Programs Available in SUMELF

The SUMELF program is designed to hold methods and modules that are used by multiple programs used in the grand scheme for simulating/calculating electronic properties as well as charge and exciton diffusion in molecular crystals.

The get_molecules module

It is possible to separate a crystal into its separate molecules using the get_molecules module. This module will extract the individual molecules in a crystal structure, and save them into separate .xyz files.

To use the get_molecules module, type the following into your terminal:

# First, change directory into the directory contain the folder with your crystal files
cd path_to_crystal_database

# Second, run the get_molecules program:
SUMELF get_molecules crystal_database

This will separate the crystal into its individual molecules, and save them as individual xyz file in folder called crystal_database_molecules. You can view these molecules using your favourite GUI viewer, mine is ase gui (click here for more about ase gui).

NEED TO ADD OPTIONS TO THIS.

Info

You can also use Mercury (a CCDC program) to view the crystal. However, you will need to use the get_molecules to get the names of the molecules and the atom indices to make modifications to for the Repair_Crystals module in the ReCrystals program