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Merge pull request #4470 from akohlmey/bye-bye-python-zwei

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Remove support for Python 2.x and show corresponding errors.
This commit is contained in:
Axel Kohlmeyer
2025-02-13 19:44:07 -05:00
committed by GitHub
parent 52f068d1c5 53213fb6ff
commit 36e739b734
28 changed files with 197 additions and 197 deletions
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6
cmake/CMakeLists.txt
View File

@ -225,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
" Setting Python interpreter to: ${Python_EXECUTABLE}")
endif()
find_package(Python COMPONENTS Interpreter QUIET)
# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
endif()
set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
mark_as_advanced(LAMMPS_MACHINE)
if(LAMMPS_MACHINE)

7
cmake/Modules/CodingStandard.cmake
View File

@ -1,11 +1,11 @@
# use default (or custom) Python executable, if version is sufficient
if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
# use default (or custom) Python executable.
# Python version check is in main CMakeLists.txt file
if(Python_EXECUTABLE)
set(Python3_EXECUTABLE ${Python_EXECUTABLE})
endif()
find_package(Python3 COMPONENTS Interpreter)
if(Python3_EXECUTABLE)
if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
add_custom_target(
check-whitespace
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
@ -36,5 +36,4 @@ if(Python3_EXECUTABLE)
${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
WORKING_DIRECTORY ${LAMMPS_DIR}
COMMENT "Fix permission errors")
endif()
endif()

4
cmake/Modules/Packages/ML-IAP.cmake
View File

@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
if(NOT PKG_PYTHON)
message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
endif()
if(Python_VERSION VERSION_LESS 3.6)
message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
endif()
# Python version check is in main CMakeLists.txt file
set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)

11
doc/src/Build_extras.rst
View File

@ -1139,11 +1139,10 @@ POEMS package
PYTHON package
---------------------------
Building with the PYTHON package requires you have a the Python development
headers and library available on your system, which needs to be a Python 2.7
version or a Python 3.x version. Since support for Python 2.x has ended,
using Python 3.x is strongly recommended. See ``lib/python/README`` for
additional details.
Building with the PYTHON package requires you have a the Python
development headers and library available on your system, which
needs to be Python version 3.6 or later. See ``lib/python/README``
for additional details.
.. tabs::
@ -1159,7 +1158,7 @@ additional details.
set the Python_EXECUTABLE variable to specify which Python
interpreter should be used. Note note that you will also need to
have the development headers installed for this version,
e.g. python2-devel.
e.g. python3-devel.
.. tab:: Traditional make

6
doc/src/Build_make.rst
View File

@ -30,9 +30,9 @@ additional tools to be available and functioning.
* A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
* A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
* Python (optional, required for ``make lib-<pkg>`` in the ``src``
folder). Python scripts are currently tested with python 2.7 and
3.6 to 3.11. The procedure for :doc:`building the documentation
<Build_manual>` *requires* Python 3.5 or later.
folder). Python scripts are currently tested with 3.6 to 3.11.
The procedure for :doc:`building the documentation <Build_manual>`
*requires* Python 3.8 or later.
Getting started
^^^^^^^^^^^^^^^

2
doc/src/Build_manual.rst
View File

@ -162,7 +162,7 @@ are usually installed by default, the following packages are required:
- dvipng
- ellipse
- fncychap
- fontawesom
- fontawesome
- framed
- geometry
- gyre

14
doc/src/Intro_portability.rst
View File

@ -13,10 +13,14 @@ Programming language standards
Most of the C++ code currently requires a compiler compatible with the
C++11 standard, the KOKKOS package currently requires C++17. Most of
the Python code is written to be compatible with Python 3.5 or later or
Python 2.7. Some Python scripts *require* Python 3 and a few others
still need to be ported from Python 2 to Python 3.
the Python code is written to be compatible with Python 3.6 or later.
.. deprecated:: TBD
Python 2.x is no longer supported and trying to use it, e.g. for the
LAMMPS Python module should result in an error. If you come across
some part of the LAMMPS distribution that is not (yet) compatible with
Python 3, please notify the LAMMPS developers.
Build systems
^^^^^^^^^^^^^
@ -24,8 +28,8 @@ Build systems
LAMMPS can be compiled from source code using a (traditional) build
system based on shell scripts, a few shell utilities (grep, sed, cat,
tr) and the GNU make program. This requires running within a Bourne
shell (``/bin/sh``). Alternatively, a build system with different back ends
can be created using CMake. CMake must be at least version 3.16.
shell (``/bin/sh``). Alternatively, a build system with different back
ends can be created using CMake. CMake must be at least version 3.16.
Operating systems
^^^^^^^^^^^^^^^^^

6
doc/src/Modify_requirements.rst
View File

@ -189,10 +189,8 @@ of the contribution. As of January 2023, all previously included
Fortran code for the LAMMPS executable has been replaced by equivalent
C++ code.
Python code must be compatible with Python 3.5 and later. Large parts
of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
compatible with Python 2.7. Compatibility with Python 2.7 is desirable,
but compatibility with Python 3.5 is **required**.
Python code currently must be compatible with Python 3.6. If a later
version or Python is required, it needs to be documented.
Compatibility with older programming language standards is very
important to maintain portability and availability of LAMMPS on many

2
doc/src/Packages_details.rst
View File

@ -2428,7 +2428,7 @@ ways to use LAMMPS and Python together.
Building with the PYTHON package assumes you have a Python development
environment (headers and libraries) available on your system, which needs
to be either Python version 2.7 or Python 3.5 and later.
to be Python version 3.6 or later.
**Install:**

19
doc/src/Python_install.rst
View File

@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
module. Because of the dynamic loading, it is required that LAMMPS is
compiled in :ref:`"shared" mode <exe>`.
.. versionchanged:: TBD
LAMMPS currently only supports Python version 3.6 or later.
Two components are necessary for Python to be able to invoke LAMMPS code:
* The LAMMPS Python Package (``lammps``) from the ``python`` folder
@ -136,11 +140,6 @@ folder that the dynamic loader searches or inside of the installed
# create virtual environment in folder $HOME/myenv
python3 -m venv $HOME/myenv
For Python versions prior 3.3 you can use `virtualenv
<https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
command instead of "python3 -m venv". This step has to be done
only once.
To activate the virtual environment type:
.. code-block:: bash
@ -245,14 +244,14 @@ make MPI calls directly from Python in your script, if you desire.
We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
(aka mpi4py) and you will find installation instruction for it below.
Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
follows:
- Via ``pip`` into a local user folder with:
.. code-block:: bash
pip install --user mpi4py
python3 -m pip install --user mpi4py
- Via ``dnf`` into a system folder for RedHat/Fedora systems:
@ -261,20 +260,20 @@ follows:
# for use with OpenMPI
sudo dnf install python3-mpi4py-openmpi
# for use with MPICH
sudo dnf install python3-mpi4py-openmpi
sudo dnf install python3-mpi4py-mpich
- Via ``pip`` into a virtual environment (see above):
.. code-block:: console
$ source $HOME/myenv/activate
(myenv)$ pip install mpi4py
(myenv)$ python -m pip install mpi4py
- Via ``pip`` into a system folder (not recommended):
.. code-block:: bash
sudo pip install mpi4py
sudo python3 -m pip install mpi4py
For more detailed installation instructions and additional options,
please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.

14
doc/src/Python_overview.rst
View File

@ -44,15 +44,11 @@ Below is an example output for Python version 3.8.5.
.. warning::
The options described in this section of the manual for using Python
with LAMMPS currently support either Python 2 or 3. Specifically
version 2.7 or later and 3.6 or later. Since the Python community no
longer maintains Python 2 (see `this notice
<https://www.python.org/doc/sunset-python-2/>`_), we recommend use of
Python 3 with LAMMPS. While Python 2 code should continue to work,
that is not something we can guarantee long-term. If you notice
Python code in the LAMMPS distribution that is not compatible with
Python 3, please contact the LAMMPS developers or submit `and issue
on GitHub <https://github.com/lammps/lammps/issues>`_
with LAMMPS support only Python 3.6 or later. For use with Python
2.x you will need to use an older LAMMPS version like 29 Aug 2024
or older. If you notice Python code in the LAMMPS distribution that
is not compatible with Python 3, please contact the LAMMPS developers
or submit `and issue on GitHub <https://github.com/lammps/lammps/issues>`_
---------

6
doc/src/region2vmd.rst
View File

@ -166,11 +166,7 @@ Only the following region styles are currently supported: *block*,
*cone*, *cylinder*, *ellipsoid*, *prism*, and *sphere*. Regions formed
from unions or intersections of other regions are not supported.
For region style *cone* one of the two radii must be zero, since the
equivalent VMD graphics primitive does not support truncated cones.
Also the VMD graphics primitive does not support open cones.
Rotating regions are not supported.
Rotating regions are currently not supported.
Related commands
""""""""""""""""

16
doc/utils/sphinx-config/false_positives.txt
View File

@ -99,6 +99,7 @@ AMD
amino
Amirjalayer
Amit
amsmath
amu
Amzallag
analytical
@ -128,6 +129,7 @@ Antisymmetrized
antisymmetry
anton
Antonelli
anysize
api
apolar
Apoorva
@ -613,6 +615,7 @@ Courant
covalent
covalently
covariance
cp
cpp
cpu
cradius
@ -905,6 +908,7 @@ dUs
Duval
dV
dvector
dvipng
dVx
dW
dx
@ -1215,12 +1219,14 @@ fmz
fN
Fn
fname
fncychap
fno
Fnudge
foces
Fock
Fogarty
Foiles
fontawesome
fopenmp
forceclear
forestgreen
@ -1407,6 +1413,7 @@ Gunsteren
Gunzenmuller
Guo
gw
gyre
gyromagnetic
gz
gzip
@ -1532,10 +1539,12 @@ hydrostatically
hydroxyl
Hynninen
Hyoungki
hypcap
hyperdynamics
hyperparameters
hyperplane
hyperradius
hyperref
hyperspherical
hysteretic
hz
@ -2514,6 +2523,7 @@ Ndof
Ndouble
ndx
neb
needspace
neel
Neel
Neelov
@ -2918,6 +2928,7 @@ picogram
picograms
picosecond
picoseconds
pict
pid
piecewise
Pieniazek
@ -3689,6 +3700,7 @@ Sz
Tabbernor
tabinner
tabstyle
tabulary
Tadmor
Tafipolsky
tagID
@ -3786,6 +3798,7 @@ timestamps
timestep
timestepping
timesteps
titlesec
TiN
TiO
Tirado
@ -3962,6 +3975,7 @@ untilted
Unwin
uparrow
upenn
upquote
upto
Urbakh
Urbana
@ -4148,6 +4162,7 @@ Workum
Worley
wormlike
wpbe
wrapfig
Wriggers
writedata
Wuppertal
@ -4178,6 +4193,7 @@ Xia
Xiaohu
Xiaowang
Xie
xindy
xk
xlat
xlattice

7
lib/python/Makefile.lammps.python2
View File

@ -1,7 +0,0 @@
# 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 || (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)

0
lib/python/Makefile.lammps.python2.7 → lib/python/Makefile.lammps.python3.13
View File

27
lib/python/README
View File

@ -9,30 +9,29 @@ 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:
The file Makefile.lammps.python3 is similar to the default file, but
meant for the case that both, python 2 and python 3, are installed
simultaneously. LAMMPS only supports python 3. 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.python3.13 file:
python_SYSINC = -I/usr/local/include/python2.7
python_SYSLIB = -lpython2.7 -lnsl -ldl -lreadline -ltermcap -lpthread -lutil -lm
python_SYSPATH =
PYTHON=python2.7
python_SYSINC = -I/usr/local/include/python3.13
python_SYSLIB = -lpython3.13 -ldl -lm
python_SYSPATH = -L/usr/lib64
PYTHON=python3.13
python_SYSINC refers to the directory where Python's Python.h file is
found. LAMMPS includes this file.
python_SYSLIB refers to the libraries needed to link to from an
application (LAMMPS in this case) to "embed" Python in the
application. The Python library itself is listed (-lpython2.7) are
application. The Python library itself is listed (-lpython3.13) are
are several system libraries needed by Python.
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.
path is already included in your 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"
@ -45,7 +44,7 @@ run in embedded mode on your machine.
Here is what this Python doc page says about it:
https://docs.python.org/2/extending/embedding.html#compiling-and-linking-under-unix-like-systems
https://docs.python.org/3/extending/embedding.html#compiling-and-linking-under-unix-like-systems
"It is not necessarily trivial to find the right flags to pass to your
compiler (and linker) in order to embed the Python interpreter into

70
python/README
View File

@ -1,20 +1,27 @@
This directory contains Python code which wraps LAMMPS as a library
and allows the LAMMPS library interface to be invoked from Python,
either from a Python script or using Python interactively.
This directory contains the LAMMPS Python module that allows the LAMMPS
C library interface to be invoked from Python, either from a Python
script or using Python interactively.
Details on the Python interface to LAMMPS and how to build LAMMPS as a
shared library, for use with Python, are given in
doc/Section_python.html and in doc/Section_start.html#start_5.
https://docs.lammps.org/Build_basics.html#exe
and
https://docs.lammps.org/Python_install.html
Basically you need to follow these steps in the src directory:
Basically you need to use the flag -D BUILD_SHARED_LIBS=ON when
configuring LAMMPS with CMake and then in the build folder use the
command % cmake --build . --target install-python
or for the legacy GNU build system execute these steps in the src folder:
% make g++ mode=shlib # build for whatever machine target you wish
% make install-python # install into site-packages folder
You can replace the last step by a one-time setting of environment
variables in your shell script. Or you can run the python/install.py
script directly to give you more control over where the two relevant
files are installed. See doc/Python_install.html for details.
variables in your shell environment. Or you can run the
python/install.py script directly to give you more control over where
the two relevant files are installed. See
https://docs.lammps.org/Python_install.html for details.
You should then be able to launch Python and instantiate an instance
of LAMMPS:
@ -24,13 +31,14 @@ of LAMMPS:
>>> lmp = lammps()
If that gives no errors, you have successfully wrapped LAMMPS with
Python. See doc/Section_python.html#py_7 for tests you can then use
to run LAMMPS both in serial or parallel thru Python.
Python. See https://docs.lammps.org/Python_launch.html for examples how
to run LAMMPS both in serial or parallel from Python.
Note that you can also invoke Python code from within a LAMMPS input
script, using the "python" command. See the doc/python.html doc page
for details. The Python code you invoke can also call back to LAMMPS
using the same interface described here for wrapping LAMMPS.
script, using the "python" command. See the
https://docs.lammps.org/python.html doc page for details. The Python
code you invoke can also call back to LAMMPS using the same interface
described here for wrapping LAMMPS.
-------------------------------------------------------------------
@ -45,18 +53,19 @@ mc.py Monte Carlo energy relaxation wrapper on LAMMPS
gui.py GUI go/stop/temperature-slider to control LAMMPS
plot.py real-time temperature plot with GnuPlot via Pizza.py
matplotlib_plot.py real-time temperature plot with Matplotlib via Pizza.py
viz_tool.py real-time viz via some viz package
vizplotgui_tool.py combination of viz.py and plot.py and gui.py
viz_<tool>.py real-time viz via some viz package
vizplotgui_<tool>.py combination of viz.py and plot.py and gui.py
For the viz_tool.py and vizplotgui_tool.py commands, replace "tool"
with "gl" or "atomeye" or "pymol", depending on what visualization
package you have installed. We hope to add a VMD option soon.
For the viz_<tool>.py and vizplotgui_<tool>.py commands, replace
"<tool>" with "gl" or "atomeye" or "pymol", depending on what
visualization package you have installed. We hope to add a VMD option
soon.
Note that for GL, you need to be able to run the Pizza.py GL tool,
which is included in the pizza sub-directory. See the Pizza.py doc
pages for more info:
http://www.sandia.gov/~sjplimp/pizza.html
https://lammps.github.io/pizza/
Note that for AtomEye, you need version 3, and their is a line in the
scripts that specifies the path and name of the executable. See
@ -115,17 +124,14 @@ one-processor run, where both Python and LAMMPS will run on single
processors. Each running job will read the same input file, and write
to same log.lammps file, which isn't too useful.
However, if you have the mpi4py Python package installed and uncomment mpi4py
code in simple.py, then the above commands will invoke 1 instance of a
P-processor run. Both Python and LAMMPS will run on P processors. The job will
read the input file and write a single log.lammps file.
The split.py script can also be run in parallel. It uses mpi4py
version 2.0.0 (or later), which makes it possible to pass a
communicator when creating the LAMMPS object and thus run multiple
instances of LAMMPS at the same time, each on a different subset of
MPI ranks. Or run LAMMPS on one subset and some other program on the
rest of the MPI ranks, concurrently. See comments in the split.py
script for more details.
However, if you have the mpi4py Python package installed and uncomment
mpi4py code in simple.py, then the above commands will invoke 1 instance
of a P-processor run. Both Python and LAMMPS will run on P processors.
The job will read the input file and write a single log.lammps file.
The split.py script can also be run in parallel. It uses mpi4py version
2.0.0 (or later), which makes it possible to pass a communicator when
creating the LAMMPS object and thus run multiple instances of LAMMPS at
the same time, each on a different subset of MPI ranks. Or run LAMMPS
on one subset and some other program on the rest of the MPI ranks,
concurrently. See comments in the split.py script for more details.

3
python/lammps/__init__.py
View File

@ -23,6 +23,9 @@ def get_version_number():
if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
return 0
if version_info.major < 3 or (version_info.major == 3 and version_info.minor < 6):
raise SystemError('LAMMPS only supports Python version 3.6 or later')
vstring = None
if version_info.major == 3 and version_info.minor >= 8:
from importlib.metadata import version, PackageNotFoundError

16
python/lammps/core.py
View File

@ -83,8 +83,6 @@ class command_wrapper(object):
def _wrap_args(self, x):
if callable(x):
if sys.version_info < (3,):
raise Exception("Passing functions or lambdas directly as arguments is only supported in Python 3 or newer")
import hashlib
import __main__
sha = hashlib.sha256()
@ -105,11 +103,6 @@ class command_wrapper(object):
all the arguments, concatinates them to a single string, and executes it using
:py:meth:`lammps.command`.
Starting with Python 3.6 it also supports keyword arguments. key=value is
transformed into 'key value'. Note, since these have come last in the
parameter list, only a subset of LAMMPS commands can be used with this
syntax.
LAMMPS commands that accept callback functions (such as fix python/invoke)
can be passed functions and lambdas directly. The first argument of such
callbacks will be an lammps object constructed from the passed LAMMPS
@ -121,9 +114,6 @@ class command_wrapper(object):
def handler(*args, **kwargs):
cmd_args = [name] + [str(self._wrap_args(x)) for x in args]
if len(kwargs) > 0 and sys.version_info < (3,6):
raise Exception("Keyword arguments are only supported in Python 3.6 or newer")
# Python 3.6+ maintains ordering of kwarg keys
for k in kwargs.keys():
cmd_args.append(k)
@ -530,16 +520,10 @@ class lammps(object):
else:
# magic to convert ptr to ctypes 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))
# check if library initilialization failed
if not self.lmp:

4
src/KOKKOS/mliap_model_python_kokkos.cpp
View File

@ -68,12 +68,12 @@ MLIAPModelPythonKokkos<DeviceType>::MLIAPModelPythonKokkos(LAMMPS *lmp, char *co
// Recipe from lammps/src/pair_python.cpp :
// add current directory to PYTHONPATH
PyObject *py_path = PySys_GetObject((char *) "path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
PyList_Append(py_path, PyUnicode_FromString("."));
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
if (potentials_path != nullptr) {
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
}
PyGILState_Release(gstate);
if (coefffilename) read_coeffs(coefffilename);

4
src/ML-IAP/mliap_model_python.cpp
View File

@ -62,12 +62,12 @@ MLIAPModelPython::MLIAPModelPython(LAMMPS *lmp, char *coefffilename, bool is_chi
// Recipe from lammps/src/pair_python.cpp :
// add current directory to PYTHONPATH
PyObject *py_path = PySys_GetObject((char *) "path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
PyList_Append(py_path, PyUnicode_FromString("."));
// if LAMMPS_POTENTIALS environment variable is set, add it to PYTHONPATH as well
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
if (potentials_path != nullptr) {
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
}
PyGILState_Release(gstate);
if (coefffilename) read_coeffs(coefffilename);

24
src/Makefile
View File

@ -2,6 +2,12 @@
SHELL = /bin/bash
PYTHON = python
PYTHON_VERSION=$(word 2,$(shell $(PYTHON) -V 2>&1 | tr '.' ' '))
ifeq ($(PYTHON_VERSION),2)
PYTHON_CHECK=@echo LAMMPS requires Python 3. Try: 'make PYTHON=python3 ...' ; exit 1
else
PYTHON_CHECK=@echo
endif
DYN_LIB = -ldl
#.IGNORE:
@ -276,7 +282,7 @@ LIBDIR = $(@:lib-%=%)
# List of all targets
help:
@echo ''
$(PYTHON_CHECK)
@echo 'make clean-all delete all object files'
@echo 'make clean-machine delete object files for one machine'
@echo 'make mpi-stubs build dummy MPI library in STUBS'
@ -378,6 +384,7 @@ gitversion:
# shared = shared compile in Obj_shared_machine
.DEFAULT:
$(PYTHON_CHECK)
@if [ $@ = "serial" ]; \
then cd STUBS; $(MAKE); cd ..; fi
@test -f MAKE/Makefile.$@ -o -f MAKE/OPTIONS/Makefile.$@ -o \
@ -465,6 +472,7 @@ mpi-stubs:
sinclude ../lib/python/Makefile.lammps
install-python:
$(PYTHON_CHECK)
@rm -rf ../python/build
@$(PYTHON) ../python/install.py -p ../python/lammps -l ../src/liblammps.so -w $(PWD) -v $(PWD)/version.h
@ -483,49 +491,59 @@ tar:
check: check-whitespace check-permissions check-homepage check-errordocs check-fmtlib check-docs check-version
check-whitespace:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/whitespace.py ..
fix-whitespace:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/whitespace.py .. -f
check-permissions:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/permissions.py ..
fix-permissions:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/permissions.py .. -f
check-homepage:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/homepage.py ..
fix-homepage:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/homepage.py .. -f
check-errordocs:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/errordocs.py ..
fix-errordocs:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/errordocs.py .. -f
check-fmtlib:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/fmtlib.py ..
fix-fmtlib:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/fmtlib.py .. -f
check-docs:
$(PYTHON_CHECK)
$(MAKE) $(MFLAGS) -C ../doc anchor_check style_check package_check role_check
check-version:
$(PYTHON_CHECK)
$(PYTHON) ../tools/coding_standard/versiontags.py .. || echo
format-src:
clang-format -i --verbose --style=file *.cpp *.h */*.cpp */*.h
format-tests:
clang-format -i --verbose --style=file ../unittest/*/*.cpp ../unittest/*/*.h
# Package management
package:

2
src/PYTHON/fix_python_invoke.cpp
View File

@ -70,7 +70,7 @@ FixPythonInvoke::FixPythonInvoke(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Could not find Python function");
}
lmpPtr = PY_VOID_POINTER(lmp);
lmpPtr = PyCapsule_New((void *)lmp, nullptr, nullptr);
// nvalid = next step on which end_of_step or post_force does something
// add nextvalid() to all computes that store invocation times

4
src/PYTHON/fix_python_move.cpp
View File

@ -44,7 +44,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
// add current directory to PYTHONPATH
PyObject *py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
PyList_Append(py_path, PyUnicode_FromString("."));
// create integrator instance
@ -73,7 +73,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Could not find integrator class {} in module {}", cls_name, module_name);
}
PyObject *ptr = PY_VOID_POINTER(lmp);
PyObject *ptr = PyCapsule_New((void *)lmp, nullptr, nullptr);
PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr);
Py_CLEAR(ptr);

4
src/PYTHON/pair_python.cpp
View File

@ -54,14 +54,14 @@ PairPython::PairPython(LAMMPS *lmp) : Pair(lmp) {
PyUtils::GIL lock;
PyObject *py_path = PySys_GetObject((char *)"path");
PyList_Append(py_path, PY_STRING_FROM_STRING("."));
PyList_Append(py_path, PyUnicode_FromString("."));
// if LAMMPS_POTENTIALS environment variable is set,
// add it to PYTHONPATH as well
const char *potentials_path = getenv("LAMMPS_POTENTIALS");
if (potentials_path != nullptr) {
PyList_Append(py_path, PY_STRING_FROM_STRING(potentials_path));
PyList_Append(py_path, PyUnicode_FromString(potentials_path));
}
}

21
src/PYTHON/python_compat.h
View File

@ -16,22 +16,11 @@
#include <Python.h>
// Wrap API changes between Python 2 and 3 using macros
#if PY_MAJOR_VERSION == 2
#if defined(_MSC_VER) || defined(__MINGW32__)
#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
#define PY_LONG_FROM_STRING(X) std::stoll(X)
#else
#define PY_INT_FROM_LONG(X) PyInt_FromLong(X)
#define PY_INT_AS_LONG(X) PyInt_AsLong(X)
#define PY_LONG_FROM_STRING(X) std::stol(X)
#if PY_VERSION_HEX < 0x030600f0
#error Python version 3.6 or later is required by LAMMPS
#endif
#define PY_STRING_FROM_STRING(X) PyString_FromString(X)
#define PY_VOID_POINTER(X) PyCObject_FromVoidPtr((void *) X, nullptr)
#define PY_STRING_AS_STRING(X) PyString_AsString(X)
#elif PY_MAJOR_VERSION == 3
// Wrap API differences between platforms using macros
#if defined(_MSC_VER) || defined(__MINGW32__)
#define PY_INT_FROM_LONG(X) PyLong_FromLongLong(X)
#define PY_INT_AS_LONG(X) PyLong_AsLongLong(X)
@ -41,9 +30,5 @@
#define PY_INT_AS_LONG(X) PyLong_AsLong(X)
#define PY_LONG_FROM_STRING(X) std::stol(X)
#endif
#define PY_STRING_FROM_STRING(X) PyUnicode_FromString(X)
#define PY_VOID_POINTER(X) PyCapsule_New((void *) X, nullptr, nullptr)
#define PY_STRING_AS_STRING(X) PyUnicode_AsUTF8(X)
#endif
#endif

8
src/PYTHON/python_impl.cpp
View File

@ -361,12 +361,12 @@ void PythonImpl::invoke_function(int ifunc, char *result)
if (!str)
error->all(FLERR, "Could not evaluate Python function {} input variable: {}",
pfuncs[ifunc].name, pfuncs[ifunc].svalue[i]);
pValue = PY_STRING_FROM_STRING(str);
pValue = PyUnicode_FromString(str);
} else {
pValue = PY_STRING_FROM_STRING(pfuncs[ifunc].svalue[i]);
pValue = PyUnicode_FromString(pfuncs[ifunc].svalue[i]);
}
} else if (itype == PTR) {
pValue = PY_VOID_POINTER(lmp);
pValue = PyCapsule_New((void *)lmp, nullptr, nullptr);
} else {
error->all(FLERR, "Unsupported variable type: {}", itype);
}
@ -397,7 +397,7 @@ void PythonImpl::invoke_function(int ifunc, char *result)
auto value = fmt::format("{:.15g}", PyFloat_AsDouble(pValue));
strncpy(result, value.c_str(), Variable::VALUELENGTH - 1);
} else if (otype == STRING) {
const char *pystr = PY_STRING_AS_STRING(pValue);
const char *pystr = PyUnicode_AsUTF8(pValue);
if (pfuncs[ifunc].longstr)
strncpy(pfuncs[ifunc].longstr, pystr, pfuncs[ifunc].length_longstr);
else

3
src/safe_pointers.h
View File

@ -17,6 +17,7 @@
// collection of smart pointers for specific purposes
#include <cstdio>
#include <utility>
namespace LAMMPS_NS {
@ -36,7 +37,7 @@ class SafeFilePtr {
SafeFilePtr(FILE *_fp) : fp(_fp) {};
SafeFilePtr(const SafeFilePtr &) = delete;
SafeFilePtr(const SafeFilePtr &&) = delete;
SafeFilePtr(SafeFilePtr &&o) noexcept : fp(std::exchange(o.fp, nullptr)) {}
SafeFilePtr &operator=(const SafeFilePtr &) = delete;
~SafeFilePtr()