https://github.com/by256/rdfpy

A Python module for fast computation of 2D and 3D radial distribution functions (RDFs).
https://github.com/by256/rdfpy

chemistry pair-correlation-function pair-distribution-function particles physics radial-distribution-function rdf scattering solid-state-chemistry solid-state-physics

Last synced: 8 months ago
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A Python module for fast computation of 2D and 3D radial distribution functions (RDFs).

• Host: GitHub
• URL: https://github.com/by256/rdfpy
• Owner: by256
• License: mit
• Created: 2020-06-18T09:04:53.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2023-12-23T22:14:32.000Z (over 2 years ago)
• Last Synced: 2025-08-25T16:13:39.517Z (10 months ago)
• Topics: chemistry, pair-correlation-function, pair-distribution-function, particles, physics, radial-distribution-function, rdf, scattering, solid-state-chemistry, solid-state-physics
• Language: Python
• Homepage: https://rdfpy.readthedocs.io/
• Size: 3.33 MB
• Stars: 31
• Watchers: 3
• Forks: 13
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# 

[![Build Status](https://travis-ci.org/by256/rdfpy.svg?branch=master)](https://travis-ci.org/by256/rdfpy)

[![Documentation Status](https://readthedocs.org/projects/rdfpy/badge/?version=latest)](https://rdfpy.readthedocs.io/en/latest/?badge=latest)

[![PyPI version](https://badge.fury.io/py/rdfpy.svg)](https://pypi.org/project/rdfpy/)

[![License](http://img.shields.io/:license-mit-blue.svg?style=flat-square)](https://github.com/by256/rdfpy/blob/master/LICENSE)

**rdfpy** is a Python module for fast computation of 2D and 3D radial distribution functions (RDFs).

## Installation

```shell

$ pip install rdfpy

```

## Usage

```python

import numpy as np

from rdfpy import rdf

# create random particle coordinates in a 20x20x20 box

coords = np.random.uniform(0.0, 20.0, size=(2500, 3))  

# compute radial distribution function with step size = 0.1

g_r, radii = rdf(coords, dr=0.1)

```

You can find a more detailed example in the [Documentation](https://rdfpy.readthedocs.io/).

**Note:** In order for **rdfpy** to work correctly, your particles should spatially be in a cuboidal box, where the entire box is filled with particles.

## How does it work?

**rdfpy** achieves significant speed-up due to:

- **Fast nearest-neighbor look-up**: a k-d tree is utilized when counting the number of particles as a function of distance from an origin particle.

- **Multiprocessing**: computation of the particle count histogram is parallelized across multiple cores, with each core sharing the aforementioned k-d tree.

## Authors

**rdfpy** was developed by [Batuhan Yildirim](https://by256.github.io/) under the supervision of [Prof. Jacqueline M. Cole](https://www.phy.cam.ac.uk/directory/colej).

## Citation

If you use **rdfpy** in your work, please cite:

```

@software{rdfpy,

  author       = {Batuhan Yildirim and

                  Hamish Galloway Brown},

  title        = {by256/rdfpy: rdfpy-v1.0.0},

  month        = mar,

  year         = 2021,

  publisher    = {Zenodo},

  version      = {v1.0.0},

  doi          = {10.5281/zenodo.4625675},

  url          = {https://doi.org/10.5281/zenodo.4625675}

}

```

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4625675.svg)](https://doi.org/10.5281/zenodo.4625675)

## Funding

This project was financially supported by the [Science and Technology Facilities Council (STFC)](https://stfc.ukri.org/) and the [Royal Academy of Engineering](https://www.raeng.org.uk/) (RCSRF1819\7\10).