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Enable Metal, Facet, site and terrace specification in Molecule #2452

Merged
merged 10 commits into from
Jun 9, 2023
Merged

Enable Metal, Facet, site and terrace specification in Molecule #2452

merged 10 commits into from
Jun 9, 2023

Commits on Jun 8, 2023

  1. allow skipping of consistency checks when generating Molecule and Gro… 

    …up objects

consistency check
    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  2. add reaction 'R' bonds 

    reaction bonds
    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  3. add metal and facet attributes to Molecule and Group

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  4. add site and morphology attributes to Group and Molecule

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  5. allow read and write of adjlists with site and morphology

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  6. add site and morphology to fragment to make compatible with adjlist

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  7. enable sites to be bonded to each other to represent neighbors

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  8. set metal and facet for fragment

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  9. add test for metal, facet, site and morphology specifications

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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  10. add metal, facet, site and morphology to adjacency list documentation

    @mjohnson541
    mjohnson541 committed Jun 8, 2023
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