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Tree generation improvements #1848

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Merged
mliu49 merged 4 commits into from
Dec 14, 2019
Merged

Tree generation improvements #1848

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6094f4d
generate resonance structures when generating treegen training set
mjohnson541 Dec 12, 2019
1d5bb0f
add SABIC_aromatics to the thermolibraries used in tree generation
mjohnson541 Dec 12, 2019
e050d78
write the autoGenerated attribute to the groups.py file when saving
mjohnson541 Dec 13, 2019
c1973f0
add autoGenerated attribute to intra_H_migration for family save test
mjohnson541 Dec 13, 2019
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13 changes: 11 additions & 2 deletions rmgpy/data/kinetics/family.py
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Original file line number Diff line number Diff line change
Expand Up @@ -959,6 +959,9 @@ def save_groups(self, path):
f.write('reactantNum = {0}\n\n'.format(self.reactant_num))
if self.product_num is not None:
f.write('productNum = {0}\n\n'.format(self.product_num))

if self.auto_generated is not None:
f.write('autoGenerated = {0}\n\n'.format(self.auto_generated))

# Write the recipe
f.write('recipe(actions=[\n')
Expand Down Expand Up @@ -3798,10 +3801,12 @@ def fix_labels_mol(mol, root_labels):
if estimate_thermo:
for j, react in enumerate(r.item.reactants):
if rxns[i].reactants[j].thermo is None:
react.generate_resonance_structures()
rxns[i].reactants[j].thermo = tdb.get_thermo_data(react)

for j, react in enumerate(r.item.products):
if rxns[i].products[j].thermo is None:
react.generate_resonance_structures()
rxns[i].products[j].thermo = tdb.get_thermo_data(react)

rxns[i].kinetics = r.data
Expand Down Expand Up @@ -3877,7 +3882,9 @@ def fix_labels_mol(mol, root_labels):
if estimate_thermo:
for r in rrev.reactants:
if r.thermo is None:
r.thermo = tdb.get_thermo_data(deepcopy(r))
therm_spc = deepcopy(r)
therm_spc.generate_resonance_structures()
r.thermo = tdb.get_thermo_data(therm_spc)

rev_rxns.append(rrev)

Expand Down Expand Up @@ -3916,7 +3923,9 @@ def fix_labels_mol(mol, root_labels):
if estimate_thermo:
for r in rrev.reactants:
if r.thermo is None:
r.thermo = tdb.get_thermo_data(deepcopy(r))
therm_spc = deepcopy(r)
therm_spc.generate_resonance_structures()
r.thermo = tdb.get_thermo_data(therm_spc)
rxns[i] = rrev

if self.own_reverse and get_reverse:
Expand Down
2 changes: 2 additions & 0 deletions rmgpy/test_data/testing_database/kinetics/families/intra_H_migration/groups.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,8 @@

reversible = True

autoGenerated = False

recipe(actions=[
['BREAK_BOND', '*2', 1, '*3'],
['FORM_BOND', '*1', 1, '*3'],
Expand Down
2 changes: 1 addition & 1 deletion scripts/generateTree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -73,7 +73,7 @@ def main():
path=dbdir,
thermo_libraries=['Klippenstein_Glarborg2016', 'BurkeH2O2', 'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo',
'primaryThermoLibrary', 'primaryNS', 'NitrogenCurran', 'NOx2018', 'FFCM1(-)',
'SulfurLibrary', 'SulfurGlarborgH2S'],
'SulfurLibrary', 'SulfurGlarborgH2S', 'SABIC_aromatics'],
transport_libraries=[],
reaction_libraries=[],
seed_mechanisms=[],
Expand Down