epipy documentation

This website contains the documentation and tutorials for Epipy: a python interface for EPISOL (kernel for 3DRISM calculations).

Contents:

• Home
• Background for Integral Equation Theory and 3DRISM
• Installing Epipy and EPISOL
• episol package
• Jupyter Notebook Tutorial Gallery

What is this?

Epipy is the python interface for EPISOL and relies on its kernel to perform 3DRISM calculations. Epipy helps the user to setup and automatically modify input files then calls the EPISOL kernel to perform the calculation. Episol solves the 3-dimens ional reference interaction site model (3DRISM) equation.

\(h_v({\bf r}) = c_v({\bf r}) + \sum_{v'}\int \rho_{v'}^b c_{v'}({\bf r}')(h_{vv'}(r_{vv'})+s_{vv'}(r_{vv'}))d^3{\bf r}'\)

Via applying the following closure relation in a sef-consistent manner.

\(h_v({\bf r}) = e ^{-u_v({\bf r})/k_BT+h_v({\bf r})-c_v({\bf r})+B_v({\bf r})} - 1\)

Offering 22 available bridge functionals. Epipy also includes some helpful functions for post-processing, including extratcing compressed 3DRISM output and loading into an array. Calculations require ONLY a topology , and structure file (ideally .gro).

from episol import epipy

example = epipy("structure.gro","topology.top")

Setting grid-resolution, and number of SCF cycles follows:

example.rism(step=1000,resolution=0.5)

and finally, calling the kernel to perform the cacluation

example.kernel()

This writes the relevant grid-based data to a .ts4s file, and epipy will automatically extract our desired values given a selection command

data = example.select_grid('guv')

See our example library for example calculations..

Why?

I originally created epipy for use in high-throughput calculations across a distributed computing environment. It calls on the EPISOL. library to perform 3DRISM calculations. I made epipy fit into one file/module to make it as efficient as possible. Big updates are planned so stay tuned, and report any bugs/issues here.

How to cite

If you liked this. please cite:

Swanson, P. C.; Cao, S.; Huang, X. A Python Tutorial for 3DRISM Solvation Calculations of Chemical and Biological Molecules. The Journal of Chemical Physics 2025, 163 (17). https://doi.org/10.1063/5.0299937.