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Load and dump TS YAML files in Arkane #1551

Merged
merged 15 commits into from Mar 15, 2019
Merged

Load and dump TS YAML files in Arkane #1551

merged 15 commits into from Mar 15, 2019

Commits on Mar 14, 2019

  1. Don't prettify the yaml file by removing extra lines 

    Doing so interfers with reading the line brakes, so whe reading we get:
1 O u0 p2 c0 {2,S} {9,S} 2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} 3 C u0 p0
c0 {2,S} {6,S} {7,S} {8,S} 4 H u0 p0 c0 {2,S} 5 H u0 p0 c0 {2,S} 6 H u0
p0 c0 {3,S} 7 H u0 p0 c0 {3,S} 8 H u0 p0 c0 {3,S} 9 H u0 p0 c0 {1,S}
instead of:
1 O u0 p2 c0 {2,S} {9,S}
2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
4 H u0 p0 c0 {2,S}
5 H u0 p0 c0 {2,S}
6 H u0 p0 c0 {3,S}
7 H u0 p0 c0 {3,S}
8 H u0 p0 c0 {3,S}
9 H u0 p0 c0 {1,S}
    @alongd
    alongd committed Mar 14, 2019
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  2. Load all lines when reading energy in QChem 

    For some reason ARC fails without this modification when sp calculations
are done in QChem. It is indeed less efficient, since the entire file is
loaded to memory.
    @alongd
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  3. Added a QChem LoadEnergy test 

    Using the 'Total energy in the final basis set' phrase
    @alongd
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  4. Renamed the species YAML folder to simply species

    @alongd
    alongd committed Mar 14, 2019
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  5. Allow ArkaneSpecies to process TSs as well

    @alongd
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  6. Set ArkaneSpecies properties after loading the objects 

    Some properties are important to parse, but are not objects and cannot
be updated automatically.
`imaginary_frequency` contains a ScalarQuantity instance, but it is not
an object in itself in RMG/Arkane, just an attribute of TransitionState
(.frequency). It's important to parse it for tunneling.
Structure information is important to parse since YAML file generation
depends on it.
    @alongd
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  7. Minor: Styling improvements in Arkane kinetics.py

    @alongd
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  8. Save a YAML file for TSs after computing kinetics 

    Iff structures of all reactant/s and product/s are given
    @alongd
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  9. Allow Statmech to process TSs from YAML 

    Also, renames `TS` as `is_ts`
    @alongd
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  10. Minor: comments in Arkane thermo

    @alongd
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  11. Allow RMGObject to process lists even if they don't contain RMGObjects

    @alongd
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  12. Added the NH2 + N2H3 = NH + N2H4 Arkane reaction example 

    Showing how to use species (and TS) YAML files to run Arkane
    @alongd
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  13. Modified the H+C2H4=C2H5 Arkane example to save YAML files

    @alongd
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  14. Modified commonTest according to the recent ArkaneSpecies changes

    @alongd
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  15. Minor improvements to yaml dumping for ArkaneSpecies 

    Provide file stream directly to yaml.dump
Remove optional Dumper argument and associated imports
Add str representer to dump multiline strings as block literals
    @mliu49 @alongd
    mliu49 authored and alongd committed Mar 14, 2019
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