Resources

• Github and Gitlab repositories.
• Useful analysis scripts
• Posters at past conferences.
• Books on Methods for Statistical Mechanics
• Suggested Molecular Dynamics packages
• Instructions on how to use the shell
• Instructions on Python
• Mathematical libraries
• Lectures

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Applications

Vicsek model on Heroku https://vicsek.herokuapp.com

Scripts

Useful scripts for analysis, post-processing or just didactical purposes. Click here.

Posters

Large scale posters accepted in past conferences. Click here.

Methods for Statistical Mechanics

Suggested reading:

• Daan Frenkel and Berend Smit, Understanding Molecular Simulation http://www.sciencedirect.com/science/book/978012267351 [in particular chapter 1,2,3,4]
• Werner Krauth, Statistical Mechanics: Algorithms and Computations   http://ukcatalogue.oup.com/product/9780198515364.do

Molecular Dynamics and Monte Carlo

• LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) http://lammps.sandia.gov
• Event driven molecular dynamics, DynamO, http://dynamomd.org
• DL_MONTE, http://www.scd.stfc.ac.uk//research/app/ccg/software/DL_MONTE/40692.aspx

Using the Terminal

• Tutorial for the usage of the command line https://www.codecademy.com/courses/learn-the-command-line
• Another tutorial for the usage of the shell http://linuxsurvival.com/
• Bash tutorial http://ryanstutorials.net/bash-scripting-tutorial/
• Submitting a job to an HPC cluster and some useful UNIX commands https://www.acrc.bris.ac.uk/acrc/pdf/BlueCrystalRefCard2.pdf

Python

• Tutorial for Python basics: http://www.codecademy.com/
• Python for scientific computing: http://scipy-lectures.github.io/index.html
• Anaconda Python (recommended for Windows) https://www.continuum.io/downloads

Mathematical methods

• Computational Geometry Algorithms Library, http://www.cgal.org

Lecture slides

• Undulatory nature of light: [pdf]