Commit 7caf6cf4 authored by Richard Berger's avatar Richard Berger
Browse files

Change how a Python pair style is loaded 

Implements a class loader which takes a fully qualified Python class
name, loads the module and creates an object instance.

To add flexibility, the current working directory and the
directory specified by the LAMMPS_POTENTIALS environment variable are
added to the module search path.
parent a6f0d700

examples/python/in.pair_python_hybrid

+3 −3
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ mass * 1.0 
velocity	all create 3.0 87287



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python lj-melt-potential.py lj NULL

pair_coeff	* * python potentials.LAMMPSLJCutPotential lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



neighbor	0.3 bin
@@ -31,7 +31,7 @@ clear 
read_restart    hybrid.restart



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python lj-melt-potential.py lj NULL

pair_coeff	* * python potentials.LAMMPSLJCutPotential lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



fix		1 all nve
@@ -47,7 +47,7 @@ atom_style atomic 
read_data       hybrid.data



pair_style	hybrid lj/cut 2.5 python 2.5

pair_coeff	* * python lj-melt-potential.py lj NULL

pair_coeff	* * python potentials.LAMMPSLJCutPotential lj NULL

pair_coeff      * 2 lj/cut 1.0 1.0



neighbor	0.3 bin

examples/python/in.pair_python_melt

+3 −3
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ mass * 1.0 
velocity	all create 3.0 87287



pair_style	python 2.5

pair_coeff	* * lj-melt-potential.py lj

pair_coeff	* * potentials.LAMMPSLJCutPotential lj



neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no
@@ -30,7 +30,7 @@ clear 
read_restart    melt.restart



pair_style	python 2.5

pair_coeff	* * lj-melt-potential.py lj

pair_coeff	* * potentials.LAMMPSLJCutPotential lj



fix		1 all nve
@@ -45,7 +45,7 @@ atom_style atomic 
read_data       melt.data



pair_style	python 2.5

pair_coeff	* * lj-melt-potential.py lj

pair_coeff	* * potentials.LAMMPSLJCutPotential lj



neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

examples/python/lj-melt-potential.py→examples/python/potentials.py

+0 −3
Original line number Diff line number Diff line
@@ -32,6 +32,3 @@ class LAMMPSLJCutPotential(object): 
        lj3 = coeff[4]

        lj4 = coeff[5]

        return (r6inv * (lj3*r6inv - lj4))
 


lammps_pair_style = LAMMPSLJCutPotential()

src/PYTHON/pair_python.cpp

+48 −12
Original line number Diff line number Diff line
@@ -42,12 +42,26 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) { 
  reinitflag = 0;



  python->init();



  py_potential = NULL;



  // add current directory to PYTHONPATH

  PyObject * py_path = PySys_GetObject("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);



  if (allocated) {

    memory->destroy(setflag);

    memory->destroy(cutsq);
@@ -234,34 +248,56 @@ void PairPython::coeff(int narg, char **arg) 
    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;



  FILE *fp = fopen(arg[2],"r");

  if (fp == NULL)

    error->all(FLERR,"Cannot open python pair potential class file");

  strcpy(cls_name, lastpos+1);



  PyGILState_STATE gstate = PyGILState_Ensure();



  int err = PyRun_SimpleFile(fp,arg[2]);

  if (err) {

  PyObject * pModule = PyImport_ImportModule(module_name);

  if (!pModule) {

    PyErr_Print();

    PyErr_Clear();

    PyGILState_Release(gstate);

    error->all(FLERR,"Loading python pair style class failure");

    error->all(FLERR,"Loading python pair style module 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");

  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_GetAttrString(pModule,"lammps_pair_style");

  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 find 'lammps_pair_style instance'");

    error->all(FLERR,"Could not instantiate instance of pair style class'");

  }

  py_potential = (void *) py_pair_instance; // XXX do we need to increment reference counter?



  py_potential = (void *) py_pair_instance;



  PyObject *py_map_coeff = PyObject_GetAttrString(py_pair_instance,"map_coeff");

  if (!py_map_coeff) {

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