Recreating Results from the Main Paper

The directories below contain all the graphing data and information needed to recreate the results presented in the main paper.

• analysis_data: The final graph from the research is provided for verification and potential modification.
• exciation-data: Raw data and instructions for running the analysis can be found in the excitation-data directory.

General Programs Needed

1. DFTB+ Program

Download from: DFTB+ GitHub Repository

2. PBC-0-3 Parameter Set

Download from: PBC-0-3 Parameters

3. Python Versions

Both python3 and python2 are required along with the following libraries:

• networkx
• numpy
• matplotlib

4. Visualization Software

• OVITO or VMD for visualizing data.

5. LAMMPS (for some postprocessing)

Download from: LAMMPS GitHub Repository