Refactor PYTHON package and wrapper classes

src/.gitignore

@@ -846,8 +846,8 @@
 /pppm_tip4p_cg.h
 /prd.cpp
 /prd.h
-/python.cpp
+/python_impl.cpp
-/python.h
+/python_impl.h
 /reader_molfile.cpp
 /reader_molfile.h
 /reaxc_allocate.cpp

src/PYTHON/Install.sh

@@ -26,16 +26,14 @@ action () {
   fi
 }
 
-# force rebuild of files with LMP_KOKKOS switch
+# force rebuild of files using python header
-# also variable so its *.d dependence on changed python_wrapper.h is rebuilt
 
-touch ../python_wrapper.h
+touch ../python.h
-touch ../variable.cpp
 
 # 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

src/PYTHON/python_impl.cpp

@@ -43,10 +43,8 @@ enum{NONE,INT,DOUBLE,STRING,PTR};
 
 /* ---------------------------------------------------------------------- */
 
-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
@@ -59,7 +57,7 @@ Python::Python(LAMMPS *lmp) : Pointers(lmp)
 
 /* ---------------------------------------------------------------------- */
 
-Python::~Python()
+PythonImpl::~PythonImpl()
 {
   // clean up
   PyGILState_STATE gstate = PyGILState_Ensure();
@@ -85,7 +83,7 @@ Python::~Python()
 
 /* ---------------------------------------------------------------------- */
 
-void Python::command(int narg, char **arg)
+void PythonImpl::command(int narg, char **arg)
 {
   if (narg < 2) error->all(FLERR,"Invalid python command");
 
@@ -244,7 +242,7 @@ void Python::command(int narg, char **arg)
 
 /* ------------------------------------------------------------------ */
 
-void Python::invoke_function(int ifunc, char *result)
+void PythonImpl::invoke_function(int ifunc, char *result)
 {
   PyGILState_STATE gstate = PyGILState_Ensure();
   PyObject *pValue;
@@ -344,7 +342,7 @@ void Python::invoke_function(int ifunc, char *result)
 
 /* ------------------------------------------------------------------ */
 
-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;
@@ -353,7 +351,7 @@ int Python::find(char *name)
 
 /* ------------------------------------------------------------------ */
 
-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;
@@ -365,14 +363,14 @@ int Python::variable_match(char *name, char *varname, int numeric)
 
 /* ------------------------------------------------------------------ */
 
-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
@@ -482,7 +480,7 @@ int Python::create_entry(char *name)
 
 /* ------------------------------------------------------------------ */
 
-void Python::deallocate(int i)
+void PythonImpl::deallocate(int i)
 {
   delete [] pfuncs[i].itype;
   delete [] pfuncs[i].ivarflag;

src/PYTHON/python_impl.h

@@ -0,0 +1,130 @@
+/* -*- 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.
+
+*/

src/lammps.cpp

@@ -45,6 +45,7 @@
 #include "accelerator_kokkos.h"
 #include "accelerator_omp.h"
 #include "timer.h"
+#include "python.h"
 #include "memory.h"
 #include "version.h"
 #include "error.h"
@@ -67,6 +68,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator)
   error = new Error(this);
   universe = new Universe(this,communicator);
   output = NULL;
+  python = NULL;
 
   screen = NULL;
   logfile = NULL;
@@ -585,6 +587,7 @@ LAMMPS::~LAMMPS()
 
   if (world != universe->uworld) MPI_Comm_free(&world);
 
+  delete python;
   delete kokkos;
   delete [] suffix;
   delete [] suffix2;
@@ -639,6 +642,8 @@ void LAMMPS::create()
                               // 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);
 }
 
 /* ----------------------------------------------------------------------
@@ -759,6 +764,9 @@ void LAMMPS::destroy()
 
   delete timer;
   timer = NULL;
+
+  delete python;
+  python = NULL;
 }
 
 /* ----------------------------------------------------------------------

src/lammps.h

@@ -54,6 +54,8 @@ class LAMMPS {
   class KokkosLMP *kokkos;       // KOKKOS accelerator class
   class AtomKokkos *atomKK;      // KOKKOS version of Atom class
 
+  class Python * python;         // Python interface
+
   class CiteMe *citeme;          // citation info
 
   LAMMPS(int, char **, MPI_Comm);

src/pointers.h

@@ -56,7 +56,8 @@ class Pointers {
     infile(ptr->infile),
     screen(ptr->screen),
     logfile(ptr->logfile),
-    atomKK(ptr->atomKK) {}
+    atomKK(ptr->atomKK),
+    python(ptr->python) {}
   virtual ~Pointers() {}
 
  protected:
@@ -83,6 +84,7 @@ class Pointers {
   FILE *&logfile;
 
   class AtomKokkos *&atomKK;
+  class Python *&python;
 };
 
 }

src/python.cpp

@@ -0,0 +1,99 @@
+/* ----------------------------------------------------------------------
+   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 "python.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+Python::Python(LAMMPS *lmp) : Pointers(lmp)
+{
+  // implementation of Python interface is only loaded on demand
+  // and only if PYTHON package has been installed and compiled into binary
+  impl = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+Python::~Python()
+{
+  delete impl;
+}
+
+/* ---------------------------------------------------------------------- */
+
+PythonInterface::~PythonInterface()
+{
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Python::init()
+{
+#if LMP_PYTHON
+  impl = new PythonImpl(lmp);
+#else
+  error->all(FLERR,"Python support missing! Compile with PYTHON package installed!");
+#endif
+}
+
+/* ---------------------------------------------------------------------- */
+bool Python::is_enabled() const {
+#if LMP_PYTHON
+  return true;
+#else
+  return false;
+#endif
+}
+
+/* ---------------------------------------------------------------------- */
+
+void Python::command(int narg, char **arg)
+{
+  if(!impl) init();
+  impl->command(narg, arg);
+}
+
+/* ------------------------------------------------------------------ */
+
+void Python::invoke_function(int ifunc, char *result)
+{
+  if(!impl) init();
+  impl->invoke_function(ifunc, result);
+}
+
+/* ------------------------------------------------------------------ */
+
+int Python::find(char *name)
+{
+  if(!impl) init();
+  return impl->find(name);
+}
+
+/* ------------------------------------------------------------------ */
+
+int Python::variable_match(char *name, char *varname, int numeric)
+{
+  if(!impl) init();
+  return impl->variable_match(name, varname, numeric);
+}
+
+/* ------------------------------------------------------------------ */
+
+char * Python::long_string(int ifunc)
+{
+  if(!impl) init();
+  return impl->long_string(ifunc);
+}

src/python.h

@@ -18,50 +18,42 @@
 
 namespace LAMMPS_NS {
 
-class Python : protected Pointers {
+class PythonInterface {
- public:
+public:
-  int python_exists;
+  virtual ~PythonInterface();
-  bool external_interpreter;
+  virtual void command(int, char **) = 0;
+  virtual void invoke_function(int, char *) = 0;
+  virtual int find(char *) = 0;
+  virtual int variable_match(char *, char *, int) = 0;
+  virtual char * long_string(int ifunc) = 0;
+};
 
+class Python : protected Pointers {
+public:
   Python(class LAMMPS *);
   ~Python();
+
   void command(int, char **);
   void invoke_function(int, char *);
   int find(char *);
   int variable_match(char *, char *, int);
-  char *long_string(int);
+  char * long_string(int ifunc);
 
- private:
+  bool is_enabled() const;
-  int ninput,noutput,length_longstr;
-  char **istr;
-  char *ostr,*format;
-  void *pyMain;
 
-  struct PyFunc {
+private:
-    char *name;
+  PythonInterface * impl;
-    int ninput,noutput;
+  void init();
-    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
 
+#if LMP_PYTHON
+#include "python_impl.h"
+#endif
+
 /* ERROR/WARNING messages:
 
 E: Invalid python command

src/variable.cpp

@@ -34,7 +34,7 @@
 #include "random_mars.h"
 #include "math_const.h"
 #include "atom_masks.h"
-#include "python_wrapper.h"
+#include "python.h"
 #include "memory.h"
 #include "info.h"
 #include "error.h"
@@ -111,10 +111,6 @@ Variable::Variable(LAMMPS *lmp) : Pointers(lmp)
   precedence[MULTIPLY] = precedence[DIVIDE] = precedence[MODULO] = 6;
   precedence[CARAT] = 7;
   precedence[UNARY] = precedence[NOT] = 8;
-
-  // Python wrapper, real or dummy
-
-  python = new Python(lmp);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -144,7 +140,6 @@ Variable::~Variable()
   delete randomequal;
   delete randomatom;
 
-  delete python;
 }
 
 /* ----------------------------------------------------------------------
@@ -464,7 +459,7 @@ void Variable::set(int narg, char **arg)
 
   } else if (strcmp(arg[1],"python") == 0) {
     if (narg != 3) error->all(FLERR,"Illegal variable command");
-    if (!python->python_exists)
+    if (!python->is_enabled())
       error->all(FLERR,"LAMMPS is not built with Python embedded");
     int ivar = find(arg[0]);
     if (ivar >= 0) {
@@ -735,7 +730,7 @@ void Variable::set_arrays(int i)
 
 void Variable::python_command(int narg, char **arg)
 {
-  if (!python->python_exists)
+  if (!python->is_enabled())
     error->all(FLERR,"LAMMPS is not built with Python embedded");
   python->command(narg,arg);
 }

src/variable.h

@@ -78,8 +78,6 @@ class Variable : protected Pointers {
   int precedence[18];      // precedence level of math operators
                            // set length to include up to XOR in enum
 
-  class Python *python;    // ptr to embedded Python interpreter
-
   struct Tree {            // parse tree for atom-style or vector-style vars
     double value;          // single scalar
     double *array;         // per-atom or per-type list of doubles