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Allow auto-library-completion to seed libraries #161

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Allow auto-library-completion to seed libraries #161

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bbf8d96
Allow auto-library-completion to seed libraries
alongd Nov 28, 2024
42f903c
Seed the primaryH2O2 kinetic library
alongd Nov 28, 2024
482fbba
Tests: Seed a kinetic library
alongd Nov 28, 2024
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3 changes: 2 additions & 1 deletion data/libraries.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ primary:
- DFT_QCI_thermo
- CBS_QB3_1dHR
kinetics:
- primaryH2O2
- name: primaryH2O2
seed: true

nitrogen:
thermo:
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10 changes: 8 additions & 2 deletions t3/main.py
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Expand Up @@ -1558,6 +1558,7 @@ def auto_complete_rmg_libraries(database: dict) -> dict:
"""
database['thermo_libraries'] = database['thermo_libraries'] or list()
database['kinetics_libraries'] = database['kinetics_libraries'] or list()
database['seed_mechanisms'] = database['seed_mechanisms'] or list()
if database['chemistry_sets'] is not None:
libraries_dict = read_yaml_file(path=os.path.join(DATA_BASE_PATH, 'libraries.yml'))
low_credence = database['use_low_credence_libraries']
Expand All @@ -1571,10 +1572,15 @@ def auto_complete_rmg_libraries(database: dict) -> dict:
if isinstance(entry, str) and entry not in libraries:
libraries.append(entry)
elif isinstance(entry, dict):
if entry['credence'] != 'low' and entry['name'] not in libraries:
if 'credence' in entry and entry['credence'] != 'low' and entry['name'] not in libraries:
libraries.append(entry['name'])
if entry['credence'] == 'low' and low_credence and entry['name'] not in libraries:
if 'credence' in entry and entry['credence'] == 'low' and low_credence and entry['name'] not in libraries:
low_credence_libraries.append(entry['name'])
if 'seed' in entry and entry['seed'] and entry['name'] not in libraries \
and entry['name'] not in database['seed_mechanisms']:
database['seed_mechanisms'].append(entry['name'])
if 'seed' in entry and not entry['seed'] and entry['name'] not in libraries:
libraries.append(entry['name'])
libraries.extend(low_credence_libraries)
del database['chemistry_sets']
del database['use_low_credence_libraries']
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6 changes: 4 additions & 2 deletions tests/test_main.py
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Expand Up @@ -1076,7 +1076,8 @@ def test_auto_complete_rmg_libraries():
assert database_2['thermo_libraries'] == ['primaryThermoLibrary', 'BurkeH2O2', 'Spiekermann_refining_elementary_reactions',
'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo', 'CBS_QB3_1dHR', 'NH3', 'NitrogenCurran',
'CHON_G4', 'CN', 'NOx2018']
assert database_2['kinetics_libraries'] == ['primaryH2O2', 'primaryNitrogenLibrary', 'HydrazinePDep', 'Ethylamine']
assert database_2['kinetics_libraries'] == ['primaryNitrogenLibrary', 'HydrazinePDep', 'Ethylamine']
assert database_2['seed_mechanisms'] == ['primaryH2O2']
assert 'chemistry_sets' not in database_2

database_3 = t3.rmg['database'].copy()
Expand All @@ -1086,7 +1087,8 @@ def test_auto_complete_rmg_libraries():
assert database_3['thermo_libraries'] == ['primaryThermoLibrary', 'BurkeH2O2', 'Spiekermann_refining_elementary_reactions',
'thermo_DFT_CCSDTF12_BAC', 'DFT_QCI_thermo', 'CBS_QB3_1dHR', 'NH3', 'NitrogenCurran',
'CHON_G4', 'CN', 'NOx2018', 'primaryNS', 'CHN', 'CHON', 'BurcatNS']
assert database_3['kinetics_libraries'] == ['primaryH2O2', 'primaryNitrogenLibrary', 'HydrazinePDep', 'Ethylamine']
assert database_3['kinetics_libraries'] == ['primaryNitrogenLibrary', 'HydrazinePDep', 'Ethylamine']
assert database_2['seed_mechanisms'] == ['primaryH2O2']
assert 'chemistry_sets' not in database_3


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