HOW TO RUN THE MOLECULAR DYNAMICS EXERCISES

The Molecular Dynamics exercises were originally constructed to generate some animations that show movies of simulated atoms flying around under their mutual interaction.  This was done using the Visual Python (VPython) package, which provides graphical primitives (spheres, lines, cylinders, etc.) whose positions, size, and other properties can be updated within a simulation.  As a result, VPython has been used by many in conjunction with physical simulations, to describe the motion of bodies under various forces.

We have upgraded the core simulation software to be compatible with Python version 3, but VPython has not yet been upgraded as such.  Therefore, while the computational exercises can be carried out, the accompanying animations are not readily accessible.  This is not a big deal, but there is a workaround, if you are using the Cornell PECF lab machines for your work in the course.

(1) First, go to a directory containing a version of the course software compatible with Python version 2.7: 

cd /home/Faculty/myers/ComputationalMethods/ComputerExercises/PythonSoftware2

(2) Next, run the answer file for one of the Molecular Dynamics exercises, such as ExponentialAtmosphereA.py, explicitly invoking a Python 2.7 version of the interpreter:

python2.7 ExponentialAtmosphereA.py

(3) You should see atoms flying around in a VPython window, as part of the exercise demo.