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InvalidMicrocanonicalRateError

Open PoojaNem opened this issue 1 year ago • 1 comments

Hello Everyone,

I am working on kinetic model generation for n-decane combustion in air. Based on the reactor pressure, temperature and mixture composition I intend to produce a mechanism with pressure dependence. While running this case, I end up with the error (shown below):

image

I have looked into several similar issues previously reported on GitHub, but could not understand the source of the error.

Any suggestion to resolve this concern will be helpful. I have attached the RMG input, error and thermo database file (slightly different from existing file in RMG database). Let me know if further details are needed from my end.

input.txt error.txt JetSurF2.txt

Installation Information OS: Windows 11, WSL2, Ubuntu 22.04 Installation method: Installation by Source Using Anaconda Environment for Unix-based Systems: Linux and Mac OSX RMG version information: RMG-Py: Latest version RMG-database: Latest database

PoojaNem avatar Apr 18 '24 14:04 PoojaNem

Here's the complete text of the error, which I think shows the actual problem:

Updating PDepNetwork #523
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCCCCCC)C([O])=O.
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C=C([O])OCCCCCCC.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for CCCCCCCC=C([O])[O].
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C([C]=O)CCCCCCC.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Statmech node 'RsCHrr' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH]C(CCCCCCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2][C](CCCCCCC)C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C([CH]CCCCCC)C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C([CH]CCCCCC)[C]([O])O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(C[CH]CCCCC)C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(C[CH]CCCCC)[C]([O])O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CC[CH]CCCC)C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CC[CH]CCCC)[C]([O])O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCC[CH]CCC)C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCC[CH]CCC)[C]([O])O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCCC[CH]CC)C([O])[O].
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2][C](CCCCCCC)C(=O)O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for C=C(CCCCCCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCCCCCC)=C([O])[O].
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C([CH]CCCCCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CC[CH]CCCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCC[CH]CCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCCC[CH]CC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(C[CH]CCCCC)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C(CCCCC[CH]C)C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]CCCCCCC([CH2])C([O])=O.
Warning: Statmech node 'Oxy' and all its parents have data = None
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for CCCCCCC[C](C)C([O])=O.
Warning: Statmech node 'O_R0' and all its parents have data = None
Warning: Statmech node 'C_R0' and all its parents have data = None
Warning: Maximum number of iterations reached when fitting spectral data for [CH2]C([CH]CCCCCC)C(=O)O.
Calculating densities of states for PDepNetwork #523 network...
Using 718 grains from -536.40 to 963.56 kJ/mol in steps of 2.09 kJ/mol to compute densities of states
Calculating phenomenological rate coefficients for [CH2]C(CCCCCCC)C([O])=O(2772) <=> C[CH]CCCCCC(C)C([O])=O(4314)...
Using 718 grains from -536.40 to 963.56 kJ/mol in steps of 2.09 kJ/mol to compute the k(T,P) values at 2100 K
Warning: Significant corrections to k(E) to be consistent with high-pressure limit for path reaction "[CH2]C(CCCCCCC)C([O])=O(2772) <=> CCCCCCCCC=C([O])[O](4276)".
Warning: For path reaction [CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290):
Warning:     Expected kf(2100 K) = 22938.6
Warning:       Actual kf(2100 K) = 7734.82
Warning:     Expected Keq(2100 K) = 1.20613e-09
Warning:       Actual Keq(2100 K) = 0
Warning: Increasing number of grains, decreasing grain size and trying again. (Current badness: 0.5)
Using 1434 grains from -536.40 to 962.51 kJ/mol in steps of 1.05 kJ/mol to compute the k(T,P) values at 2100 K
Warning: For path reaction [CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290):
Warning:     Expected kf(2100 K) = 22938.6
Warning:       Actual kf(2100 K) = 7646.57
Warning:     Expected Keq(2100 K) = 1.20613e-09
Warning:       Actual Keq(2100 K) = 0
Warning: Increasing number of grains, decreasing grain size and trying again. (Current badness: 0.5)
Using 2866 grains from -536.40 to 961.99 kJ/mol in steps of 0.52 kJ/mol to compute the k(T,P) values at 2100 K
Warning: For path reaction [CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290):
Warning:     Expected kf(2100 K) = 22938.6
Warning:       Actual kf(2100 K) = 7602.51
Warning:     Expected Keq(2100 K) = 1.20613e-09
Warning:       Actual Keq(2100 K) = 0
Warning: Increasing number of grains, decreasing grain size and trying again. (Current badness: 0.5)
Using 5731 grains from -536.40 to 961.99 kJ/mol in steps of 0.26 kJ/mol to compute the k(T,P) values at 2100 K
Warning: For path reaction [CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290):
Warning:     Expected kf(2100 K) = 22938.6
Warning:       Actual kf(2100 K) = 7595.19
Warning:     Expected Keq(2100 K) = 1.20613e-09
Warning:       Actual Keq(2100 K) = 0
Warning: Increasing number of grains, decreasing grain size and trying again. (Current badness: 0.5)
Using 11461 grains from -536.40 to 961.99 kJ/mol in steps of 0.13 kJ/mol to compute the k(T,P) values at 2100 K
Warning: Significant corrections to k(E) to be consistent with high-pressure limit for path reaction "[CH2]C(CCCCCCC)C([O])=O(2772) <=> CCCCCCCCC=C([O])[O](4276)".
Warning: For path reaction [CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290):
Warning:     Expected kf(2100 K) = 22938.6
Warning:       Actual kf(2100 K) = 7591.52
Warning:     Expected Keq(2100 K) = 1.20613e-09
Warning:       Actual Keq(2100 K) = 0
Error: Invalid k(E) values computed for path reaction "[CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290)".
Error: Increasing number of grains did not decrease error enough (Current badness: 0.5, previous 0.5). Something must be wrong with network PDepNetwork #523
Traceback (most recent call last):
  File "/home/pnema/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
    python(**vars(ns))
  File "/home/pnema/miniconda3/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 "/home/pnema/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/home/pnema/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/home/pnema/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/pnema/RMG/RMG-Py/rmg.py", line 118, in <module>
    main()
  File "/home/pnema/RMG/RMG-Py/rmg.py", line 112, in main
    rmg.execute(**kwargs)
  File "/home/pnema/RMG/RMG-Py/rmgpy/rmg/main.py", line 944, in execute
    self.reaction_model.enlarge(objectToEnlarge)
  File "/home/pnema/RMG/RMG-Py/rmgpy/rmg/model.py", line 709, in enlarge
    self.update_unimolecular_reaction_networks()
  File "/home/pnema/RMG/RMG-Py/rmgpy/rmg/model.py", line 1919, in update_unimolecular_reaction_networks
    network.update(self, self.pressure_dependence)
  File "/home/pnema/RMG/RMG-Py/rmgpy/rmg/pdep.py", line 879, in update
    K = self.calculate_rate_coefficients(Tlist, Plist, method)
  File "/home/pnema/RMG/RMG-Py/rmgpy/pdep/network.py", line 268, in calculate_rate_coefficients
    self.set_conditions(T, P)
  File "/home/pnema/RMG/RMG-Py/rmgpy/pdep/network.py", line 411, in set_conditions
    raise error
  File "/home/pnema/RMG/RMG-Py/rmgpy/pdep/network.py", line 399, in set_conditions
    self.calculate_microcanonical_rates()
  File "/home/pnema/RMG/RMG-Py/rmgpy/pdep/network.py", line 841, in calculate_microcanonical_rates
    'Invalid k(E) values computed for path reaction "{0}".'.format(rxn), k_ratio, Keq_ratio)
rmgpy.exceptions.InvalidMicrocanonicalRateError: ('Invalid k(E) values computed for path reaction "[CH2]C(CCCCCCC)C([O])=O(2772) <=> [CH2]C(CCCCCCC)[C]1OO1(4290)".', 3.0216075010375487, 1.0)

The Warning: Actual Keq(2100 K) = 0 which comes up after Warning: Statmech node 'Oxy' and all its parents have data = None leads me to believe that one of these species contains some group that Arkane just can't estimate something for, though I don't know much detail beyond that. @oscarwumit have you seen something like this before?

JacksonBurns avatar Jun 06 '24 20:06 JacksonBurns

This issue is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant issue, otherwise it will automatically be closed in 30 days.

github-actions[bot] avatar Sep 05 '24 08:09 github-actions[bot]