The module contains patch files for the Stable release 29 October 2020 version of LAMMPS, to enable accessing simulation force-filed parameters from python.

Purpose of Module

When performing alchemical free energy calculations, it is necessary to change the attributes of various particles in a simulations - Atom properties such as charge and mass or Force field properties such as \epsilon or \sigma of Lennard-Jones potentials.

The LAMMPS library along with its Python interface provides the ability to directly access and change many such attributes in a running simulation. However, for pair potentials while it is possible to change their parameters it is currently not possible to read the existing parameters from a running simulations. This is required for the alchemical free energy calculations using the Particle Insertion approach as described in the Particle Insertion Core module, where the scaling of the forcefield attribute depends on the existing attributes.

This module address this limitation by extending the LAMMPS library and the Python interface to add a function allowing read access to pair-potential parameters. It also adds an extract method to the the pair_*.cpp files associated with some commonly used pair-potential in LAMMPS as described in fix adapt.

Background Information

LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is a very versatile MD engine. The current stable release of which can be obtained from the link LAMMPS stable 29Oct2020. In particular, due to it’s powerful library and python interface it allows great control and easy scripting of any time of simulation

The Particle Insertion approach for alchemical free energy calculations is currently only implemented using the LAMMPS MD engine. The set of patches in this module exist to accommodate the requirements of those modules.

Building and Testing

Download and extract the LAMMPS source. Before building LAMMPS download the patch file and apply the patch using the patch command from the root of the LAMMPS source directory.

patch < lmp_pyExt.patch

Follow the normal LAMMPS building instructions at to build and install LAMMPS along with the applied patch. Make sure to enable pkg_python when building.

Source Code

Available as a patch file from here