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molecular-dynamics

Molecule visualization

Skeleton code and visualization for a basic molecular dynamics simulator, provided as part of the 15-462/662 final exam at CMU. Visualization via Polyscope.

The code will build and run as-is, but to make the simulator work you will have to implement the routines marked TODO in src/MolecularDynamics.cpp. The correct behavior for these routines is described in the exam found in 15462_Final_FA2021.pdf.

Several test files can be found in the data/ subdirectory.

Note that you do not have to build and run this version of the code for the exam (which can be more difficult to compile, due to the visualization routines). It is provided "just for fun." See Piazza for the official exam code.

Disclaimer: This simulator is an extremely simplified version of a real molecular dynamics simulator, intended purely for pedagogical purposes. It should not be used for serious scientific work.

Build the code

Unix-like machines: configure (with cmake) and compile

cd molecular-dynamics
mkdir build
cd build
cmake ..
make -j6

Windows / Visual Studio

Install CMake, and use either the CMake GUI or the command line interface (as on unix) to generate a Visual Studio solution. Build the solution with Visual Studio.

Run the code

./bin/md /path/to/a/molecule.mol

Edit the code

Copy your solutions into src/MolecularDynamics.cpp. Modify the main file src/main.cpp to change UI/visualization. CMakeLists.txt contains a few comments for adding additional files.