/Zeolite

Primary LanguagePython

Zeolite

In Progress ..

Requirements:

  • molmod
  • ASE
  • Q-Chem

Step 1: generate_structures:

objective:

Generate unique zeolite structures (1 or 2 Al atoms substituting Si, and compensating cations/protons)

syntax:

python main.py

  • functions.py [common useful functions]
  • adsorbate.py [scripts specific to adding adsorbates]

options:

  • choice of adsorbate (H, NH3, Pd)

inputs:

  • xyz file of original zeolite structure (placed under original_structures folders)
  • index of T-atom (Si atoms) to be replaced with the first Al atom
  • number of terminal H atoms in the original structure (needed to eliminate dangling bonds from terminal Si in the cluster)
  • adsorbed metals oxidation states and compositions

outputs:

  • generate structures of the zeolites (under structures_saved)
  • data file (json) containing information on each generated structure (under data directory)

Step 2: Create input

objective:

Create Q-Chem input files for desired structures

syntax:

python create_input.py

inputs:

  • index of the first structure
  • index of the last structure
  • calculation type (optimization or single-point)

outputs:

generate input file for each calculation in a new folder (under calculations directory)

Step 4: Calculations

Run desired calculations (under calculations directory)

Step 5:

TBA