kinpy2 1.0.2

Reaction kinetics intergration from user-friendly input

Kinpy2

Excel-based setup for reaction kinetics integrator

Install

pip install kinpy2

Use

1. Generate *.k file with reaction equations and run

python -m kinpy2 parse equations.k

2. Input energies of intermediates and TSs into mytable.xlsx file. Optionally, to obtain energies one can use

python -m kinpy2 energy

this runs GoodVibes and creates an energies.xlsx table. One can copy-paste these energies into mytable.xlsx

3. Generate kinetics integration script calc_kinetics.py by running

python -m kinpy2 gen mytable.xlsx

One can tweak the energy barriers in the generated file mytable_new.xlsx and re-run script generation via

python -m kinpy2 gen mytable.xlsx --noprep

4. Execute the integration script by running

python calc_kinetics.py

Kinetics trajectories are stored at res.csv.

All file names can be set using CLI flags. See help messages

python -m kinpy2 gen --help