Refactor PYTHON package and wrapper classes

/pppm_tip4p_cg.h

/prd.cpp

/prd.h

/python.cpp

/python.h

/python_impl.cpp

/python_impl.h

/reader_molfile.cpp

/reader_molfile.h

/reaxc_allocate.cpp

  fi

}

# force rebuild of files with LMP_KOKKOS switch

# also variable so its *.d dependence on changed python_wrapper.h is rebuilt

# force rebuild of files using python header

touch ../python_wrapper.h

touch ../variable.cpp

touch ../python.h

# all package files with no dependencies

for file in *.cpp *.h; do

  test -f ${file} && action $file

  action $file

done

# edit 2 Makefile.package files to include/exclude package info

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

Python::Python(LAMMPS *lmp) : Pointers(lmp)

PythonImpl::PythonImpl(LAMMPS *lmp) : Pointers(lmp)

{

  python_exists = 1;

  pyMain = NULL;

  // pfuncs stores interface info for each Python function

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

Python::~Python()

PythonImpl::~PythonImpl()

{

  // clean up

  PyGILState_STATE gstate = PyGILState_Ensure();

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

void Python::command(int narg, char **arg)

void PythonImpl::command(int narg, char **arg)

{

  if (narg < 2) error->all(FLERR,"Invalid python command");

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

void Python::invoke_function(int ifunc, char *result)

void PythonImpl::invoke_function(int ifunc, char *result)

{

  PyGILState_STATE gstate = PyGILState_Ensure();

  PyObject *pValue;

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

int Python::find(char *name)

int PythonImpl::find(char *name)

{

  for (int i = 0; i < nfunc; i++)

    if (strcmp(name,pfuncs[i].name) == 0) return i;

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

int Python::variable_match(char *name, char *varname, int numeric)

int PythonImpl::variable_match(char *name, char *varname, int numeric)

{

  int ifunc = find(name);

  if (ifunc < 0) return -1;

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

char *Python::long_string(int ifunc)

char *PythonImpl::long_string(int ifunc)

{

  return pfuncs[ifunc].longstr;

}

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

int Python::create_entry(char *name)

int PythonImpl::create_entry(char *name)

{

  // ifunc = index to entry by name in pfuncs vector, can be old or new

  // free old vectors if overwriting old pfunc

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

void Python::deallocate(int i)

void PythonImpl::deallocate(int i)

{

  delete [] pfuncs[i].itype;

  delete [] pfuncs[i].ivarflag;

/* -*- 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.

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

#ifndef LMP_PYTHON_IMPL_H

#define LMP_PYTHON_IMPL_H

#include "pointers.h"

namespace LAMMPS_NS {

class PythonImpl : protected Pointers, public PythonInterface {

 public:

  bool external_interpreter;

  PythonImpl(class LAMMPS *);

  ~PythonImpl();

  void command(int, char **);

  void invoke_function(int, char *);

  int find(char *);

  int variable_match(char *, char *, int);

  char *long_string(int);

 private:

  int ninput,noutput,length_longstr;

  char **istr;

  char *ostr,*format;

  void *pyMain;

  struct PyFunc {

    char *name;

    int ninput,noutput;

    int *itype,*ivarflag;

    int *ivalue;

    double *dvalue;

    char **svalue;

    int otype;

    char *ovarname;

    char *longstr;

    int length_longstr;

    void *pFunc;

  };

  PyFunc *pfuncs;

  int nfunc;

  int create_entry(char *);

  void deallocate(int);

};

}

#endif

/* ERROR/WARNING messages:

E: Invalid python 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.

E: Python invoke of undefined function

Cannot invoke a function that has not been previously defined.

E: Python variable does not match Python function

This matching is defined by the python-style variable and the python

command.

E: Cannot embed Python when also extending Python with LAMMPS

When running LAMMPS via Python through the LAMMPS library interface

you cannot also user the input script python command.

E: Could not initialize embedded Python

The main module in Python was not accessible.

E: Could not open Python file

The specified file of Python code cannot be opened.  Check that the

path and name are correct.

E: Could not process Python file

The Python code in the specified file was not run successfully by

Python, probably due to errors in the Python code.

E: Could not process Python string

The Python code in the here string was not run successfully by Python,

probably due to errors in the Python code.

E: Could not find Python function

The provided Python code was run successfully, but it not

define a callable function with the required name.

E: Python function is not callable

The provided Python code was run successfully, but it not

define a callable function with the required name.

E: Could not create Python function arguments

This is an internal Python error, possibly because the number

of inputs to the function is too large.

E: Could not evaluate Python function input variable

Self-explanatory.

E: Python function evaluation failed

The Python function did not run successfully and/or did not return a

value (if it is supposed to return a value).  This is probably due to

some error condition in the function.

*/

#include "accelerator_kokkos.h"

#include "accelerator_omp.h"

#include "timer.h"

#include "python.h"

#include "memory.h"

#include "version.h"

#include "error.h"

  error = new Error(this);

  universe = new Universe(this,communicator);

  output = NULL;

  python = NULL;

  screen = NULL;

  logfile = NULL;

  if (world != universe->uworld) MPI_Comm_free(&world);

  delete python;

  delete kokkos;

  delete [] suffix;

  delete [] suffix2;

                              // must be after modify so can create Computes

  update = new Update(this);  // must be after output, force, neighbor

  timer = new Timer(this);

  python = new Python(this);

}

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

  delete timer;

  timer = NULL;

  delete python;

  python = NULL;

}

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