Implement fix python mentioned in issue #454

Allows to call a python function at defined points in the integration loop

examples/python/in.fix_python

@@ -0,0 +1,50 @@
+# 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

src/.gitignore

@@ -850,6 +850,8 @@
 /prd.h
 /python_impl.cpp
 /python_impl.h
+/fix_python.cpp
+/fix_python.h
 /reader_molfile.cpp
 /reader_molfile.h
 /reaxc_allocate.cpp

src/PYTHON/fix_python.cpp

@@ -0,0 +1,106 @@
+/* ----------------------------------------------------------------------
+   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);
+}

src/PYTHON/fix_python.h

@@ -0,0 +1,54 @@
+/* -*- 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.
+
+*/