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Thu, May 23, 08:47

simple.cpp
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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: simpleCC 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 "lammps.h" // these are LAMMPS include files
#include "input.h"
#include "atom.h"
#include "library.h"
using namespace LAMMPS_NS;
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: simpleCC 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 input->one() on the line
LAMMPS *lmp = NULL;
if (lammps == 1) lmp = new LAMMPS(0,NULL,comm_lammps);
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) {
lmp->input->one("run 10");
int natoms = static_cast<int> (lmp->atom->natoms);
x = new double[3*natoms];
v = new double[3*natoms];
lammps_gather_atoms(lmp,"x",1,3,x);
lammps_gather_atoms(lmp,"v",1,3,v);
double epsilon = 0.1;
x[0] += epsilon;
lammps_scatter_atoms(lmp,"x",1,3,x);
// these 2 lines are the same
// lammps_command(lmp,"run 1");
lmp->input->one("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 = static_cast<int> (lmp->atom->natoms);
type = new int[natoms];
for (int i = 0; i < natoms; i++) type[i] = 1;
lmp->input->one("delete_atoms group all");
lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0);
lmp->input->one("run 10");
}
delete [] x;
delete [] v;
delete [] type;
// close down LAMMPS
delete lmp;
// close down MPI
if (lammps == 1) MPI_Comm_free(&comm_lammps);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Finalize();
}

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