https://github.com/readdy/readdy

Python / C++ based particle reaction-diffusion simulator
https://github.com/readdy/readdy

cplusplus particles python reaction-diffusion simulation

Last synced: about 2 months ago
JSON representation

Python / C++ based particle reaction-diffusion simulator

• Host: GitHub
• URL: https://github.com/readdy/readdy
• Owner: readdy
• License: bsd-3-clause
• Created: 2016-05-24T09:41:44.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2022-07-11T14:14:21.000Z (about 3 years ago)
• Last Synced: 2025-03-17T17:21:31.334Z (7 months ago)
• Topics: cplusplus, particles, python, reaction-diffusion, simulation
• Language: C++
• Homepage: https://readdy.github.io/
• Size: 7.14 MB
• Stars: 59
• Watchers: 5
• Forks: 12
• Open Issues: 17
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

          
# ![ReaDDy](https://readdy.github.io/assets/readdy_black_150px.png "ReaDDy logo") #

[![Build Status](https://dev.azure.com/clonker/readdy/_apis/build/status/readdy.readdy?branchName=master)](https://dev.azure.com/clonker/readdy/_build/latest?definitionId=5&branchName=master)

ReaDDy (**Rea**ction **D**iffusion **Dy**namics) is an open source particle based reaction-diffusion simulator that can be configured and run via Python.

Currently supported platforms are Mac and Linux.

# Installation

The preferred way of installing the software is by using the conda package manager:

```bash

# optional: create environment for readdy, switch to that environment

conda create -n readdy

conda activate readdy

# add conda-forge channel

conda config --env --add channels conda-forge

# install readdy with a specified Python version

conda install python=3.9 readdy

```

# Documentation

A documentation and a few examples are provided at [https://readdy.github.io/](https://readdy.github.io/).

# Core features

- particle based simulation of reaction-diffusion systems in 3D

- particles diffuse via Brownian dynamics

- reactions between single instances of particles (unimolecularly and bimolecularly)

- particle interaction potentials for modeling

  - space exclusion

  - molecular crowding

  - aggregation

- particle complexes via harmonic bonds, angles, and cosine dihedrals for modeling, e.g.,

  - domain structure

  - polymer chains

- spatially and temporally triggered changes in the particle complexes

- simulation output in a compact hdf5 file

- single-threaded and pthread-parallelized implementations available