The module contains patch files for the Stable release 29 October 2020 version of LAMMPS, to enable accessing simulation force-filed parameters from python.
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 or 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
pair_*.cpp files associated with some commonly used pair-potential in LAMMPS as described in
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.
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 https://lammps.sandia.gov/doc/Build.html to build and install LAMMPS along with the applied
patch. Make sure to enable
pkg_python when building.