ReactionMechanismGenerator / ReactionMechanismGenerator/ARC
Not identifing H_abstraction family
@alongd is already working on this.
Since Dec 4, 2023.
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Description
Describe the bug
I tried to calculate the rate of the H_abstraction reaction : H2N2_116 + ammonia_5 <=> NH2_3 + H3N2_4, without including TS guess. I got this reaction from RMG output that identified it as H_abstraction. While running ARC the reaction wasn't identified as H_abstraction as expected.
How to reproduce
Here is some more examples that ARC didn't identified to be H_abstraction but they are.
job_types:
rotors: false
allow_nonisomorphic_2d: True
compute_thermo: false
freq_scale_factor: 1
species:
- label: 'H4N2_1'
smiles: 'NN'
- label: 'H2_2'
smiles: '[H][H]'
- label: 'NH2_3'
smiles: '[NH2]'
- label: 'H3N2_4'
smiles: '[NH]N'
- label: 'ammonia_5'
smiles: 'N'
- label: 'HN2_6'
smiles: '[N]=N'
- label: 'N2H2_19'
smiles: 'N=N'
- label: 'H_8'
smiles: '[H]'
- label: 'H2N2_116'
smiles: '[NH][NH]'
- label: 'H2N2_113'
smiles: '[N]N'
reactions:
- label: H2N2_116 + ammonia_5 <=> NH2_3 + H3N2_4
- label: H2N2_116 + H4N2_1 <=> H3N2_4 + H3N2_4
- label: N2H2_19 + H2N2_116 <=> HN2_6 + H3N2_4
- label: H_8 + H3N2_4 <=> H2_2 + H2N2_116
ARC.log output:
Setting multiplicity of reaction NH2_3 + H3N2_4 <=> H2N2_116 + ammonia_5 to 3
Considering reaction: H2N2_116 + ammonia_5 <=> NH2_3 + H3N2_4
Setting multiplicity of reaction H3N2_4 + H3N2_4 <=> H2N2_116 + H4N2_1 to 3
Considering reaction: H2N2_116 + H4N2_1 <=> H3N2_4 + H3N2_4
Setting multiplicity of reaction HN2_6 + H3N2_4 <=> N2H2_19 + H2N2_116 to 3
Considering reaction: N2H2_19 + H2N2_116 <=> HN2_6 + H3N2_4
Setting multiplicity of reaction H2_2 + H2N2_116 <=> H_8 + H3N2_4 to 3
Considering reaction: H_8 + H3N2_4 <=> H2_2 + H2N2_116
Here is a graphic image of the species of the first reaction:

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