Electrochemistry! (finally) a.k.a. RMG-electrocat#2598

Merged

rwest merged 109 commits intomainfrom echem-rebase

Nov 27, 2024

+6,231-685

Commits on Nov 21, 2024

Add reaction library to test example for liquidSurfaceReactor

mjohnson541
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added Faraday's Constant and vacuum permittivity

davidfarinajr
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added Potential as V quantity

davidfarinajr
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added H+ and e atomtypes and increment/decrement charge attributes

davidfarinajr
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Added increment_charge and decrement_charge to Rx
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added gain_charge and lose_charge actions

davidfarinajr
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added is_proton and is_electron methods

davidfarinajr
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added updated charge method and revised update Molecule method

davidfarinajr
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added get_net_charge method for Species

davidfarinajr
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do not raise charge exception by default

davidfarinajr
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try to generate_resonance_structures, and return a deep copy of the molecule if it fails

davidfarinajr
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added molecule.pxd declarations

davidfarinajr
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do not forbid ions

davidfarinajr
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added SurfaceChargeTransfer and SurfaceChargeTransferBEP kinetic models

davidfarinajr
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making rules for SurfaceChargeTransfer training reactions

davidfarinajr
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added electrons reaction attr and reaction methods for charge transfer reactions

davidfarinajr
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adding charged species and electrons to family.py

davidfarinajr
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added group unit tests

davidfarinajr
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added Molecule unit tests

davidfarinajr
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added reaction tests for charge transfer reactions

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added family test for Surface_Proton_Electron_Reduction_Alpha family

davidfarinajr
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update charge before updating lone pairs for solvation transform_lone_pairs method

davidfarinajr
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update_atomtypes -> update in translator.py

davidfarinajr
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added adsorption_groups attr to thermoDB

davidfarinajr
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added fluorine to thermo correct_binding_energy method

davidfarinajr
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added Li/Li0/Li+ atomtype

mjohnson541
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add LiH and LiF to atom energy corrections fitting species list

mjohnson541
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handle SurfaceChargeTransfer in to_rms

mjohnson541
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filter out resonance structures that try to put - charges on Li

mjohnson541
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ensure atomtypes get updated on loading in thermo entries

mjohnson541
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add solute data to KineticsModel and Arrhenius

mjohnson541
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add index of refraction to SolventData objects

mjohnson541
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added ArrheniusChargeTransfer kinetics type

mjohnson541
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added ArrheniusChargeTransferBM type

mjohnson541
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add ChargeTransfer types to kinetics/__init__.py

mjohnson541
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handle ChargeTransfer kinetics with in reaction.py

mjohnson541
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handle ArrheniusChargeTransfer => Arrheniusq

mjohnson541
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add charge transfer types to database context

mjohnson541
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enable use of non-surface charge transfer families

mjohnson541
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enable surface and bulk potentials to be specified separately

mjohnson541
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avoid issue with auto decay reactions

mjohnson541
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Added Charge Transfer types to average_kinetics

rwest
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update rule fitting

mjohnson541
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Allow approximating a solvent not in the database with another solvent

mjohnson541
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standardize ascend option in cross validate

mjohnson541
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Average kinetics when n=1 or E0<0*

mjohnson541
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fix BM fitting

mjohnson541
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add functions for solvent correcting kinetics

mjohnson541
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add functionality for site specific solvent corrections

mjohnson541
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apply_solvent_correction in fix_barrier_height

mjohnson541
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enable solvent parameters to be directly specified in input file

mjohnson541
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fix KineticsModel outputs

mjohnson541
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add SoluteTSData object

mjohnson541
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add SoluteTSDIffData object

mjohnson541
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add function to convert SoluteData and SoluteTSDiffData to SoluteTSData

mjohnson541
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Enable LibraryReaction to handle SoluteTSData

mjohnson541
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Enable TemplateReaction to handle new TS solvent corrections

mjohnson541
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Enable database to understand new objects

mjohnson541
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only use kinetics that have arrhenius forms for tree generation

mjohnson541
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enable solute data to be pulled from further up the tree as necessary

mjohnson541
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enable fitting of TS solute rules

mjohnson541
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allow training reaction notebook to handle reactions without gas phase kinetics

mjohnson541
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added arrhenius test

mjohnson541
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Fix ArrheniusBM.get_activation_energy unit test.

rwest
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modifed arrbm fit_to_data unit test

davidfarinajr
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handle charge properly in fragment smiles hack

mjohnson541
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skip nodes that are empty when pulling solute data

mjohnson541
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update product template after generation

mjohnson541
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add Li adsorption to test data
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don't check collision limit for reactions without kinetics

mjohnson541
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fix charge handling in make sample molecule

mjohnson541
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Refactor some rate fitting in rule generation.

rwest
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Minor refactor.

rwest
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Consistently use T=298. K for fitting and evaluating Blowers-Masel rates.

rwest
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Fixes and tweaks to Blowers Masel classes' fit_to_reactions methods.

rwest
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allow cat of regression diff to fail, print a warning instead

JacksonBurns
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combine the messy Cython declarations (and remove dupes) in reaction.py

JacksonBurns
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Ported all echem-related unit tests to new style

JacksonBurns
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skip a test in solvation

JacksonBurns
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add missing kwarg to fragment update method

JacksonBurns
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Fixed some tests from bad automated conversions

JacksonBurns
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enable fitting of TS solute rules

mjohnson541
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allow inclusion of refractive index in Solvent object

mjohnson541
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change TS solvation handling to new system

mjohnson541
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added Marcus kinetics

mjohnson541
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allow direct specification of viscosity and electrode distance for the RMS reactor

mjohnson541
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handle electronchange when constructing RMS objects

mjohnson541
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handle Marcus in RMS yaml constructionn

mjohnson541
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handle Marcus kinetics in fix_barrier_height

mjohnson541
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handle solvation for Marcus kinetics

mjohnson541
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handle kinetics averaging for Marcus

mjohnson541
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handle Marcus kinetics within tree generation and rule generation

mjohnson541
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add ethylene carbonate and acetonitrile SEI examples

mjohnson541
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fix bug with species initialization

mjohnson541
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Fixed a typo in test lose charge
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Add set_reference_potential for SurfaceChargeTransfer
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Set reference potential now always sets to 300 K
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Fixed A-factor correction for SurfaceChargeTransfer
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Added CO2RR example
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Extra error logging in HBI thermo estimation.

rwest
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Ignore PCET vdW families for surface coverage test
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Changed rate coefficient test to use rtol
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update_charge skips cutting labels
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Fixed Fragment test
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Commits on Nov 24, 2024

Changed RMS branch to for_rmg

ssun30
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rwest
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Use the lithium_rebase branch of RMG-database for CI
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fixup! enable use of non-surface charge transfer families

rwest
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Small efficiency gain checking for charged species.

rwest
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Commits on Nov 27, 2024

Switch back to using main branch of RMG-database
rwest
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