HOOMD-blue tutorials

These jupyter notebooks provide a tutorial for the HOOMD-blue simulation software and are included in HOOMD-blue's documentation.

Outline

• Introducing HOOMD-blue
• Introducing Molecular Dynamics
• Logging
• Parallel Simulations With MPI
• Custom Actions In Python
• Organizing and Executing Simulations
• Modelling Rigid Bodies
• Modelling Patchy Particles

Executing the tutorials

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

Clone the hoomd-examples repository and start jupyter notebook

$ git clone https://github.com/glotzerlab/hoomd-examples
$ cd hoomd-examples
$ jupyter lab

Prerequisites

These examples use the following python packages:

• fresnel
• freud
• GSD
• HOOMD-blue
• jupyterlab
• matplotlib
• pillow

Conda users can install these from conda-forge:

conda install -c conda-forge fresnel freud  gsd hoomd jupyterlab matplotlib