Data Structure

Example on how you should structure your files

Your data should be structured in order to use rgmol without any issues

project
├── molecule_1
|   ├── rgmol
|   ├── molecule_1.out
|   └── molecule_1.molden.input
|   ├── molecule_1_m.out
|   └── molecule_1_m.molden.input
├── molecule_2
|   ├── rgmol
|   ├── molecule_2.out
|   └── molecule_2.molden.input
└── script.py

The molecule_1_m is the molecule 1 with an electron removed.

The rgmol folder

The rgmol folders will be created and used automatically by rgmol after the calculation of kernel eigenmodes.

This folder will contain the eigenmodes with the extension .npy as well as the voxel parameters, the eigenvalues and the contribution of the transition densities.

More information on the way they are written can be found here.