RMG-generated network__.py doesn't run in measure.py #40
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The commit e1f226c changed the method for writing a measure input file, but not the call to it from rmg/model.py
When reading in from the smiles '[CH]' the carbon ends up with a radicalElectrons count of 0 instead of 3. Strangely, [CH2] and [CH3] work fine. This causes problems in data/thermo.py when trying to find the thermo for [CH].
…oner. As soon as the input file has been read in, we write an output file which has 0 species and 0 reactions. The species pictures etc. from the previous run have been wiped by this point already, but it can be confusing to have the previous output file still there when you're running a new job.
Whenever the latest chemXXXX.inp file is written, it is copied (or rather hard-linked) to chemkin/chem.inp, so that you can always just look at this file and get the latest.
It used to write
isomer("HCCOH")
reactants("C2H", "OH")
instead of
isomer("HCCOH(31)")
reactants("C2H(3)", "OH(32)")
This closes #40
|
Hmm. Only the last of these commits actually deals with this issue, so perhaps I shouldn't have turned it into a pull request, but in any event merging it will close the issue. |
This is close to something I've been using in RMG-Java.
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When I run RMG-py it generates a pdep/network73_1.py file, which contains the lines
The species labels are missing their numbers.
In order to run in standalone measure.py without giving a KeyError on the line
it should read: