git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3551 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/compute_rdf.cpp
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src/compute_rdf.cpp
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/* ----------------------------------------------------------------------
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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 "compute_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 "pair.h"
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#include "neighbor.h"
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#include "neigh_request.h"
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#include "neigh_list.h"
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#include "group.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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ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg < 8 || (narg-6) % 2) error->all("Illegal compute rdf command");
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array_flag = 1;
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size_array_rows = 1;
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size_array_cols = 1;
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extarray = 1;
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maxbin = atoi(arg[5]);
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npairs = 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 type in compute rdf command");
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npairs++;
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rdfpair[itype][jtype] = npairs;
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}
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hist = memory->create_2d_double_array(maxbin,npairs+1,"rdf:hist");
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array = memory->create_2d_double_array(maxbin,npairs+1,"rdf:array");
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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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}
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/* ---------------------------------------------------------------------- */
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ComputeRDF::~ComputeRDF()
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{
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memory->destroy_2d_int_array(rdfpair);
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memory->destroy_2d_double_array(hist);
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delete [] nrdfatoms;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRDF::init()
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{
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if (force->pair) delr = force->pair->cutforce / maxbin;
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else error->all("Compute rdf requires a pair style be defined");
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delrinv = 1.0/delr;
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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]->compute = 1;
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neighbor->requests[irequest]->occasional = 1;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeRDF::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 ComputeRDF::compute_array()
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{
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invoked_array = update->ntimestep;
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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 < maxbin; i++)
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for (int j = 0; j < npairs; 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[bin][ipair-1]++;
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if (newton_pair || j < nlocal)
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if (jpair) hist[bin][jpair-1]++;
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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],array[0],maxbin*npairs,MPI_DOUBLE,MPI_SUM,world);
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}
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