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ReactionMechanismGenerator / RMG-Py

Python version of the amazing Reaction Mechanism Generator (RMG).
http://reactionmechanismgenerator.github.io/RMG-Py/
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AtomTypeError when used Seed mechanism with the liquid reactor #2301

Closed qqppoqq closed 1 year ago

qqppoqq commented 2 years ago

Bug Description

Generating thermo for new species... Species O renamed O(S) based on thermo library name Error: Could not update atomtypes for this molecule: multiplicity 1 1 O u0 p1 c+1 {3,S} {5,D} 2 C u0 p0 c0 {3,S} {4,S} {6,S} {7,S} 3 C u0 p0 c0 {1,S} {2,S} {8,S} {9,S} 4 C u0 p0 c0 {2,S} {5,S} {10,S} {11,S} 5 C u2 p0 c-1 {1,D} {4,S} 6 H u0 p0 c0 {2,S} 7 H u0 p0 c0 {2,S} 8 H u0 p0 c0 {3,S} 9 H u0 p0 c0 {3,S} 10 H u0 p0 c0 {4,S} 11 H u0 p0 c0 {4,S}

Traceback (most recent call last): File "/home/liuqi/anaconda3/envs/rmg_env/bin/rmg.py", line 118, in main() File "/home/liuqi/anaconda3/envs/rmg_env/bin/rmg.py", line 112, in main rmg.execute(**kwargs) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/main.py", line 733, in execute trimolecular_react=self.trimolecular_react) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/model.py", line 614, in enlarge self.apply_thermo_to_species(procnum) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/model.py", line 824, in apply_thermo_to_species self.generate_thermo(spc, rename=True) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/rmg/model.py", line 831, in generate_thermo submit(spc, self.solvent_name) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/thermo/thermoengine.py", line 175, in submit spc.thermo = evaluator(spc, solvent_name=solvent_name) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/thermo/thermoengine.py", line 160, in evaluator thermo = generate_thermo_data(spc, solvent_name=solvent_name) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/thermo/thermoengine.py", line 143, in generate_thermo_data return process_thermo_data(spc, thermo0, thermo_class, solvent_name) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/thermo/thermoengine.py", line 66, in process_thermo_data solute_data = solvation_database.get_solute_data(spc) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/solvation.py", line 694, in get_solute_data solute_data = self.get_solute_data_from_groups(species) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/solvation.py", line 751, in get_solute_data_from_groups solute_data = self.estimate_solute_via_group_additivity(molecule) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/solvation.py", line 861, in estimate_solute_via_group_additivity saturated_struct, added_to_pairs = self.transform_lone_pairs(saturated_struct) File "/home/liuqi/anaconda3/envs/rmg_env/lib/python3.7/site-packages/rmgpy/data/solvation.py", line 796, in transform_lone_pairs saturated_struct.update() File "rmgpy/molecule/molecule.py", line 1137, in rmgpy.molecule.molecule.Molecule.update File "rmgpy/molecule/molecule.py", line 1362, in rmgpy.molecule.molecule.Molecule.update_atomtypes File "rmgpy/molecule/molecule.py", line 1357, in rmgpy.molecule.molecule.Molecule.update_atomtypes File "rmgpy/molecule/atomtype.py", line 813, in rmgpy.molecule.atomtype.get_atomtype File "rmgpy/molecule/atomtype.py", line 841, in rmgpy.molecule.atomtype.get_atomtype rmgpy.exceptions.AtomTypeError: Unable to determine atom type for atom C..-, which has 1 single bonds, 1 double bonds (1 to O, 0 to S, 0 others), 0 triple bonds, 0 quadruple bonds, 0 benzene bonds, 0 lone pairs, and -1 charge.

How To Reproduce

database( thermoLibraries=['primaryThermoLibrary','JetSurF1.0'], reactionLibraries=[], seedMechanisms=['JetSurF1.0'], kineticsFamilies='default', kineticsDepositories='default', kineticsEstimator='rate rules', )

species( label='Phenol, 3-methyl-', reactive=True, structure=SMILES("CC1=CC(=CC=C1)O"), ) species( label='water', reactive=True, structure=SMILES("O"), )

Reaction systems

liquidReactor( temperature=(500,'K'), initialConcentrations={ "Phenol, 3-methyl-": (6.154e-3,'mol/cm^3'), "water": (4.953e-6,'mol/cm^3') }, terminationTime=(5,'s'), )

solvation( solvent='water' )

simulator( atol=1e-16, rtol=1e-8, )

model( toleranceMoveToCore=0.1, toleranceKeepInEdge=0.01, toleranceInterruptSimulation=1, maximumEdgeSpecies=100000, minCoreSizeForPrune=50, minSpeciesExistIterationsForPrune=2, filterReactions=False, filterThreshold=1e8, )

options( name='SeedName', generateSeedEachIteration=True, saveSeedToDatabase=False, units='si', generateOutputHTML=True, generatePlots=False, saveSimulationProfiles=False, verboseComments=False, saveEdgeSpecies=False, keepIrreversible=False, trimolecularProductReversible=True, saveSeedModulus=-1 )

generatedSpeciesConstraints( allowed=['input species', 'seed mechanisms', 'reaction libraries'], maximumCarbonAtoms=8, maximumOxygenAtoms=2, maximumNitrogenAtoms=0, maximumSiliconAtoms=0, maximumSulfurAtoms=0, maximumRadicalElectrons=1, maximumSingletCarbenes=1, maximumCarbeneRadicals=0, )

Expected Behavior

It wouldn't crash.

Installation Information

Describe your installation method and system information.

Additional Context

When I use the simple reactor there is no problem, but when I change the reactor to the liquid reactor, this problem happened.

github-actions[bot] commented 1 year ago

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