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lammps/src/PYTHON/pair_python.cpp
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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 authors: 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 "update.h"
#include "neigh_list.h"
#include "python.h"
#include "error.h"
#include "python_compat.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
respa_enable = 0;
single_enable = 1;
writedata = 0;
restartinfo = 0;
one_coeff = 1;
reinitflag = 0;
cut_global = 0.0;
py_potential = NULL;
skip_types = NULL;
python->init();
// add current directory to PYTHONPATH
PyObject * py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
const char * potentials_path = getenv("LAMMPS_POTENTIALS");
if (potentials_path != NULL) {
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
}
}
/* ---------------------------------------------------------------------- */
PairPython::~PairPython()
{
if (py_potential) Py_DECREF((PyObject*) py_potential);
delete[] skip_types;
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;
// prepare access to compute_force and compute_energy functions
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *py_pair_instance = (PyObject *) py_potential;
PyObject *py_compute_force = PyObject_GetAttrString(py_pair_instance,"compute_force");
if (!py_compute_force) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'compute_force' method'");
}
if (!PyCallable_Check(py_compute_force)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'compute_force' is not callable");
}
PyObject *py_compute_energy = PyObject_GetAttrString(py_pair_instance,"compute_energy");
if (!py_compute_energy) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'compute_energy' method'");
}
if (!PyCallable_Check(py_compute_energy)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'compute_energy' is not callable");
}
PyObject *py_compute_args = PyTuple_New(3);
if (!py_compute_args) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
}
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
// 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];
py_itype = PY_INT_FROM_LONG(itype);
PyTuple_SetItem(py_compute_args,1,py_itype);
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];
// with hybrid/overlay we might get called for skipped types
if (skip_types[itype] || skip_types[jtype]) continue;
py_jtype = PY_INT_FROM_LONG(jtype);
PyTuple_SetItem(py_compute_args,2,py_jtype);
if (rsq < cutsq[itype][jtype]) {
py_rsq = PyFloat_FromDouble(rsq);
PyTuple_SetItem(py_compute_args,0,py_rsq);
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
if (!py_value) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Calling 'compute_force' function failed");
}
fpair = factor_lj*PyFloat_AsDouble(py_value);
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) {
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
evdwl = factor_lj*PyFloat_AsDouble(py_value);
} else evdwl = 0.0;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
Py_DECREF(py_compute_args);
PyGILState_Release(gstate);
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
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 python potential file exists and source it
char * full_cls_name = arg[2];
char * lastpos = strrchr(full_cls_name, '.');
if (lastpos == NULL) {
error->all(FLERR,"Python pair style requires fully qualified class name");
}
size_t module_name_length = strlen(full_cls_name) - strlen(lastpos);
size_t cls_name_length = strlen(lastpos)-1;
char * module_name = new char[module_name_length+1];
char * cls_name = new char[cls_name_length+1];
strncpy(module_name, full_cls_name, module_name_length);
module_name[module_name_length] = 0;
strcpy(cls_name, lastpos+1);
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject * pModule = PyImport_ImportModule(module_name);
if (!pModule) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Loading python pair style module failure");
}
// create LAMMPS atom type to potential file type mapping in python class
// by calling 'lammps_pair_style.map_coeff(name,type)'
PyObject *py_pair_type = PyObject_GetAttrString(pModule, cls_name);
if (!py_pair_type) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find pair style class in module'");
}
delete [] module_name;
delete [] cls_name;
PyObject * py_pair_instance = PyObject_CallObject(py_pair_type, NULL);
if (!py_pair_instance) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not instantiate instance of pair style class'");
}
py_potential = (void *) py_pair_instance;
PyObject *py_check_units = PyObject_GetAttrString(py_pair_instance,"check_units");
if (!py_check_units) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'check_units' method'");
}
if (!PyCallable_Check(py_check_units)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'check_units' is not callable");
}
PyObject *py_units_args = PyTuple_New(1);
if (!py_units_args) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not create tuple for 'check_units' function arguments");
}
PyObject *py_name = PY_STRING_FROM_STRING(update->unit_style);
PyTuple_SetItem(py_units_args,0,py_name);
PyObject *py_value = PyObject_CallObject(py_check_units,py_units_args);
if (!py_value) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Calling 'check_units' function failed");
}
Py_DECREF(py_units_args);
PyObject *py_map_coeff = PyObject_GetAttrString(py_pair_instance,"map_coeff");
if (!py_map_coeff) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'map_coeff' method'");
}
if (!PyCallable_Check(py_map_coeff)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'map_coeff' is not callable");
}
PyObject *py_map_args = PyTuple_New(2);
if (!py_map_args) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not create tuple for 'map_coeff' function arguments");
}
delete[] skip_types;
skip_types = new int[ntypes+1];
skip_types[0] = 1;
for (int i = 1; i <= ntypes ; i++) {
if (strcmp(arg[2+i],"NULL") == 0) {
skip_types[i] = 1;
continue;
} else skip_types[i] = 0;
PyObject *py_type = PY_INT_FROM_LONG(i);
py_name = PY_STRING_FROM_STRING(arg[2+i]);
PyTuple_SetItem(py_map_args,0,py_name);
PyTuple_SetItem(py_map_args,1,py_type);
py_value = PyObject_CallObject(py_map_coeff,py_map_args);
if (!py_value) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Calling 'map_coeff' function failed");
}
for (int j = i; j <= ntypes ; j++) {
setflag[i][j] = 1;
cutsq[i][j] = cut_global*cut_global;
}
}
Py_DECREF(py_map_args);
PyGILState_Release(gstate);
}
/* ---------------------------------------------------------------------- */
double PairPython::init_one(int, int)
{
return cut_global;
}
/* ---------------------------------------------------------------------- */
double PairPython::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
// with hybrid/overlay we might get called for skipped types
if (skip_types[itype] || skip_types[jtype]) {
fforce = 0.0;
return 0.0;
}
// prepare access to compute_force and compute_energy functions
PyGILState_STATE gstate = PyGILState_Ensure();
PyObject *py_pair_instance = (PyObject *) py_potential;
PyObject *py_compute_force
= PyObject_GetAttrString(py_pair_instance,"compute_force");
if (!py_compute_force) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'compute_force' method'");
}
if (!PyCallable_Check(py_compute_force)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'compute_force' is not callable");
}
PyObject *py_compute_energy
= PyObject_GetAttrString(py_pair_instance,"compute_energy");
if (!py_compute_energy) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'compute_energy' method'");
}
if (!PyCallable_Check(py_compute_energy)) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Python 'compute_energy' is not callable");
}
PyObject *py_rsq, *py_itype, *py_jtype, *py_value;
PyObject *py_compute_args = PyTuple_New(3);
if (!py_compute_args) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not create tuple for 'compute' function arguments");
}
py_itype = PY_INT_FROM_LONG(itype);
PyTuple_SetItem(py_compute_args,1,py_itype);
py_jtype = PY_INT_FROM_LONG(jtype);
PyTuple_SetItem(py_compute_args,2,py_jtype);
py_rsq = PyFloat_FromDouble(rsq);
PyTuple_SetItem(py_compute_args,0,py_rsq);
py_value = PyObject_CallObject(py_compute_force,py_compute_args);
if (!py_value) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Calling 'compute_force' function failed");
}
fforce = factor_lj*PyFloat_AsDouble(py_value);
py_value = PyObject_CallObject(py_compute_energy,py_compute_args);
if (!py_value) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Calling 'compute_energy' function failed");
}
double evdwl = factor_lj*PyFloat_AsDouble(py_value);
Py_DECREF(py_compute_args);
PyGILState_Release(gstate);
return evdwl;
}
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