sevyharris
commented
3 years ago Thanks to PR 2208 the ValueError: 'O2' is not in list error is fixed and the Sulfur test passes! However the Nitrogen test (run on Github Actions) now fails for non-identical thermo and kinetics:
Running rmg/nitrogen test case
Benchmark code directory: /home/runner/work/RMG-tests/RMG-tests/code/benchmark/RMG-Py
Running benchmark job
Benchmark job completed
Testing code directory: /home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py
Running testing job
Testing job completed
Comparing results
Benchmark model folder: /home/runner/work/RMG-tests/RMG-tests/results/benchmark/rmg/nitrogen
Testing model folder: /home/runner/work/RMG-tests/RMG-tests/results/testmodel/rmg/nitrogen
Core for rmg/nitrogen:
Test model has 41 species.
Original model has 41 species.
Test model has 360 reactions.
Original model has 360 reactions.
Edge for rmg/nitrogen:
Test model has 132 species.
Original model has 132 species.
Test model has 998 reactions.
Original model has 998 reactions.
Non-identical thermo!
original: O1[C]=N1
tested: O1[C]=N1
Hf(300K) |S(300K) |Cp(300K) |Cp(400K) |Cp(500K) |Cp(600K) |Cp(800K) |Cp(1000K) |Cp(1500K)
116.46| 53.90| 11.62| 12.71| 13.49| 13.96| 14.14| 13.85| 13.58
141.64| 58.66| 12.26| 12.27| 12.09| 11.96| 12.26| 12.72| 12.15
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
Non-identical kinetics!
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
k(1bar)|300K |400K |500K |600K |800K |1000K |1500K |2000K
k(T): | -50.17| -34.42| -24.95| -18.64| -10.73| -5.97| 0.40| 3.60
k(T): | -68.50| -48.17| -35.96| -27.81| -17.60| -11.47| -3.27| 0.85
Kinetics: Arrhenius(A=(1.55936e+11,'s^-1'), n=0.551, Ea=(86.101,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [R3_linear;multiplebond_intra;radadd_intra] for rate rule [R3_linear;multiplebond_intra;radadd_intra_O]
Kinetics: Arrhenius(A=(1.55936e+11,'s^-1'), n=0.551, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated using template [R3_linear;multiplebond_intra;radadd_intra] for rate rule [R3_linear;multiplebond_intra;radadd_intra_O]
Identical kinetics comments
Execution time, Benchmark:
Execution time (DD:HH:MM:SS): 00:00:01:53
Execution time, Tested:
Execution time (DD:HH:MM:SS): 00:00:01:42
Memory used, Benchmark:
Memory used: 1421.00 MB
Memory used, Tested:
Memory used: 1431.86 MB
Traceback (most recent call last):
File "/usr/share/miniconda/envs/testing/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
python(**vars(ns))
File "/usr/share/miniconda/envs/testing/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python
scope = runpy.run_path(script, run_name="__main__")
File "/usr/share/miniconda/envs/testing/lib/python3.7/runpy.py", line 263, in run_path
pkg_name=pkg_name, script_name=fname)
File "/usr/share/miniconda/envs/testing/lib/python3.7/runpy.py", line 96, in _run_module_code
mod_name, mod_spec, pkg_name, script_name)
File "/usr/share/miniconda/envs/testing/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py/rmgpy/tools/regression.py", line 199, in <module>
main()
File "/home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py/rmgpy/tools/regression.py", line 195, in main
run(benchmark, tested, *args)
File "/home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py/rmgpy/tools/regression.py", line 157, in run
observables={'species': observables}
File "/home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py/rmgpy/tools/observablesregression.py", line 138, in __init__
quiet=True)
File "/home/runner/work/RMG-tests/RMG-tests/code/testing/RMG-Py/rmgpy/tools/canteramodel.py", line 305, in load_chemkin_model
self.model = ct.Solution(out_name)
File "interfaces/cython/cantera/base.pyx", line 29, in cantera._cantera._SolutionBase.__cinit__
File "interfaces/cython/cantera/base.pyx", line 50, in cantera._cantera._SolutionBase._init_cti_xml
cantera._cantera.CanteraError:
***********************************************************************
CanteraError thrown by ct2ctml_string:
Error converting input file "/home/runner/work/RMG-tests/RMG-tests/results/benchmark/rmg/nitrogen/chemkin/chem_annotated.cti" to CTML.
Python command was: '/usr/share/miniconda/envs/testing/bin/python'
The exit code was: 7
-------------- start of converter log --------------
Python 3.7.11 (default, Jul 27 2021, 14:35:47)
[GCC 7.5.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
(InteractiveConsole)
Traceback (most recent call last):
File "<console>", line 8, in <module>
File "/usr/share/miniconda/envs/testing/lib/python3.7/site-packages/cantera/ctml_writer.py", line 2694, in convert
write(outName)
File "/usr/share/miniconda/envs/testing/lib/python3.7/site-packages/cantera/ctml_writer.py", line 377, in write
x.write(sys.stdout)
File "/usr/share/miniconda/envs/testing/lib/python3.7/site-packages/cantera/ctml_writer.py", line 152, in write
filename.write(''.join(s))
BlockingIOError: [Errno 11] write could not complete without blocking
--------------- end of converter log ---------------
***********************************************************************
Bug Description
RMG fails while running the Nitrogen, Sulfur, and Oxidation regression tests in RMG-tests/test/rmg/ (It also fails the superminimal and liquid_oxidation tests, but for different reasons that probably need separate issues. It does pass the aromatics and eg1 tests)
How To Reproduce
Expected Behavior
I would expect this test to run without error because it is a part of the regression suite in RMG-tests.
Installation Information
Describe your installation method and system information.
Additional Context
I found this bug while running RMG-tests in Github Actions on a copy of the main RMG-Py branch. The details of the Github Actions run can be found here. I get the same result running on my local machine.
This is the error message:
This is the RMG Log: