git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/fix_msd.cpp
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286
src/fix_msd.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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 "stdlib.h"
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#include "string.h"
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#include "fix_msd.h"
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#include "atom.h"
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#include "update.h"
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#include "domain.h"
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#include "group.h"
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#include "modify.h"
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#include "memory.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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FixMSD::FixMSD(int narg, char **arg) : Fix(narg, arg)
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{
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if (narg != 5) error->all("Illegal fix msd command");
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nevery = atoi(arg[3]);
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if (nevery <= 0) error->all("Illegal fix msd command");
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first = 1;
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restart_peratom = 1;
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MPI_Comm_rank(world,&me);
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if (me == 0) {
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fp = fopen(arg[4],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix msd file %s",arg[4]);
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error->one(str);
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}
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}
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if (me == 0) {
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fprintf(fp,"Mean-squared Displacement for group %s\n",
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group->names[igroup]);
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fprintf(fp,"TimeStep x y z total\n");
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}
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// perform initial allocation of atom-based array
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// register with atom class
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xoriginal = NULL;
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grow_arrays(atom->nmax);
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atom->add_callback(0);
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atom->add_callback(1);
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// xoriginal = initial unwrapped positions of atoms
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double **x = atom->x;
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int *mask = atom->mask;
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int *image = atom->image;
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int nlocal = atom->nlocal;
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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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int xbox,ybox,zbox;
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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] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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xoriginal[i][0] = x[i][0] + xbox*xprd;
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xoriginal[i][1] = x[i][1] + ybox*yprd;
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xoriginal[i][2] = x[i][2] + zbox*zprd;
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} else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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}
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// nmsd = # of atoms in group
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nmsd = 0;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) nmsd++;
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int nmsd_all;
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MPI_Allreduce(&nmsd,&nmsd_all,1,MPI_INT,MPI_SUM,world);
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nmsd = nmsd_all;
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if (nmsd == 0) error->all("Fix msd group has no atoms");
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}
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/* ---------------------------------------------------------------------- */
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FixMSD::~FixMSD()
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{
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if (me == 0) fclose(fp);
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// if atom class still exists:
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// unregister this fix so atom class doesn't invoke it any more
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if (atom) atom->delete_callback(id,0);
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if (atom) atom->delete_callback(id,1);
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// delete locally stored array
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memory->destroy_2d_double_array(xoriginal);
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}
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/* ---------------------------------------------------------------------- */
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int FixMSD::setmask()
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{
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int mask = 0;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixMSD::init()
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{
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// warn if more than one msd fix
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int count = 0;
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"msd") == 0) count++;
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if (count > 1 && me == 0) error->warning("More than one msd fix");
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}
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/* ---------------------------------------------------------------------- */
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void FixMSD::setup()
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{
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if (first) end_of_step();
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first = 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixMSD::end_of_step()
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{
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double **x = atom->x;
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int *mask = atom->mask;
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int *image = atom->image;
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int nlocal = atom->nlocal;
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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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int xbox,ybox,zbox;
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double dx,dy,dz;
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double msd[4];
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msd[0] = msd[1] = msd[2] = msd[3] = 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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xbox = (image[i] & 1023) - 512;
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ybox = (image[i] >> 10 & 1023) - 512;
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zbox = (image[i] >> 20) - 512;
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dx = x[i][0] + xbox*xprd - xoriginal[i][0];
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dy = x[i][1] + ybox*yprd - xoriginal[i][1];
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dz = x[i][2] + zbox*zprd - xoriginal[i][2];
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msd[0] += dx*dx;
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msd[1] += dy*dy;
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msd[2] += dz*dz;
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msd[3] += dx*dx + dy*dy + dz*dz;
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}
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double msd_all[4];
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MPI_Allreduce(msd,msd_all,4,MPI_DOUBLE,MPI_SUM,world);
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msd_all[0] /= nmsd;
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msd_all[1] /= nmsd;
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msd_all[2] /= nmsd;
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msd_all[3] /= nmsd;
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if (me == 0) fprintf(fp,"%d %g %g %g %g\n",update->ntimestep,
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msd_all[0],msd_all[1],msd_all[2],msd_all[3]);
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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int FixMSD::memory_usage()
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{
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int bytes = atom->nmax*3 * sizeof(double);
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return bytes;
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}
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/* ----------------------------------------------------------------------
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allocate atom-based array
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------------------------------------------------------------------------- */
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void FixMSD::grow_arrays(int nmax)
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{
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xoriginal =
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memory->grow_2d_double_array(xoriginal,nmax,3,"fix_msd:xoriginal");
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}
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/* ----------------------------------------------------------------------
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copy values within local atom-based array
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------------------------------------------------------------------------- */
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void FixMSD::copy_arrays(int i, int j)
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{
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xoriginal[j][0] = xoriginal[i][0];
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xoriginal[j][1] = xoriginal[i][1];
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xoriginal[j][2] = xoriginal[i][2];
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based array for exchange with another proc
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------------------------------------------------------------------------- */
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int FixMSD::pack_exchange(int i, double *buf)
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{
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buf[0] = xoriginal[i][0];
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buf[1] = xoriginal[i][1];
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buf[2] = xoriginal[i][2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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unpack values in local atom-based array from exchange with another proc
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------------------------------------------------------------------------- */
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int FixMSD::unpack_exchange(int nlocal, double *buf)
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{
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xoriginal[nlocal][0] = buf[0];
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xoriginal[nlocal][1] = buf[1];
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xoriginal[nlocal][2] = buf[2];
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return 3;
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}
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/* ----------------------------------------------------------------------
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pack values in local atom-based arrays for restart file
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------------------------------------------------------------------------- */
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int FixMSD::pack_restart(int i, double *buf)
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{
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buf[0] = 4;
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buf[1] = xoriginal[i][0];
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buf[2] = xoriginal[i][1];
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buf[3] = xoriginal[i][2];
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return 4;
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}
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/* ----------------------------------------------------------------------
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unpack values from atom->extra array to restart the fix
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------------------------------------------------------------------------- */
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void FixMSD::unpack_restart(int nlocal, int nth)
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{
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double **extra = atom->extra;
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// skip to Nth set of extra values
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int m = 0;
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for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
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m++;
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xoriginal[nlocal][0] = extra[nlocal][m++];
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xoriginal[nlocal][1] = extra[nlocal][m++];
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xoriginal[nlocal][2] = extra[nlocal][m++];
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}
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/* ----------------------------------------------------------------------
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maxsize of any atom's restart data
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------------------------------------------------------------------------- */
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int FixMSD::maxsize_restart()
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{
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return 4;
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}
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/* ----------------------------------------------------------------------
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size of atom nlocal's restart data
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------------------------------------------------------------------------- */
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int FixMSD::size_restart(int nlocal)
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{
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return 4;
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}
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