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sjplimp
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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 author: Axel Kohlmeyer (Temple U)
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------------------------------------------------------------------------- */
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#include "group_ndx.h"
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#include "atom.h"
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#include "comm.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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#include <stdio.h>
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#include <stdlib.h>
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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helper function. integer comparison for qsort()
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---------------------------------------------------------------------- */
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static int cmpint(const void *p1, const void *p2)
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{
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const int i1 = * static_cast<const int *>(p1);
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const int i2 = * static_cast<const int *>(p2);
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if (i1 == i2) return 0;
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else {
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if (i1 < i2) return -1;
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else return 1;
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}
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}
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/* ----------------------------------------------------------------------
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helper function. writes out one group to a gromacs style index file
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---------------------------------------------------------------------- */
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static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
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int np, MPI_Comm world, FILE *screen, FILE *logfile)
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{
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char fmt[8];
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int *sendlist, *recvlist;
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bigint num = group->count(gid);
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int lnum, cols;
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if (me == 0) {
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if (screen) fprintf(screen, " writing group %s... ", group->names[gid]);
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if (logfile) fprintf(logfile, " writing group %s... ", group->names[gid]);
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// the "all" group in LAMMPS is called "System" in gromacs
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if (gid == 0) {
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fputs("[ System ]\n", fp);
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} else {
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fprintf(fp,"[ %s ]\n", group->names[gid]);
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}
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// derive format string for index lists
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bigint j = atom->natoms;
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int i = 0;
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while (j > 0) {
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++i;
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j /= 10;
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}
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sprintf(fmt,"%%%dd ", i);
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cols = 80 / (i+1);
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}
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if (num > 0) {
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const int * const mask = atom->mask;
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const int * const tag = atom->tag;
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const int groupbit = group->bitmask[gid];
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const int nlocal = atom->nlocal;
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int i,j;
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sendlist = new int[nlocal];
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recvlist = new int[num];
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lnum = 0;
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) sendlist[lnum++] = tag[i];
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MPI_Status status;
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MPI_Request request;
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int nrecv,allrecv;
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if (me == 0) {
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for (i = 0; i < lnum; i++)
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recvlist[i] = sendlist[i];
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allrecv = lnum;
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for (int i=1; i < np; ++i) {
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MPI_Irecv(recvlist+allrecv,num-allrecv,MPI_INT,i,0, world,&request);
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MPI_Send(&nrecv,0,MPI_INT,i,0,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&nrecv);
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allrecv += nrecv;
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}
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// sort received list
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qsort((void *)recvlist, num, sizeof(int), cmpint);
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} else {
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MPI_Recv(&nrecv,0,MPI_INT,0,0,world,&status);
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MPI_Rsend(sendlist,lnum,MPI_INT,0,0,world);
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}
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delete [] sendlist;
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}
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if (me == 0) {
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int i, j;
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for(i = 0, j = 0; i < num; ++i) {
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fprintf(fp,fmt,recvlist[i]);
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++j;
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if (j == cols) {
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fputs("\n",fp);
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j = 0;
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}
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}
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if (j > 0) fputs("\n",fp);
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if (screen) fputs("done\n",screen);
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if (logfile) fputs("done\n",logfile);
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}
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if (num > 0) delete[] recvlist;
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}
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/* ---------------------------------------------------------------------- */
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void Group2Ndx::command(int narg, char **arg)
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{
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FILE *fp;
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if (narg < 1) error->all(FLERR,"Illegal group2ndx command");
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if (atom->tag_enable == 0)
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error->all(FLERR,"Must have atom IDs for group2ndx command");
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if (comm->me == 0) {
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fp = fopen(arg[0], "w");
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if (fp == NULL)
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error->one(FLERR,"Cannot open index file for writing");
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if (screen)
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fprintf(screen, "Writing groups to index file %s:\n",arg[0]);
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if (logfile)
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fprintf(logfile,"Writing groups to index file %s:\n",arg[0]);
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}
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if (narg == 1) { // write out all groups
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for (int i=0; i < group->ngroup; ++i) {
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write_group(fp,i,atom,group,comm->me,comm->nprocs,world,screen,logfile);
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}
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} else { // write only selected groups
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for (int i=1; i < narg; ++i) {
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int gid = group->find(arg[i]);
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if (gid < 0) error->all(FLERR, "Non-existing group requested");
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write_group(fp,gid,atom,group,comm->me,comm->nprocs,world,screen,logfile);
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}
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}
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if (comm->me == 0) {
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if (screen) fputs("\n",screen);
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if (logfile) fputs("\n",logfile);
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fclose(fp);
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}
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}
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@ -0,0 +1,55 @@
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/* -*- 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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#ifdef COMMAND_CLASS
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CommandStyle(group2ndx,Group2Ndx)
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#else
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#ifndef LMP_GROUP_NDX_H
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#define LMP_GROUP_NDX_H
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#include "pointers.h"
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namespace LAMMPS_NS {
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class Group2Ndx : protected Pointers {
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public:
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Group2Ndx(class LAMMPS *lmp) : Pointers(lmp) {};
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void command(int, char **);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Must have atom IDs for group2ndx command
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There are no atom IDs defined in the system, but they are required
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to identify atoms in a gromacs style index file.
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E: Cannot open index file for writing
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Self-explanatory. Check your filename, permissions, and disk space or quota.
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*/
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