Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/couple/lammps_quest/lmpqst.cpp
b956107fc6f1lammps-icms

Last Change
Raw File

lmpqst.cpp
View Options

// lmpqst = umbrella driver to couple LAMMPS + Quest
// for MD using quantum forces
// Syntax: lmpqst Niter in.lammps in.quest
// Niter = # of MD iterations
// in.lammps = LAMMPS input script
// in.quest = Quest input script
#include "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "many2one.h"
#include "one2many.h"
#include "files.h"
#include "memory.h"
#include "error.h"
#define QUOTE_(x) #x
#define QUOTE(x) QUOTE_(x)
#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/fix.h)
#include QUOTE(LMPPATH/src/fix_external.h)
#include "qstexe.h"
using namespace LAMMPS_NS;
#define ANGSTROM_per_BOHR 0.529
#define EV_per_RYDBERG 13.6056923
void quest_callback(void *, int, int, int *, double **, double **);
struct Info {
int me;
Memory *memory;
LAMMPS *lmp;
char *quest_input;
};
/* ---------------------------------------------------------------------- */
int main(int narg, char **arg)
{
int 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 != 4) error->all("Syntax: lmpqst Niter in.lammps in.quest");
int niter = atoi(arg[1]);
n = strlen(arg[2]) + 1;
char *lammps_input = new char[n];
strcpy(lammps_input,arg[2]);
n = strlen(arg[3]) + 1;
char *quest_input = new char[n];
strcpy(quest_input,arg[3]);
// instantiate LAMMPS
LAMMPS *lmp = new LAMMPS(0,NULL,MPI_COMM_WORLD);
// create simulation in LAMMPS from in.lammps
lmp->input->file(lammps_input);
// make info avaiable to callback function
Info info;
info.me = me;
info.memory = memory;
info.lmp = lmp;
info.quest_input = quest_input;
// set callback to Quest inside fix external
int ifix = lmp->modify->find_fix("2");
FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix];
fix->set_callback(quest_callback,&info);
// run LAMMPS for Niter
// each time it needs forces, it will invoke quest_callback
sprintf(str,"run %d",niter);
lmp->input->one(str);
// clean up
delete lmp;
delete memory;
delete error;
delete [] lammps_input;
delete [] quest_input;
MPI_Finalize();
}
/* ----------------------------------------------------------------------
callback to Quest with atom IDs and coords from each proc
invoke Quest to compute forces, load them into f for LAMMPS to use
f can be NULL if proc owns no atoms
------------------------------------------------------------------------- */
void quest_callback(void *ptr, int ntimestep, int nlocal,
int *id, double **x, double **f)
{
int i,j;
char str[128];
Info *info = (Info *) ptr;
// boxlines = LAMMPS box size converted into Quest lattice vectors
char **boxlines = NULL;
if (info->me == 0) {
boxlines = new char*[3];
for (i = 0; i < 3; i++) boxlines[i] = new char[128];
}
double boxxlo = *((double *) lammps_extract_global(info->lmp,"boxxlo"));
double boxxhi = *((double *) lammps_extract_global(info->lmp,"boxxhi"));
double boxylo = *((double *) lammps_extract_global(info->lmp,"boxylo"));
double boxyhi = *((double *) lammps_extract_global(info->lmp,"boxyhi"));
double boxzlo = *((double *) lammps_extract_global(info->lmp,"boxzlo"));
double boxzhi = *((double *) lammps_extract_global(info->lmp,"boxzhi"));
double xprd = (boxxhi-boxxlo)/ANGSTROM_per_BOHR;
double yprd = (boxyhi-boxylo)/ANGSTROM_per_BOHR;
double zprd = (boxzhi-boxzlo)/ANGSTROM_per_BOHR;
if (info->me == 0) {
sprintf(boxlines[0],"%g %g %g\n",xprd,0.0,0.0);
sprintf(boxlines[1],"%g %g %g\n",0.0,yprd,0.0);
sprintf(boxlines[2],"%g %g %g\n",0.0,0.0,zprd);
}
// xlines = x for atoms on each proc converted to text lines
// xlines is suitable for insertion into Quest input file
// convert LAMMPS Angstroms to Quest bohr
int natoms;
MPI_Allreduce(&nlocal,&natoms,1,MPI_INT,MPI_SUM,MPI_COMM_WORLD);
Many2One *lmp2qst = new Many2One(MPI_COMM_WORLD);
lmp2qst->setup(nlocal,id,natoms);
char **xlines = NULL;
double **xquest = NULL;
if (info->me == 0) {
xquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:xquest");
xlines = new char*[natoms];
for (i = 0; i < natoms; i++) xlines[i] = new char[128];
}
if (info->me == 0) lmp2qst->gather(&x[0][0],3,&xquest[0][0]);
else lmp2qst->gather(&x[0][0],3,NULL);
if (info->me == 0) {
for (i = 0; i < natoms; i++) {
xquest[i][0] /= ANGSTROM_per_BOHR;
xquest[i][1] /= ANGSTROM_per_BOHR;
xquest[i][2] /= ANGSTROM_per_BOHR;
}
for (i = 0; i < natoms; i++) {
sprintf(xlines[i],"%d %d %g %g %g\n",i+1,1,
xquest[i][0],xquest[i][1],xquest[i][2]);
}
}
// one-processor tasks:
// whack all lcao.* files
// cp quest_input to lcao.in
// replace atom coords section of lcao.in with new atom coords
// run Quest on one proc, save screen output to file
// flines = atom forces extracted from Quest screen file
// fquest = atom forces
// convert Quest Ryd/bohr to LAMMPS eV/Angstrom
char **flines = NULL;
double **fquest = NULL;
if (info->me == 0) {
fquest = info->memory->create_2d_double_array(natoms,3,"lmpqst:fquest");
flines = new char*[natoms];
for (i = 0; i < natoms; i++) flines[i] = new char[128];
}
if (info->me == 0) {
system("rm lcao.*");
sprintf(str,"cp %s lcao.in",info->quest_input);
system(str);
sprintf(str,"cp %s lcao.x",QUOTE(QUEST));
system(str);
replace("lcao.in","primitive lattice vectors",3,boxlines);
replace("lcao.in","atom, type, position vector",natoms,xlines);
system("lcao.x > lcao.screen");
extract("lcao.screen","atom x force "
"y force z force",natoms,flines);
int itmp;
for (i = 0; i < natoms; i++)
sscanf(flines[i],"%d %lg %lg %lg",&itmp,
&fquest[i][0],&fquest[i][1],&fquest[i][2]);
for (i = 0; i < natoms; i++) {
fquest[i][0] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
fquest[i][1] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
fquest[i][2] *= EV_per_RYDBERG / ANGSTROM_per_BOHR;
}
}
// convert fquest on one proc into f for atoms on each proc
One2Many *qst2lmp = new One2Many(MPI_COMM_WORLD);
qst2lmp->setup(natoms,nlocal,id);
double *fvec = NULL;
if (f) fvec = &f[0][0];
if (info->me == 0) qst2lmp->scatter(&fquest[0][0],3,fvec);
else qst2lmp->scatter(NULL,3,fvec);
// clean up
// some data only exists on proc 0
delete lmp2qst;
delete qst2lmp;
info->memory->destroy_2d_double_array(xquest);
info->memory->destroy_2d_double_array(fquest);
if (boxlines) {
for (i = 0; i < 3; i++) delete [] boxlines[i];
delete [] boxlines;
}
if (xlines) {
for (i = 0; i < natoms; i++) delete [] xlines[i];
delete [] xlines;
}
if (flines) {
for (i = 0; i < natoms; i++) delete [] flines[i];
delete [] flines;
}
}
c4science · Help