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Simplified rmgdb.loop_families() #717

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Simplified rmgdb.loop_families() #717

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637c4f5
Simplified rmgdb.loop_families()
alongd Dec 4, 2023
7cfb2a6
f!
alongd Dec 5, 2023
dc45e29
Check in ReactionTest before setting cls.rmgdb.kinetics.families to None
alongd Dec 5, 2023
0b7adf4
f! rmgdb
alongd Dec 5, 2023
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3 changes: 2 additions & 1 deletion arc/reaction_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,8 @@ def setUpClass(cls):
"""
cls.maxDiff = None
cls.rmgdb = rmgdb.make_rmg_database_object()
cls.rmgdb.kinetics.families = None
if cls.rmgdb.kinetics is not None:
cls.rmgdb.kinetics.families = None
rmgdb.load_families_only(cls.rmgdb, "all")

cls.h2_xyz = {'coords': ((0, 0, 0.3736550), (0, 0, -0.3736550)), 'isotopes': (1, 1), 'symbols': ('H', 'H')}
Expand Down
127 changes: 42 additions & 85 deletions arc/rmgdb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,10 +6,9 @@
from typing import TYPE_CHECKING, List, Optional, Tuple, Union

from rmgpy import settings as rmg_settings
from rmgpy.data.kinetics.common import find_degenerate_reactions
from rmgpy.data.rmg import RMGDatabase
from rmgpy.exceptions import KineticsError
from rmgpy.reaction import same_species_lists, Reaction
from rmgpy.reaction import Reaction

from arc.common import get_logger, generate_resonance_structures
from arc.exceptions import InputError
Expand Down Expand Up @@ -213,6 +212,24 @@
return None, False


def match_family_by_label(rmgdb: RMGDatabase,
family_label: str,
) -> Optional['KineticsFamily']:
Comment on lines +215 to +217

Check notice

Code scanning / CodeQL

Explicit returns mixed with implicit (fall through) returns Note

Mixing implicit and explicit returns may indicate an error as implicit returns always return None.
"""
Find a family in the RMG database by its label.

Args:
rmgdb (RMGDatabase): The RMG database instance.
family_label (str): The family label.

Returns: Optional[KineticsFamily]
The corresponding family object instance.
"""
for family in rmgdb.kinetics.families.values():
if family.label == family_label:
return family


def loop_families(rmgdb: RMGDatabase,
reaction: Reaction,
) -> List[Tuple['KineticsFamily', list]]:
Expand All @@ -227,79 +244,20 @@
Returns: List[Tuple['KineticsFamily', list]]
Entries are tuples of a corresponding RMG KineticsFamily instance and a list of degenerate reactions.
"""
reaction = reaction.copy() # Use a copy to avoid changing atom order in the molecules by RMG.
for spc in reaction.reactants + reaction.products:
generate_resonance_structures(spc)
fam_list = list()
for family in rmgdb.kinetics.families.values():
family.save_order = True
degenerate_reactions = list()
family_reactions_by_r = list() # Family reactions for the specified reactants.
family_reactions_by_rnp = list() # Family reactions for the specified reactants and products.

if len(reaction.reactants) == 1:
for reactant0 in reaction.reactants[0].molecule:
fam_rxn = family.generate_reactions(reactants=[reactant0],
products=reaction.products,
delete_labels=False,
rxn_copy = reaction.copy()
reactions_f = rmgdb.kinetics.generate_reactions(reactants=rxn_copy.reactants,
products=rxn_copy.products,
only_families=True,
resonance=True,
)
reactions_r = rmgdb.kinetics.generate_reactions(reactants=rxn_copy.products,
products=rxn_copy.reactants,
only_families=True,
resonance=True,
)
if fam_rxn:
family_reactions_by_r.extend(fam_rxn)
elif len(reaction.reactants) == 2:
for reactant0 in reaction.reactants[0].molecule:
for reactant1 in reaction.reactants[1].molecule:
fam_rxn = family.generate_reactions(reactants=[reactant0, reactant1],
products=reaction.products,
delete_labels=False,
)
if fam_rxn:
family_reactions_by_r.extend(fam_rxn)
elif len(reaction.reactants) == 3:
for reactant0 in reaction.reactants[0].molecule:
for reactant1 in reaction.reactants[1].molecule:
for reactant2 in reaction.reactants[2].molecule:
fam_rxn = family.generate_reactions(reactants=[reactant0, reactant1, reactant2],
products=reaction.products,
delete_labels=False,
)
if fam_rxn:
family_reactions_by_r.extend(fam_rxn)

if len(reaction.products) == 1:
for fam_rxn in family_reactions_by_r:
for product0 in reaction.products[0].molecule:
if same_species_lists([product0], fam_rxn.products, save_order=True):
family_reactions_by_rnp.append(fam_rxn)
degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
same_reactants=False,
kinetics_database=rmgdb.kinetics,
save_order=True
)
elif len(reaction.products) == 2:
for fam_rxn in family_reactions_by_r:
for product0 in reaction.products[0].molecule:
for product1 in reaction.products[1].molecule:
if same_species_lists([product0, product1], fam_rxn.products, save_order=True):
family_reactions_by_rnp.append(fam_rxn)
degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
same_reactants=False,
kinetics_database=rmgdb.kinetics,
save_order=True
)
elif len(reaction.products) == 3:
for fam_rxn in family_reactions_by_r:
for product0 in reaction.products[0].molecule:
for product1 in reaction.products[1].molecule:
for product2 in reaction.products[2].molecule:
if same_species_lists([product0, product1, product2], fam_rxn.products, save_order=True):
family_reactions_by_rnp.append(fam_rxn)
degenerate_reactions = find_degenerate_reactions(rxn_list=family_reactions_by_rnp,
same_reactants=False,
kinetics_database=rmgdb.kinetics,
save_order=True
)
if degenerate_reactions:
fam_list.append((family, degenerate_reactions))
fam_list = list()
for rxn in reactions_f + reactions_r:
fam_list.append((match_family_by_label(rmgdb=rmgdb, family_label=rxn.family), rxn))
return fam_list


Expand Down Expand Up @@ -331,17 +289,16 @@
break
# Families:
fam_list = loop_families(rmgdb, reaction)
for family, degenerate_reactions in fam_list:
for deg_rxn in degenerate_reactions:
template = family.retrieve_template(deg_rxn.template)
kinetics = family.estimate_kinetics_using_rate_rules(template)[0]
kinetics.change_rate(deg_rxn.degeneracy)
kinetics = kinetics.to_arrhenius(dh_rxn298) # Convert ArrheniusEP to Arrhenius using the dHrxn at 298K
deg_rxn.kinetics = kinetics
deg_rxn.comment = f'Family: {deg_rxn.family}'
deg_rxn.reactants = reaction.reactants
deg_rxn.products = reaction.products
rmg_reactions.extend(degenerate_reactions)
for family, rxn in fam_list:
template = family.retrieve_template(rxn.template)
kinetics = family.estimate_kinetics_using_rate_rules(template)[0]
kinetics.change_rate(rxn.degeneracy)
kinetics = kinetics.to_arrhenius(dh_rxn298) # Convert ArrheniusEP to Arrhenius using the dHrxn at 298K
rxn.kinetics = kinetics
rxn.comment = f'Family: {rxn.family}'
rxn.reactants = reaction.reactants
rxn.products = reaction.products
rmg_reactions.append(rxn)
worked_through_nist_fams = []
# NIST:
for family, degenerate_reactions in fam_list:
Expand Down
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