Surface auto tree gen support with metal attrs#2187

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davidfarinajr wants to merge 36 commits intomainfrom

surface_arrbm

Commits on Oct 1, 2021

added `get_metal_label` entry method

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use `get_rate_coefficient_units_from_reaction_order` to get A units for ArrBM

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`get_w0` with metals and vdw bonds

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added SurfaceArrheniusBM kinetics class

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added `add_van_der_waals_bond` mol method

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added `is_surface_bond` Bond method

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`get_bde` for metal bonds using MetalDB

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added `test_get_bde` unit test

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added metal attrs to Reaction

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change logging from warning to info

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added metal attrs to reaction when loading entries

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reactions on different metals are not duplicate

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added metal and facet to input, RMG and CoreEdgeReactionModel classes

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select the best kinetics with metal and facet attrs

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added `vdw_bonds` family attr

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added `split_template` family method

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use SurfaceArrheniusBM for surace reactions with autotree gen methods

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save training reactions with metal attrs

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set family reactant_num to length of template if not specified

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using get_metal_label function

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get_training_set for surface families

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`get_kinetics_from_depository` fixup

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added metal attrs to kinetics database and generate reactions

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added metal attrs to kinetics Groups and descend tree algorithm

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added facets to autotree gen extend node

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do not regularize rings if the molecule contains surface site

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added notebook to estimate A factors for surface reactions

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use cathub db branch for tests

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use `with` for mp pool

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family product num is length of template products if not specified

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raise InvalidActionError if nonexistent bond when applying recipe for `get_w0` method

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added `reactantNum` and `productNum` to `intra_H_migration` testing groups

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saving DB metal attrs

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commented out `check_surface_thermo_groups_have_surface_attributes` db test

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fixup! commented out `check_surface_thermo_groups_have_surface_attributes` db test

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added rxn metal attrs to own reverse reactions in family `get_training_set`

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