pykbi: Python module to work on radial distribution functions and Kirkwood-Buff integrals

Kirkwood-Buff theory bridges microscopic structure and macroscopic properties of isotropic liquids. The classical version of the theory deals with open and infinite systems[1], while the new correction allows us to work on closed and finite systems[2]. The code contains modules to correct finite-size effects in Radial Distribution functions (RDFs) from Molecular Simulations, and integrate RDFs obtained from both open and closed ensembles.

The methods in this module is included in the references below. pykbi works with radial distribution functions obtained from various softwares, so it is up to the user to read in and make radial distance and the pair correlation function available as vectors. The integral can be done for both open and closed systems. In addition, it has included correction methods to correct for finite-size effects.

This package accompanies the paper "Kirkwood-Buff integrals from molecular simulation" [3].

Installation

The program can be installed from pip, using:

pip3 install pykbi

or it can be installed directly from github:

pip3 install git+git://github.com/sondresc/pykbi.git

or you can clone the code, and install manually:

git clone https://github.com/sondresc/pykbi
cd pykbi
python setup.py install

References

1. J. G. Kirkwood and F. P. Buff, J. Chem. Phys. 19, 774(1951).
2. P. Kruger, S. K. Schnell, D. Bedeaux, S. Kjelstrup, T. J. H. Vlugt, J.-M. Simon, J. Phys. Chem. Lett. 4, 2(2013).
3. N. Dawass, P. Kruger, S. K. Schnell, J.-M. Simon, T. J. H. Vlugt, Fluid Phase Equilibria 486, (2019).