https://github.com/glotzerlab/hoomd-examples

HOOMD-blue example scripts.
https://github.com/glotzerlab/hoomd-examples

hard-particle hoomd-blue jupyter molecular-dynamics monte-carlo-simulation particle-system python simulation tutorial

Last synced: 2 months ago
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HOOMD-blue example scripts.

• Host: GitHub
• URL: https://github.com/glotzerlab/hoomd-examples
• Owner: glotzerlab
• License: bsd-3-clause
• Created: 2019-02-12T22:04:08.000Z (almost 6 years ago)
• Default Branch: trunk-minor
• Last Pushed: 2024-08-01T13:46:41.000Z (6 months ago)
• Last Synced: 2024-08-01T15:23:03.512Z (6 months ago)
• Topics: hard-particle, hoomd-blue, jupyter, molecular-dynamics, monte-carlo-simulation, particle-system, python, simulation, tutorial
• Language: Jupyter Notebook
• Size: 62 MB
• Stars: 33
• Watchers: 12
• Forks: 15
• Open Issues: 4
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Authors: AUTHORS.md

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README

        
# HOOMD-blue tutorials

These [jupyter] notebooks provide a tutorial for the [HOOMD-blue] simulation software and are

included in HOOMD-blue's [documentation].

[jupyter]: https://jupyter.org

[HOOMD-blue]: https://glotzerlab.engin.umich.edu/hoomd-blue

[documentation]: http://hoomd-blue.readthedocs.io

## Outline

* [Introducing HOOMD-blue](00-Introducing-HOOMD-blue/00-index.ipynb)

* [Introducing Molecular Dynamics](01-Introducing-Molecular-Dynamics/00-index.ipynb)

* [Logging](02-Logging/00-index.ipynb)

* [Parallel Simulations With MPI](03-Parallel-Simulations-With-MPI/00-index.ipynb)

* [Custom Actions In Python](04-Custom-Actions-In-Python/00-index.ipynb)

* [Organizing and Executing Simulations](05-Organizing-and-Executing-Simulations/00-index.ipynb)

* [Modelling Rigid Bodies](06-Modelling-Rigid-Bodies/00-index.ipynb)

* [Modelling Patchy Particles](07-Modelling-Patchy-Particles/00-index.ipynb)

* [Multiparticle Collision Dynamics](09-Multiparticle-Collision-Dynamics/00-index.ipynb)

## Executing the tutorials

You can [install HOOMD-blue] and run these examples interactively.

[install HOOMD-blue]: http://hoomd-blue.readthedocs.io

Clone the **hoomd-examples** repository and open the notebooks with the tool you

prefer.

## Prerequisites

These examples use the following python packages:

* [fresnel](https://github.com/glotzerlab/fresnel)

* [freud](http://glotzerlab.engin.umich.edu/freud/)

* [GSD](https://github.com/glotzerlab/gsd)

* [HOOMD-blue](http://glotzerlab.engin.umich.edu/hoomd-blue/)

* [matplotlib](http://matplotlib.org/)

* [pillow](https://python-pillow.org/)

* [signac](https://signac.io/)

* [signac-flow](https://signac.io/)

You can install these from [conda-forge](https://conda-forge.org/):

```bash

mamba install fresnel freud gsd hoomd matplotlib pillow signac signac-flow

```