2.1. Overview

The LAMMPS distribution includes a python directory with the Python code needed to run LAMMPS from Python. The python/lammps package contains the “lammps” Python module that wraps the LAMMPS C-library interface. This module makes it is possible to do the following either from a Python script, or interactively from a Python prompt:

  • create one or more instances of LAMMPS

  • invoke LAMMPS commands or read them from an input script

  • run LAMMPS incrementally

  • extract LAMMPS results

  • and modify internal LAMMPS data structures.

From a Python script you can do this in serial or in parallel. Running Python interactively in parallel does not generally work, unless you have a version of Python that extends Python to enable multiple instances of Python to read what you type.

To do all of this, you must build LAMMPS in “shared” mode and make certain that your Python interpreter can find the lammps Python package and the LAMMPS shared library file.

The Python wrapper for LAMMPS uses the ctypes package in Python, which auto-generates the interface code needed between Python and a set of C-style library functions. Ctypes has been part of the standard Python distribution since version 2.5. You can check which version of Python you have by simply typing “python” at a shell prompt. Below is an example output for Python version 3.8.5.

$ python
Python 3.8.5 (default, Aug 12 2020, 00:00:00)
[GCC 10.2.1 20200723 (Red Hat 10.2.1-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

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), 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.

LAMMPS can work together with Python in three ways. First, Python can wrap LAMMPS through the its library interface, so that a Python script can create one or more instances of LAMMPS and launch one or more simulations. In Python terms, this is referred to as “extending” Python with a LAMMPS module.

_images/python-invoke-lammps.png

Launching LAMMPS via Python

Second, the lower-level Python interface in the lammps Python class can be used indirectly through the provided PyLammps and IPyLammps wrapper classes, also written in Python. These wrappers try to simplify the usage of LAMMPS in Python by providing a more object-based interface to common LAMMPS functionality. They also reduce the amount of code necessary to parameterize LAMMPS scripts through Python and make variables and computes directly accessible.

_images/pylammps-invoke-lammps.png

Using the PyLammps / IPyLammps wrappers

Third, LAMMPS can use the Python interpreter, so that a LAMMPS 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 call back to LAMMPS to query or change its attributes through the LAMMPS Python module mentioned above. In Python terms, this is called “embedding” Python into LAMMPS. When used in this mode, Python can perform script operations that the simple LAMMPS input script syntax can not.

_images/lammps-invoke-python.png

Calling Python code from LAMMPS