMSDNonGauss::ComputeMSDNonGauss(LAMMPS *lmp, int narg, char **arg) :
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ComputeMSD(lmp, narg, arg)
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{
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size_vector = 3;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMSDNonGauss::compute_vector()
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{
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invoked_vector = update->ntimestep;
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// cm = current center of mass
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double cm[3];
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if (comflag) group->xcm(igroup,masstotal,cm);
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else cm[0] = cm[1] = cm[2] = 0.0;
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// dx,dy,dz = displacement of atom from original position
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// original unwrapped position is stored by fix
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// relative to center of mass if comflag is set
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// for triclinic, need to unwrap current atom coord via h matrix
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double **xoriginal = fix->astore;
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double **x = atom->x;
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int *mask = atom->mask;
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imageint *image = atom->image;
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int nlocal = atom->nlocal;
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double *h = domain->h;
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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double dx,dy,dz;
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int xbox,ybox,zbox;
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double msd[2];
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msd[0] = msd[1] = 0.0;
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if (domain->triclinic == 0) {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = x[i][0] + xbox*xprd - cm[0] - xoriginal[i][0];
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dy = x[i][1] + ybox*yprd - cm[1] - xoriginal[i][1];
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dz = x[i][2] + zbox*zprd - cm[2] - xoriginal[i][2];
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msd[0] += dx*dx + dy*dy + dz*dz;
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msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
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}
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xbox = (image[i] & IMGMASK) - IMGMAX;
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ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
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zbox = (image[i] >> IMG2BITS) - IMGMAX;
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dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox -
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cm[0] - xoriginal[i][0];
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dy = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1] - xoriginal[i][1];
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dz = x[i][2] + h[2]*zbox - cm[2] - xoriginal[i][2];
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msd[0] += dx*dx + dy*dy + dz*dz;
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msd[1] += (dx*dx + dy*dy + dz*dz)*(dx*dx + dy*dy + dz*dz);
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}
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}
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MPI_Allreduce(msd,vector,2,MPI_DOUBLE,MPI_SUM,world);
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if (nmsd) {
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vector[0] /= nmsd;
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vector[1] /= nmsd;
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vector[2] = (3*vector[1])/(5*vector[0]*vector[0]) - 1;
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}
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}
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