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[Python 3.9] Reimplement Clar Optimization with Scipy MILP #2694

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Commits on Jul 24, 2024

  1. Refactoring clar optimization and utilize scipy MILP

    1. Replace lpsolve APIs with the scipy milp APIs. The new implementation potentially have a slightly better performance (due to vectorization, less data transfer, comparable solver performance, etc.) and improved readability.
    2. Decouple the MILP solving step (as _solve_clar_milp ) from the MILP formulation step. The motivation is to avoid unnecessary computation. The original approach includes molecule analysis (specifically `get_aromatic_rings`) into the recursive calls. However, this is not necessary, as molecules are just copied and not modified at all. Therefore analyzing once is enough.
    xiaoruiDong authored and JacksonBurns committed Jul 24, 2024
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  5. Fix list style in clar optimization

    Co-authored-by: Hao-Wei Pang <45482070+hwpang@users.noreply.github.com>
    2 people authored and JacksonBurns committed Jul 24, 2024
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  6. Update year in license

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  7. imports sorting by formatter

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  8. Add improvements by @amarkpayne

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  9. Add constraints for element balance

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  11. Formatting by formatter

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  12. Catch TypeError

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  13. WIP

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  14. Modify based on review comment

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  15. Better way to initialize empty list

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  18. Add warning for easy debugging

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  19. Switch to use scipy

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  22. Remove options of solver

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  24. Use keyword variable

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  25. Add comment

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  26. Add comment to test

    hwpang authored and JacksonBurns committed Jul 24, 2024
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  30. ugh, typo

    JacksonBurns committed Jul 24, 2024
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Commits on Jul 25, 2024

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  7. add back the cclib version restriction

    we are not compatible with the latest version, will be resolved in this PR: #2639
    JacksonBurns committed Jul 25, 2024
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Commits on Jul 26, 2024

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Commits on Aug 5, 2024

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  3. fix usage of warning

    JacksonBurns committed Aug 5, 2024
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  4. Merge pull request #2695 from ReactionMechanismGenerator/feat/isodesm…

    …ic_scipy
    
    [Python 3.9] Improve isodesmic and add element balance constraints
    JacksonBurns authored Aug 5, 2024
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Commits on Aug 21, 2024

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