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Enable Restarting RMG Jobs from a Seed Mechanism #1641

Merged
merged 17 commits into from
Aug 12, 2019
Merged

Enable Restarting RMG Jobs from a Seed Mechanism #1641

merged 17 commits into from
Aug 12, 2019

Commits on Aug 10, 2019

  1. Save the seed mechanism at the beginning of each iteration

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  2. Make seed mechanism generation every iteration the default behavior

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  3. Prevent the loss of the seed mechanism if an exception is encountered

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  4. Save filter tensors with seed mechanism

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  5. Add flag in RMG input for restarting from a seed mechanism

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  6. Load in a seed mechanism and filter tensors for restarting jobs

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  7. Do not perform forbidden species checking for auto generated libraries 

    We now perform this check when/if these edge species are moved to the core
    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  8. Automatically generate a restart from seed file

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  9. Add documentation for restarting from a seed mechanism

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  10. Delete the cPickle restart feature!!!! 

    Has been deprecated for a while, and is now completely replaced by the restart from seed mechanism feature.
    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  11. Add minimal restart example

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  12. Use reaction filtering in the minimal example

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  13. Make the name of the seed mechanism fixed and case consistent 

    We will still use the job name when outputting to the database, but the name should be fixed in the output directory
    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  14. Use degeneracy from a seed mechanism if auto-generated

    @amarkpayne
    amarkpayne committed Aug 10, 2019
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  15. Use longDesc property instead of private variable

    @mliu49 @amarkpayne
    mliu49 authored and amarkpayne committed Aug 10, 2019
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  16. Refactor comment parsing for template reactions in kinetics library 

    More robust methods to determine template and family name
Make sure to strip family name
    @mliu49 @amarkpayne
    mliu49 authored and amarkpayne committed Aug 10, 2019
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  17. Remove leading spaces from kinetics comments from libraries 

    Otherwise, indents are retained over each read/write operation
    @mliu49 @amarkpayne
    mliu49 authored and amarkpayne committed Aug 10, 2019
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