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Non-cat changes to master from cat branch, 2 #1542

Merged
merged 9 commits into from
Feb 6, 2019
Merged

Non-cat changes to master from cat branch, 2 #1542

merged 9 commits into from
Feb 6, 2019

Commits on Feb 6, 2019

  1. Snapshots (PNGs and CSVs) now track moles not mole fractions. 

    Unsure if this has consequences on flux diagrams or
sensitivity analyses, etc. but I think it's a helpful 
start towards making more sense of simulation outputs,
especially for two-phase heterogeneous systems.
    @rwest
    rwest committed Feb 6, 2019
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  2. Brief notes in documentation about change of 'solver' output.

    @rwest
    rwest committed Feb 6, 2019
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  3. Add quadruple bonds 

    A combination of commits with these messages:

replaced part of the adjlist in the test that I accidentally deleted

added in a quadruple bond to orders

Added in quadruple bond type in converter
added in more instances of quadruple bonds

Adding Cq to R and R!H atom types

added in todos to add unit tests for quadruple bonded elements
    @rwest
    rwest committed Feb 6, 2019
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  4. Updates since AtomType.getFeatures() now includes quadruple bonds 

    It's unfortunate how fragile this code is, using integer
indexing.
Had to change getFeatures to include Benzene in its corrcect spot,
    @mazeau @rwest
    mazeau authored and rwest committed Feb 6, 2019
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  5. changed H bonds to 0.1 in the definitions 

    A combination of several commits, with these messages:

changed the remove H bonds to remove anything close to 0.1

Hydrogen-bonds now have order 0.1

This way of doing things is a bit fragile, and not very satisfying.
But I think this fixes at least a couple of places where this change
needs to be made.

Detect 0.1 bond orders (for H bonds) more robustly.

Now passes last unit test.
(It was something like 0.1000000000000149)
    @mazeau @rwest
    mazeau authored and rwest committed Feb 6, 2019
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  6. Hydrogen bonds have order 0.1 (instead of 0) (more)

    @rwest
    rwest committed Feb 6, 2019
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  7. Adding van der Waals bonds (which have order 0) 

    Reaction recipes can make Van der Waals bonds (with order 0)

Remove 'vdW' from bond types accepted (should be 0).

This is a hold-over from when bond types were strings
not floating point numbers.
    @rwest
    rwest committed Feb 6, 2019
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  8. Minor comments added to molecule/groupTest unit tests.

    @rwest
    rwest committed Feb 6, 2019
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  9. More helpful error logging when failing to load reaction library. 

    Might not make a difference if you could see the logging.info call two lines earlier,
but when running unit tests (databaseTest) that is not necessarily the case.
    @rwest
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