bslakman / my_scripts

Some helpful scripts that are not totally part of (nor totally separate from) other projects

my_scripts

Python scripts

• 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.py script, 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.py and tsGroups.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

Shell scripts

• ck2cti.sh: runs the Cantera ck2cti.py from an RMG-generated Chemkin file without having to manually type the in/out file paths every time
• submit.sh: runs input.py on the West nodes on the Discovery cluster

Jupyter notebooks

• Classification.ipynb: classifies silicon hydride AutoTST successes and failures to try to predict whether a reaction will work or not