Getting started

Here are some instructions on running a lignin pyrolysis simulation using ligpy. The package structure diagram is included here for reference while following these steps.

1. Make sure that the elemental analysis of the type of lignin you would like to simulate is specified in the file elementalanalysis.dat. This file is located in the ligpy/data/ folder and it contains instructions on how to format new entries.
2. Create your own version of generate_bash_script.py to write the command line function call to ligpy.py. Alternatively you can run ligpy directly from the command line with python ligpy.py <arguments>. (Note: Future users will need to modify ddasac_utils.py, and while doing so they can specify their own directory structure for saving the results; the existing code requires a specific directory structure to already exist on cmole at the University of Washington.)
3. Run your script. ligpy.py will handle calls to all the necessary modules to complete the simulation and save the results.
4. Explore your results. If you have formatted them in the same way that the sample results (in ligpy/sample_results/) are formatted then only minor modifications will be required in analysis_tools.py to use the existing Jupyter notebook (explore_ligpy_results.ipynb), otherwise you can create your own analysis scripts to suit your purposes.

Updating or revising the kinetic scheme

We are publishing the code for this model with the hope that it makes it easy to revise, improve, and expand the kinetic scheme. Changing the kinetic scheme only requires modification of the files complete_reaction_list.dat and complete_rateconstant_list.dat. The formatting for these files is described in the README in ligpy/data/. Once you’ve added reactions or updated kinetic parameters in these files the rest of the code will update the set of equations that is solved automatically.