From e38c93664cfc8ebd18e00fb4df7a526aea5a8147 Mon Sep 17 00:00:00 2001 From: Colin Grambow Date: Wed, 13 May 2020 16:08:44 -0400 Subject: [PATCH 1/3] Update reference species for atom energy fitting Add experimental atomization energies, geometries, and zero-point vibrational energies from CCCBDB. --- input/reference_sets/main/Ammonia.yml | 38 ++++++++++++++++ input/reference_sets/main/Chloromethane.yml | 43 +++++++++++++++++++ input/reference_sets/main/Dibromine.yml | 28 ++++++++++++ input/reference_sets/main/Dichlorine.yml | 28 ++++++++++++ input/reference_sets/main/Difluorine.yml | 28 ++++++++++++ input/reference_sets/main/Dihydrogen.yml | 26 +++++++++++ input/reference_sets/main/Dinitrogen.yml | 28 ++++++++++++ input/reference_sets/main/Dioxygen.yml | 28 ++++++++++++ input/reference_sets/main/Disulfur.yml | 28 ++++++++++++ .../reference_sets/main/Hydrogen bromide.yml | 28 ++++++++++++ .../reference_sets/main/Hydrogen chloride.yml | 28 ++++++++++++ .../reference_sets/main/Hydrogen fluoride.yml | 28 ++++++++++++ .../reference_sets/main/Hydrogen sulfide.yml | 31 +++++++++++++ input/reference_sets/main/Methane.yml | 43 +++++++++++++++++++ input/reference_sets/main/Methyl.yml | 38 ++++++++++++++++ input/reference_sets/main/Water.yml | 33 ++++++++++++++ 16 files changed, 504 insertions(+) diff --git a/input/reference_sets/main/Ammonia.yml b/input/reference_sets/main/Ammonia.yml index f0b1833594..6f178b9847 100644 --- a/input/reference_sets/main/Ammonia.yml +++ b/input/reference_sets/main/Ammonia.yml @@ -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 diff --git a/input/reference_sets/main/Chloromethane.yml b/input/reference_sets/main/Chloromethane.yml index 4c0a8ceaa6..dd5b993e2d 100644 --- a/input/reference_sets/main/Chloromethane.yml +++ b/input/reference_sets/main/Chloromethane.yml @@ -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 diff --git a/input/reference_sets/main/Dibromine.yml b/input/reference_sets/main/Dibromine.yml index 7575d8c9ec..2ccf5d105a 100644 --- a/input/reference_sets/main/Dibromine.yml +++ b/input/reference_sets/main/Dibromine.yml @@ -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 diff --git a/input/reference_sets/main/Dichlorine.yml b/input/reference_sets/main/Dichlorine.yml index 3d6cfd7e15..97bb9df3c9 100644 --- a/input/reference_sets/main/Dichlorine.yml +++ b/input/reference_sets/main/Dichlorine.yml @@ -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 diff --git a/input/reference_sets/main/Difluorine.yml b/input/reference_sets/main/Difluorine.yml index f08174fb5e..50213cbc5a 100644 --- a/input/reference_sets/main/Difluorine.yml +++ b/input/reference_sets/main/Difluorine.yml @@ -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 diff --git a/input/reference_sets/main/Dihydrogen.yml b/input/reference_sets/main/Dihydrogen.yml index 7a5a9be3a1..5d440f1484 100644 --- a/input/reference_sets/main/Dihydrogen.yml +++ b/input/reference_sets/main/Dihydrogen.yml @@ -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 diff --git a/input/reference_sets/main/Dinitrogen.yml b/input/reference_sets/main/Dinitrogen.yml index 6aa7676a1c..857f7d775f 100644 --- a/input/reference_sets/main/Dinitrogen.yml +++ b/input/reference_sets/main/Dinitrogen.yml @@ -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 diff --git a/input/reference_sets/main/Dioxygen.yml b/input/reference_sets/main/Dioxygen.yml index f6ea257b56..2d8fddbd65 100644 --- a/input/reference_sets/main/Dioxygen.yml +++ b/input/reference_sets/main/Dioxygen.yml @@ -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 diff --git a/input/reference_sets/main/Disulfur.yml b/input/reference_sets/main/Disulfur.yml index 21d3e0cb0f..94851d5383 100644 --- a/input/reference_sets/main/Disulfur.yml +++ b/input/reference_sets/main/Disulfur.yml @@ -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: diff --git a/input/reference_sets/main/Hydrogen bromide.yml b/input/reference_sets/main/Hydrogen bromide.yml index c99f6f6a69..260002d2a8 100644 --- a/input/reference_sets/main/Hydrogen bromide.yml +++ b/input/reference_sets/main/Hydrogen bromide.yml @@ -52,5 +52,33 @@ reference_data: units: kJ/mol value: -35.57 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.2 + uncertainty_type: +|- + units: kJ/mol + value: 362.4 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.0 + - - 0.0 + - 0.0 + - 1.4144 + isotopes: + - 79 + - 1 + symbols: + - Br + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 15.72432 smiles: Br symmetry_number: 1.0 diff --git a/input/reference_sets/main/Hydrogen chloride.yml b/input/reference_sets/main/Hydrogen chloride.yml index 4146c13abe..35edaa1fcb 100644 --- a/input/reference_sets/main/Hydrogen chloride.yml +++ b/input/reference_sets/main/Hydrogen chloride.yml @@ -52,5 +52,33 @@ reference_data: units: kJ/mol value: -92.173 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.1 + uncertainty_type: +|- + units: kJ/mol + value: 427.8 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.0 + - - 0.0 + - 0.0 + - 1.2746 + isotopes: + - 35 + - 1 + symbols: + - Cl + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 17.75122 smiles: Cl symmetry_number: 1.0 diff --git a/input/reference_sets/main/Hydrogen fluoride.yml b/input/reference_sets/main/Hydrogen fluoride.yml index 6391e9457c..33bfdba969 100644 --- a/input/reference_sets/main/Hydrogen fluoride.yml +++ b/input/reference_sets/main/Hydrogen fluoride.yml @@ -52,5 +52,33 @@ reference_data: units: kJ/mol value: -272.726 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.8 + uncertainty_type: +|- + units: kJ/mol + value: 566.6 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.0 + - - 0.0 + - 0.0 + - 0.9168 + isotopes: + - 19 + - 1 + symbols: + - F + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 24.5327 smiles: F symmetry_number: 1.0 diff --git a/input/reference_sets/main/Hydrogen sulfide.yml b/input/reference_sets/main/Hydrogen sulfide.yml index 019c7d66c0..76482d98e2 100644 --- a/input/reference_sets/main/Hydrogen sulfide.yml +++ b/input/reference_sets/main/Hydrogen sulfide.yml @@ -49,6 +49,12 @@ molecular_weight: multiplicity: 1 reference_data: CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.5 + uncertainty_type: +|- + units: kJ/mol + value: 724.7 class: ReferenceDataEntry thermo_data: H298: @@ -58,5 +64,30 @@ reference_data: units: kJ/mol value: -20.6 class: ThermoData + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.1030 + - - 0.0 + - 0.9616 + - -0.8239 + - - 0.0 + - -0.9616 + - -0.8239 + isotopes: + - 32 + - 1 + - 1 + symbols: + - S + - H + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 38.424 smiles: S symmetry_number: 2.0 diff --git a/input/reference_sets/main/Methane.yml b/input/reference_sets/main/Methane.yml index 1af27b37c8..2bc29d7e8c 100644 --- a/input/reference_sets/main/Methane.yml +++ b/input/reference_sets/main/Methane.yml @@ -70,5 +70,48 @@ reference_data: units: kJ/mol value: -74.525 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.5 + uncertainty_type: +|- + units: kJ/mol + value: 1642.0 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.0 + - - 0.6276 + - 0.6276 + - 0.6276 + - - 0.6276 + - -0.6276 + - -0.6276 + - - -0.6276 + - 0.6276 + - -0.6276 + - - -0.6276 + - -0.6276 + - 0.6276 + isotopes: + - 12 + - 1 + - 1 + - 1 + - 1 + symbols: + - C + - H + - H + - H + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 113.41 smiles: C symmetry_number: 12.0 diff --git a/input/reference_sets/main/Methyl.yml b/input/reference_sets/main/Methyl.yml index 0430669f9b..1e78f93094 100644 --- a/input/reference_sets/main/Methyl.yml +++ b/input/reference_sets/main/Methyl.yml @@ -65,5 +65,43 @@ reference_data: units: kJ/mol value: 146.41400000000007 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.7 + uncertainty_type: +|- + units: kJ/mol + value: 1209.3 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.0 + - - 1.0790 + - 0.0 + - 0.0 + - - -0.5395 + - -0.9344 + - 0.0 + - - -0.5395 + - 0.9344 + - 0.0 + isotopes: + - 12 + - 1 + - 1 + - 1 + symbols: + - C + - H + - H + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 76.110 smiles: '[CH3]' symmetry_number: 6.0 diff --git a/input/reference_sets/main/Water.yml b/input/reference_sets/main/Water.yml index 059888b946..8407bdea9d 100644 --- a/input/reference_sets/main/Water.yml +++ b/input/reference_sets/main/Water.yml @@ -58,5 +58,38 @@ reference_data: units: kJ/mol value: -241.842 class: ThermoData + CCCBDB: + atomization_energy: + class: ScalarQuantity + uncertainty: 0.1 + uncertainty_type: +|- + units: kJ/mol + value: 917.8 + class: ReferenceDataEntry + xyz_dict: + coords: + class: np_array + object: + - - 0.0 + - 0.0 + - 0.1173 + - - 0.0 + - 0.7572 + - -0.4692 + - - 0.0 + - -0.7572 + - -0.4692 + isotopes: + - 16 + - 1 + - 1 + symbols: + - O + - H + - H + zpe: + class: ScalarQuantity + units: kJ/mol + value: 53.880 smiles: O symmetry_number: 2.0 From cf18865602e239ca463c40a3aefe4c247ecfff27 Mon Sep 17 00:00:00 2001 From: Colin Grambow Date: Thu, 14 May 2020 13:52:21 -0400 Subject: [PATCH 2/3] Update wB97M-V/def2-TZVPD atom energies --- input/quantum_corrections/data.py | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/input/quantum_corrections/data.py b/input/quantum_corrections/data.py index 569b3adda7..a4e8a64ee2 100644 --- a/input/quantum_corrections/data.py +++ b/input/quantum_corrections/data.py @@ -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 From 764319ef5aa3bdef3e7300b60fa9774137af23d2 Mon Sep 17 00:00:00 2001 From: Colin Grambow Date: Fri, 15 May 2020 19:33:11 -0400 Subject: [PATCH 3/3] Add frequency scaling factor for wB97M-V/def2-TZVPD --- input/quantum_corrections/data.py | 1 + 1 file changed, 1 insertion(+) diff --git a/input/quantum_corrections/data.py b/input/quantum_corrections/data.py index a4e8a64ee2..964907a7cb 100644 --- a/input/quantum_corrections/data.py +++ b/input/quantum_corrections/data.py @@ -453,6 +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'