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
• Placing Barriers in the Simulation Box
• Multiparticle Collision Dynamics
• Modelling Flexible Active Interfaces

Executing the tutorials

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

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

Prerequisites

These examples use the following python packages:

• fresnel
• freud
• GSD
• HOOMD-blue
• matplotlib
• pillow
• row
• signac

You can install these from conda-forge:

micromamba install fresnel freud gsd hoomd matplotlib pillow row signac