Creating ASE database via running post processing notbook

[sakim8048]

SQLite database for adsorbates, transition state and rate coefficients can be created via post processing notebook.

Adsorbates and slab geometries, energies, frequencies, DFT parameters will be added to adsorbate.db. Transition state geometries, energies, frequencies, DFT parameters will be saved in TS_geometry.db Rate coefficients calculated via post processing will be saved in rate_coeff.db.

The database are created and edited only when the user uses post processing notebook, giving users options of creating databases for geometries of their own interest. (Pick and chose to save)

pynta postprocessing.ipynb: A section for DFT functional, Pseudopotentials, lattice parameters added write_adsorbate_db(), write_ts_db(), write_slab_db(), write_rate_db() added

postprocessing.py: write_adsorbate_db() : create and write adsorbate.db for unique adsorbates (ones that calculates frequencies)

write_slab_db(): update slab info to adsorbate database

write_ts_db() : create and write ts_geometry.db for unique transition states geometries

parse_all_surface_arrhenius(): iterate by indices {key} and parse surface arrhenius information for unique TS

• input: "farrs" for forward rate, "rarrs" reverse rate
• return: rate_data

parse_surface_arrhenius(): parse SurfaceArrhenius from molecule. Define the SurfaceArrhenius named tuple for the example and extract dA, dn, dEa from the comment from the output.

write_rate_db(): create rate_coeff.db. Save prefector, n, Ea, dA, dn, dEa in a string form from rate_data