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lmpspk.cpp
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Sat, Jul 13, 05:42
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rLAMMPS lammps
lmpspk.cpp
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// lmpspk = umbrella driver to couple LAMMPS + SPPARKS
// for a strain-induced grain growth model
// Syntax: lmpspk Niter Ndelta Sfactor in.spparks
// Niter = # of outer iterations
// Ndelta = time to run MC in each iteration
// Sfactor = multiplier on strain effect
// in.spparks = SPPARKS input script
#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "lammps_data_write.h"
#include "many2many.h"
#include "memory.h"
#include "error.h"
#define QUOTE_(x) #x
#define QUOTE(x) QUOTE_(x)
#include "spkpath.h"
#include QUOTE(SPKPATH/src/spparks.h)
#include QUOTE(SPKPATH/src/library.h)
#include QUOTE(SPKPATH/src/input.h)
#include "lmppath.h"
#include QUOTE(LMPPATH/src/lammps.h)
#include QUOTE(LMPPATH/src/library.h)
#include QUOTE(LMPPATH/src/input.h)
#include QUOTE(LMPPATH/src/modify.h)
#include QUOTE(LMPPATH/src/compute.h)
using namespace SPPARKS_NS;
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
int main(int narg, char **arg)
{
int i,n;
char str[128];
// setup MPI
MPI_Init(&narg,&arg);
MPI_Comm comm = MPI_COMM_WORLD;
int me,nprocs;
MPI_Comm_rank(comm,&me);
MPI_Comm_size(comm,&nprocs);
Memory *memory = new Memory(comm);
Error *error = new Error(comm);
// command-line args
if (narg != 5)
error->all("Syntax: lmpspk Niter Ndelta Sfactor in.spparks");
int niter = atoi(arg[1]);
double delta = atof(arg[2]);
double sfactor = atof(arg[3]);
n = strlen(arg[4]) + 1;
char *spparks_input = new char[n];
strcpy(spparks_input,arg[4]);
// instantiate LAMMPS and SPPARKS
SPPARKS *spk = new SPPARKS(0,NULL,MPI_COMM_WORLD);
LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
// create simulation in SPPARKS from in.spparks
spk->input->file(spparks_input);
// extract permanent info from SPPARKS
int dimension,nglobal,nlocal_spparks,nspins;
double boxxlo,boxxhi,boxylo,boxyhi,boxzlo,boxzhi;
int *id_spparks,*spins;
double **xyz;
double *strain;
dimension = *((int *) spparks_extract(spk,"dimension"));
nglobal = *((int *) spparks_extract(spk,"nglobal"));
nlocal_spparks = *((int *) spparks_extract(spk,"nlocal"));
boxxlo = *((double *) spparks_extract(spk,"boxxlo"));
boxxhi = *((double *) spparks_extract(spk,"boxxhi"));
boxylo = *((double *) spparks_extract(spk,"boxylo"));
boxyhi = *((double *) spparks_extract(spk,"boxyhi"));
if (dimension == 3) {
boxzlo = *((double *) spparks_extract(spk,"boxzlo"));
boxzhi = *((double *) spparks_extract(spk,"boxzhi"));
} else {
boxzlo = -0.5;
boxzhi = 0.5;
}
id_spparks = (int *) spparks_extract(spk,"id");
spins = (int *) spparks_extract(spk,"site");
xyz = (double **) spparks_extract(spk,"xyz");
nspins = *((int *) spparks_extract(spk,"nspins"));
strain = (double *) spparks_extract(spk,"strain");
// write a LAMMPS input script using SPPARKS params
if (me == 0) {
FILE *fp = fopen("in.lammps","w");
if (fp == NULL) error->one("Could not create LAMMPS input script");
fprintf(fp,"units lj\n");
sprintf(str,"dimension %d\n",dimension);
fprintf(fp,str);
fprintf(fp,"atom_style atomic\n\n");
fprintf(fp,"read_data data.lammps\n");
fprintf(fp,"mass * 1.0\n\n");
fprintf(fp,"pair_style lj/cut 2.5\n");
fprintf(fp,"pair_coeff * * 1.0 1.2\n");
for (i = 0; i < nspins; i++) {
sprintf(str,"pair_coeff %d %d 1.0 1.0\n",i+1,i+1);
fprintf(fp,str);
}
fprintf(fp,"\n");
fprintf(fp,"compute da all displace/atom\n\n");
fprintf(fp,"dump 1 all atom 10 dump.md\n");
fprintf(fp,"thermo 1\n");
fclose(fp);
}
// write a LAMMPS data file using SPPARKS data
LAMMPSDataWrite *lwd = new LAMMPSDataWrite(MPI_COMM_WORLD);
lwd->file("data.lammps");
lwd->header("%d atoms",nglobal);
lwd->header("%d atom types",nspins);
lwd->header("%g %g xlo xhi",boxxlo,boxxhi);
lwd->header("%g %g ylo yhi",boxylo,boxyhi);
lwd->header("%g %g zlo zhi",boxzlo,boxzhi);
lwd->atoms(nlocal_spparks);
lwd->atoms(id_spparks);
lwd->atoms(spins);
lwd->atoms(3,xyz);
lwd->execute();
delete lwd;
// create simulation in LAMMPS from created input script
lmp->input->file("in.lammps");
// create transfer operators
Many2Many *spk2lmp = new Many2Many(MPI_COMM_WORLD);
Many2Many *lmp2spk = new Many2Many(MPI_COMM_WORLD);
// timestep loop
// run SPPARKS for delta time
// use SPPARKS spins to reset LAMMPS atom types
// perform LAMMPS minimization
// use atom displacements to reset strain values in SPPARKS
// realloc displace as necessary since nlocal_lammps may change
// re-create both xfers every iteration since LAMMPS may migrate atoms
int nmax = 0;
double *displace = NULL;
int nlocal_lammps;
int *id_lammps,*type;
double **displace_lammps;
for (int iter = 0; iter < niter; iter++) {
sprintf(str,"run %g",delta);
spk->input->one(str);
nlocal_lammps = *((int *) lammps_extract_global(lmp,"nlocal"));
id_lammps = (int *) lammps_extract_atom(lmp,"id");
type = (int *) lammps_extract_atom(lmp,"type");
spk2lmp->setup(nlocal_spparks,id_spparks,nlocal_lammps,id_lammps);
spk2lmp->exchange(spins,type);
lmp->input->one("minimize 0.001 0.001 10 1000");
nlocal_lammps = *((int *) lammps_extract_global(lmp,"nlocal"));
id_lammps = (int *) lammps_extract_atom(lmp,"id");
displace_lammps = (double **) lammps_extract_compute(lmp,"da",1,2);
if (nlocal_lammps > nmax) {
memory->sfree(displace);
nmax = nlocal_lammps;
displace = (double *)
memory->smalloc(nmax*sizeof(double),"lmpspk:displace");
}
for (i = 0; i < nlocal_lammps; i++)
displace[i] = sfactor*displace_lammps[i][3];
lmp2spk->setup(nlocal_lammps,id_lammps,nlocal_spparks,id_spparks);
lmp2spk->exchange(displace,strain);
}
memory->sfree(displace);
// clean up
delete spk2lmp;
delete lmp2spk;
delete spk;
delete lmp;
delete [] spparks_input;
delete memory;
delete error;
MPI_Finalize();
}
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