12.10. Call Python from a LAMMPS input script
LAMMPS has several commands which can be used to invoke Python code directly from an input script:
The python command which can be used to define and execute a Python function that you write the code for. The Python function can also be assigned to a LAMMPS python-style variable via the variable command. Each time the variable is evaluated, either in the LAMMPS input script itself, or by another LAMMPS command that uses the variable, this will trigger the Python function to be invoked.
The Python code for the function can be included directly in the input script or in an auxiliary file. The function can have arguments which are mapped to LAMMPS variables (also defined in the input script) and it can return a value to a LAMMPS variable. This is thus a mechanism for your input script to pass information to a piece of Python code, ask Python to execute the code, and return information to your input script.
Note that a Python function can be arbitrarily complex. It can import other Python modules, instantiate Python classes, call other Python functions, etc. The Python code that you provide can contain more code than the single function. It can contain other functions or Python classes, as well as global variables or other mechanisms for storing state between calls from LAMMPS to the function.
The Python function you provide can consist of “pure” Python code that only performs operations provided by standard Python. However, the Python function can also “call back” to LAMMPS through its Python-wrapped library interface, in the manner described in the Python run doc page. This means it can issue LAMMPS input script commands or query and set internal LAMMPS state. As an example, this can be useful in an input script to create a more complex loop with branching logic, than can be created using the simple looping and branching logic enabled by the next and if commands.
See the python doc page and the variable doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations and callbacks to LAMMPS.
The fix python/invoke command can execute Python code at selected timesteps during a simulation run.
The pair_style python command allows you to define pairwise potentials as python code which encodes a single pairwise interaction. This is useful for rapid development and debugging of a new potential.
To use any of these commands, you only need to build LAMMPS with the PYTHON package installed:
make yes-python make machine
Note that this will link LAMMPS with the Python library on your system, which typically requires several auxiliary system libraries to also be linked. The list of these libraries and the paths to find them are specified in the lib/python/Makefile.lammps file. You need to insure that file contains the correct information for your version of Python and your machine to successfully build LAMMPS. See the lib/python/README file for more info.
If you want to write Python code with callbacks to LAMMPS, then you must also follow the steps summarized in the Python run doc page. I.e. you must build LAMMPS as a shared library and insure that Python can find the python/lammps.py file and the shared library.