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lammps/src/USER-COLVARS/ndx_group.cpp
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ndx_group.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 "ndx_group.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "memory.h"
#include "force.h"
#include "error.h"
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
using namespace LAMMPS_NS;
#define BUFLEN 4096
#define DELTA 16384
static char *find_section(FILE *fp, const char *name)
{
char linebuf[BUFLEN];
char *n,*p,*t,*r;
while ((p = fgets(linebuf,BUFLEN,fp))) {
t = strtok(p," \t\n\r\f");
if ((t != NULL) && *t == '[') {
t = strtok(NULL," \t\n\r\f");
if (t != NULL) {
n = t;
t = strtok(NULL," \t\n\r\f");
if ((t != NULL) && *t == ']') {
if ((name == NULL) || strcmp(name,n) == 0) {
int l = strlen(n);
r = new char[l+1];
strncpy(r,n,l+1);
return r;
}
}
}
}
}
return NULL;
}
static tagint *read_section(FILE *fp, bigint &num)
{
char linebuf[BUFLEN];
char *p,*t;
tagint *tagbuf;
bigint nmax;
num = 0;
nmax = DELTA;
tagbuf = (tagint *)malloc(sizeof(tagint)*nmax);
while ((p = fgets(linebuf,BUFLEN,fp))) {
t = strtok(p," \t\n\r\f");
while (t != NULL) {
// start of a new section. we are done here.
if (*t == '[') return tagbuf;
tagbuf[num++] = ATOTAGINT(t);
if (num == nmax) {
nmax += DELTA;
tagbuf = (tagint *)realloc(tagbuf,sizeof(tagint)*nmax);
}
t = strtok(NULL," \t\n\r\f");
}
}
return tagbuf;
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::command(int narg, char **arg)
{
int len;
bigint num;
FILE *fp;
char *name = NULL;
tagint *tags;
if (narg < 1) error->all(FLERR,"Illegal ndx2group command");
if (atom->tag_enable == 0)
error->all(FLERR,"Must have atom IDs for ndx2group command");
if (comm->me == 0) {
fp = fopen(arg[0], "r");
if (fp == NULL)
error->one(FLERR,"Cannot open index file for reading");
if (screen)
fprintf(screen, "Reading groups from index file %s:\n",arg[0]);
if (logfile)
fprintf(logfile,"Reading groups from index file %s:\n",arg[0]);
}
if (narg == 1) { // restore all groups
do {
if (comm->me == 0) {
len = 0;
// find the next section.
// if we had processed a section, before we need to step back
if (name != NULL) {
rewind(fp);
char *tmp = find_section(fp,name);
delete[] tmp;
delete[] name;
name = NULL;
}
name = find_section(fp,NULL);
if (name != NULL) {
len=strlen(name);
// skip over group "all", which is called "System" in gromacs
if (strcmp(name,"System") == 0) continue;
if (screen)
fprintf(screen," Processing group '%s'\n",name);
if (logfile)
fprintf(logfile," Processing group '%s'\n",name);
}
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 0) {
MPI_Bcast(name,len,MPI_CHAR,0,world);
// read tags for atoms in group and broadcast
num = 0;
tags = read_section(fp,num);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world);
create(name,num,tags);
free(tags);
}
} else {
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 0) {
delete[] name;
name = new char[len+1];
MPI_Bcast(name,len+1,MPI_CHAR,0,world);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1));
MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world);
create(name,num,tags);
free(tags);
}
}
} while (len);
} else { // restore selected groups
for (int idx=1; idx < narg; ++idx) {
if (comm->me == 0) {
len = 0;
// find named section, search from beginning of file
if (name != NULL) delete[] name;
rewind(fp);
name = find_section(fp,arg[idx]);
if (name != NULL) len=strlen(name);
if (screen)
fprintf(screen," %s group '%s'\n",
len ? "Processing" : "Skipping",arg[idx]);
if (logfile)
fprintf(logfile,"%s group '%s'\n",
len ? "Processing" : "Skipping",arg[idx]);
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 0) {
MPI_Bcast(name,len+1,MPI_CHAR,0,world);
// read tags for atoms in group and broadcast
num = 0;
tags = read_section(fp,num);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world);
create(name,num,tags);
free(tags);
}
} else {
MPI_Bcast(&len,1,MPI_INT,0,world);
if (len > 0) {
delete[] name;
name = new char[len+1];
MPI_Bcast(name,len+1,MPI_CHAR,0,world);
MPI_Bcast(&num,1,MPI_LMP_BIGINT,0,world);
tags = (tagint *)malloc(sizeof(tagint)*(num ? num : 1));
MPI_Bcast(tags,num,MPI_LMP_TAGINT,0,world);
create(name,num,tags);
free(tags);
}
}
}
}
delete[] name;
if (comm->me == 0) {
if (screen) fputs("\n",screen);
if (logfile) fputs("\n",logfile);
fclose(fp);
}
}
/* ---------------------------------------------------------------------- */
void Ndx2Group::create(char *name, bigint num, tagint *tags)
{
// wipe out all members if the group exists. gid==0 is group "all"
int gid = group->find(name);
if (gid > 0) {
char *cmd[2];
cmd[0] = name;
cmd[1] = (char *)"clear";
group->assign(2,cmd);
}
// map from global to local
const int nlocal = atom->nlocal;
int *flags = (int *)calloc(nlocal,sizeof(int));
for (bigint i=0; i < num; ++i) {
const int id = atom->map(tags[i]);
if (id < nlocal && id >= 0)
flags[id] = 1;
}
group->create(name,flags);
free(flags);
}
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