9.8. Database Scripts

This section details usage for scripts available in RMG-database/scripts folder.

9.8.1. evansPolanyi.py

This script will generate an Evans-Polanyi plot for a single kinetics depository.

Usage:

python evansPolanyi.py [-h] <family> <kinetics_depository> [<kinetics_depository> ...]
Positional arguments::

<family> the family to use <kinetics_depository> the kineticsDepository to use, e.g., training, NIST

Optional arguments:

-h, --help    show help message and exit

9.8.2. exportKineticsLibraryToChemkin.py

This script exports an individual RMG-Py kinetics library to a chemkin and dictionary file. Thermo is taken from RMG’s estimates and libraries. In order to use more specific thermo, you must tweak the thermoLibraries and estimators in use when loading the database. The script will save the chem.inp and species_dictionary.txt files in the local directory.

Usage:

python exportKineticsLibrarytoChemkin.py [-h] LIBRARYNAME

Positional arguments:

LIBRARYNAME    the libraryname of the RMG-Py format kinetics library

Optional arguments:

-h, --help     show help message and exit

9.8.3. importChemkinLibrary.py

This script imports a chemkin file (along with RMG dictionary) from a local directory and saves a set of RMG-Py kinetics library and thermo library files. These py files are automatically added to the input/kinetics/libraries and input/thermo/libraries folder under the user-specified name for the chemkin library.

Usage:

python importChemkinLibrary.py [-h] CHEMKIN DICTIONARY NAME

Positional arguments:

CHEMKIN     The path of the chemkin file
DICTIONARY  The path of the RMG dictionary file
NAME        Name of the chemkin library to be saved

Optional arguments:

-h, --help  show help message and exit

9.8.4. process_family_images.py

This script processes reaction family template images (saved as eps files) into user friendly files (pdf and pngs). This should typically be run whenever a new family is added or an existing family is updated.

Notes:

  • Make sure you have a working LaTeX installation with pdflatex

  • Make sure you have a working GhostScript installation for epstopdf

  • Make sure you have ImageMagick installed for png generation

  • ImageMagick may have security limitations in place which prevent reading eps files. To circumvent these, edit the /etc/ImageMagick-6/policy.xml file by changing <policy domain="coder" rights="none" pattern="EPS" /> to <policy domain="coder" rights="read|write" pattern="EPS" />

Usage:

python process_family_images.py