Brief descriptions of files in this folder.
complete_rateconstant_list.dat
This file contains the parameters for calculating the reaction rate constants in the final kinetic scheme. Each row corresponds to a reaction from complete_reaction_list.dat and lists "A n E" for that reaction.
complete_reaction_list.dat
Each row in this file describes a reaction in the kinetic scheme. Reactants are written with a negative stoichiometric coefficient, followed by an underscore, then the reactant name. Products have a positive stoichiometric coefficient. Different molecules are separated by commas.
compositionlist.dat
This file is automatically generated every time ligpy.py is run - it is built based on the information in elemental_analysis.dat. In this file each species of lignin is described by the number of moles of each pseudocomponent from the model (LIGC, LIGH, LIGO).
elemental_analysis.dat
This file is the only file in this folder that future users will likely edit directly. It contains experimental results for the elemental analysis of various lignin species that you might want to model with ligpy (mass fractions of C, H, O). If a species of lignin is not present in this file you will not be able to model it.
faravelli_rateconstantlist.dat
faravelli_reactionlist.dat
These files describe the rate constants and reactions from the original Faravelli et al. paper that our model is modified from. It is included for reference.
rates_and_ODEs.txt
This file is not used by any modules in the program, it is only included so users can see what equations are being solved by the ODE solver.