This module is unlike most others in that the code is presented in its entirety, and the exercises consist primarily of running code and analyzing the resulting data.

Linked at the left is Python code that implements the DigitalMaterial library to support molecular dynamics computations. The Python code is adapted from (mostly abandoned) C++ code developed previously as part of the Digital Material project. The original C++ class design is described here. If you're interested in delving into the Python code and adding to it, you might find that design document useful. But for the purposes of this course module, you do not need to access the old C++ implementation.

The simulations include animations that are fun to watch but are not crucial for completing the exercises. You need Visual Python (vpython) to run the animations, although building and/or installing vpython on your own machine can be problematic. vpython is installed on the PECF computer lab machines in Rockefeller B3, so if you are working on your own machine, you might want to login to one of the PECF machines just to run some of the animations.

• Perfume Walk Exercise
• Pressure Exercise
• Equilibration Exercise
• Exponential Atmosphere Exercise
• Pair Distribution Function Exercise
• Instructions for running the MD simulations

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