VlachosGroup / renview

The Reaction Network Viewer (ReNView) generates a graphic representation of the reaction fluxes within the system essential for identifying dominant reaction pathways and mechanism reduction.

Reaction Network Viewer (ReNView)

The Reaction Network Viewer (ReNView) generates a graphic representation of the reaction fluxes within the system essential for identifying dominant reaction pathways and mechanism reduction.

Documentation

See our documentation page for examples, and equations used.

Developer

Udit Gupta ([e-mail])

Dependencies

• Python3
• Numpy : Used for vector and matrix operations
• Pandas: Used to import data from input files and process headers
• Graphviz: Used to generate visualizations from text files

Getting Started

1. Install using pip::

pip install ReNView

Files for using the Visualization tool

1. species_comp.out - A species composition file specifying species name, phase, and the elemental composition of the molecule. In case of heterogeneous systems, surface coverages can also be provided for node coloring.

2. reaction_rates.out - A reactions file specifying the forward, reverse, net rate, partial equilibrium index, and reaction string. The reaction string should contain species names as mentioned in the species_comp.out file.

Features in the visualization tool:

• Network Visualization
• Species Visualization
• Legend generation

License

This project is licensed under the GNU LGPL License - see the LICENSE.md file for details

Publications

• Gupta, U.; Vlachos, D. G. Reaction Network Viewer (ReNView): An Open-Source Framework for Reaction Path Visualization of Chemical Reaction Systems. SoftwareX 2020, 11, 100442. https://doi.org/10.1016/J.SOFTX.2020.100442.

Contributing

If you have a suggestion or find a bug, please post to our Issues page with the enhancement or bug tag respectively.

Finally, if you would like to add to the body of code, please:

• fork the development branch
• make the desired changes
• write the appropriate unit tests
• submit a pull request.

Questions

If you are having issues, please post to our Issues page with the help wanted or question tag. We will do our best to assist.

Funding

This material is based upon work supported by the Department of Energy's Office of Energy Efficient and Renewable Energy's Advanced Manufacturing Office under Award Number DE-EE0007888-9.5.

Special Thanks

• Dr. Jeffrey Frey (capsule compatibility)
• Gerhard Wittreich (testing)
• Hilal Ezgi Toraman (testing)
• Jonathan Lym (testing)
• Jaynell Keely (Logo design)