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Merge pull request #415 from ReactionMechanismGenerator/atom_energies
Atom energy fitting
2 parents f973f1d + 764319e commit b076b63

17 files changed

+513
-12
lines changed

‎input/quantum_corrections/data.py‎

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Original file line numberDiff line numberDiff line change
@@ -73,20 +73,16 @@
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'F': -0.000614, 'Si': -0.000682, 'Cl': -0.001338, 'Br': -0.005597, 'B': -0.000046}
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# Atomic energies
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# All model chemistries here should be lower-case because the user input is changed to lower-case
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atom_energies = {
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# Note: If your model chemistry does not include spin orbit coupling, you should add the corrections
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# to the energies here
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'wb97m-v/def2-tzvpd': {
82-
'H': -0.4941110259 + SOC['H'],
83-
'C': -37.8458797086 + SOC['C'],
84-
'N': -54.5915786724 + SOC['N'],
85-
'O': -75.0762279005 + SOC['O'],
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'S': -398.0789126541 + SOC['S'],
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'F': -99.7434924415 + SOC['F'],
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'Cl': -460.1100357269 + SOC['Cl'],
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'Br': -2573.9684615505 + SOC['Br']
78+
'H': -0.49338216995809725,
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'C': -37.84772407774059,
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'N': -54.59351384873174,
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'O': -75.0774947462408,
82+
'F': -99.74200231175924,
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'S': -398.0820818202818,
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'Cl': -460.1117669506163,
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'Br': -2573.9713149056824
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},
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# cbs-qb3 and cbs-qb3-paraskevas have the same corrections
@@ -457,6 +453,7 @@
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'wb97xd/6-311++g(d,p)': 0.988, # [4]
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'wb97xd/def2tzvp': 0.988, # [4]
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'wb97xd/def2svp': 0.986, # [4]
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'wb97m-v/def2-tzvpd': 1.002, # [4]
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'apfd/def2tzvp': 0.993, # [4]
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'apfd/def2tzvpp': 0.992, # [4]
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'mp2_rmp2_pvdz': 0.953, # [2], taken as 'MP2/cc-pVDZ'

‎input/reference_sets/main/Ammonia.yml‎

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@@ -64,5 +64,43 @@ reference_data:
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units: kJ/mol
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value: -45.557
6666
class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.5
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uncertainty_type: +|-
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units: kJ/mol
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value: 1157.9
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- -0.9377
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- -0.3816
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- - 0.8121
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- 0.4689
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- -0.3816
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- - -0.8121
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- 0.4689
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- -0.3816
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isotopes:
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- 14
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- 1
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- 1
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- 1
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symbols:
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- N
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- H
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- H
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- H
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 86.305
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smiles: N
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symmetry_number: 3.0

‎input/reference_sets/main/Chloromethane.yml‎

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@@ -70,5 +70,48 @@ reference_data:
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units: kJ/mol
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value: -82.10000000000007
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.8
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uncertainty_type: +|-
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units: kJ/mol
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value: 1552.9
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 1.7810
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- - 1.0424
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- 0.0
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- -0.3901
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- - -0.5212
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- 0.9027
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- -0.3901
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- - -0.5212
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- -0.9027
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- -0.3901
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isotopes:
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- 12
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- 35
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- 1
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- 1
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- 1
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symbols:
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- C
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- Cl
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- H
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- H
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- H
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 96.156
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smiles: CCl
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symmetry_number: 3.0

‎input/reference_sets/main/Dibromine.yml‎

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@@ -52,5 +52,33 @@ reference_data:
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units: kJ/mol
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value: 30.89
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.3
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uncertainty_type: +|-
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units: kJ/mol
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value: 190.2
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 1.1405
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- - 0.0
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- 0.0
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- -1.1405
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isotopes:
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- 79
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- 79
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symbols:
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- Br
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- Br
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 1.9332
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smiles: BrBr
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symmetry_number: 2.0

‎input/reference_sets/main/Dichlorine.yml‎

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@@ -50,5 +50,33 @@ reference_data:
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units: kJ/mol
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value: 0.0
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.0
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uncertainty_type: +|-
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units: kJ/mol
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value: 239.3
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 1.9879
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isotopes:
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- 35
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- 35
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symbols:
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- Cl
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- Cl
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 3.340240
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smiles: '[Cl][Cl]'
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symmetry_number: 2.0

‎input/reference_sets/main/Difluorine.yml‎

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@@ -50,5 +50,33 @@ reference_data:
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units: kJ/mol
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value: 0.0
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.6
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uncertainty_type: +|-
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units: kJ/mol
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value: 154.5
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 1.4119
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isotopes:
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- 19
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- 19
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symbols:
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- F
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- F
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 5.447936
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smiles: FF
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symmetry_number: 2.0

‎input/reference_sets/main/Dihydrogen.yml‎

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@@ -50,5 +50,31 @@ reference_data:
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units: kJ/mol
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value: 0.0
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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units: kJ/mol
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value: 432.1
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 0.7414
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isotopes:
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- 1
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- 1
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symbols:
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- H
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- H
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 26.07031
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smiles: '[H][H]'
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symmetry_number: 2.0

‎input/reference_sets/main/Dinitrogen.yml‎

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@@ -50,5 +50,33 @@ reference_data:
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units: kJ/mol
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value: 0.0
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.8
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uncertainty_type: +|-
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units: kJ/mol
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value: 941.6
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.5488
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- - 0.0
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- 0.0
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- -0.5488
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isotopes:
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- 14
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- 14
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symbols:
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- N
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- N
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 14.06543
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smiles: N#N
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symmetry_number: 2.0

‎input/reference_sets/main/Dioxygen.yml‎

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@@ -51,5 +51,33 @@ reference_data:
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units: kJ/mol
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value: 0.0
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class: ThermoData
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.2
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uncertainty_type: +|-
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units: kJ/mol
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value: 493.7
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 1.2075
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isotopes:
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- 16
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- 16
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symbols:
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- O
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- O
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 9.419155
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smiles: '[O][O]'
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symmetry_number: 2.0

‎input/reference_sets/main/Disulfur.yml‎

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@@ -43,6 +43,34 @@ molecular_weight:
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value: 64.13000613827143
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multiplicity: 3
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reference_data:
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CCCBDB:
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atomization_energy:
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class: ScalarQuantity
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uncertainty: 0.4
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uncertainty_type: +|-
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units: kJ/mol
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value: 421.6
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class: ReferenceDataEntry
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xyz_dict:
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coords:
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class: np_array
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object:
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- - 0.0
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- 0.0
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- 0.0
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- - 0.0
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- 0.0
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- 1.8892
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isotopes:
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- 32
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- 32
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symbols:
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- S
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- S
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zpe:
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class: ScalarQuantity
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units: kJ/mol
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value: 4.33274
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NIST Chemistry WebBook:
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class: ReferenceDataEntry
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thermo_data:

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