WIP: RMG-Electrocat - #2000

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davidfarinajr wants to merge 36 commits into

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Commits on Jul 29, 2021

added Faraday's Constant `F`
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f2e644d
added Potential as `V` quantity
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c108446
added `H+` and `e` atomtypes, increment/decrement charge attributes
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dc56485
added atomtype unit tests
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14eebc8
added `gain_charge` and `lose_charge` actions
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2e5b3a6
added `is_proton` and `is_electron` group methods
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a8eb291
added group unit tests
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50fd05c
added `is_electron` and `is_proton` methods to Atom and Mol
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f4e40e8
added GAIN and LOSE CHARGE actions to Atoms
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3feb806
added updated charge method and revised `update` Molecule method
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b055183
do not raise charge exception by default when creating molecule from adj list
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c56a711
H -> H0 in find_h_bonds Molecule method
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67856dd
try to generate_resonance_structures, and return a deep copy of the molecule if it fails
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91b4f5c
added molecule.pxd declarations
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6da1615
added Species `is_electron` and `is_proton` methods
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81958fe
do not raise charge exception by default when creating species from adj list
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b64c0c4
added `get_net_charge` method for Species
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018889a
do not forbid ions
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178b34e
added `SurfaceChargeTransfer` and `SurfaceChargeTransferBEP` kinetic models
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8a7426e
added unit tests for SurfaceChargeTranser kinetic model
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090ec07
added Molecule unit tests
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c587c21
added `electrons` reaction attr and reaction methods for charge transfer reactions
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04362cc
added reaction tests for charge transfer reactions
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3d4bdaa
adding charged species and electrons to family.py
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d41ac9b
added family test for `Surface_Proton_Electron_Reduction_Alpha` family
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01c5f22
added support for loading `SurfaceChargeTransfer` kinetics from the database
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78e7959
update charge before updating lone pairs for solvation `transform_lone_pairs` method
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1d059b8
making rules for SurfaceChargeTransfer training reactions
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657def1
added SurfaceChargeTransfer kinetics import
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c0603f8
added H+ and e to translator
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d6c079c
update_atomtypes -> update in translator.py
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bae3eab
added `SurfaceChargeTransfer` to yml
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00f7073
added `ElectrodeReactor`
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3117b33
added `ElectrodeReactor` to input.py
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ad16c47
adding `potential` and `ElectrodeReactor` to main.py and model.py
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5decbb6
used `electrocat` DB branch for testing
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091fe9b