RMG-Electrochem#2316

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mjohnson541 wants to merge 110 commits intomainfrom

electrochem

Commits on Jul 27, 2023

Add reaction library to test example for liquidSurfaceReactor
mjohnson541
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added Faraday's Constant `F`

davidfarinajr
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added Potential as `V` quantity

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

davidfarinajr
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added atomtype unit tests

davidfarinajr
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added `gain_charge` and `lose_charge` actions

davidfarinajr
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added `is_proton` and `is_electron` group methods

davidfarinajr
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added group unit tests

davidfarinajr
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added `is_electron` and `is_proton` methods to Atom and Mol

davidfarinajr
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added GAIN and LOSE CHARGE actions to Atoms

davidfarinajr
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added updated charge method and revised `update` Molecule method

davidfarinajr
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do not raise charge exception by default when creating molecule from adj list

davidfarinajr
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H -> H0 in find_h_bonds Molecule method

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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added Species `is_electron` and `is_proton` methods

davidfarinajr
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do not raise charge exception by default when creating species from adj list

davidfarinajr
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added `get_net_charge` method for Species

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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added unit tests for SurfaceChargeTranser kinetic model

davidfarinajr
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added Molecule unit tests

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

davidfarinajr
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added reaction tests for charge transfer reactions

davidfarinajr
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adding charged species and electrons to family.py

davidfarinajr
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added family test for `Surface_Proton_Electron_Reduction_Alpha` family

davidfarinajr
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added support for loading `SurfaceChargeTransfer` kinetics from the database

davidfarinajr
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update charge before updating lone pairs for solvation `transform_lone_pairs` method

davidfarinajr
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making rules for SurfaceChargeTransfer training reactions

davidfarinajr
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added SurfaceChargeTransfer kinetics import

davidfarinajr
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added H+ and e to translator

davidfarinajr
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update_atomtypes -> update in translator.py

davidfarinajr
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added `SurfaceChargeTransfer` to yml

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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add LiH and LiF to atom energy corrections fitting species list
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add Li atom spin
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don't check Li partial charges in adjlists
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add Li atomtype
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add atom information for Li
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handle Lithium electron calculations
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handle SurfaceChargeTransfer in to_rms
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add Li to R and R!H lists
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filter out resonance structures that try to put - charges on Li
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add Li McGowan volume
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add is_lithium for GroupAtom
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add additional Li BDEs
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add Li to bond dictionaries in thermo
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ensure atomtypes get updated on loading in thermo entries
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add solute data to KineticsModel and Arrhenius
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add ArrheniusChargeTransfer kinetics type
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create ArrheniusChargeTransferBM type
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add ChargeTransfer types to kinetics/__init__.py
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avoid issue with auto decay reactions
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handle ChargeTransfer kinetics with in reaction.py
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add handling ArrheniusChargeTransfer and fix handling SurfaceChargeTransfer for rms output
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Revert "Remove charge transfer types from average_kinetics (to be reverted)"

rwest
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enable access to SoluteData object in kinetics database
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update rule fitting
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enable use of non-surface charge transfer families
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add charge transfer types to database context
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add Li0 and Li+ atomtypes
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enable surface and bulk potentials to be specified separately
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Allow approximating a solvent not in the database with another solvent
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standardize ascend option in cross validate
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Average kinetics when n=1 or E0<0
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add comment to averaged kinetics
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fix BM fitting
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add functions for solvent correcting kinetics
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add functionality for site specific solvent corrections
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apply_solvent_correction in fix_barrier_height
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enable solvent parameters to be directly specified in input file
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adapt fix_barrier_height calls
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handle ArrheniusChargeTransfer => Arrheniusq
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add index of refraction to SolventData objects
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fix KineticsModel outputs
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add SoluteTSData object
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add SoluteTSDIffData object
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add function to convert SoluteData and SoluteTSDiffData to SoluteTSData
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Enable database to understand new objects
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Enable LibraryReaction to handle SoluteTSData
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Enable TemplateReaction to handle new TS solvent corrections
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only use kinetics that have arrhenius forms for tree generation
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enable solute data to be pulled from further up the tree as necessary
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enable fitting of TS solute rules
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allow training reaction notebook to handle reactions without gas phase kinetics
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fix arrhenius test
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fix atomtype test
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add is_lithium to fragment
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handle charge properly in fragment smiles hack
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skip nodes that are empty when pulling solute data
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remove test that solvent is in initial species
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adapt corrTest
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update product template after generation
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add Li adsorption to test data
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add adsorptionLi.py to testing database
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don't check collision limit for reactions without kinetics
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skip coverage dependence checks for electrochem families
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add additional special groups to skip sample molecule generation
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fix charge handling in make sample molecule
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Refactor some rate fitting in rule generation.

rwest
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Minor refactor.

rwest
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Fix ArrheniusBM.get_activation_energy unit test.

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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modifed arrbm `fit_to_data` unit test

davidfarinajr
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TEMPORARY: set database branch to lithium
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fix atomtype charge checking
mjohnson541
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fix typo in database test
mjohnson541
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Commits on Jul 28, 2023

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