Implement fix python mentioned in issue #454

# 3d Lennard-Jones melt

units		lj

atom_style	atomic

lattice		fcc 0.8442

region		box block 0 10 0 10 0 10

create_box	1 box

create_atoms	1 box

mass		1 1.0

velocity	all create 3.0 87287

pair_style	lj/cut 2.5

pair_coeff	1 1 1.0 1.0 2.5

neighbor	0.3 bin

neigh_modify	every 20 delay 0 check no

python         end_of_step_callback here """

from __future__ import print_function

from lammps import lammps

def end_of_step_callback(lmp):

  L = lammps(ptr=lmp)

  t = L.extract_global("ntimestep", 0)

  print("### END OF STEP ###", t)

def post_force_callback(lmp, v):

  L = lammps(ptr=lmp)

  t = L.extract_global("ntimestep", 0)

  print("### POST_FORCE ###", t)

"""

fix		1 all nve

fix     2 all python end_of_step end_of_step_callback

fix     3 all python post_force post_force_callback

#dump		id all atom 50 dump.melt

#dump		2 all image 25 image.*.jpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	2 pad 3

#dump		3 all movie 25 movie.mpg type type &

#		axes yes 0.8 0.02 view 60 -30

#dump_modify	3 pad 3

thermo		50

run		250

/prd.h

/python_impl.cpp

/python_impl.h

/fix_python.cpp

/fix_python.h

/reader_molfile.cpp

/reader_molfile.h

/reaxc_allocate.cpp

/* ----------------------------------------------------------------------

   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.

------------------------------------------------------------------------- */

#include <stdio.h>

#include <string.h>

#include "fix_python.h"

#include "atom.h"

#include "force.h"

#include "update.h"

#include "respa.h"

#include "error.h"

#include "python.h"

using namespace LAMMPS_NS;

using namespace FixConst;

// Wrap API changes between Python 2 and 3 using macros

#if PY_MAJOR_VERSION == 2

#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)

#elif PY_MAJOR_VERSION == 3

#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)

#endif

/* ---------------------------------------------------------------------- */

FixPython::FixPython(LAMMPS *lmp, int narg, char **arg) :

  Fix(lmp, narg, arg)

{

  if (narg != 5) error->all(FLERR,"Illegal fix python command");

  // ensure Python interpreter is initialized

  python->init();

  if (strcmp(arg[3],"post_force") == 0) {

    selected_callback = POST_FORCE;

  } else if (strcmp(arg[3],"end_of_step") == 0) {

    selected_callback = END_OF_STEP;

  }

  // get Python function

  PyGILState_STATE gstate = PyGILState_Ensure();

  PyObject * pyMain = PyImport_AddModule("__main__");

  if (!pyMain) {

    PyGILState_Release(gstate);

    error->all(FLERR,"Could not initialize embedded Python");

  }

  char * fname = arg[4];

  pFunc = PyObject_GetAttrString(pyMain, fname);

  if (!pFunc) {

    PyGILState_Release(gstate);

    error->all(FLERR,"Could not find Python function");

  }

  PyGILState_Release(gstate);

}

/* ---------------------------------------------------------------------- */

int FixPython::setmask()

{

  return selected_callback;

}

/* ---------------------------------------------------------------------- */

void FixPython::end_of_step()

{

  PyGILState_STATE gstate = PyGILState_Ensure();

  PyObject * ptr = PY_VOID_POINTER(lmp);

  PyObject * arglist = Py_BuildValue("(O)", ptr);

  PyObject * result = PyEval_CallObject(pFunc, arglist);

  Py_DECREF(arglist);

  PyGILState_Release(gstate);

}

/* ---------------------------------------------------------------------- */

void FixPython::post_force(int vflag)

{

  PyGILState_STATE gstate = PyGILState_Ensure();

  PyObject * ptr = PY_VOID_POINTER(lmp);

  PyObject * arglist = Py_BuildValue("(Oi)", ptr, vflag);

  PyObject * result = PyEval_CallObject(pFunc, arglist);

  Py_DECREF(arglist);

  PyGILState_Release(gstate);

}

/* -*- c++ -*- ----------------------------------------------------------

   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.

------------------------------------------------------------------------- */

#ifdef FIX_CLASS

FixStyle(python,FixPython)

#else

#ifndef LMP_FIX_PYTHON_H

#define LMP_FIX_PYTHON_H

#include "fix.h"

#include <Python.h>

namespace LAMMPS_NS {

class FixPython : public Fix {

 public:

  FixPython(class LAMMPS *, int, char **);

  virtual ~FixPython() {}

  int setmask();

  virtual void end_of_step();

  virtual void post_force(int);

 private:

  PyObject * pFunc;

  int selected_callback;

};

}

#endif

#endif

/* ERROR/WARNING messages:

E: Illegal ... command

Self-explanatory.  Check the input script syntax and compare to the

documentation for the command.  You can use -echo screen as a

command-line option when running LAMMPS to see the offending line.

*/