Python package with a set of functions for calculating the g(r) using the Widom test-particle insertion method, and/or for fitting the g(r) to solve for the pair-potential using particle coordinates from e.g. confocal microscopy or cryo-TEM.
The codes for this package were developed as part of the work in reference [1], where the iterative use of test-particle insertion to solve for the pair potential was based on [2] with correction for periodic or finite boundary conditions based on equations described in [3,4].
[1] Bransen, M. (2024). Measuring interactions between colloidal (nano)particles. PhD thesis, Utrecht University.
[2] Stones, A. E., Dullens, R. P. A., & Aarts, D. G. A. L. (2019). Model-Free Measurement of the Pair Potential in Colloidal Fluids Using Optical Microscopy. Physical Review Letters, 123(9), 098002.
[3] Seserno, M. (2014). How to calculate a three-dimensional g(r) under periodic boundary conditions.
[4] Kopera, B. A. F., & Retsch, M. (2018). Computing the 3D Radial Distribution Function from Particle Positions: An Advanced Analytic Approach. Analytical Chemistry, 90(23), 13909–13914.
This package can be installed directly from GitHub using pip:
pip install git+https://github.com/MaartenBransen/potentials_from_particle_insertion
When using the Anaconda distribution, it is safer to run the conda version of pip as follows:
conda install pip
conda install git
pip install git+https://github.com/MaartenBransen/potentials_from_particle_insertion
To update to the most recent version, use pip install with the --upgrade flag set:
pip install --upgrade git+https://github.com/MaartenBransen/potentials_from_particle_insertion
After installing it can be imported like any normal package by writing e.g.
import potentials_from_particle_insertionto import everything, or something like
from potentials_from_particle_insertion import rdf_dist_hist_3d, run_iterationto only import specific functions.
For a complete API reference see the documentation or download index.html from the gh-pages branch and open it with your browser. There are example usage scripts in /examples/ for solving for the pair-potential of a randomly generated ideal gas in 2D and 3D in periodic and nonperiodic boundary conditions respectively, as well as examples for multi-component systems and using fit functions.