tx258/lammps-gran-kokkos
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

basic feature complete version of lj melt example with python interaction function

Browse Source
This commit is contained in:
Axel Kohlmeyer
2017-05-15 00:15:41 -04:00
parent f484ab6dfb
commit 6e113c1eaf
2 changed files with 133 additions and 18 deletions
Download Patch File Download Diff File Expand all files Collapse all files

150
src/PYTHON/pair_python.cpp
View File

@ -30,6 +30,22 @@
using namespace LAMMPS_NS;
// Wrap API changes between Python 2 and 3 using macros
#if PY_MAJOR_VERSION == 2
#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)
#define PY_STRING_AS_STRING(X) PyString_AsString(X)
#elif PY_MAJOR_VERSION == 3
#define PY_INT_FROM_LONG(X) PyLong_FromLong(X)
#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)
#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
#endif
/* ---------------------------------------------------------------------- */
PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
@ -78,6 +94,48 @@ void PairPython::compute(int eflag, int vflag)
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++) {
@ -89,6 +147,9 @@ void PairPython::compute(int eflag, int vflag)
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)];
@ -100,12 +161,20 @@ void PairPython::compute(int eflag, int vflag)
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
py_jtype = PY_INT_FROM_LONG(jtype);
PyTuple_SetItem(py_compute_args,2,py_jtype);
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;
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)/rsq;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
@ -117,17 +186,19 @@ void PairPython::compute(int eflag, int vflag)
}
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;
}
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();
}
/* ----------------------------------------------------------------------
@ -177,30 +248,72 @@ void PairPython::coeff(int narg, char **arg)
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// check if potential python file exists
// check if python potential file exists and source it
FILE *fp = fopen(arg[2],"r");
if (fp == NULL)
error->all(FLERR,"Cannot open python pair potential class file");
PyGILState_STATE gstate = PyGILState_Ensure();
int err = PyRun_SimpleFile(fp,arg[2]);
if (err) {
PyGILState_Release(gstate);
error->all(FLERR,"Loading python pair style class failure");
}
fclose(fp);
// create LAMMPS atom type to potential file type mapping in python class
// by calling 'lammps_pair_style.map_coeff(name,type)'
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");
PyObject *py_pair_instance = PyObject_GetAttrString(pModule,"lammps_pair_style");
if (!py_pair_instance) {
PyErr_Print();
PyErr_Clear();
PyGILState_Release(gstate);
error->all(FLERR,"Could not find 'lammps_pair_style instance'");
}
py_potential = (void *) py_pair_instance; // XXX do we need to increment reference counter?
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");
}
PyObject *py_type, *py_name, *py_value;
for (int i = 1; i <= ntypes ; i++) {
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++) {
if (strcmp(arg[2+i],"NULL") != 0) {
setflag[i][j] = 1;
@ -208,6 +321,7 @@ void PairPython::coeff(int narg, char **arg)
}
}
}
Py_DECREF(py_map_args);
PyGILState_Release(gstate);
}

1
src/PYTHON/pair_python.h
View File

@ -45,6 +45,7 @@ class PairPython : public Pair {
protected:
double cut_global;
void * py_potential;
virtual void allocate();
};