328 lines
9.1 KiB
C++
328 lines
9.1 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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/* ----------------------------------------------------------------------
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Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "math.h"
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#include "stdlib.h"
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#include "fix_rdf.h"
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#include "atom.h"
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#include "update.h"
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#include "force.h"
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#include "domain.h"
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#include "output.h"
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#include "group.h"
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#include "modify.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "pair.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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FixRDF::FixRDF(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 8 || (narg-6) % 2) error->all("Illegal fix rdf command");
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nevery = atoi(arg[3]);
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if (nevery <= 0) error->all("Illegal fix rdf command");
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first = 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 rdf file %s",arg[4]);
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error->one(str);
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}
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}
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maxbin = atoi(arg[5]);
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n_rdf_pairs = 0;
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rdfpair = memory->create_2d_int_array(atom->ntypes+1,atom->ntypes+1,
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"rdf:rdfpair");
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++)
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rdfpair[i][j] = 0;
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int itype,jtype;
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for (int i = 6; i < narg; i+=2) {
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itype = atoi(arg[i]);
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jtype = atoi(arg[i+1]);
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if (itype < 1 || jtype < 1 || itype > atom->ntypes || jtype > atom->ntypes)
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error->all("Invalid atom types in fix rdf command");
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n_rdf_pairs++;
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rdfpair[itype][jtype] = n_rdf_pairs;
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}
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hist = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist");
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hist_all = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist_all");
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int *nrdfatom = new int[atom->ntypes+1];
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for (int i = 1; i <= atom->ntypes; i++) nrdfatom[i] = 0;
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int *mask = atom->mask;
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int *type = atom->type;
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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) nrdfatom[type[i]]++;
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nrdfatoms = new int[atom->ntypes+1];
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MPI_Allreduce(&nrdfatom[1],&nrdfatoms[1],atom->ntypes,MPI_INT,MPI_SUM,world);
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delete [] nrdfatom;
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gr_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,"rdf:gr_ave");
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ncoord_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,
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"rdf:nccord_ave");
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}
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/* ---------------------------------------------------------------------- */
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FixRDF::~FixRDF()
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{
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if (me == 0) fclose(fp);
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memory->destroy_2d_int_array(rdfpair);
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memory->destroy_2d_int_array(hist);
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memory->destroy_2d_int_array(hist_all);
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delete [] nrdfatoms;
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memory->destroy_2d_double_array(gr_ave);
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memory->destroy_2d_double_array(ncoord_ave);
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}
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/* ---------------------------------------------------------------------- */
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int FixRDF::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 FixRDF::init()
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{
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if (force->pair) delr = force->pair->cutforce / maxbin;
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else error->all("Fix rdf requires a pair style be defined");
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// need an occasional half neighbor list
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int irequest = neighbor->request((void *) this);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->fix = 1;
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neighbor->requests[irequest]->occasional = 1;
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delrinv = 1.0/delr;
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nframes = 0;
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// set running averages to 0.0
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int i,j,bin,irdf;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = 1; j <= atom->ntypes; j++)
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if (rdfpair[i][j]) {
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irdf = rdfpair[i][j] - 1;
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for (bin = 0; bin < maxbin; bin++)
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gr_ave[irdf][bin] = ncoord_ave[irdf][bin] = 0.0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixRDF::init_list(int id, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void FixRDF::setup(int vflag)
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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 FixRDF::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 nlocal = atom->nlocal;
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int *type = atom->type;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int nall = atom->nlocal + atom->nghost;
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int newton_pair = force->newton_pair;
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int i,j,ii,jj,inum,jnum,itype,jtype,ipair,jpair,bin;
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double xtmp,ytmp,ztmp,delx,dely,delz,r;
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int *ilist,*jlist,*numneigh,**firstneigh;
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// invoke half neighbor list (will copy or build if necessary)
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neighbor->build_one(list->index);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// zero the histogram counts
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for (int i = 0; i < n_rdf_pairs; i++)
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for (int j = 0; j < maxbin; j++)
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hist[i][j] = 0;
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// tally the RDF
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// both atom i and j must be in fix group
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// itype,jtype must have been specified by user
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// weighting factor must be != 0.0 for this pair
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// could be 0 and still be in neigh list for long-range Coulombics
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// count the interaction once even if neighbor pair is stored on 2 procs
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// if itype = jtype, count the interaction twice
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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if (mask[i] & groupbit) {
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j >= nall) {
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if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)
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continue;
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j %= nall;
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}
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if (mask[j] & groupbit) {
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jtype = type[j];
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ipair = rdfpair[itype][jtype];
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jpair = rdfpair[jtype][itype];
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if (!ipair && !jpair) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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r = sqrt(delx*delx + dely*dely + delz*delz);
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bin = static_cast<int> (r * delrinv);
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if (bin >= maxbin) continue;
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if (ipair) hist[ipair-1][bin]++;
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if (newton_pair || j < nlocal)
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if (jpair) hist[jpair-1][bin]++;
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}
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}
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}
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}
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// sum histogram across procs
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MPI_Allreduce(hist[0],hist_all[0],n_rdf_pairs*maxbin,MPI_INT,MPI_SUM,world);
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nframes++;
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if (me == 0) {
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// print RDF for current snapshot
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double rlower,rcenter,rupper,nideal,gr;
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double PI = 4.0*atan(1.0);
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double constant = 4.0*PI / (3.0*domain->xprd*domain->yprd*domain->zprd);
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int irdf;
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fprintf(fp,"# Timestep %d\n",update->ntimestep);
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fprintf(fp,"%s","r");
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++)
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if (rdfpair[i][j])
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fprintf(fp,", %s%d,%d%s, %s%d,%d%s",
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"g(",i,j,",r)","ncoord(",i,j,",r)");
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double *ncoord = new double[n_rdf_pairs];
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for (int i = 0; i < n_rdf_pairs; i++) ncoord[i] = 0;
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for (bin = 0; bin < maxbin; bin++) {
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rlower = bin*delr;
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rcenter = rlower + 0.5*delr;
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rupper = rlower + delr;
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fprintf(fp,"\n%f ",rcenter);
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++)
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if (rdfpair[i][j]) {
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nideal = constant*nrdfatoms[j] *
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(rupper*rupper*rupper - rlower*rlower*rlower);
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irdf = rdfpair[i][j] - 1;
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gr = hist_all[irdf][bin] / (nrdfatoms[i]*nideal);
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ncoord[irdf] += gr*nideal;
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fprintf(fp,"%f %f ",gr,ncoord[irdf]);
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gr_ave[irdf][bin] =
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((nframes-1)*gr_ave[irdf][bin] + gr) / nframes;
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ncoord_ave[irdf][bin] =
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((nframes-1)*ncoord_ave[irdf][bin] + ncoord[irdf]) / nframes;
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}
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}
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fprintf(fp,"\n");
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delete [] ncoord;
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// if last time in run that RDF is computed, print running averages
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if (update->ntimestep + nevery > update->endstep) {
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fprintf(fp,"# Run Average\n");
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fprintf(fp,"%s","r");
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++)
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if (rdfpair[i][j])
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fprintf(fp,", %s%d,%d%s, %s%d,%d%s",
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"g(",i,j,",r)","ncoord(",i,j,",r)");
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for (bin = 0; bin < maxbin; bin++) {
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rlower = bin*delr;
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rcenter = rlower + 0.5*delr;
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rupper = rlower + delr;
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fprintf(fp,"\n%f ",rcenter);
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = 1; j <= atom->ntypes; j++)
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if (rdfpair[i][j]) {
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irdf = rdfpair[i][j] - 1;
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fprintf(fp,"%f %f ",gr_ave[irdf][bin],ncoord_ave[irdf][bin]);
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}
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}
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fprintf(fp,"\n");
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}
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}
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}
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