volcanic: Automated Generator of Volcano Plots

Contents

• About
• Install
• Examples

About ↑

The code runs on pure python with minimal dependencies:

• numpy
• scipy
• matplotlib
• pandas

Install ↑

Download and add volcanic.py to your path. No strings attached. Run as:

python volcanic.py [-h] [-version] -i [FILENAMES] [-df DFILENAMES] [-nd ND] [-v VERB] [-r RUNMODE] [-lsfer | -thermo | -kinetic | -es | -tof | -all] [-T TEMP] [-pm PLOTMODE] [-ic IC] [-fc FC]
                [-rm RMARGIN] [-lm LMARGIN] [-np NPOINTS] [-d] [-is IMPUTER_STRAT] [-refill]

You can also execute:

python setup.py install

to install volcanic as a python module. Afterwards, you can call volcanic as:

python -m volcanic [-h] [-version] -i [FILENAMES] [-df DFILENAMES] [-nd ND] [-v VERB] [-r RUNMODE] [-lsfer | -thermo | -kinetic | -es | -tof | -all] [-T TEMP] [-pm PLOTMODE] [-ic IC] [-fc FC]
                [-rm RMARGIN] [-lm LMARGIN] [-np NPOINTS] [-d] [-is IMPUTER_STRAT] [-refill]

Options can be consulted using the -h flag in either case.

Examples ↑

The examples subdirectory contains a copious amount of tests which double as examples. Any of the data files can be run as:

python volcanic.py -i [FILENAME]

This will query the user for options and generate the volcano plots as png images. Options can be consulted with the -h flag.

The input of volcanic.py is a pandas compatible dataframe, which includes plain .csv and .xls files.

Regarding format, volcanic.py expects headers for all columns. The first column must contain names/identifiers. Then, volcanic.py expects a number of columns with relative free energies for the species in the catalytic cycle (in order of appearance), whose headers must contain "TS" if the species is a transition state, and a final column whose header is "Product" containing the reaction energy. Non-energy descriptors can be input as a separate file using the -df flag or as extra columns whose headers contain the word "Descriptor".

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