diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt
index ff26d18e069d818ff5a3cead58180545a9b2690d..8bdd101b3d58751db6a87f4cb391eee36508fe2b 100644
--- a/doc/src/Section_python.txt
+++ b/doc/src/Section_python.txt
@@ -118,11 +118,6 @@ check which version of Python you have installed, by simply typing
11.2 Overview of using Python from a LAMMPS script :link(py_2),h4
-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
-
LAMMPS has a "python"_python.html command which can be used in an
input script to define and execute a Python function that you write
the code for. The Python function can also be assigned to a LAMMPS
diff --git a/doc/src/python.txt b/doc/src/python.txt
index 69025d791c2eba13dfc4782c6139edbf2413c1f1..e8a76c0e3e310ede29541e074842e1d28f76c3db 100644
--- a/doc/src/python.txt
+++ b/doc/src/python.txt
@@ -50,7 +50,7 @@ def factorial(n):
return n * factorial(n-1)
""" :pre
-python loop input 1 SELF return v_value format -f here """
+python loop input 1 SELF return v_value format pf here """
def loop(lmpptr,N,cut0):
from lammps import lammps
lmp = lammps(ptr=lmpptr) :pre
@@ -59,7 +59,7 @@ def loop(lmpptr,N,cut0):
for i in range(N):
cut = cut0 + i*0.1
- lmp.set_variable("cut",cut) # set a variable in LAMMPS
+ lmp.set_variable("cut",cut) # set a variable in LAMMPS
lmp.command("pair_style lj/cut $\{cut\}") # LAMMPS commands
lmp.command("pair_coeff * * 1.0 1.0")
lmp.command("run 100")
@@ -67,11 +67,6 @@ def loop(lmpptr,N,cut0):
[Description:]
-NOTE: It is not currently possible to use the "python"_python.html
-command described in this section with Python 3, only with Python 2.
-The C API changed from Python 2 to 3 and the LAMMPS code is not
-compatible with both.
-
Define a Python function or execute a previously defined function.
Arguments, including LAMMPS variables, can be passed to the function
from the LAMMPS input script and a value returned by the Python
@@ -477,16 +472,7 @@ python"_Section_python.html. Note that it is important that the
stand-alone LAMMPS executable and the LAMMPS shared library be
consistent (built from the same source code files) in order for this
to work. If the two have been built at different times using
-different source files, problems may occur.
-
-As described above, you can use the python command to invoke a Python
-function which calls back to LAMMPS through its Python-wrapped library
-interface. However you cannot do the opposite. I.e. you cannot call
-LAMMPS from Python and invoke the python command to "callback" to
-Python and execute a Python function. LAMMPS will generate an error
-if you try to do that. Note that we think there actually should be a
-way to do that, but haven't yet been able to figure out how to do it
-successfully.
+different source files, problems may occur.
[Related commands:]
diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt
index 5d3491782e98b891f025b76d037525e54f293b74..a4a7a4041ec82ab8faf9a70a87bc83c5b90dc9fa 100644
--- a/doc/src/tutorial_pylammps.txt
+++ b/doc/src/tutorial_pylammps.txt
@@ -55,7 +55,7 @@ using the generated {auto} Makefile.
cd $LAMMPS_DIR/src :pre
# generate custom Makefile
-python2 Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre
+python Make.py -jpg -png -s ffmpeg exceptions -m mpi -a file :pre
# add packages if necessary
make yes-MOLECULE :pre
diff --git a/examples/python/funcs.py b/examples/python/funcs.py
index 2f4830676e0ec4694905c88250a6552a784b263b..f38aca53f23ccabce6325987cea3065b6a7cda49 100644
--- a/examples/python/funcs.py
+++ b/examples/python/funcs.py
@@ -1,9 +1,10 @@
# Python function that implements a loop of short runs
# calls back to LAMMPS via "lmp" instance
# lammps() must be called with ptr=lmpptr for this to work
+from __future__ import print_function
def loop(N,cut0,thresh,lmpptr):
- print "LOOP ARGS",N,cut0,thresh,lmpptr
+ print("LOOP ARGS",N,cut0,thresh,lmpptr)
from lammps import lammps
lmp = lammps(ptr=lmpptr)
natoms = lmp.get_natoms()
@@ -12,11 +13,12 @@ def loop(N,cut0,thresh,lmpptr):
cut = cut0 + i*0.1
lmp.set_variable("cut",cut) # set a variable in LAMMPS
+
lmp.command("pair_style lj/cut ${cut}") # LAMMPS command
#lmp.command("pair_style lj/cut %d" % cut) # LAMMPS command option
lmp.command("pair_coeff * * 1.0 1.0") # ditto
lmp.command("run 10") # ditto
pe = lmp.extract_compute("thermo_pe",0,0) # extract total PE from LAMMPS
- print "PE",pe/natoms,thresh
+ print("PE",pe/natoms,thresh)
if pe/natoms < thresh: return
diff --git a/examples/python/in.python b/examples/python/in.python
index cb2013fdd32310d1e5f5e0febe26011a81b0a129..c5aa504d43159375715f293c6a27e5166f8b0d24 100644
--- a/examples/python/in.python
+++ b/examples/python/in.python
@@ -25,13 +25,14 @@ run 10
# example of catching a syntax error
python simple here """
+from __future__ import print_function
+
def simple():
- import exceptions
- print "Inside simple function"
+ print("Inside simple function")
try:
foo += 1
- except Exception, e:
- print "FOO error:",e
+ except Exception as e:
+ print("FOO error:", e)
"""
python simple invoke
diff --git a/lib/python/Makefile.lammps b/lib/python/Makefile.lammps
index 85389946945540667ef70c4118c39357814f7350..4289674e996ecbb69c3e8274cfcaeacd3a2efb09 100644
--- a/lib/python/Makefile.lammps
+++ b/lib/python/Makefile.lammps
@@ -1,6 +1,7 @@
# Settings that the LAMMPS build will import when this package library is used
# See the README file for more explanation
-python_SYSINC = $(shell which python2-config > /dev/null 2>&1 && python2-config --includes || python-config --includes )
-python_SYSLIB = $(shell which python2-config > /dev/null 2>&1 && python2-config --ldflags || python-config --ldflags)
+python_SYSINC = $(shell which python-config > /dev/null 2>&1 && python-config --includes || :)
+python_SYSLIB = $(shell which python-config > /dev/null 2>&1 && python-config --ldflags || :)
python_SYSPATH =
+PYTHON=python
diff --git a/lib/python/Makefile.lammps.python2 b/lib/python/Makefile.lammps.python2
index 85389946945540667ef70c4118c39357814f7350..7b54b4c3dfc68d9476b6c358645ed7ff4c766f74 100644
--- a/lib/python/Makefile.lammps.python2
+++ b/lib/python/Makefile.lammps.python2
@@ -1,6 +1,7 @@
# Settings that the LAMMPS build will import when this package library is used
# See the README file for more explanation
-python_SYSINC = $(shell which python2-config > /dev/null 2>&1 && python2-config --includes || python-config --includes )
-python_SYSLIB = $(shell which python2-config > /dev/null 2>&1 && python2-config --ldflags || python-config --ldflags)
+python_SYSINC = $(shell which python2-config > /dev/null 2>&1 && python2-config --includes || (which python-config > /dev/null 2>&1 && python-config --includes || :))
+python_SYSLIB = $(shell which python2-config > /dev/null 2>&1 && python2-config --ldflags || (which python-config > /dev/null 2>&1 && python-config --ldflags || :))
python_SYSPATH =
+PYTHON=$(shell which python2 > /dev/null 2>&1 && echo python2 || echo python)
diff --git a/lib/python/Makefile.lammps.python2.7 b/lib/python/Makefile.lammps.python2.7
index b5807086f278deb8eb4cf0b14ce9e809911884a0..07c6a94b2145801f5140bea785686cd27bec3506 100644
--- a/lib/python/Makefile.lammps.python2.7
+++ b/lib/python/Makefile.lammps.python2.7
@@ -4,3 +4,4 @@
python_SYSINC = -I/usr/local/include/python2.7
python_SYSLIB = -lpython2.7 -lnsl -ldl -lreadline -ltermcap -lpthread -lutil -lm -Xlinker -export-dynamic
python_SYSPATH =
+PYTHON=python2.7
diff --git a/lib/python/Makefile.lammps.python3 b/lib/python/Makefile.lammps.python3
new file mode 100644
index 0000000000000000000000000000000000000000..5c43b45ff6cd47bc402c2560c8512cbc08cbdce1
--- /dev/null
+++ b/lib/python/Makefile.lammps.python3
@@ -0,0 +1,7 @@
+# Settings that the LAMMPS build will import when this package library is used
+# See the README file for more explanation
+
+python_SYSINC = $(shell which python3-config > /dev/null 2>&1 && python3-config --includes || (which python-config > /dev/null 2>&1 && python-config --includes || :))
+python_SYSLIB = $(shell which python3-config > /dev/null 2>&1 && python3-config --ldflags || (which python-config > /dev/null 2>&1 && python-config --ldflags || :))
+python_SYSPATH =
+PYTHON=$(shell which python3 > /dev/null 2>&1 && echo python3 || echo python)
diff --git a/lib/python/README b/lib/python/README
index ddccc1a21ac839bba55bc2e364a5ef75ebbeb4b3..8de2bc4bd71df8fd67cd894fa295851b182b56dc 100644
--- a/lib/python/README
+++ b/lib/python/README
@@ -1,26 +1,26 @@
The Makefile.lammps file in this directory is used when building
LAMMPS with its PYTHON package installed. The file has several
settings needed to compile and link LAMMPS with the Python library.
-You should choose a Makefile.lammps.* file compatible with your system
-and your version of Python, and copy it to Makefile.lammps before
-building LAMMPS itself. You may need to edit one of the provided
-files to match your system.
-Note that is not currently possible to use the PYTHON package with
-Python 3, only with Python 2. The C API changed from Python 2 to 3
-and the LAMMPS code is not compatible with both.
-
-If you create a new Makefile.lammps file suitable for some version of
-Python on some system, that is not a match to one of the provided
-Makefile.lammps.* files, you can send it to the developers, and we can
-include it in the distribution for others to use.
-
-To illustrate, these are example settings from the
-Makefile.lammps.python2.7 file:
+The default Makefile.lammps will automatically choose the default
+python interpreter of your system and will infer the flags from
+the python-config utility, that is usually bundled with the python
+installation. If needed, you can copy one of the other provided
+Makefile.lammps.* files to to Makefile.lammps before building
+LAMMPS itself.
+
+The files Makefile.lammps.python2 and Makefile.lammps.python3 are
+similar to the default file, but meant for the case that both,
+python 2 and python 3, are installed simultaneously and you want
+to prefer one over the other. If neither of these files work, you
+may have to create a custom Makefile.lammps file suitable for
+the version of Python on your system. To illustrate, these are
+example settings from the Makefile.lammps.python2.7 file:
python_SYSINC = -I/usr/local/include/python2.7
python_SYSLIB = -lpython2.7 -lnsl -ldl -lreadline -ltermcap -lpthread -lutil -lm
-python_SYSPATH =
+python_SYSPATH =
+PYTHON=python2.7
python_SYSINC refers to the directory where Python's Python.h file is
found. LAMMPS includes this file.
@@ -30,10 +30,13 @@ application (LAMMPS in this case) to "embed" Python in the
application. The Python library itself is listed (-lpython2.7) are
are several system libraries needed by Python.
-python_SYSPATH = refers to the path (e.g. -L/usr/local/lib) where the
+python_SYSPATH refers to the path (e.g. -L/usr/local/lib) where the
Python library can be found. You may not need this setting if the
path is already included in your LD_LIBRARY_PATH environment variable.
+PYTHON is the name of the python interpreter. It is used for
+installing the LAMMPS python module with "make install-python"
+
-------------------------
Note that the trickiest issue to figure out for inclusion in
diff --git a/python/lammps.py b/python/lammps.py
index a36abb87e8fd408f953f58f0f5b14b2cb9f38e55..d428a097a81589b3bae8c18355a9bf40fd2db1ca 100644
--- a/python/lammps.py
+++ b/python/lammps.py
@@ -30,7 +30,7 @@ from collections import namedtuple
import os
import select
import re
-
+import sys
class MPIAbortException(Exception):
def __init__(self, message):
@@ -151,9 +151,16 @@ class lammps(object):
else:
# magic to convert ptr to ctypes ptr
- pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
- pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
- self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
+ if sys.version_info >= (3, 0):
+ # Python 3 (uses PyCapsule API)
+ pythonapi.PyCapsule_GetPointer.restype = c_void_p
+ pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
+ self.lmp = c_void_p(pythonapi.PyCapsule_GetPointer(ptr, None))
+ else:
+ # Python 2 (uses PyCObject API)
+ pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
+ pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
+ self.lmp = c_void_p(pythonapi.PyCObject_AsVoidPtr(ptr))
def __del__(self):
if self.lmp and self.opened:
@@ -305,7 +312,7 @@ class lammps(object):
def set_variable(self,name,value):
if name: name = name.encode()
if value: value = str(value).encode()
- return self.lib.lammps_set_variable(self.lmp,name,str(value))
+ return self.lib.lammps_set_variable(self.lmp,name,value)
# return current value of thermo keyword
diff --git a/src/.gitignore b/src/.gitignore
index 4fd04312085209539f4dc618eaa0a1b269543cdb..1327704e4731a8ac1f9ee8ecbffb171e723a2fa8 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -848,8 +848,6 @@
/pppm_tip4p_cg.h
/prd.cpp
/prd.h
-/python.cpp
-/python.h
/python_impl.cpp
/python_impl.h
/reader_molfile.cpp
diff --git a/src/Makefile b/src/Makefile
index 60c939bab2d9ab97aa88b1299d2962a3037ec016..32f9c3787c4836e585d205b386395531ca7ee41a 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -223,7 +223,8 @@ mpi-stubs:
@cd STUBS; $(MAKE) clean; $(MAKE)
# install LAMMPS shared lib and Python wrapper for Python usage
-
+# include python package settings to automatically adapt name of python interpreter
+sinclude ../lib/python/Makefile.lammps
install-python:
@$(PYTHON) ../python/install.py
diff --git a/src/PYTHON/Install.sh b/src/PYTHON/Install.sh
index 71288cf3774127d44970449d7fcf06921caf0e2b..9d2783ba0ce88458160ba8fc456a954dce720725 100755
--- a/src/PYTHON/Install.sh
+++ b/src/PYTHON/Install.sh
@@ -26,11 +26,9 @@ action () {
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
diff --git a/src/PYTHON/python.cpp b/src/PYTHON/python_impl.cpp
similarity index 87%
rename from src/PYTHON/python.cpp
rename to src/PYTHON/python_impl.cpp
index c2ff7f03c7bcd4fc0f3fef83b74f996430d7c498..8c59ef19150ff891bdc0f0a5274c50aa36dc78c8 100644
--- a/src/PYTHON/python.cpp
+++ b/src/PYTHON/python_impl.cpp
@@ -25,25 +25,51 @@ enum{NONE,INT,DOUBLE,STRING,PTR};
#define VALUELENGTH 64 // also in variable.cpp
+// Wrap API changes between Python 2 and 3 using macros
+#if PY_MAJOR_VERSION == 2
+#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
+#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
+#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
+#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, NULL)
+#define PY_STRING_AS_STRING(X) PyString_AsString(X)
+
+#elif PY_MAJOR_VERSION == 3
+#define PY_INT_FROM_LONG(X) PyLong_FromLong(X)
+#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
+#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
+#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, NULL, NULL)
+#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
+#endif
+
/* ---------------------------------------------------------------------- */
-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
nfunc = 0;
pfuncs = NULL;
- external_interpreter = false;
+ // one-time initialization of Python interpreter
+ // pymain stores pointer to main module
+ external_interpreter = Py_IsInitialized();
+
+ Py_Initialize();
+ PyEval_InitThreads();
+
+ PyGILState_STATE gstate = PyGILState_Ensure();
+
+ PyObject *pModule = PyImport_AddModule("__main__");
+ if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
+
+ pyMain = (void *) pModule;
+
+ PyGILState_Release(gstate);
}
/* ---------------------------------------------------------------------- */
-Python::~Python()
+PythonImpl::~PythonImpl()
{
if(pyMain) {
// clean up
@@ -71,7 +97,7 @@ 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");
@@ -156,22 +182,7 @@ void Python::command(int narg, char **arg)
int ifunc = create_entry(arg[0]);
- // one-time initialization of Python interpreter
- // pymain stores pointer to main module
- PyGILState_STATE gstate;
-
- if (pyMain == NULL) {
- external_interpreter = Py_IsInitialized();
- Py_Initialize();
- PyEval_InitThreads();
- gstate = PyGILState_Ensure();
-
- PyObject *pModule = PyImport_AddModule("__main__");
- if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
- pyMain = (void *) pModule;
- } else {
- gstate = PyGILState_Ensure();
- }
+ PyGILState_STATE gstate = PyGILState_Ensure();
// send Python code to Python interpreter
// file: read the file via PyRun_SimpleFile()
@@ -230,7 +241,7 @@ 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;
@@ -259,8 +270,10 @@ void Python::invoke_function(int ifunc, char *result)
error->all(FLERR,"Could not evaluate Python function input variable");
}
- pValue = PyInt_FromLong(atoi(str));
- } else pValue = PyInt_FromLong(pfuncs[ifunc].ivalue[i]);
+ pValue = PY_INT_FROM_LONG(atoi(str));
+ } else {
+ pValue = PY_INT_FROM_LONG(pfuncs[ifunc].ivalue[i]);
+ }
} else if (itype == DOUBLE) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
@@ -271,7 +284,9 @@ void Python::invoke_function(int ifunc, char *result)
}
pValue = PyFloat_FromDouble(atof(str));
- } else pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
+ } else {
+ pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
+ }
} else if (itype == STRING) {
if (pfuncs[ifunc].ivarflag[i]) {
str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
@@ -279,10 +294,13 @@ void Python::invoke_function(int ifunc, char *result)
PyGILState_Release(gstate);
error->all(FLERR,"Could not evaluate Python function input variable");
}
- pValue = PyString_FromString(str);
- } else pValue = PyString_FromString(pfuncs[ifunc].svalue[i]);
+
+ pValue = PY_STRING_FROM_STRING(str);
+ } else {
+ pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
+ }
} else if (itype == PTR) {
- pValue = PyCObject_FromVoidPtr((void *) lmp,NULL);
+ pValue = PY_VOID_POINTER(lmp);
}
PyTuple_SetItem(pArgs,i,pValue);
}
@@ -306,11 +324,11 @@ void Python::invoke_function(int ifunc, char *result)
if (pfuncs[ifunc].noutput) {
int otype = pfuncs[ifunc].otype;
if (otype == INT) {
- sprintf(result,"%ld",PyInt_AsLong(pValue));
+ sprintf(result,"%ld",PY_INT_AS_LONG(pValue));
} else if (otype == DOUBLE) {
sprintf(result,"%.15g",PyFloat_AsDouble(pValue));
} else if (otype == STRING) {
- char *pystr = PyString_AsString(pValue);
+ char *pystr = PY_STRING_AS_STRING(pValue);
if (pfuncs[ifunc].longstr)
strncpy(pfuncs[ifunc].longstr,pystr,pfuncs[ifunc].length_longstr);
else strncpy(result,pystr,VALUELENGTH-1);
@@ -323,7 +341,7 @@ 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;
@@ -332,7 +350,7 @@ 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;
@@ -344,14 +362,14 @@ 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
@@ -461,7 +479,7 @@ int Python::create_entry(char *name)
/* ------------------------------------------------------------------ */
-void Python::deallocate(int i)
+void PythonImpl::deallocate(int i)
{
delete [] pfuncs[i].itype;
delete [] pfuncs[i].ivarflag;
diff --git a/src/PYTHON/python_impl.h b/src/PYTHON/python_impl.h
new file mode 100644
index 0000000000000000000000000000000000000000..07975b3fdfd7907e7710386e95a9b615f70106a6
--- /dev/null
+++ b/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.
+
+*/
diff --git a/src/lammps.cpp b/src/lammps.cpp
index cc3133f2d9520463be814c0efd1c3a99a4357fd5..bde7ca035d6a7dc68a1b85b07b7ef67a42eab706 100644
--- a/src/lammps.cpp
+++ b/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;
}
/* ----------------------------------------------------------------------
diff --git a/src/lammps.h b/src/lammps.h
index 02490a183640688ba175747943dba42ba249cb88..c432784a0b14c92f571dc032040f22e35ec30f96 100644
--- a/src/lammps.h
+++ b/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);
diff --git a/src/pointers.h b/src/pointers.h
index dd528c3a747efaa5ff8765840161433a38474c54..82b49c1dad05e6988ec02bd1b5646ee2078b6442 100644
--- a/src/pointers.h
+++ b/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;
};
}
diff --git a/src/python.cpp b/src/python.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..fa1639b0754b141b57f450c84e54ffcca7f2b684
--- /dev/null
+++ b/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
+ if (!impl) 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)
+{
+ init();
+ impl->command(narg, arg);
+}
+
+/* ------------------------------------------------------------------ */
+
+void Python::invoke_function(int ifunc, char *result)
+{
+ init();
+ impl->invoke_function(ifunc, result);
+}
+
+/* ------------------------------------------------------------------ */
+
+int Python::find(char *name)
+{
+ init();
+ return impl->find(name);
+}
+
+/* ------------------------------------------------------------------ */
+
+int Python::variable_match(char *name, char *varname, int numeric)
+{
+ init();
+ return impl->variable_match(name, varname, numeric);
+}
+
+/* ------------------------------------------------------------------ */
+
+char * Python::long_string(int ifunc)
+{
+ init();
+ return impl->long_string(ifunc);
+}
diff --git a/src/PYTHON/python.h b/src/python.h
similarity index 84%
rename from src/PYTHON/python.h
rename to src/python.h
index 78889b994fb50e6c400e177ae622fd2b67f0291a..73f635460967fe3ad7fc686c5471a149b5959952 100644
--- a/src/PYTHON/python.h
+++ b/src/python.h
@@ -18,50 +18,42 @@
namespace LAMMPS_NS {
-class Python : protected Pointers {
- public:
- int python_exists;
- bool external_interpreter;
+class PythonInterface {
+public:
+ virtual ~PythonInterface();
+ 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);
-
- 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);
+ char * long_string(int ifunc);
+
+ bool is_enabled() const;
+ void init();
+
+private:
+ PythonInterface * impl;
};
}
#endif
+#if LMP_PYTHON
+#include "python_impl.h"
+#endif
+
/* ERROR/WARNING messages:
E: Invalid python command
diff --git a/src/python_wrapper.h b/src/python_wrapper.h
deleted file mode 100644
index 97d7de31ef150a972571586dcfdb73066b724ce3..0000000000000000000000000000000000000000
--- a/src/python_wrapper.h
+++ /dev/null
@@ -1,47 +0,0 @@
-/* -*- 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_WRAPPER_H
-#define LMP_PYTHON_WRAPPER_H
-
-// true interface to embedded Python
-// used when PYTHON package is installed
-
-#ifdef LMP_PYTHON
-
-#include "python.h"
-
-#else
-
-// dummy interface to PYTHON
-// needed for compiling when PYTHON is not installed
-
-namespace LAMMPS_NS {
-
-class Python {
- public:
- int python_exists;
-
- Python(class LAMMPS *) {python_exists = 0;}
- ~Python() {}
- void command(int, char **) {}
- void invoke_function(int, char *) {}
- int find(char *) {return -1;}
- int variable_match(char *, char *, int) {return -1;}
- char *long_string(int) {return NULL;}
-};
-
-}
-
-#endif
-#endif
diff --git a/src/variable.cpp b/src/variable.cpp
index 3eea50a463cf2f99720238cdbb3a25793e60e885..6e16597c636b9e9e07f9f484cdbcb8721b8c5352 100644
--- a/src/variable.cpp
+++ b/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);
}
diff --git a/src/variable.h b/src/variable.h
index 76607e96b404ab3ade4ec4cb9fe134bdc0f396ed..886dd7b42219dec379f3f4c69dbd54e32d8faf69 100644
--- a/src/variable.h
+++ b/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