Merge pull request #1375 from akohlmey/install-python-for-cmake

endif()

if(PKG_PYTHON)

  find_package(PythonInterp REQUIRED)

  find_package(PythonLibs REQUIRED)

  add_definitions(-DLMP_PYTHON)

  include_directories(${PYTHON_INCLUDE_DIR})

  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})

  if(BUILD_LIB AND BUILD_SHARED_LIBS)

    if(NOT PYTHON_INSTDIR)

      execute_process(COMMAND ${PYTHON_EXECUTABLE}

        -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"

        OUTPUT_VARIABLE PYTHON_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)

    endif()

    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})

  endif()

endif()

find_package(JPEG QUIET)

  DESTINATION ${CMAKE_INSTALL_SYSCONFDIR}/profile.d

)

###############################################################################

# Install LAMMPS lib and python module into site-packages folder with

# "install-python" target.  Behaves exactly like "make install-python" for

# conventional build.  Only available, if a shared library is built.

# This is primarily for people that only want to use the Python wrapper.

###############################################################################

if(BUILD_LIB AND BUILD_SHARED_LIBS)

  find_package(PythonInterp)

  if (PYTHONINTERP_FOUND)

    add_custom_target(

      install-python

      ${PYTHON_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h

      -m ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py

      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}

      WORKING_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/../python

      COMMENT "Installing LAMMPS Python module")

  else()

    add_custom_target(

      install-python

      ${CMAKE_COMMAND} -E echo "Must have Python installed to install the LAMMPS Python module")

  endif()

else()

  add_custom_target(

    install-python

    ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")

endif()

###############################################################################

# Add LAMMPS python module to "install" target. This is taylored for building

# LAMMPS for package managers and with different prefix settings.

# This requires either a shared library or that the PYTHON package is included.

###############################################################################

if((BUILD_LIB AND BUILD_SHARED_LIBS) OR (PKG_PYTHON))

  find_package(PythonInterp)

  if (PYTHONINTERP_FOUND)

    execute_process(COMMAND ${PYTHON_EXECUTABLE}

      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"

      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)

    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")

    install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../python/lammps.py DESTINATION ${PYTHON_INSTDIR})

  endif()

endif()

###############################################################################

# Testing

#

MOLECULE package and compile LAMMPS with C++ exceptions, PNG, JPEG and FFMPEG

output support enabled.

Step 1a: For the CMake based build system, the steps are:

mkdir $LAMMPS_DIR/build-shared

cd  $LAMMPS_DIR/build-shared :pre

# MPI, PNG, Jpeg, FFMPEG are auto-detected

cmake ../cmake -DPKG_MOLECULE=yes -DLAMMPS_EXCEPTIONS=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes

make :pre

Step 1b: For the legacy, make based build system, the steps are:

cd $LAMMPS_DIR/src :pre

# add packages if necessary

Step 2: Installing the LAMMPS Python package :h6

PyLammps is part of the lammps Python package. To install it simply install

that package into your current Python installation.

that package into your current Python installation with:

cd $LAMMPS_DIR/python

python install.py :pre

make install-python :pre

NOTE: Recompiling the shared library requires re-installing the Python package

Creating a virtualenv with lammps installed :h6

# create virtualenv name 'testing' :pre

# create virtualenv named 'testing'

virtualenv $HOME/python/testing :pre

# activate 'testing' environment

source testing/bin/activate :pre

source $HOME/python/testing/bin/activate :pre

Now configure and compile the LAMMPS shared library as outlined above.

When using CMake and the shared library has already been build, you

need to re-run CMake to update the location of the python executable

to the location in the virtual environment with:

cmake . -DPYTHON_EXECUTABLE=$(which python) :pre

# install LAMMPS package in virtualenv

(testing) cd $LAMMPS_DIR/python

(testing) python install.py :pre

(testing) make install-python :pre

# install other useful packages

(testing) pip install matplotlib jupyter mpi4py :pre

For Python to invoke LAMMPS, there are 2 files it needs to know about:

python/lammps.py

src/liblammps.so :ul

liblammps.so or liblammps.dylib :ul

Lammps.py is the Python wrapper on the LAMMPS library interface.

Liblammps.so is the shared LAMMPS library that Python loads, as

described above.

The python source code in lammps.py is the Python wrapper on the

LAMMPS library interface. The liblammps.so or liblammps.dylib file

is the shared LAMMPS library that Python loads dynamically.

You can insure Python can find these files in one of two ways:

You can achieve that Python can find these files in one of two ways:

set two environment variables

run the python/install.py script :ul

set two environment variables pointing to the location in the source tree

run "make install-python" or run the python/install.py script explicitly :ul

When calling "make install-python" LAMMPS will try to install the

python module and the shared library into the python site-packages folders;

either the system-wide ones, or the local users ones (in case of insufficient

permissions for the global install). Python will then find the module

and shared library file automatically. The exact location of these folders

depends on your python version and your operating system.

If you set the paths to these files as environment variables, you only

have to do it once.  For the csh or tcsh shells, add something like

setenv PYTHONPATH $\{PYTHONPATH\}:/home/sjplimp/lammps/python

setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre

If you use the python/install.py script, you need to invoke it every

time you rebuild LAMMPS (as a shared library) or make changes to the

python/lammps.py file.

You can invoke install.py from the python directory as

% python install.py \[libdir\] \[pydir\] :pre

The optional libdir is where to copy the LAMMPS shared library to; the

default is /usr/local/lib.  The optional pydir is where to copy the

lammps.py file to; the default is the site-packages directory of the

version of Python that is running the install script.

Note that libdir must be a location that is in your default

LD_LIBRARY_PATH, like /usr/local/lib or /usr/lib.  And pydir must be a

location that Python looks in by default for imported modules, like

its site-packages dir.  If you want to copy these files to

non-standard locations, such as within your own user space, you will

need to set your PYTHONPATH and LD_LIBRARY_PATH environment variables

accordingly, as above.

On MacOSX you may also need to set DYLD_LIBRARY_PATH accordingly.

For Bourne/Korn shells accordingly into the corresponding files using

the "export" shell builtin.

If the install.py script does not allow you to copy files into system

directories, prefix the python command with "sudo".  If you do this,

make sure that the Python that root runs is the same as the Python you

run.  E.g. you may need to do something like

If you use "make install-python" or the python/install.py script, you need

to invoke it every time you rebuild LAMMPS (as a shared library) or

make changes to the python/lammps.py file, so that the site-packages

files are updated with the new version.

% sudo /usr/local/bin/python install.py \[libdir\] \[pydir\] :pre

If the default settings of "make install-python" are not what you want,

you can invoke install.py from the python directory manually as

You can also invoke install.py from the make command in the src

directory as

% python install.py -m \<python module\> -l <shared library> -v <version.h file> \[-d \<pydir\>\] :pre

% make install-python :pre

The -m flag points to the lammps.py python module file to be installed,

the -l flag points to the LAMMPS shared library file to be installed,

the -v flag points to the version.h file in the LAMMPS source

and the optional -d flag to a custom (legacy) installation folder :ul

In this mode you cannot append optional arguments.  Again, you may

need to prefix this with "sudo".  In this mode you cannot control

which Python is invoked by root.

If you use a legacy installation folder, you will need to set your

PYTHONPATH and LD_LIBRARY_PATH (and/or DYLD_LIBRARY_PATH) environment

variables accordingly, as described above.

Note that if you want Python to be able to load different versions of

the LAMMPS shared library (see "this section"_Python_shlib.html), you will

LAMMPS can work together with Python in three ways.  First, Python can

wrap LAMMPS through the its "library interface"_Howto_library.html, so

that a Python script can create one or more instances of LAMMPS and

launch one or more simulations.  In Python lingo, this is "extending"

Python with LAMMPS.

launch one or more simulations.  In Python lingo, this is called

"extending" Python with a LAMMPS module.

Second, a lower-level Python interface can be used indirectly through

provided PyLammps and IPyLammps wrapper classes, written in Python.

the provided PyLammps and IPyLammps wrapper classes, written in Python.

These wrappers try to simplify the usage of LAMMPS in Python by

providing an object-based interface to common LAMMPS functionality.

They also reduces the amount of code necessary to parameterize LAMMPS

accessible.

Third, LAMMPS can use the Python interpreter, so that a LAMMPS

input script can invoke Python code directly, and pass information

back-and-forth between the input script and Python functions you

write.  This Python code can also callback to LAMMPS to query or change

its attributes.  In Python lingo, this is "embedding" Python in

LAMMPS.  When used in this mode, Python can perform operations that

the simple LAMMPS input script syntax cannot.

input script or styles can invoke Python code directly, and pass

information back-and-forth between the input script and Python

functions you write.  This Python code can also callback to LAMMPS

to query or change its attributes through the LAMMPS Python module

mentioned above.  In Python lingo, this is "embedding" Python in

LAMMPS.  When used in this mode, Python can perform script operations

that the simple LAMMPS input script syntax can not.

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