Merge pull request #409 from ReactionMechanismGenerator/std_modelchem

Standardize model chemistry
ReactionMechanismGenerator · May 21, 2020 · ed06b2b · ed06b2b
2 parents b076b63 + 28c6e48
commit ed06b2b
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diff --git a/input/quantum_corrections/data.py b/input/quantum_corrections/data.py
diff --git a/input/quantum_corrections/lot_constraints.yml b/input/quantum_corrections/lot_constraints.yml
@@ -0,0 +1,6 @@
+# [1]: Dispersion model in Q-Chem and Gaussian are different
+METHODS_THAT_REQUIRE_SOFTWARE:
+    - B97-D,  # [1]
+    - B97-D3  # [1]
+    - wB97X-D  # [1]
+    - wB97X-D3  # [1]
diff --git a/input/reference_sets/main/(E)-Diazene.yml b/input/reference_sets/main/(E)-Diazene.yml
@@ -5,7 +5,7 @@ adjacency_list: |
   3 H u0 p0 c0 {1,S}
   4 H u0 p0 c0 {2,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -42,7 +42,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: H2N2
 inchi: InChI=1S/H2N2/c1-2/h1-2H
 inchi_key: RAABOESOVLLHRU-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/(Methylamino)methyl.yml b/input/reference_sets/main/(Methylamino)methyl.yml
@@ -11,7 +11,7 @@ adjacency_list: |
   8 H u0 p0 c0 {3,S}
   9 H u0 p0 c0 {3,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -73,7 +73,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C2H6N
 inchi: InChI=1S/C2H6N/c1-3-2/h3H,1H2,2H3
 inchi_key: AQIAIZBHFAKICS-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/(Methylthio)cyclopentane.yml b/input/reference_sets/main/(Methylthio)cyclopentane.yml
@@ -20,7 +20,7 @@ adjacency_list: |
   18 H u0 p0 c0 {7,S}
   19 H u0 p0 c0 {7,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -132,7 +132,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C6H12S
 inchi: InChI=1S/C6H12S/c1-7-6-4-2-3-5-6/h6H,2-5H2,1H3
 inchi_key: OTQVGYMGQKHLMY-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/(Methylthio)ethane.yml b/input/reference_sets/main/(Methylthio)ethane.yml
@@ -13,7 +13,7 @@ adjacency_list: |
   11 H u0 p0 c0 {4,S}
   12 H u0 p0 c0 {4,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -90,7 +90,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C3H8S
 inchi: InChI=1S/C3H8S/c1-3-4-2/h3H2,1-2H3
 inchi_key: WXEHBUMAEPOYKP-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/(R)-(-)-2-Butanol.yml b/input/reference_sets/main/(R)-(-)-2-Butanol.yml
@@ -16,7 +16,7 @@ adjacency_list: |
   14 H u0 p0 c0 {4,S}
   15 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -108,7 +108,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C4H10O
 inchi: InChI=1S/C4H10O/c1-3-4(2)5/h4-5H,3H2,1-2H3
 inchi_key: BTANRVKWQNVYAZ-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/(Z)-2-Pentene.yml b/input/reference_sets/main/(Z)-2-Pentene.yml
@@ -16,7 +16,7 @@ adjacency_list: |
   14 H u0 p0 c0 {5,S}
   15 H u0 p0 c0 {4,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -108,7 +108,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C5H10
 inchi: InChI=1S/C5H10/c1-3-5-4-2/h3,5H,4H2,1-2H3
 inchi_key: QMMOXUPEWRXHJS-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-(Methylthio)butane.yml b/input/reference_sets/main/1-(Methylthio)butane.yml
@@ -19,7 +19,7 @@ adjacency_list: |
   17 H u0 p0 c0 {6,S}
   18 H u0 p0 c0 {6,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -126,7 +126,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C5H12S
 inchi: InChI=1S/C5H12S/c1-3-4-5-6-2/h3-5H2,1-2H3
 inchi_key: WCXXISMIJBRDQK-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Butanethiol.yml b/input/reference_sets/main/1-Butanethiol.yml
@@ -16,7 +16,7 @@ adjacency_list: |
   14 H u0 p0 c0 {5,S}
   15 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -108,7 +108,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C4H10S
 inchi: InChI=1S/C4H10S/c1-2-3-4-5/h5H,2-4H2,1H3
 inchi_key: WQAQPCDUOCURKW-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Butene.yml b/input/reference_sets/main/1-Butene.yml
@@ -13,7 +13,7 @@ adjacency_list: |
   11 H u0 p0 c0 {4,S}
   12 H u0 p0 c0 {4,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -90,7 +90,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C4H8
 inchi: InChI=1S/C4H8/c1-3-4-2/h3H,1,4H2,2H3
 inchi_key: VXNZUUAINFGPBY-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Butyne.yml b/input/reference_sets/main/1-Butyne.yml
@@ -11,7 +11,7 @@ adjacency_list: |
   9  H u0 p0 c0 {2,S}
   10 H u0 p0 c0 {4,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -78,7 +78,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C4H6
 inchi: InChI=1S/C4H6/c1-3-4-2/h1H,4H2,2H3
 inchi_key: KDKYADYSIPSCCQ-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Hydroxyethyl.yml b/input/reference_sets/main/1-Hydroxyethyl.yml
@@ -10,7 +10,7 @@ adjacency_list: |
   7 H u0 p0 c0 {3,S}
   8 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -67,7 +67,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C2H5O
 inchi: InChI=1S/C2H5O/c1-2-3/h2-3H,1H3
 inchi_key: GAWIXWVDTYZWAW-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Methyl-1H-Pyrrole.yml b/input/reference_sets/main/1-Methyl-1H-Pyrrole.yml
@@ -14,7 +14,7 @@ adjacency_list: |
   12 H u0 p0 c0 {6,S}
   13 H u0 p0 c0 {4,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -96,7 +96,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C5H7N
 inchi: InChI=1S/C5H7N/c1-6-4-2-3-5-6/h2-5H,1H3
 inchi_key: OXHNLMTVIGZXSG-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Methylcyclopentene.yml b/input/reference_sets/main/1-Methylcyclopentene.yml
@@ -17,7 +17,7 @@ adjacency_list: |
   15 H u0 p0 c0 {4,S}
   16 H u0 p0 c0 {6,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -114,7 +114,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C6H10
 inchi: InChI=1S/C6H10/c1-6-4-2-3-5-6/h4H,2-3,5H2,1H3
 inchi_key: ATQUFXWBVZUTKO-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Methylethenyl.yml b/input/reference_sets/main/1-Methylethenyl.yml
@@ -10,7 +10,7 @@ adjacency_list: |
   7 H u0 p0 c0 {2,S}
   8 H u0 p0 c0 {2,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -67,7 +67,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C3H5
 inchi: InChI=1S/C3H5/c1-3-2/h1H2,2H3
 inchi_key: NMTZQIYQFZGXQT-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Pentanethiol.yml b/input/reference_sets/main/1-Pentanethiol.yml
@@ -19,7 +19,7 @@ adjacency_list: |
   17 H u0 p0 c0 {6,S}
   18 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -126,7 +126,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C5H12S
 inchi: InChI=1S/C5H12S/c1-2-3-4-5-6/h6H,2-5H2,1H3
 inchi_key: ZRKMQKLGEQPLNS-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Pentanol.yml b/input/reference_sets/main/1-Pentanol.yml
@@ -19,7 +19,7 @@ adjacency_list: |
   17 H u0 p0 c0 {6,S}
   18 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -126,7 +126,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C5H12O
 inchi: InChI=1S/C5H12O/c1-2-3-4-5-6/h6H,2-5H2,1H3
 inchi_key: AMQJEAYHLZJPGS-UHFFFAOYSA-N

diff --git a/input/reference_sets/main/1-Propanethiol.yml b/input/reference_sets/main/1-Propanethiol.yml
@@ -13,7 +13,7 @@ adjacency_list: |
   11 H u0 p0 c0 {4,S}
   12 H u0 p0 c0 {1,S}
 calculated_data:
-  wb97m-v/def2-tzvpd:
+  LevelOfTheory(method='wb97mv',basis='def2tzvpd',software='qchem'):
     class: CalculatedDataEntry
     thermo_data:
       H298:
@@ -90,7 +90,11 @@ calculated_data:
 charge: 0
 class: ReferenceSpecies
 datetime: 2020-02-24 11:05
-default_xyz_chemistry: wb97m-v/def2-tzvpd
+default_xyz_chemistry:
+  basis: def2tzvpd
+  class: LevelOfTheory
+  method: wb97mv
+  software: qchem
 formula: C3H8S
 inchi: InChI=1S/C3H8S/c1-2-3-4/h4H,2-3H2,1H3
 inchi_key: SUVIGLJNEAMWEG-UHFFFAOYSA-N