ForbiddenStructureException

[123wa-zj]

When I restart from seed mechanism I get the following error:

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.py", line 118, in
main()
File "rmg.py", line 112, in main
rmg.execute(**kwargs)
File "/rmg/RMG-Py/rmgpy/rmg/main.py", line 751, in execute
self.initialize(**kwargs)
File "/rmg/RMG-Py/rmgpy/rmg/main.py", line 684, in initialize
"inside of the Species Constraints block in your input file.".format(spec.label)
rmgpy.exceptions.ForbiddenStructureException: Species constraints forbids input species O=O RMG expects the triplet form of oxygen for correct usage in reaction families. Please change your input to SMILES='[O][O]' If you actually want to use the singlet state, set the allowSingletO2=True inside of the Species Constraints block in your input file.

But I set the forbidden in the input file. Finally I found it in my edge species dictionary. What should I do to restart it correctly.

This is input file:

database(
thermoLibraries = ['FFCM1(-)','BurkeH2O2','GRI-Mech3.0','GRI-Mech3.0-N','USC-Mech-ii','primaryThermoLibrary',
'primaryNS','NitrogenCurran','DFT_QCI_thermo','CBS_QB3_1dHR','SABIC_aromatics'],
reactionLibraries = ['FFCM1(-)','BurkeH2O2inArHe','2005_Senosiain_OH_C2H2','GRI-Mech3.0','GRI-Mech3.0-N'],
seedMechanisms = [],
kineticsDepositories = 'default',
kineticsFamilies = 'default',
kineticsEstimator = 'rate rules',
)

Constraints on generated species

generatedSpeciesConstraints(
allowed=['input species','seed mechanisms','reaction libraries'],
maximumCarbonAtoms=7,
maximumRadicalElectrons=2,
allowSingletO2 = False,
)

forbidden(
label='SingletO2',
structure=SMILES("O=O"),
)

List of species

species(
label='Ar',
reactive=False,
structure=SMILES("[Ar]"),
)
species(
label='CH4',
reactive=True,
structure=SMILES("C"),
)
species(
label='C2H6',
reactive=True,
structure=SMILES("CC"),
)
species(
label='C3H8',
reactive=True,
structure=SMILES("CCC"),
)
species(
label='CO2',
reactive=True,
structure=SMILES("C(=O)=O"),
)
species(
label='N2',
reactive=True,
structure=adjacencyList("""
1 N u0 p1 c0 {2,T}
2 N u0 p1 c0 {1,T}
"""),
)
species(
label='O2',
reactive=True,
structure=SMILES("[O][O]"),
)
species(
label='H2',
reactive=True,
structure=SMILES("[H][H]"),
)
species(
label='CO',
reactive=True,
structure=SMILES("[C-]#[O+]"),
)
species(
label='C2H2',
reactive=True,
structure=SMILES("C#C"),
)
species(
label='C6H6',
reactive=True,
structure=SMILES("c1ccccc1"),
)
species(
label = 'C3H3-1',
reactive=True,
structure=SMILES('[CH]=C=C'),
)
species(
label = 'C3H3-2',
reactive=True,
structure=SMILES('[C]#CC'),
)
species(
label='C4H4',
reactive=True,
structure=SMILES("C#CC=C"),
)
species(
label='C5H6',
reactive=True,
structure=SMILES("C1C=CCC=1"),
)
species(
label='C5H5',
reactive=True,
structure=SMILES("[CH]1C=CC=C1"),
)
species(
label = 'CH3OO',
reactive=True,
structure=adjacencyList("""
multiplicity 2
1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S}
2 O u0 p2 c0 {1,S} {6,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 O u1 p2 c0 {2,S}
"""),
)
species(
label = 'N',
reactive=True,
structure=adjacencyList("""
multiplicity 4
1 N u3 p1 c0
"""),
)

Reaction systems

simpleReactor(
temperature=[(1150,'K'),(1800,'K')],
pressure=(1.0,'bar'),
initialMoleFractions={
"CH4": 0.16,
"C2H6": 0.02,
"C3H8": 0.01,
"CO2": 0.006,
"N2": 0.004,
"O2": [0.1,0.75],
"Ar": 0.97
},
balanceSpecies = "Ar",
terminationTime=(2,'s'),
terminationConversion={'CH4': 0.99,},
nSims=14,
)
simpleReactor(
temperature=[(1150,'K'),(1800,'K')],
pressure=(1.0,'bar'),
initialMoleFractions={
"CH4": 0.48,
"C2H6": 0.006,
"C3H8": 0.006,
"CO2": [0.06,0.180.6],
"N2": 0.006,
"O2": 0.70.48,
"Ar": 0.95
},
balanceSpecies = "Ar",
terminationTime=(2,'s'),
terminationConversion={'CH4': 0.99,},
nSims=14,
)

simulator(
atol=1e-16,
rtol=1e-8,
#sens_atol=1e-6,
#sens_rtol=1e-4,
)

model(
toleranceMoveToCore=0.01,
toleranceKeepInEdge=0.001,
toleranceInterruptSimulation=1e8,
maximumEdgeSpecies=100000,
filterReactions=True,
maxNumObjsPerIter=5,
toleranceBranchReactionToCore=0.001,
branchingIndex=0.5,
branchingRatioMax=1.0,
)

pressureDependence(
method='modified strong collision',
maximumGrainSize=(0.5,'kcal/mol'),
minimumNumberOfGrains=250,
temperatures=(298,3000,'K',8),
pressures=(0.1,100,'bar',6),
interpolation=('Chebyshev', 6, 4),
)

options(
name='seed',
units='si',
generateSeedEachIteration=True,
generateOutputHTML=False,
generatePlots=False,
saveEdgeSpecies=False,
saveSimulationProfiles=False,
saveSeedToDatabase=False,
verboseComments=True,
keepIrreversible=False,
)
Also，although my the model large, my memory was 32GB but it was killed after a long long time.Strangely my resource monitor did not detect that RMG took up more than 24GB of memory.

Installation Information

Describe your installation method and system information if applicable.

• OS (include version if known): win11
• Installation method: Docker
• RMG version information:3.2