The ./main folder contains Jupyter notebook that runs the simulation. Will eventually port notebook to python script. The ./main folder will also contains a bash or zsh script to automatically submit multiple jobs.
The ./main/modules folder presently contains code for the Z2 gates and building circuits. It will eventually also contain code for pauli_twirling, saving run data, and post-run analaysis.
The ./main/inputs folder will contain yaml files with simulation parameters for different runs.
The ./main/json folder will contain each run's info, input, and output json files.
The remaining folders are for literature (currently empty) and code development and testing.