pair_python.cpp
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Created: Fri, Nov 8, 00:52

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 = delxdelx + delydely + 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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