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pair_python.cpp
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Thu, Jul 3, 08:06

pair_python.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 and Richard Berger (Temple U)
------------------------------------------------------------------------- */
#include <Python.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_python.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "python.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
respa_enable = 0;
single_enable = 0;
writedata = 0;
restartinfo = 0;
one_coeff = 1;
reinitflag = 0;
python->init();
}
/* ---------------------------------------------------------------------- */
PairPython::~PairPython()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
}
}
/* ---------------------------------------------------------------------- */
void PairPython::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
const double r = sqrt(rsq);
printf("compute f at r=%g for types %d,%d with factor %g\n",
r,itype,jtype,factor_lj);
fpair = 0.0;
fpair *= factor_lj;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
printf("compute e at r=%g for types %d,%d with factor %g\n",
r,itype,jtype,factor_lj);
evdwl = 0.0;
evdwl *= factor_lj;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPython::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPython::settings(int narg, char **arg)
{
if (narg != 1)
error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
}
/* ----------------------------------------------------------------------
set coeffs for all type pairs
------------------------------------------------------------------------- */
void PairPython::coeff(int narg, char **arg)
{
const int ntypes = atom->ntypes;
if (narg != 3+ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
// make sure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// check if potential python file exists
FILE *fp = fopen(arg[2],"r");
if (fp == NULL)
error->all(FLERR,"Cannot open python pair potential class file");
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *pModule = PyImport_AddModule("__main__");
if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
int err = PyRun_SimpleFile(fp,arg[2]);
if (err) error->all(FLERR,"Loading python pair style class failure");
fclose(fp);
PyObject *py_pair_instance =
PyObject_GetAttrString(pModule,"lammps_pair_style");
if (!py_pair_instance) {
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'lammps_pair_style instance'");
}
for (int i = 1; i <= ntypes ; i++) {
for (int j = i; j <= ntypes ; j++) {
if (strcmp(arg[2+i],"NULL") != 0) {
setflag[i][j] = 1;
cutsq[i][j] = cut_global*cut_global;
}
}
}
PyGILState_Release(gstate);
}
/* ---------------------------------------------------------------------- */
double PairPython::init_one(int, int)
{
return cut_global;
}

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