scripts

Custom scripts mainly for VASP calculation and catalysis related content.

jworkflow

Custom Python scripts based mainly on pymatgen and are used to analyze VASP calculation results and catalysis related content

Requirement

• pymatgen
• ase
• sklearn
• matplotlib
• numpy
• pandas
• openpyxl

Overview

• slab.py: Cleave surface, find adsorption sites, and add adsorbates in batches. Modify the slab structure by layer.
• dada_process.py: Extract VASP calculation results like slab relaxation, adsorbate adsorption energy and free energy correction. Process POSCAR files for frequency and differential charge density calculations.
• reaction.py: Calculate adsorption energy, find stablest adsorption structure from VASP calculations, find potential determinted step and calculate energy profile.
• plot.py: Plot slab structures and energy profile.
• electronic.py: Gather DOS and COHP information from vasprun.xml and cohpcar.lobster file respectively.
• dataset.py: Store molecular structures and energies, and reaction formulas.

Tutorial

See Tutorial Jupyter Notebooks in 'jworkflow/Tutorial-xxx.ipynb'.