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Remove kinetic group additivity methods from code and documentation #2612

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Feb 16, 2024
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Merged

Remove kinetic group additivity methods from code and documentation #2612

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f695b05
Removed references to kinetic group additivity values from codebase
jonwzheng Feb 14, 2024
9ab9c40
Removed references of kinetic group additivity from the RMG documenta…
jonwzheng Feb 14, 2024
d207493
Update to get_kinetics_for_template docstring to fix accidental remov…
jonwzheng Feb 14, 2024
6c1d8aa
fix malformed table in kinetics documentation
jonwzheng Feb 16, 2024
c0ea448
fix typo in docstring for getting kinetics from reaction template
jonwzheng Feb 16, 2024
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2 changes: 1 addition & 1 deletion documentation/source/reference/data/index.rst
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Expand Up @@ -50,7 +50,7 @@ Class Description
=========================== ====================================================
:class:`DepositoryReaction` A reaction with kinetics determined from querying a kinetics depository
:class:`LibraryReaction` A reaction with kinetics determined from querying a kinetics library
:class:`TemplateReaction` A reaction with kinetics determined from querying a kinetics group additivity or rate rules method
:class:`TemplateReaction` A reaction with kinetics determined from querying a rate rules method
:class:`ReactionRecipe` A sequence of actions that represent the process of a chemical reaction
--------------------------- ----------------------------------------------------
:class:`KineticsDepository` A depository of all kinetics parameters for one or more reactions
Expand Down
6 changes: 2 additions & 4 deletions documentation/source/users/rmg/kinetics.rst
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Expand Up @@ -40,11 +40,9 @@ parameters
+-------+--------------------------------------------------------------------------------------+
|Rank 8 |B3LYP & lower DFT (rotors if necessary) |
+-------+--------------------------------------------------------------------------------------+
|Rank 9 |Group Additivity |
|Rank 9 |Direct Estimate/Guess |
+-------+--------------------------------------------------------------------------------------+
|Rank 10|Direct Estimate/Guess |
+-------+--------------------------------------------------------------------------------------+
|Rank 11|Average of Rates |
|Rank 10|Average of Rates |
+-------+--------------------------------------------------------------------------------------+
|Rank 0 |General Estimate (Never used in generation) |
+-------+--------------------------------------------------------------------------------------+
Expand Down
39 changes: 13 additions & 26 deletions rmgpy/data/kinetics/family.py
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Expand Up @@ -77,7 +77,7 @@ class TemplateReaction(Reaction):
Attribute Type Description
=============== ========================= =====================================
`family` ``str`` The kinetics family that the reaction was created from.
`estimator` ``str`` Whether the kinetics came from rate rules or group additivity.
`estimator` ``str`` The name of the kinetic estimator; currently only rate rules is supported.
`reverse` :class:`TemplateReaction` The reverse reaction, for families that are their own reverse.
`is_forward` ``bool`` Whether the reaction was generated in the forward direction of the family.
`labeled_atoms` ``dict`` Keys are 'reactants' or 'products', values are dictionaries.
Expand Down Expand Up @@ -2396,23 +2396,20 @@ def get_reaction_template(self, reaction):
def get_kinetics_for_template(self, template, degeneracy=1, method='rate rules'):
"""
Return an estimate of the kinetics for a reaction with the given
`template` and reaction-path `degeneracy`. There are two possible methods
to use: 'group additivity' (new possible RMG-Py behavior) and 'rate rules' (old
RMG-Java behavior, and default RMG-Py behavior).
`template` and reaction-path `degeneracy`. There is currently only one method to use:
'rate rules' (old RMG-Java behavior, and default RMG-Py behavior). Group additivity was removed in August 2023.

Returns a tuple (kinetics, entry):
If it's estimated via 'rate rules' and an exact match is found in the tree,
then the entry is returned as the second element of the tuple.
But if an average is used, or the 'group additivity' method, then the tuple
returned is (kinetics, None).
But if an average is used, then the tuple returned is (kinetics, None).

"""
if method.lower() == 'group additivity':
return self.estimate_kinetics_using_group_additivity(template, degeneracy), None
elif method.lower() == 'rate rules':
if method.lower() == 'rate rules':
return self.estimate_kinetics_using_rate_rules(template, degeneracy) # This returns kinetics and entry data
else:
raise ValueError('Invalid value "{0}" for method parameter; '
'should be "group additivity" or "rate rules".'.format(method))
'currently only "rate rules" is supported.'.format(method))

def get_kinetics_from_depository(self, depository, reaction, template, degeneracy):
"""
Expand Down Expand Up @@ -2458,8 +2455,8 @@ def _select_best_kinetics(self, kinetics_list):
def get_kinetics(self, reaction, template_labels, degeneracy=1, estimator='', return_all_kinetics=True):
"""
Return the kinetics for the given `reaction` by searching the various
depositories as well as generating a result using the user-specified `estimator`
of either 'group additivity' or 'rate rules'. Unlike
depositories as well as generating a result using the user-specified `estimator`.
Currently, only 'rate rules' is a supported estimator. Unlike
the regular :meth:`get_kinetics()` method, this returns a list of
results, with each result comprising of

Expand All @@ -2468,7 +2465,7 @@ def get_kinetics(self, reaction, template_labels, degeneracy=1, estimator='', re
3. the entry - this will be `None` if from a template estimate
4. is_forward a boolean denoting whether the matched entry is in the same
direction as the inputted reaction. This will always be True if using
rates rules or group additivity. This can be `True` or `False` if using
rates rules. This can be `True` or `False` if using
a depository

If return_all_kinetics==False, only the first (best?) matching kinetics is returned.
Expand All @@ -2489,7 +2486,9 @@ def get_kinetics(self, reaction, template_labels, degeneracy=1, estimator='', re
for kinetics, entry, is_forward in kinetics_list0:
kinetics_list.append([kinetics, depository, entry, is_forward])

# If estimator type of rate rules or group additivity is given, retrieve the kinetics.
# If estimator type of rate rules is given, retrieve the kinetics.
# TODO: Since group additivity was removed, this logic can be condensed into just 1 branch.

if estimator:
try:
kinetics, entry = self.get_kinetics_for_template(template, degeneracy, method=estimator)
Expand All @@ -2502,7 +2501,6 @@ def get_kinetics(self, reaction, template_labels, degeneracy=1, estimator='', re
return kinetics, estimator, entry, True
kinetics_list.append([kinetics, estimator, entry, True])
# If no estimation method was given, prioritize rate rule estimation.
# If returning all kinetics, add estimations from both rate rules and group additivity.
else:
try:
kinetics, entry = self.get_kinetics_for_template(template, degeneracy, method='rate rules')
Expand All @@ -2513,15 +2511,6 @@ def get_kinetics(self, reaction, template_labels, degeneracy=1, estimator='', re
# If kinetics were undeterminable for rate rules estimation, do nothing.
pass

try:
kinetics2, entry2 = self.get_kinetics_for_template(template, degeneracy, method='group additivity')
if not return_all_kinetics:
return kinetics2, 'group additivity', entry2, True
kinetics_list.append([kinetics2, 'group additivity', entry2, True])
except KineticsError:
# If kinetics were undeterminable for group additivity estimation, do nothing.
pass

if not return_all_kinetics:
raise UndeterminableKineticsError(reaction)

Expand Down Expand Up @@ -3599,8 +3588,6 @@ def cross_validate_old(self, folds=5, T=1000.0, random_state=1, estimator='rate
template = self.retrieve_template(template_labels)
if estimator == 'rate rules':
kinetics, entry = self.estimate_kinetics_using_rate_rules(template, degeneracy=1)
elif estimator == 'group additivity':
kinetics = self.estimate_kinetics_using_group_additivity(template, degeneracy=1)
else:
raise ValueError('{0} is not a valid value for input `estimator`'.format(estimator))

Expand Down
4 changes: 2 additions & 2 deletions rmgpy/rmg/main.py
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Expand Up @@ -112,7 +112,7 @@ class RMG(util.Subject):
`seed_mechanisms` The seed mechanisms included in the model
`kinetics_families` The kinetics families to use for reaction generation
`kinetics_depositories` The kinetics depositories to use for looking up kinetics in each family
`kinetics_estimator` The method to use to estimate kinetics: 'group additivity' or 'rate rules'
`kinetics_estimator` The method to use to estimate kinetics: currently, only 'rate rules' is supported
`solvent` If solvation estimates are required, the name of the solvent.
`liquid_volumetric_mass_transfer_coefficient_power_law` If kLA estimates are required, the coefficients for kLA power law
---------------------------------------------------------- ------------------------------------------------
Expand Down Expand Up @@ -183,7 +183,7 @@ def clear(self):
self.seed_mechanisms = None
self.kinetics_families = None
self.kinetics_depositories = None
self.kinetics_estimator = "group additivity"
self.kinetics_estimator = "rate rules"
self.solvent = None
self.diffusion_limiter = None
self.surface_site_density = None
Expand Down
12 changes: 0 additions & 12 deletions rmgpy/rmg/model.py
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Expand Up @@ -996,18 +996,6 @@ def generate_kinetics(self, reaction):
# Use the one for which the kinetics is the forward kinetics
keep_reverse = gibbs_is_positive and is_forward and rev_is_forward
reason = "Both directions matched the same entry in {0}, but this direction is exergonic.".format(reaction.family)
elif self.kinetics_estimator == "group additivity" and (
kinetics.comment.find("Fitted to 1 rate") > 0 and not rev_kinetics.comment.find("Fitted to 1 rate") > 0
):
# forward kinetics were fitted to only 1 rate, but reverse are hopefully better
keep_reverse = True
reason = "Other direction matched a group only fitted to 1 rate."
elif self.kinetics_estimator == "group additivity" and (
not kinetics.comment.find("Fitted to 1 rate") > 0 and rev_kinetics.comment.find("Fitted to 1 rate") > 0
):
# reverse kinetics were fitted to only 1 rate, but forward are hopefully better
keep_reverse = False
reason = "Other direction matched a group only fitted to 1 rate."
elif entry is not None and rev_entry is not None:
# Both directions matched explicit rate rules
# Keep the direction with the lower (but nonzero) rank
Expand Down
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