Coverage-dependent thermochemistry for catalysis#2646

Merged

rwest merged 49 commits intoReactionMechanismGenerator:mainfrom

12Chao:cov_dep_therm

Apr 10, 2026

Commits on Apr 9, 2026

Add thermodynamic coverage dependent models in surface reactor

12Chao
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add thermo coverage dependence instance while reading the file

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add import copy package

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add the instances for thermo coverage dependence

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add polynomial thermodynamic coverage model to Wilhoit, NASA, and thermodata

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declare _thermo_coverage_dependence in the pxd files

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fix the typos, and add the missing import command line

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Add thermo_coverage_dependence as new property to NASA

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Move thermo_coverage_dependence from NASAPolynomial to NASA

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Add unit test for coverage dependent thermodynamics in RMG thermo classes

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check thermo_coverage_dependence is not empty

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Fix the bug for calculating thermo coverage dependent correct values

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add a big matrix for species Gibbs free energy corrections

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correct Gibbs free energy for each species based on its 3-parameter polynomial thermo coverage depedent model

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use stoichiometric matrix to calculate the correct value for Keq

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Add unit tests for thermo coverage dependent models in surface solver tests

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use isomorphic check to check if thermo coverage dependent species are in the model

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delete unused instances

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Add solver unit test for thermodynamic coverage dependent models

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save thermo coverage dependent models as numpy arrays instead a list of rmg quantities

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create a subclass of numpy array overriding __repr__ method

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create thermo coverage dep polynomial model in numpy array class with new __repr__ method

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use adjacency list as the key of thermo cov dep models

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adjust the method to read data from numpy arrays instead list

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Write thermo coverage dependent data to Cantera yaml file

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Use chemkin strings instead of labels when writing to yaml files

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Write the thermo coverage dependent data to yaml files in right format

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Add thermo_coverag_dependence as an instance for class RMG

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fix the bug that the coverage kinetics cannot be written to chemkin

12Chao
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write data as RMG object instead of floats to keep the units consistent

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add thermo_coverage_dependence to initialize

bjkreitz
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fix type in wilhoit.pyx

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fix coefficients check in nasaTest.py

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fix test_thermo_coverage_dependence

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fix thermodataTest.py

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fix convertTest.py

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fix wilhoit test_thermo_coverage_dependence and test_wilhoit_as_dict

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fix solverSurfaceTest.py by adding units

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calculate rxns_free_energy_change via np.matmul

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remove Chaos bugfix that the coverage kinetics cannot be written to chemkin

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remove cantera dependence

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remove np_list function

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Optimization: avoiding exponentials and stacks.
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optimization: removing loops, and making cython declarations
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Don't save empty dictionary when thermo coverage is None
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Small optimization and simplification.
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update tests for coverage-dependence data as_dict
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Fix YAML dumping style for consistency in output files.
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Changing coverage-dependent thermo cantera yaml output.
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