Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/fix_rdf.cpp
d0e374e4c3a8efficient_neuronet

Last Change
Raw File

fix_rdf.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Paul Crozier (SNL), Jeff Greathouse (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "stdlib.h"
#include "fix_rdf.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "output.h"
#include "group.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "pair.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixRDF::FixRDF(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 8 || (narg-6) % 2) error->all("Illegal fix rdf command");
nevery = atoi(arg[3]);
if (nevery <= 0) error->all("Illegal fix rdf command");
first = 1;
MPI_Comm_rank(world,&me);
if (me == 0) {
fp = fopen(arg[4],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix rdf file %s",arg[4]);
error->one(str);
}
}
maxbin = atoi(arg[5]);
n_rdf_pairs = 0;
rdfpair = memory->create_2d_int_array(atom->ntypes+1,atom->ntypes+1,
"rdf:rdfpair");
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
rdfpair[i][j] = 0;
int itype,jtype;
for (int i = 6; i < narg; i+=2) {
itype = atoi(arg[i]);
jtype = atoi(arg[i+1]);
if (itype < 1 || jtype < 1 || itype > atom->ntypes || jtype > atom->ntypes)
error->all("Invalid atom types in fix rdf command");
n_rdf_pairs++;
rdfpair[itype][jtype] = n_rdf_pairs;
}
hist = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist");
hist_all = memory->create_2d_int_array(n_rdf_pairs,maxbin,"rdf:hist_all");
int *nrdfatom = new int[atom->ntypes+1];
for (int i = 1; i <= atom->ntypes; i++) nrdfatom[i] = 0;
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) nrdfatom[type[i]]++;
nrdfatoms = new int[atom->ntypes+1];
MPI_Allreduce(&nrdfatom[1],&nrdfatoms[1],atom->ntypes,MPI_INT,MPI_SUM,world);
delete [] nrdfatom;
gr_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,"rdf:gr_ave");
ncoord_ave = memory->create_2d_double_array(n_rdf_pairs,maxbin,
"rdf:nccord_ave");
}
/* ---------------------------------------------------------------------- */
FixRDF::~FixRDF()
{
if (me == 0) fclose(fp);
memory->destroy_2d_int_array(rdfpair);
memory->destroy_2d_int_array(hist);
memory->destroy_2d_int_array(hist_all);
delete [] nrdfatoms;
memory->destroy_2d_double_array(gr_ave);
memory->destroy_2d_double_array(ncoord_ave);
}
/* ---------------------------------------------------------------------- */
int FixRDF::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixRDF::init()
{
if (force->pair) delr = force->pair->cutforce / maxbin;
else error->all("Fix rdf requires a pair style be defined");
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->occasional = 1;
delrinv = 1.0/delr;
nframes = 0;
// set running averages to 0.0
int i,j,bin,irdf;
for (i = 1; i <= atom->ntypes; i++)
for (j = 1; j <= atom->ntypes; j++)
if (rdfpair[i][j]) {
irdf = rdfpair[i][j] - 1;
for (bin = 0; bin < maxbin; bin++)
gr_ave[irdf][bin] = ncoord_ave[irdf][bin] = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void FixRDF::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void FixRDF::setup(int vflag)
{
if (first) end_of_step();
first = 0;
}
/* ---------------------------------------------------------------------- */
void FixRDF::end_of_step()
{
double **x = atom->x;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *type = atom->type;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int nall = atom->nlocal + atom->nghost;
int newton_pair = force->newton_pair;
int i,j,ii,jj,inum,jnum,itype,jtype,ipair,jpair,bin;
double xtmp,ytmp,ztmp,delx,dely,delz,r;
int *ilist,*jlist,*numneigh,**firstneigh;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero the histogram counts
for (int i = 0; i < n_rdf_pairs; i++)
for (int j = 0; j < maxbin; j++)
hist[i][j] = 0;
// tally the RDF
// both atom i and j must be in fix group
// itype,jtype must have been specified by user
// weighting factor must be != 0.0 for this pair
// could be 0 and still be in neigh list for long-range Coulombics
// count the interaction once even if neighbor pair is stored on 2 procs
// if itype = jtype, count the interaction twice
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j >= nall) {
if (special_coul[j/nall] == 0.0 && special_lj[j/nall] == 0.0)
continue;
j %= nall;
}
if (mask[j] & groupbit) {
jtype = type[j];
ipair = rdfpair[itype][jtype];
jpair = rdfpair[jtype][itype];
if (!ipair && !jpair) continue;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
r = sqrt(delx*delx + dely*dely + delz*delz);
bin = static_cast<int> (r * delrinv);
if (bin >= maxbin) continue;
if (ipair) hist[ipair-1][bin]++;
if (newton_pair || j < nlocal)
if (jpair) hist[jpair-1][bin]++;
}
}
}
}
// sum histogram across procs
MPI_Allreduce(hist[0],hist_all[0],n_rdf_pairs*maxbin,MPI_INT,MPI_SUM,world);
nframes++;
if (me == 0) {
// print RDF for current snapshot
double rlower,rcenter,rupper,nideal,gr;
double PI = 4.0*atan(1.0);
double constant = 4.0*PI / (3.0*domain->xprd*domain->yprd*domain->zprd);
int irdf;
fprintf(fp,"%s %d \n","TIMESTEP", update->ntimestep);
fprintf(fp,"%s","r");
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
if (rdfpair[i][j])
fprintf(fp,", %s%d,%d%s, %s%d,%d%s",
"g(",i,j,",r)","ncoord(",i,j,",r)");
double *ncoord = new double[n_rdf_pairs];
for (int i = 0; i < n_rdf_pairs; i++) ncoord[i] = 0;
for (bin = 0; bin < maxbin; bin++) {
rlower = bin*delr;
rcenter = rlower + 0.5*delr;
rupper = rlower + delr;
fprintf(fp,"\n%f ",rcenter);
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
if (rdfpair[i][j]) {
nideal = constant*nrdfatoms[j] *
(rupper*rupper*rupper - rlower*rlower*rlower);
irdf = rdfpair[i][j] - 1;
gr = hist_all[irdf][bin] / (nrdfatoms[i]*nideal);
ncoord[irdf] += gr*nideal;
fprintf(fp,"%f %f ",gr,ncoord[irdf]);
gr_ave[irdf][bin] =
((nframes-1)*gr_ave[irdf][bin] + gr) / nframes;
ncoord_ave[irdf][bin] =
((nframes-1)*ncoord_ave[irdf][bin] + ncoord[irdf]) / nframes;
}
}
fprintf(fp,"\n");
delete [] ncoord;
// if last time in run that RDF is computed, print running averages
if (update->ntimestep + nevery > update->endstep) {
fprintf(fp,"%s \n","RUN AVERAGE");
fprintf(fp,"%s","r");
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
if (rdfpair[i][j])
fprintf(fp,", %s%d,%d%s, %s%d,%d%s",
"g(",i,j,",r)","ncoord(",i,j,",r)");
for (bin = 0; bin < maxbin; bin++) {
rlower = bin*delr;
rcenter = rlower + 0.5*delr;
rupper = rlower + delr;
fprintf(fp,"\n%f ",rcenter);
for (int i = 1; i <= atom->ntypes; i++)
for (int j = 1; j <= atom->ntypes; j++)
if (rdfpair[i][j]) {
irdf = rdfpair[i][j] - 1;
fprintf(fp,"%f %f ",gr_ave[irdf][bin],ncoord_ave[irdf][bin]);
}
}
fprintf(fp,"\n");
}
}
}
c4science · Help