RMG forbidding the species without addition of the constraints block in the input file.

[shikharnigam8]

Bug Description

I am running the inbuilt RMG example "ethane-oxidation". This example ran without any error. However, I face the following error on the addition of "combustion_core/version4" reaction library in the input file. The constraint block in the input file is not active.
input.txt

On doing this, my simulation is terminating with an error saying "rmgpy.exceptions.ForbiddenStructureException: Species constraints forbids species CH from reaction library combustion_core/version4. Please reformulate constraints, remove the species, or explicitly allow it".
@rwest

How To Reproduce

I have attached the input file.

Expected Behavior

Since, the constraint block is not used in the input file, the simulation should terminate without any error.

Installation Information

Describe your installation method and system information.

• OS (include version if known): Linux Subsystem on Windows 10
• Installation method: Source with anaconda
• RMG version information:
  • RMG-Py: Latest version
  • RMG-database: Latest database

Additional Context

Add any other context about the problem here.

[rwest]

You could try

generatedSpeciesConstraints(
    allowed=['input species','seed mechanisms','reaction libraries'],
)

My guess is the maximumCarbeneRadicals is limiting you.

Perhaps the defaults, and/or other tips, should be in the documentation.
(edit it here )

You can figure them out from
https://github.com/ReactionMechanismGenerator/RMG-Py/blob/master/rmgpy/constraints.py

[shikharnigam8]

Of course, on explicitly adding the constraint block in the input file, the simulation is running fine. However, we are not sure about the source of this error, if we don't add the constraint block in the input file.
We further checked "forbiddenstructures.py" file, but we did not find any such specie there.
Could you help us to locate the error?

[rwest]

The constraints.py file I pointed you to above has this block

    max_carbene_radicals = species_constraints.get('maximumCarbeneRadicals', 0)
    if max_carbene_radicals != -1:
        if struct.get_singlet_carbene_count() > 0 and struct.get_radical_count() > max_carbene_radicals:
            return True

On the first line, if maximumCarbeneRadicals is not set, then it defaults to 0.
Your original message says the problem is CH in the combustion_core/version4 library. Checking that dictionary.txt we find the structure is

CH
multiplicity 2
1 C u1 p1 c0 {2,S}
2 H u0 p0 c0 {1,S}

We can then confirm this is counting as a singlet carbene with a radical, for the purposes of this constraint:

In [1]: from rmgpy.molecule import Molecule

In [2]: Molecule().from_adjacency_list("""CH
   ...: multiplicity 2
   ...: 1 C u1 p1 c0 {2,S}
   ...: 2 H u0 p0 c0 {1,S}""")
Out[2]: Molecule(smiles="[CH]")

In [3]: _.get_singlet_carbene_count(), _.get_radical_count()
Out[3]: (1, 1)

Checking the history of that file we can find that the carbene radical constraint was added in the pull request #1187, which contains some explanation and commentary.

As I suggested above, perhaps someone should add a little to the documentation about the default values (because the pull request comments will be hard to find).

[github-actions]

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