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Fix pressure dependent network generation in RMG jobs #1658

Merged
merged 7 commits into from Jul 21, 2019
Merged

Fix pressure dependent network generation in RMG jobs #1658

merged 7 commits into from Jul 21, 2019

Commits on Jul 20, 2019

  1. Refactor reaction generation and processing for reactEdge phase 

    Motivation:
- processNewReactions requires a newSpecies argument which was not
being properly identified after multiprocessing changes in #1459

Background:
- The newSpecies argument is retained from early RMG when reactions
were generated right after adding a new species to the core.
- Hence, newSpecies referred to the newly added core species which
was used to generate the new reactions.
- The overall model generation algorithm has since changed, so
identifying newSpecies is not as straightforward.
- The multiprocessing PR changed newSpecies to be any core species,
missing the original purpose of identifying the species from which
the reaction was generated.

Changes:
- Use the species tuples created during reaction generation to
keep track of which species were used to generate the reaction
- Update unit tests which are affected by the changes in return values
from react and react_all
    @mliu49
    mliu49 committed Jul 20, 2019
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  2. Update docstrings in rmgpy.rmg.react module 

    Also rename the spc_tuples arg in the react method to spc_fam_tuples
to reflect updated usage.
    @mliu49
    mliu49 committed Jul 20, 2019
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  3. Remove getSpecies and retrive_species which are no longer used

    @mliu49
    mliu49 committed Jul 20, 2019
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  4. Remove unused imports in rmgpy.rmg.model

    @mliu49
    mliu49 committed Jul 20, 2019
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  5. Reorganize imports in rmgpy.rmg.model 

    Sort alphabetically and also remove relative imports
    @mliu49
    mliu49 committed Jul 20, 2019
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  6. Revert "Update arkane/explorerTest.py." 

    This reverts commit d59da68.

Lesson to be learned: If a unit test fails, make sure you
understand why before changing the correct answer...
    @mliu49
    mliu49 committed Jul 20, 2019
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  7. Add test class for CoreEdgeReactionModel.enlarge 

    With tests for pdep network generation
    @mliu49
    mliu49 committed Jul 20, 2019
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