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Tue, Jul 30, 19:17

simple.c
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
/* c_driver = simple example of how an umbrella program
can invoke LAMMPS as a library on some subset of procs
Syntax: simpleC P in.lammps
P = # of procs to run LAMMPS on
must be <= # of procs the driver code itself runs on
in.lammps = LAMMPS input script
See README for compilation instructions */
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "mpi.h"
#include "library.h" /* this is a LAMMPS include file */
int main(int narg, char **arg)
{
/* setup MPI and various communicators
driver runs on all procs in MPI_COMM_WORLD
comm_lammps only has 1st P procs (could be all or any subset) */
MPI_Init(&narg,&arg);
if (narg != 3) {
printf("Syntax: simpleC P in.lammps\n");
exit(1);
}
int me,nprocs;
MPI_Comm_rank(MPI_COMM_WORLD,&me);
MPI_Comm_size(MPI_COMM_WORLD,&nprocs);
int nprocs_lammps = atoi(arg[1]);
if (nprocs_lammps > nprocs) {
if (me == 0)
printf("ERROR: LAMMPS cannot use more procs than available\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
int lammps;
if (me < nprocs_lammps) lammps = 1;
else lammps = MPI_UNDEFINED;
MPI_Comm comm_lammps;
MPI_Comm_split(MPI_COMM_WORLD,lammps,0,&comm_lammps);
/* open LAMMPS input script */
FILE *fp;
if (me == 0) {
fp = fopen(arg[2],"r");
if (fp == NULL) {
printf("ERROR: Could not open LAMMPS input script\n");
MPI_Abort(MPI_COMM_WORLD,1);
}
}
/* run the input script thru LAMMPS one line at a time until end-of-file
driver proc 0 reads a line, Bcasts it to all procs
(could just send it to proc 0 of comm_lammps and let it Bcast)
all LAMMPS procs call lammps_command() on the line */
void *lmp = NULL;
if (lammps == 1) lammps_open(0,NULL,comm_lammps,&lmp);
int n;
char line[1024];
while (1) {
if (me == 0) {
if (fgets(line,1024,fp) == NULL) n = 0;
else n = strlen(line) + 1;
if (n == 0) fclose(fp);
}
MPI_Bcast(&n,1,MPI_INT,0,MPI_COMM_WORLD);
if (n == 0) break;
MPI_Bcast(line,n,MPI_CHAR,0,MPI_COMM_WORLD);
if (lammps == 1) lammps_command(lmp,line);
}
/* run 10 more steps
get coords from LAMMPS
change coords of 1st atom
put coords back into LAMMPS
run a single step with changed coords */
double *x = NULL;
double *v = NULL;
if (lammps == 1) {
lammps_command(lmp,"run 10");
int natoms = lammps_get_natoms(lmp);
x = (double *) malloc(3*natoms*sizeof(double));
lammps_gather_atoms(lmp,"x",1,3,x);
v = (double *) malloc(3*natoms*sizeof(double));
lammps_gather_atoms(lmp,"v",1,3,v);
double epsilon = 0.1;
x[0] += epsilon;
lammps_scatter_atoms(lmp,"x",1,3,x);
lammps_command(lmp,"run 1");
}
// extract force on single atom two different ways
if (lammps == 1) {
double **f = (double **) lammps_extract_atom(lmp,"f");
printf("Force on 1 atom via extract_atom: %g\n",f[0][0]);
double *fx = (double *) lammps_extract_variable(lmp,"fx","all");
printf("Force on 1 atom via extract_variable: %g\n",fx[0]);
}
/* use commands_string() and commands_list() to invoke more commands */
char *strtwo = "run 10\nrun 20";
if (lammps == 1) lammps_commands_string(lmp,strtwo);
char *cmds[2];
cmds[0] = "run 10";
cmds[1] = "run 20";
if (lammps == 1) lammps_commands_list(lmp,2,cmds);
/* delete all atoms
create_atoms() to create new ones with old coords, vels
initial thermo should be same as step 20 */
int *type = NULL;
if (lammps == 1) {
int natoms = lammps_get_natoms(lmp);
type = (int *) malloc(natoms*sizeof(double));
int i;
for (i = 0; i < natoms; i++) type[i] = 1;
lammps_command(lmp,"delete_atoms group all");
lammps_create_atoms(lmp,natoms,NULL,type,x,v);
lammps_command(lmp,"run 10");
}
if (x) free(x);
if (v) free(v);
if (type) free(type);
// close down LAMMPS
lammps_close(lmp);
/* close down MPI */
if (lammps == 1) MPI_Comm_free(&comm_lammps);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}

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