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Resonance structures of adsorbates don't put radicals on the surface. #1828

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Resonance structures of adsorbates don't put radicals on the surface. #1828

wants to merge 5 commits into from

Commits on Aug 18, 2020

  1. More informative error logging when adsorption thermo fails. 

    If you can't find adsorption energy group value,
log the adjacency list of the molecule.
    @rwest
    rwest committed Aug 18, 2020
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  2. Make Atom.apply_action more consistent (and slightly faster) 

    Tiny change. Increases readability and presumably speed.
    @rwest
    rwest committed Aug 18, 2020
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  3. Don't add radicals or lone pairs to surface sites. 

    This may hide bugs, or it may be exactly the right
thing to do. I'm not entirely sure.
But it currently seems like a good idea.

The presumption is:
surface sites of metals should not have unpaired
or pairs of electrons - they just have a big sea
of delocalized electrons at their disposal.

See #1820
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  4. When making a Species allow adsorbate resonance structures different … 

    …multiplicity.

When a metal surface is involved, your adsorbate may
have different multiplicity in different resonance forms
because you may hybridize a radical onto the metal
where it "disappears". 

It is an attempt to address 
#1820
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  5. Unit test that Surface_Adsorption_vdW doesn't adsorb radicals. 

    Trying to forbid them using the forbidden structures doesn't 
seem to be working (a bug in is_subgraph_isomorphic?) but
making the top level node have multiplicity [1,3] excludes
anything with multiplicity 2 and seems to work on a 
generate_reactions level. Probably a better solution anyway, 
as it's inefficient to match the node, apply the recipe, generate
the products, and *then* discard them as forbidden.
    @rwest
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