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Add surf-graph as an option to place adsorbates #159

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brookwander opened this issue Sep 15, 2022 · 1 comment
Open

Add surf-graph as an option to place adsorbates #159

brookwander opened this issue Sep 15, 2022 · 1 comment
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enhancement New feature or request

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@brookwander
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brookwander commented Sep 15, 2022

Use cases:

  1. Surfgraph will be applied to place small and large molecule adsorbates (C3+) on catalyst surfaces found in the OC20 dataset.
  2. Test surfgraph with other catlas tool additions that team is incorporating.

Scope:
What will be done:

  1. Examine surfgraph site detection method and compare with CATKIT applied in Catlas.
  2. Determine how adsorbates are placed in surfgraph and add into Catlas workflow.
  3. Conduct several tests that will be used to incorporate surfgraph in Catlas workflow.
  4. Add documentation for addition of surfgraph/adsorbate placement methods added to Catlas.

What will not be done:

Execution plan:
This should be detailed, you should consider the infrastructure currently in catlas. What specific functions need changing? Are there several significantly different alternatives to implement? What are some advantages and disadvantages to different approaches
You should also use this section to delegate tasks. Upfront tasks should be outlined, and then you can work with your subteam to delegate them.

Incorporate site_detection.py in Catlas [check for differences in adsorbate placement in this code & CATKIT]
Require to import surfgraph.chemical_environment packages, ase.constraints, specify class functions in site_detection.py

Sources:
https://surfgraph.readthedocs.io/en/latest/Usage.html#generate-sites-py
https://gitlab.com/jgreeley-group/graph-theory-surfaces/-/tree/master

Task Owner Due by Dependent?

Consider any problems / risk:

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