Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix species information for select reference species #406

Merged
merged 1 commit into from
May 1, 2020
Merged

Fix species information for select reference species #406

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
39 changes: 20 additions & 19 deletions input/reference_sets/main/Benzylide.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,18 +1,19 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 3
1 C u0 p0 c0 {2,D} {6,S} {7,S}
2 C u0 p0 c0 {1,D} {3,S} {8,S}
3 C u0 p0 c0 {2,S} {4,D} {9,S}
4 C u0 p0 c0 {3,D} {5,S} {10,S}
5 C u0 p0 c0 {4,S} {6,D} {11,S}
6 C u0 p0 c0 {1,S} {5,D} {12,S}
7 C u2 p1 c-1 {1,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {4,S}
11 H u0 p0 c0 {5,S}
12 H u0 p0 c0 {6,S}
1 C u0 p0 c0 {2,D} {6,S} {10,S}
2 C u0 p0 c0 {1,D} {3,S} {11,S}
3 C u0 p0 c0 {2,S} {4,D} {12,S}
4 C u0 p0 c0 {3,D} {5,S} {7,S}
5 C u0 p0 c0 {4,S} {6,D} {13,S}
6 C u0 p0 c0 {1,S} {5,D} {14,S}
7 C u0 p1 c-1 {4,S} {8,S} {9,S}
8 H u0 p0 c0 {7,S}
9 H u0 p0 c0 {7,S}
10 H u0 p0 c0 {1,S}
11 H u0 p0 c0 {2,S}
12 H u0 p0 c0 {3,S}
13 H u0 p0 c0 {5,S}
14 H u0 p0 c0 {6,S}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -102,16 +103,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: C7H5
inchi: InChI=1S/C7H5/c1-7-5-3-2-4-6-7/h2-6H/q-1
inchi_key: WSUGBBJIWXKXIY-UHFFFAOYSA-N
formula: C7H7
inchi: InChI=1S/C7H7/c1-7-5-3-2-4-6-7/h2-6H,1H2/q-1
inchi_key: QJHNLKRMBCYQKX-UHFFFAOYSA-N
index: 402
label: Benzylide
molecular_weight:
class: ScalarQuantity
units: amu
value: 89.11460813569646
multiplicity: 3
value: 91.13048838065595
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -123,5 +124,5 @@ reference_data:
units: kJ/mol
value: 123.10000000000007
class: ThermoData
smiles: '[C-]C1=CC=CC=C1'
smiles: 'c1ccc(cc1)[CH2-]'
symmetry_number: 2.0
20 changes: 10 additions & 10 deletions input/reference_sets/main/Ethynol anion.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 2
1 O u0 p2 c0 {2,D}
2 C u0 p0 c0 {1,D} {3,D}
3 C u1 p1 c-1 {2,D}
1 C u0 p1 c-1 {2,S} {3,D}
2 H u0 p0 c0 {1,S}
3 C u0 p0 c0 {1,D} {4,D}
4 O u0 p2 c0 {3,D}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -43,16 +43,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: C2O
inchi: InChI=1S/C2O/c1-2-3/q-1
inchi_key: BLDNDSGBHRVRNO-UHFFFAOYSA-N
formula: C2HO
inchi: InChI=1S/C2HO/c1-2-3/h1H/q-1
inchi_key: BSJVBKBNZLEKLO-UHFFFAOYSA-N
index: 119
label: Ethynol anion
molecular_weight:
class: ScalarQuantity
units: amu
value: 40.02080261436369
multiplicity: 2
value: 41.028742736843434
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -64,5 +64,5 @@ reference_data:
units: kJ/mol
value: -47.26
class: ThermoData
smiles: '[C-]=C=O'
smiles: '[CH-]=C=O'
symmetry_number: 1.0
18 changes: 9 additions & 9 deletions input/reference_sets/main/Formyl anion.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 2
1 O u0 p2 c0 {2,D}
2 C u1 p1 c-1 {1,D}
1 C u0 p1 c-1 {2,S} {3,D}
2 H u0 p0 c0 {1,S}
3 O u0 p2 c0 {1,D}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -37,16 +37,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: CO
inchi: InChI=1S/CO/c1-2/q-1
inchi_key: DCMZLVSOPGZIFI-UHFFFAOYSA-N
formula: CHO
inchi: InChI=1S/CHO/c1-2/h1H/q-1
inchi_key: CKJNUZNMWOVDFN-UHFFFAOYSA-N
index: 44
label: Formyl anion
molecular_weight:
class: ScalarQuantity
units: amu
value: 28.010101539606868
multiplicity: 2
value: 29.01804166208662
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -58,5 +58,5 @@ reference_data:
units: kJ/mol
value: 12.02
class: ThermoData
smiles: '[C-]=O'
smiles: '[CH-]=O'
symmetry_number: 1.0
17 changes: 9 additions & 8 deletions input/reference_sets/main/Methanide.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 3
1 C u2 p1 c-1 {2,S}
1 C u0 p1 c-1 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -42,16 +43,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: CH
inchi: InChI=1S/CH/h1H/q-1
inchi_key: VPIURJINGFGPNS-UHFFFAOYSA-N
formula: CH3
inchi: InChI=1S/CH3/h1H3/q-1
inchi_key: LGRLWUINFJPLSH-UHFFFAOYSA-N
index: 16
label: Methanide
molecular_weight:
class: ScalarQuantity
units: amu
value: 13.018641197236564
multiplicity: 3
value: 15.034521442196064
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -63,5 +64,5 @@ reference_data:
units: kJ/mol
value: 137.63
class: ThermoData
smiles: '[CH]'
smiles: '[CH3-]'
symmetry_number: 3.0
23 changes: 12 additions & 11 deletions input/reference_sets/main/Vinoxide.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,11 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 3
1 O u0 p2 c0 {2,D}
2 C u0 p0 c0 {1,D} {3,S} {4,S}
3 C u2 p1 c-1 {2,S}
4 H u0 p0 c0 {2,S}
1 C u0 p1 c-1 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 C u0 p0 c0 {1,S} {5,D} {6,S}
5 O u0 p2 c0 {4,D}
6 H u0 p0 c0 {4,S}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -54,16 +55,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: C2HO
inchi: InChI=1S/C2HO/c1-2-3/h2H/q-1
inchi_key: FKOCRZRGMPDZME-UHFFFAOYSA-N
formula: C2H3O
inchi: InChI=1S/C2H3O/c1-2-3/h2H,1H2/q-1
inchi_key: MGKBHFTXPZTTHS-UHFFFAOYSA-N
index: 157
label: Vinoxide
molecular_weight:
class: ScalarQuantity
units: amu
value: 41.028742736843434
multiplicity: 3
value: 43.04462298180294
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -75,5 +76,5 @@ reference_data:
units: kJ/mol
value: -160.63
class: ThermoData
smiles: '[C-]C=O'
smiles: '[CH2-]C=O'
symmetry_number: 1.0
20 changes: 10 additions & 10 deletions input/reference_sets/main/Vinyl anion.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
RMG_version: 3.0.0
adjacency_list: |
multiplicity 2
1 C u0 p0 c0 {2,D} {3,S} {4,S}
2 C u1 p1 c-1 {1,D}
3 H u0 p0 c0 {1,S}
1 C u0 p0 c0 {2,D} {4,S} {5,S}
2 C u0 p1 c-1 {1,D} {3,S}
3 H u0 p0 c0 {2,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
calculated_data:
wb97m-v/def2-tzvpd:
class: CalculatedDataEntry
Expand Down Expand Up @@ -49,16 +49,16 @@ charge: -1
class: ReferenceSpecies
datetime: 2020-02-24 11:05
default_xyz_chemistry: wb97m-v/def2-tzvpd
formula: C2H2
inchi: InChI=1S/C2H2/c1-2/h1H2/q-1
inchi_key: VSVANFQZMKLBSU-UHFFFAOYSA-N
formula: C2H3
inchi: InChI=1S/C2H3/c1-2/h1H,2H2/q-1
inchi_key: IEARPTNIYZTWOZ-UHFFFAOYSA-N
index: 70
label: Vinyl anion
molecular_weight:
class: ScalarQuantity
units: amu
value: 26.037282394473127
multiplicity: 2
value: 27.04522251695288
multiplicity: 1
reference_data:
ATcT:
class: ReferenceDataEntry
Expand All @@ -70,5 +70,5 @@ reference_data:
units: kJ/mol
value: 232.59
class: ThermoData
smiles: '[C-]=C'
smiles: 'C=[CH-]'
symmetry_number: 2.0