nkm-ml / notebook_tutorials

A home for the Jupyter notebook tutorials created by and for our lab

Notebook Tutorials

Use the binder above to use these notebooks in your browser.

Or if you'd like to run these notebooks on your local machine, the conda environment used in these tutorials can be created using the following command:

conda env create -f environment.yml

Once your environment has been created, the environment can be activated and the interactive notebooks run using the following commands:

conda activate cmelab
jupyter lab

Tutorials

These tutorials highlight the following tools from MoSDeF and Glotzer group: mbuild, foyer, hoomd, freud, fresnel

1. Initializing a system to a specific density - MD_density.ipynb This tutorial will explain some of the common pitfalls of initializing a system at high density and how to overcome them by using a "shrink step."
2. Radial Distribution Function - radial-distribution-function.ipynb demonstrates how to calculate the RDF and shows how the temperature affects the system
3. Organic Photovoltaic Simulation - opv_sim.ipynb demonstrates how to set up, run, and analyze a molecular dynamics simulation of a conjugated polymer.
4. Temperature/Thermostat - (WIP) temperature-thermostat.ipynb
5. Intro to Molecular Dynamics - (WIP) MD_intro.ipynb