DatabaseError: Unable to determine thermo parameters for <Molecule "C#CC=C[Ni]">: no data for node R* or any of its ancestors #70
Milestone
Comments
|
this is the notebook I started working on |
|
If you want to load the just the thermo groups file, you should create a It might be easier to load the full thermo database though, which would also allow you to test |
|
same error for |
|
Error after trying to run ethylene butene things |
|
Think I'm seeing something similar. I was getting... so I added more informative error logging in rwest@270e5fc to print the full adjacency list. Why on earth does the X have an unpaired electron? |
|
Yeah, what is going on with this? |
|
Is some gas phase reaction family being applied and making the radical or something? Where does it come from? Need to see what made that species. |
|
I can go back and rerun the last commit I made before July 22? Though I have a hunch it's one of the surface families that doesn't have any forbidden species |
|
Before just running something again, add extra debugging traps, like putting assert not self.is_surface_site(), "Attempted to increment radical count of a surface site."in I just ran it with that and got Traceback (most recent call last):
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 79, in _react_species_star
return react_species(*args)
File "/Users/rwest/Code/Cat/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 "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/database.py", line 543, in generate_reactions_from_families
successful = family.add_reverse_attribute(rxn)
File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/family.py", line 1721, in add_reverse_attribute
ensure_independent_atom_ids(rxn.products)
File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/data/kinetics/common.py", line 214, in ensure_independent_atom_ids
species.generate_resonance_structures(keep_isomorphic=True)
File "rmgpy/species.py", line 266, in rmgpy.species.Species.generate_resonance_structures
File "rmgpy/species.py", line 276, in rmgpy.species.Species.generate_resonance_structures
File "rmgpy/molecule/molecule.py", line 2092, in rmgpy.molecule.molecule.Molecule.generate_resonance_structures
File "rmgpy/molecule/molecule.py", line 2094, in rmgpy.molecule.molecule.Molecule.generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 150, in rmgpy.molecule.resonance.generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 235, in rmgpy.molecule.resonance.generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 244, in rmgpy.molecule.resonance._generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 280, in rmgpy.molecule.resonance._generate_resonance_structures
File "rmgpy/molecule/resonance.py", line 311, in rmgpy.molecule.resonance.generate_allyl_delocalization_resonance_structures
File "rmgpy/molecule/resonance.py", line 328, in rmgpy.molecule.resonance.generate_allyl_delocalization_resonance_structures
File "rmgpy/molecule/molecule.py", line 414, in rmgpy.molecule.molecule.Atom.increment_radical
AssertionError: Attempted to increment radical count of a surface site.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 111, in <module>
main()
File "/Users/rwest/Code/Cat/RMG-Py/rmg.py", line 96, in main
cProfile.runctx(command, global_vars, local_vars, stats_file)
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/cProfile.py", line 20, in runctx
filename, sort)
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/profile.py", line 62, in runctx
prof.runctx(statement, globals, locals)
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/cProfile.py", line 100, in runctx
exec(cmd, globals, locals)
File "<string>", line 1, in <module>
File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/main.py", line 891, in execute
trimolecular_react=self.trimolecular_react)
File "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/model.py", line 595, in enlarge
procnum=procnum)
File "/Users/rwest/Code/Cat/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 "/Users/rwest/Code/Cat/RMG-Py/rmgpy/rmg/react.py", line 70, in react
reactions = p.map(_react_species_star, spc_fam_tuples)
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Users/rwest/anaconda/envs/rmg3/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
AssertionError: Attempted to increment radical count of a surface site.which reveals it's not a reaction recipe that's making the radical surface but the resonance structure generation, specifically |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Total error message:
This has happened in 7 models... and it's always only for that one molecule. However, putting that species in the list of species to include in the core in the Pt(111)/base input file does not raise this error. It should definitely match the C-*R3 node in the adsorptionPt tree.
I tried to see if it was a problem with the tree itself in a jupyter notebook, but it turns out, according to the RMG website
and I didn't feel like doing that so I couldn't test to see how far that molecule could descend the tree :(
The text was updated successfully, but these errors were encountered: