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Merge pull request #415 from ReactionMechanismGenerator/atom_energies
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Atom energy fitting
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@amarkpayne
amarkpayne authored May 20, 2020
2 parents f973f1d + 764319e commit b076b63
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Showing 17 changed files with 513 additions and 12 deletions.
21 changes: 9 additions & 12 deletions input/quantum_corrections/data.py
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Expand Up @@ -73,20 +73,16 @@
'F': -0.000614, 'Si': -0.000682, 'Cl': -0.001338, 'Br': -0.005597, 'B': -0.000046}

# Atomic energies
# All model chemistries here should be lower-case because the user input is changed to lower-case
atom_energies = {
# Note: If your model chemistry does not include spin orbit coupling, you should add the corrections
# to the energies here

'wb97m-v/def2-tzvpd': {
'H': -0.4941110259 + SOC['H'],
'C': -37.8458797086 + SOC['C'],
'N': -54.5915786724 + SOC['N'],
'O': -75.0762279005 + SOC['O'],
'S': -398.0789126541 + SOC['S'],
'F': -99.7434924415 + SOC['F'],
'Cl': -460.1100357269 + SOC['Cl'],
'Br': -2573.9684615505 + SOC['Br']
'H': -0.49338216995809725,
'C': -37.84772407774059,
'N': -54.59351384873174,
'O': -75.0774947462408,
'F': -99.74200231175924,
'S': -398.0820818202818,
'Cl': -460.1117669506163,
'Br': -2573.9713149056824
},

# cbs-qb3 and cbs-qb3-paraskevas have the same corrections
Expand Down Expand Up @@ -457,6 +453,7 @@
'wb97xd/6-311++g(d,p)': 0.988, # [4]
'wb97xd/def2tzvp': 0.988, # [4]
'wb97xd/def2svp': 0.986, # [4]
'wb97m-v/def2-tzvpd': 1.002, # [4]
'apfd/def2tzvp': 0.993, # [4]
'apfd/def2tzvpp': 0.992, # [4]
'mp2_rmp2_pvdz': 0.953, # [2], taken as 'MP2/cc-pVDZ'
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38 changes: 38 additions & 0 deletions input/reference_sets/main/Ammonia.yml
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Expand Up @@ -64,5 +64,43 @@ reference_data:
units: kJ/mol
value: -45.557
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.5
uncertainty_type: +|-
units: kJ/mol
value: 1157.9
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- -0.9377
- -0.3816
- - 0.8121
- 0.4689
- -0.3816
- - -0.8121
- 0.4689
- -0.3816
isotopes:
- 14
- 1
- 1
- 1
symbols:
- N
- H
- H
- H
zpe:
class: ScalarQuantity
units: kJ/mol
value: 86.305
smiles: N
symmetry_number: 3.0
43 changes: 43 additions & 0 deletions input/reference_sets/main/Chloromethane.yml
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Expand Up @@ -70,5 +70,48 @@ reference_data:
units: kJ/mol
value: -82.10000000000007
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.8
uncertainty_type: +|-
units: kJ/mol
value: 1552.9
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 1.7810
- - 1.0424
- 0.0
- -0.3901
- - -0.5212
- 0.9027
- -0.3901
- - -0.5212
- -0.9027
- -0.3901
isotopes:
- 12
- 35
- 1
- 1
- 1
symbols:
- C
- Cl
- H
- H
- H
zpe:
class: ScalarQuantity
units: kJ/mol
value: 96.156
smiles: CCl
symmetry_number: 3.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Dibromine.yml
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Expand Up @@ -52,5 +52,33 @@ reference_data:
units: kJ/mol
value: 30.89
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.3
uncertainty_type: +|-
units: kJ/mol
value: 190.2
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 1.1405
- - 0.0
- 0.0
- -1.1405
isotopes:
- 79
- 79
symbols:
- Br
- Br
zpe:
class: ScalarQuantity
units: kJ/mol
value: 1.9332
smiles: BrBr
symmetry_number: 2.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Dichlorine.yml
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Expand Up @@ -50,5 +50,33 @@ reference_data:
units: kJ/mol
value: 0.0
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.0
uncertainty_type: +|-
units: kJ/mol
value: 239.3
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 1.9879
isotopes:
- 35
- 35
symbols:
- Cl
- Cl
zpe:
class: ScalarQuantity
units: kJ/mol
value: 3.340240
smiles: '[Cl][Cl]'
symmetry_number: 2.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Difluorine.yml
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Expand Up @@ -50,5 +50,33 @@ reference_data:
units: kJ/mol
value: 0.0
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.6
uncertainty_type: +|-
units: kJ/mol
value: 154.5
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 1.4119
isotopes:
- 19
- 19
symbols:
- F
- F
zpe:
class: ScalarQuantity
units: kJ/mol
value: 5.447936
smiles: FF
symmetry_number: 2.0
26 changes: 26 additions & 0 deletions input/reference_sets/main/Dihydrogen.yml
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Expand Up @@ -50,5 +50,31 @@ reference_data:
units: kJ/mol
value: 0.0
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
units: kJ/mol
value: 432.1
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 0.7414
isotopes:
- 1
- 1
symbols:
- H
- H
zpe:
class: ScalarQuantity
units: kJ/mol
value: 26.07031
smiles: '[H][H]'
symmetry_number: 2.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Dinitrogen.yml
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Expand Up @@ -50,5 +50,33 @@ reference_data:
units: kJ/mol
value: 0.0
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.8
uncertainty_type: +|-
units: kJ/mol
value: 941.6
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.5488
- - 0.0
- 0.0
- -0.5488
isotopes:
- 14
- 14
symbols:
- N
- N
zpe:
class: ScalarQuantity
units: kJ/mol
value: 14.06543
smiles: N#N
symmetry_number: 2.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Dioxygen.yml
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Expand Up @@ -51,5 +51,33 @@ reference_data:
units: kJ/mol
value: 0.0
class: ThermoData
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.2
uncertainty_type: +|-
units: kJ/mol
value: 493.7
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 1.2075
isotopes:
- 16
- 16
symbols:
- O
- O
zpe:
class: ScalarQuantity
units: kJ/mol
value: 9.419155
smiles: '[O][O]'
symmetry_number: 2.0
28 changes: 28 additions & 0 deletions input/reference_sets/main/Disulfur.yml
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Expand Up @@ -43,6 +43,34 @@ molecular_weight:
value: 64.13000613827143
multiplicity: 3
reference_data:
CCCBDB:
atomization_energy:
class: ScalarQuantity
uncertainty: 0.4
uncertainty_type: +|-
units: kJ/mol
value: 421.6
class: ReferenceDataEntry
xyz_dict:
coords:
class: np_array
object:
- - 0.0
- 0.0
- 0.0
- - 0.0
- 0.0
- 1.8892
isotopes:
- 32
- 32
symbols:
- S
- S
zpe:
class: ScalarQuantity
units: kJ/mol
value: 4.33274
NIST Chemistry WebBook:
class: ReferenceDataEntry
thermo_data:
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