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lammps/src/USER-COLVARS/group_ndx.cpp
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group_ndx.cpp
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/* ----------------------------------------------------------------------
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 author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "group_ndx.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "error.h"
#include <stdio.h>
#include <stdlib.h>
using namespace LAMMPS_NS;
/* ----------------------------------------------------------------------
helper function. integer comparison for qsort()
---------------------------------------------------------------------- */
static int cmptagint(const void *p1, const void *p2)
{
const tagint i1 = * static_cast<const tagint *>(p1);
const tagint i2 = * static_cast<const tagint *>(p2);
if (i1 == i2) return 0;
else {
if (i1 < i2) return -1;
else return 1;
}
}
/* ----------------------------------------------------------------------
helper function. writes out one group to a gromacs style index file
---------------------------------------------------------------------- */
static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
int np, MPI_Comm world, FILE *screen, FILE *logfile)
{
char fmt[8];
tagint *sendlist, *recvlist;
bigint num = group->count(gid);
int lnum, cols;
if (me == 0) {
if (screen) fprintf(screen, " writing group %s... ", group->names[gid]);
if (logfile) fprintf(logfile, " writing group %s... ", group->names[gid]);
// the "all" group in LAMMPS is called "System" in gromacs
if (gid == 0) {
fputs("[ System ]\n", fp);
} else {
fprintf(fp,"[ %s ]\n", group->names[gid]);
}
// derive format string for index lists
bigint j = atom->natoms;
int i=0;
while (j > 0) {
++i;
j /= 10;
}
sprintf(fmt,"%%%dd ", i);
cols = 80 / (i+1);
}
if (num > 0) {
const int * const mask = atom->mask;
const tagint * const tag = atom->tag;
const int groupbit = group->bitmask[gid];
const int nlocal = atom->nlocal;
int i;
sendlist = new tagint[nlocal];
recvlist = new tagint[num];
lnum = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
int nrecv,allrecv;
if (me == 0) {
MPI_Status status;
MPI_Request request;
for (i=0; i < lnum; i++)
recvlist[i] = sendlist[i];
allrecv = lnum;
for (i=1; i < np; ++i) {
MPI_Irecv(recvlist+allrecv,num-allrecv,MPI_LMP_TAGINT,i,0, world,&request);
MPI_Send(&nrecv,0,MPI_INT,i,0,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_LMP_TAGINT,&nrecv);
allrecv += nrecv;
}
// sort received list
qsort((void *)recvlist, num, sizeof(tagint), cmptagint);
} else {
MPI_Recv(&nrecv,0,MPI_INT,0,0,world,MPI_STATUS_IGNORE);
MPI_Rsend(sendlist,lnum,MPI_LMP_TAGINT,0,0,world);
}
delete [] sendlist;
}
if (me == 0) {
int i, j;
for(i=0, j=0; i < num; ++i) {
fprintf(fp,fmt,recvlist[i]);
++j;
if (j == cols) {
fputs("\n",fp);
j = 0;
}
}
if (j > 0) fputs("\n",fp);
if (screen) fputs("done\n",screen);
if (logfile) fputs("done\n",logfile);
}
if (num > 0) delete[] recvlist;
}
/* ---------------------------------------------------------------------- */
void Group2Ndx::command(int narg, char **arg)
{
FILE *fp;
if (narg < 1) error->all(FLERR,"Illegal group2ndx command");
if (atom->tag_enable == 0)
error->all(FLERR,"Must have atom IDs for group2ndx command");
if (comm->me == 0) {
fp = fopen(arg[0], "w");
if (fp == NULL)
error->one(FLERR,"Cannot open index file for writing");
if (screen)
fprintf(screen, "Writing groups to index file %s:\n",arg[0]);
if (logfile)
fprintf(logfile,"Writing groups to index file %s:\n",arg[0]);
}
if (narg == 1) { // write out all groups
for (int i=0; i < group->ngroup; ++i) {
write_group(fp,i,atom,group,comm->me,comm->nprocs,world,screen,logfile);
}
} else { // write only selected groups
for (int i=1; i < narg; ++i) {
int gid = group->find(arg[i]);
if (gid < 0) error->all(FLERR, "Non-existing group requested");
write_group(fp,gid,atom,group,comm->me,comm->nprocs,world,screen,logfile);
}
}
if (comm->me == 0) {
if (screen) fputs("\n",screen);
if (logfile) fputs("\n",logfile);
fclose(fp);
}
}
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