NH3/CH4 Co-oxidation - No enthalpy for N#N

[calvinp0]

Topic

General area which your question is related to.

• Installation of RMG
• Running an RMG job
• Using RMG API
• Arkane (formerly CanTherm)
• Dependencies
• An error message

Context

Attempting to run a simple NH3/CH4 Co-oxidation job with Nitrogen gas as the bath gas. However, when running the reaction - it complains with the following message:

Adding reaction library primaryNitrogenLibrary to model edge...
Traceback (most recent call last):
  File "/home/calvin/Downloads/daniel_rmg/../../code/RMG-Py/rmg.py", line 4, in <module>
    __main__.main()
  File "/home/calvin/code/RMG-Py/rmgpy/__main__.py", line 102, in main
    rmg.execute(**kwargs)
  File "/home/calvin/code/RMG-Py/rmgpy/rmg/main.py", line 802, in execute
    requires_rms = self.initialize(**kwargs)
  File "/home/calvin/code/RMG-Py/rmgpy/rmg/main.py", line 669, in initialize
    self.reaction_model.add_reaction_library_to_edge(library, requires_rms=requires_rms)
  File "/home/calvin/code/RMG-Py/rmgpy/rmg/model.py", line 1762, in add_reaction_library_to_edge
    r, isNew = self.make_new_reaction(rxn)  # updates self.new_species_list and self.new_reaction_list
  File "/home/calvin/code/RMG-Py/rmgpy/rmg/model.py", line 566, in make_new_reaction
    forward.fix_barrier_height(force_positive=True,solvent="")
  File "rmgpy/reaction.py", line 1002, in rmgpy.reaction.Reaction.fix_barrier_height
  File "rmgpy/reaction.py", line 1034, in rmgpy.reaction.Reaction.fix_barrier_height
  File "rmgpy/reaction.py", line 640, in rmgpy.reaction.Reaction.get_enthalpy_of_reaction
  File "rmgpy/reaction.py", line 640, in rmgpy.reaction.Reaction.get_enthalpy_of_reaction
  File "rmgpy/reaction.py", line 648, in rmgpy.reaction.Reaction.get_enthalpy_of_reaction
  File "rmgpy/species.py", line 573, in rmgpy.species.Species.get_enthalpy
Exception: Unable to calculate enthalpy for species 'nitrogen': no thermo or statmech data available.

Now, when I run it with N#N as reactive and set [Ar] as non-reactive with concentration 0, it runs fine (although of course need to allow for singlet O2).

Am I missing something in my input file?

input.py

[calvinp0]

Just to add, the input.py runs fine on RMG 3.7

[rwest]

To clarify, this species( label='nitrogen', reactive=True, structure=SMILES("N#N"))
works fine.

but this species( label='nitrogen', reactive=False, structure=SMILES("N#N"))
gives "Unable to calculate enthalpy for species 'nitrogen'"

?

Must be to do with how the reactive=False species are handled?

Also, I'm curious - why do you want it to be inert, in an ammonia oxidation model?

[calvinp0]

To clarify, this species( label='nitrogen', reactive=True, structure=SMILES("N#N")) works fine.

but this species( label='nitrogen', reactive=False, structure=SMILES("N#N")) gives "Unable to calculate enthalpy for species 'nitrogen'"

?

Must be to do with how the reactive=False species are handled?

Also, I'm curious - why do you want it to be inert, in an ammonia oxidation model?

Yeah, exactly right. When set to non-reactive then we receive the error in RMG 3.9

It was set as inert due to a student misreading an experiment article that they were trying to simulate. I see in the article now that was not the case, it is meant to be reactive.