Error when Running Halogen Example

[timmallo]

Bug Description

When running the halogen example, I get a kinetics error, not finding a reverse reaction.

How To Reproduce

1. Download RMG using Docker
2. Copy the input file code from Github for the Halogen Example
3. Make a directory in Docker to place the copied input file
4. Copy input file from Github into the new directory
5. Run the example input file using the command "python-jl /rmg/RMG-Py/rmg.py input.py"

Expected Behavior

The job ran perfectly fine for about 45 minutes before returning an error.

Installation Information

Describe your installation method and system information.

• OS: Windows 10 (Using Command Prompt/Docker)
• Installation method: Docker
• RMG version information: 3.1.1

Additional Context

Error: Debugging why no reaction was found...
Error: Checking whether the family's forbidden species have affected reaction generation...
Error: Still experiencing error: Expecting one matching reverse reaction, not 2 in reaction family F_Abstraction for forward reaction C#C[CH]F + [O]C=C([O])C=C(F)F <=> [CH]C#C + [O]C=C(C=C(F)F)OF.

Traceback (most recent call last):
File "/miniconda/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
python(**vars(ns))
File "/miniconda/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python
scope = runpy.run_path(script, run_name="main")
File "/miniconda/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "/miniconda/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "/miniconda/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/rmg/RMG-Py/rmg.py", line 118, in
main()
File "/rmg/RMG-Py/rmg.py", line 112, in main
rmg.execute(**kwargs)
File "/rmg/RMG-Py/rmgpy/rmg/main.py", line 1026, in execute
trimolecular_react=self.trimolecular_react)
File "/rmg/RMG-Py/rmgpy/rmg/model.py", line 685, in enlarge
procnum=procnum)
File "/rmg/RMG-Py/rmgpy/rmg/react.py", line 172, in react_all
return react(spc_fam_tuples, procnum), [fam_tuple[0] for fam_tuple in spc_fam_tuples]
File "/rmg/RMG-Py/rmgpy/rmg/react.py", line 66, in react
reactions = list(map(_react_species_star, spc_fam_tuples))
File "/rmg/RMG-Py/rmgpy/rmg/react.py", line 79, in _react_species_star
return react_species(*args)
File "/rmg/RMG-Py/rmgpy/rmg/react.py", line 94, in react_species
reactions = get_db('kinetics').generate_reactions_from_families(species_tuple, only_families=only_families)
File "/rmg/RMG-Py/rmgpy/data/kinetics/database.py", line 546, in generate_reactions_from_families
successful = family.add_reverse_attribute(rxn)
File "/rmg/RMG-Py/rmgpy/data/kinetics/family.py", line 1880, in add_reverse_attribute
"{1}.".format(self.label, str(rxn)))
rmgpy.exceptions.KineticsError: Did not find reverse reaction in reaction family F_Abstraction for reaction C#C[CH]F + [O]C=C([O])C=C(F)F <=> [CH]C#C + [O]C=C(C=C(F)F)OF.

[rwest]

Sorry - we added the example to RMG-Py before the relevant updates to the database were merged into RMG-database. You could try a different branch of the database like halogens_kinetics_paper, or wait a while for us to get it merged.

[JacksonBurns]

@timmallo I think when you pulled the docker container you likely used docker pull reactionmechanismgenerator/rmg:latest instead of docker pull reactionmechanismgenerator/rmg:3.1.1. The latest tag is not intended for general use and is a developer tool.

I will clarify this inside the Docker image itself.

[timmallo]

I believe I used docker pull reactionmechanismgenerator/rmg:3.1.1 . I did not know the latest tag existed.

[JacksonBurns]

I believe I used docker pull reactionmechanismgenerator/rmg:3.1.1 . I did not know the latest tag existed.

Interesting - were you running this halogen example? That one is only available in the latest image AFAIK.

[timmallo]

I used the file on github, copied the text, and manually added it to the docker container.

[JacksonBurns]

I used the file on github, copied the text, and manually added it to the docker container.

Ah I apologize, I should have re-read the original post. @rwest's comment still stands - we will get the new version out asap.

[timmallo]

All good! Thank you both for the help and speedy responses!

[JacksonBurns]

This issue will be resolved by the release of v3.2.0 and the corresponding Docker image - I have linked this issue to the PR, and it will automatically close after the release since the issue will be resolved.

[JacksonBurns]

@timmallo apologies for the delay, but the Docker image for version 3.2.0 is out! It should contain all the changes needed to run the example.

This issue will automatically be closed once #2522 is merged (which updates the docs to point to 3.2.0) but if the issue persists please feel free to re-open.