pycif.plugins.chemistries.chimere — API reference

Configuration reference: chimere plugin

pycif.plugins.chemistries.chimere.make_chemistry.create_chemicalscheme(self)

Read the mandatory chemistry files, create the optional ones and set the species attributes consistently with the data retrieved

pycif.plugins.chemistries.chimere.read_chemistry.read_chemicalscheme(chemistry, **kwargs)

Reads a chemical scheme from existing files

Parameters:

chemistry (pycif.utils.classes.chemistries.Chemistry) – the chemical scheme

Returns:

Grid dictionary with characteristics of the chemical scheme

Notes:

pycif.plugins.chemistries.chimere.utils.create_mandchem(chemistry, mandatory_files)

Create the mandatory chemistry files using the chemistry config yml file

pycif.plugins.chemistries.chimere.utils.create_optchem(chemistry, filer, fileps)

Create the chemistry files ALL_SPECIES, CHEMISTRY, REACTION_RATES,

STOICHIOMETRY and ACTIVE_SPECIES

At the moment, FAMILIES is set empty

ALL_SPECIES is created

Parameters:

• chemistry (pycif.utils.classes.chemistries.Chemistry) – chemical scheme

• filer (str) – path to the file with reactions

• fileps (str) – path to the file with prescribed species

pycif.plugins.chemistries.chimere.utils.read_react(reactions, filej)

Parse the types of reactions in the REACTIONS file and extract the data

pycif.plugins.chemistries.chimere.utils.make_inout_react_graph(filer)