This project was created as a part of the Molecular Dynamics Course at Uni Freiburg. An explanation of the project structure can be found on the report. The link to the large data files is the following.

https://mega.nz/folder/CeBj1SBK#RaQxGveHUBE82Nj6cY-f2Q

The visualization of the project data can be found in results/plots_and_figures.ipynb . A part of the source files used in this project were provided by the lecture content. The complete explanation and bibliography can be found in the report. This project has been build using Ubuntu on WSL, therefore, the possibility of running all sections of this project using alternate configurations/operating systems is not guaranteed. The data for the parallel section (MPI operations) of this project was generated using BwUniCluster 2.0.

The datastructures are provided by the Eigen library and tests are run on the implemented features using Googletest. Ovito is used to visualize the simulation. The plots are made with python using Matplotlib and are managed using a Jupyter notebook.

To build the project, do the following set of commands in the project folder.

mkdir build
cmake -DCMAKE_BUILD_TYPE=Release ../code
make

The executable should now be present in the build directory. The executable for the tests should be under build/tests/ .

The same process follows to build on the unicluster. Except -DEIGEN3_INCLUDE_DIR=<path> and -DMPI_BUILD=True flags need to be set.

This project uses a modified version of this code to create a Makay Icosahedron Structure. The files for this is present under the data folder. This project can be built in it's directory the following way.

g++ -o output.out ih.C

and run using

./output.out

if it does not run, execute the following command before running

chmod+x output.out