Rename fix python/integrate to python/move

This is to avoid confusion to what LAMMPS considers to be an
integrator like Verlet and RESPA.

src/PYTHON/fix_python_move.cpp

@@ -0,0 +1,239 @@
+/* ----------------------------------------------------------------------
+   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 author: Richard Berger (Temple U)
+------------------------------------------------------------------------- */
+
+#include <Python.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "fix_python_move.h"
+#include "atom.h"
+#include "comm.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+#include "python.h"
+#include "error.h"
+#include "python_compat.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+/* ---------------------------------------------------------------------- */
+
+FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
+  Fix(lmp, narg, arg)
+{
+  dynamic_group_allow = 1;
+  time_integrate = 1;
+
+  python->init();
+
+  py_integrator = NULL;
+
+  PyGILState_STATE gstate = PyGILState_Ensure();
+
+  // add current directory to PYTHONPATH
+  PyObject * py_path = PySys_GetObject("path");
+  PyList_Append(py_path, PY_STRING_FROM_STRING("."));
+
+
+  // create integrator instance
+  char * full_cls_name = arg[3];
+  char * lastpos = strrchr(full_cls_name, '.');
+
+  if (lastpos == NULL) {
+    error->all(FLERR,"Fix python/integrate 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);
+
+  PyObject * pModule = PyImport_ImportModule(module_name);
+  if (!pModule) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Loading python integrator 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_integrator_type = PyObject_GetAttrString(pModule, cls_name);
+  if (!py_integrator_type) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find integrator class in module'");
+  }
+
+  delete [] module_name;
+  delete [] cls_name;
+
+  PyObject * ptr = PY_VOID_POINTER(lmp);
+  PyObject * arglist = Py_BuildValue("(O)", ptr);
+  PyObject * py_integrator_obj = PyObject_CallObject(py_integrator_type, arglist);
+  Py_DECREF(arglist);
+
+  if (!py_integrator_obj) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not instantiate instance of integrator class'");
+  }
+
+  // check object interface
+  py_integrator = (void *) py_integrator_obj;
+
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixPythonMove::~FixPythonMove()
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  if(py_integrator) Py_DECREF((PyObject*) py_integrator);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixPythonMove::setmask()
+{
+  int mask = 0;
+  mask |= INITIAL_INTEGRATE;
+  mask |= FINAL_INTEGRATE;
+  mask |= INITIAL_INTEGRATE_RESPA;
+  mask |= FINAL_INTEGRATE_RESPA;
+  return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::init()
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_init = PyObject_GetAttrString(py_integrator_obj,"init");
+  if (!py_init) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'init' method'");
+  }
+  PyObject * result = PyEval_CallObject(py_init, NULL);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::initial_integrate(int vflag)
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_initial_integrate = PyObject_GetAttrString(py_integrator_obj,"initial_integrate");
+  if (!py_initial_integrate) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'initial_integrate' method'");
+  }
+  PyObject * arglist = Py_BuildValue("(i)", vflag);
+  PyObject * result = PyEval_CallObject(py_initial_integrate, arglist);
+  Py_DECREF(arglist);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::final_integrate()
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_final_integrate = PyObject_GetAttrString(py_integrator_obj,"final_integrate");
+  if (!py_final_integrate) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'final_integrate' method'");
+  }
+  PyObject * result = PyEval_CallObject(py_final_integrate, NULL);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_initial_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"initial_integrate_respa");
+  if (!py_initial_integrate_respa) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'initial_integrate_respa' method'");
+  }
+  PyObject * arglist = Py_BuildValue("(iii)", vflag, ilevel, iloop);
+  PyObject * result = PyEval_CallObject(py_initial_integrate_respa, arglist);
+  Py_DECREF(arglist);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_final_integrate_respa = PyObject_GetAttrString(py_integrator_obj,"final_integrate_respa");
+  if (!py_final_integrate_respa) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'final_integrate_respa' method'");
+  }
+  PyObject * arglist = Py_BuildValue("(ii)", ilevel, iloop);
+  PyObject * result = PyEval_CallObject(py_final_integrate_respa, arglist);
+  Py_DECREF(arglist);
+  PyGILState_Release(gstate);
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixPythonMove::reset_dt()
+{
+  PyGILState_STATE gstate = PyGILState_Ensure();
+  PyObject *py_integrator_obj = (PyObject *) py_integrator;
+  PyObject *py_reset_dt = PyObject_GetAttrString(py_integrator_obj,"reset_dt");
+  if (!py_reset_dt) {
+    PyErr_Print();
+    PyErr_Clear();
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find 'reset_dt' method'");
+  }
+  PyObject * result = PyEval_CallObject(py_reset_dt, NULL);
+  PyGILState_Release(gstate);
+}