- activation_energy.py: parses Gaussian output files to get energies of reactants, TS in gas-phase, solvents
- checkEa.py: goes through textfiles with activation energies, created from the
activation_energy.pyscript, and finds negative ones - input.py: the input script for autoTST
- manualCalc.py: generate TS geometry for one reaction based on folder you're in, using autoTST (so still semi automatic, not "manual", but on one reaction)
- modifyReactionBarriers.py: modifies existing Chemkin file for solvation kinetics. Creates a .csv file of changed reactions.
- processCanteraOutput.py: basically deprecated. puts Cantera outputs into Excel but based on specific output format that I no longer use
- reactant_energies.py: perform single point energy calculations in solvent on a set of gas phase reactant geometries - needs to be updated for SLURM
- rmg_helper_functions.py: a place for some helpful RMG functions that are reused often
- SMD.py: gathers barrier corrections from Gaussian jobs and puts them in the RMG database; creates a .csv file for doing some non-RMG machine learning
- SMD_Abraham.py: an alternative script which prints Abraham parameters to .csv file instead of atom properties
- solvationGroups.py: like
kineticsGroups.pyandtsGroups.py, generates the group values for solvation kinetics from training reactions in RMG-database - solvation_energies.py: like
reactant_energies.py, but for transition states - solvents.py: deprecated, manual version of
reactant_energies.py/solvation_energies.py - thermo_compare.py: compares thermo from a text file to thermo generated by group additivity
- V3_to_V4.py: given two chemkin files and species dictionaries, will replace rates in the second mechanism with the rate in the first
- ck2cti.sh: runs the Cantera
ck2cti.pyfrom an RMG-generated Chemkin file without having to manually type the in/out file paths every time - submit.sh: runs
input.pyon the West nodes on the Discovery cluster
- Classification.ipynb: classifies silicon hydride AutoTST successes and failures to try to predict whether a reaction will work or not