2993aec312
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15519 f3b2605a-c512-4ea7-a41b-209d697bcdaa
271 lines
7.4 KiB
C++
271 lines
7.4 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://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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#include <string.h>
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#include "compute_msd.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 "modify.h"
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#include "fix_store.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeMSD::ComputeMSD(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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id_fix(NULL)
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{
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if (narg < 3) error->all(FLERR,"Illegal compute msd command");
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vector_flag = 1;
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size_vector = 4;
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extvector = 0;
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create_attribute = 1;
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dynamic_group_allow = 0;
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// optional args
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comflag = 0;
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avflag = 0;
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"com") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command");
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if (strcmp(arg[iarg+1],"no") == 0) comflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) comflag = 1;
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else error->all(FLERR,"Illegal compute msd command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"average") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal compute msd command");
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if (strcmp(arg[iarg+1],"no") == 0) avflag = 0;
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else if (strcmp(arg[iarg+1],"yes") == 0) avflag = 1;
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else error->all(FLERR,"Illegal compute msd command");
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iarg += 2;
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} else error->all(FLERR,"Illegal compute msd command");
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}
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// create a new fix STORE style for reference positions
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// id = compute-ID + COMPUTE_STORE, fix group = compute group
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int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
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id_fix = new char[n];
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strcpy(id_fix,id);
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strcat(id_fix,"_COMPUTE_STORE");
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char **newarg = new char*[6];
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newarg[0] = id_fix;
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newarg[1] = group->names[igroup];
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newarg[2] = (char *) "STORE";
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newarg[3] = (char *) "peratom";
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newarg[4] = (char *) "1";
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newarg[5] = (char *) "3";
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modify->add_fix(6,newarg);
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fix = (FixStore *) modify->fix[modify->nfix-1];
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delete [] newarg;
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// calculate xu,yu,zu for fix store array
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// skip if reset from restart file
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if (fix->restart_reset) fix->restart_reset = 0;
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else {
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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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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) domain->unmap(x[i],image[i],xoriginal[i]);
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else xoriginal[i][0] = xoriginal[i][1] = xoriginal[i][2] = 0.0;
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// adjust for COM if requested
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if (comflag) {
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double cm[3];
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masstotal = group->mass(igroup);
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group->xcm(igroup,masstotal,cm);
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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xoriginal[i][0] -= cm[0];
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xoriginal[i][1] -= cm[1];
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xoriginal[i][2] -= cm[2];
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}
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}
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// initialize counter for average positions if requested
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naverage = 0;
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}
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// displacement vector
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vector = new double[4];
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}
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/* ---------------------------------------------------------------------- */
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ComputeMSD::~ComputeMSD()
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{
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// check nfix in case all fixes have already been deleted
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if (modify->nfix) modify->delete_fix(id_fix);
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delete [] id_fix;
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMSD::init()
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{
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// set fix which stores reference atom coords
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int ifix = modify->find_fix(id_fix);
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if (ifix < 0) error->all(FLERR,"Could not find compute msd fix ID");
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fix = (FixStore *) modify->fix[ifix];
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// nmsd = # of atoms in group
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nmsd = group->count(igroup);
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masstotal = group->mass(igroup);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeMSD::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 reference position
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// reference 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[4];
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msd[0] = msd[1] = msd[2] = msd[3] = 0.0;
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double xtmp, ytmp, ztmp;
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// update number of averages if requested
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double navfac;
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if (avflag) {
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naverage++;
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navfac = 1.0/(naverage+1);
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}
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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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xtmp = x[i][0] + xbox*xprd - cm[0];
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ytmp = x[i][1] + ybox*yprd - cm[1];
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ztmp = x[i][2] + zbox*zprd - cm[2];
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// use running average position for reference if requested
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if (avflag) {
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xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
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xoriginal[i][1] = (xoriginal[i][1]*naverage + ytmp)*navfac;
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xoriginal[i][2] = (xoriginal[i][2]*naverage + ztmp)*navfac;
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}
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dx = xtmp - xoriginal[i][0];
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dy = ytmp - xoriginal[i][1];
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dz = ztmp - 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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} 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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xtmp = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - cm[0];
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ytmp = x[i][1] + h[1]*ybox + h[3]*zbox - cm[1];
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ztmp = x[i][2] + h[2]*zbox - cm[2];
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// use running average position for reference if requested
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if (avflag) {
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xoriginal[i][0] = (xoriginal[i][0]*naverage + xtmp)*navfac;
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xoriginal[i][1] = (xoriginal[i][0]*naverage + xtmp)*navfac;
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xoriginal[i][2] = (xoriginal[i][0]*naverage + xtmp)*navfac;
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}
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dx = xtmp - xoriginal[i][0];
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dy = ytmp - xoriginal[i][1];
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dz = ztmp - 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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}
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MPI_Allreduce(msd,vector,4,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] /= nmsd;
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vector[3] /= nmsd;
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}
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}
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/* ----------------------------------------------------------------------
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initialize one atom's storage values, called when atom is created
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------------------------------------------------------------------------- */
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void ComputeMSD::set_arrays(int i)
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{
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double **xoriginal = fix->astore;
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double **x = atom->x;
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xoriginal[i][0] = x[i][0];
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xoriginal[i][1] = x[i][1];
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xoriginal[i][2] = x[i][2];
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}
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