The LAMMPS distribution includes a
python directory with the Python
code needed to run LAMMPS from Python. The
contains the “lammps” Python that wraps the
LAMMPS C-library interface. This file makes it is possible to do the
following either from a Python script, or interactively from a Python
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
file 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. >>>
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.
Second, the lower-level Python interface in the
class can be used indirectly through the provided
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.
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.