Midterm Project 2020

Your project is to write, in teams of three students, a Python molecular dynamics (MD) code to simulate a droplet of liquid Argon. We want to study how varying some of the simulation parameters affects the accuracy of the simulations and extract thermodynamic properties from the simulations. You will write a short "letter"-style paper to communicate, discuss and summarize your reasoning and your results.

For details see project_2.pdf. Note the requirements for code and report and note what constitutes admissable collaboration between teams.

Resources

Code

Starter code is available in directory code/. It is explained in the appendices of the write-up project_2.pdf.

Example data

The example directory contains output from a simulation of the Lennard-Jones fluid. You can use it to develop the analysis portion of the project even while your MD code is not yet producing results. The README shows how to read the data.

Submission

1. Create three sub-directories Submission, Grade, and Work.

2. You can try out code in the Work directory but you don’t have to use it if you don’t want to. Your grade with comments will appear in Grade.

3. Create your solution in Submission. Use git to git add files and git commit changes.

   You can create a PDF file or Jupyter notebook inside the Submission directory as well as Python code. Name your files project2.pdf or or project2.ipynb, depending on how you format your work. Files with code (if requested) should be named exactly as required in the assignment.

4. When you are ready to submit your solution, do a final git status to check that you haven’t forgotten anything, commit any uncom- mitted changes, and git push to your GitHub repository. Check on your GitHub repository web page that your files were properly submitted.

   You can push more updates up until the deadline. Changes after the deadline will not be taken into account for grading.