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This will be used implicitly by anyone using catlas to enumerate slabs. It makes it so the undercoordination of possible surface atoms is directly compared to its bulk counterpart (via wyckoff) rather than considering the min coordination for that species in the bulk. This removes the need to consider surface atoms by height as well, which could have resulted in subsurface placement in the past.
Scope: What will be done:
The Surface class from ocdata.surfaces will be brought into catlas and modified.
It will primarily use pymatgen.structure.Structure objects rather than ase.Atoms
Atom tiling will be modified to be handled on pymatgen.structure.Structure objects rather than ase.Atoms
atom coordination will be considered by full_wyckoff rather than min per species
_find_surface_atoms_by_height will be removed
Some modifications to catlas.enumerate_slabs_adslabs.enumerate_slabs to support above changes
Possibly some integration with the broken bond model to reduce compute although how to do this isn't immediately obvious because BB model as implemented does not use Voronoi nn
testing: look at the differences between adslabs enumerated (up to max miller =2)by the previous approach and this current one for 300 randomly selected bulks to quantify the impact of this approach. For a subset of differences (say 200 slabs) ensure the change is in fact an improvement. Although I don't know why it wouldn't be. Maybe try out a couple of NN approaches and compare. Voronoi is slow and has some problems. Take a look to see if this completely corrects issues with large adsorbates. Test overlap post adslab enumerations.
doc updates
What will not be done:
Full integration of existing ocdata infra. This has been something we have talked about and I think we are close to that now, but it will not be completed here.
Execution plan:
This will be a solo project all to be completed by Brook. The execution plan is well detailed in the scope section.
Consider any problems / risk:
Unforeseen issues with the new tagging method. There should be very little risk once the testing plan has been completed.
The text was updated successfully, but these errors were encountered:
Use cases:
Scope:
What will be done:
Surface
class fromocdata.surfaces
will be brought into catlas and modified.pymatgen.structure.Structure
objects rather thanase.Atoms
pymatgen.structure.Structure
objects rather thanase.Atoms
full_wyckoff
rather than min per species_find_surface_atoms_by_height
will be removedcatlas.enumerate_slabs_adslabs.enumerate_slabs
to support above changesWhat will not be done:
Execution plan:
This will be a solo project all to be completed by Brook. The execution plan is well detailed in the scope section.
Consider any problems / risk:
Unforeseen issues with the new tagging method. There should be very little risk once the testing plan has been completed.
The text was updated successfully, but these errors were encountered: