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New style adjacency list and multiplicity label #217

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d7f7fcb
Update RMG example 1,3-hexadiene with multiplicity label
bbuesser Mar 14, 2014
302f9ef
Update RMG example c3h4 with multiplicity label
bbuesser Mar 14, 2014
9f67f08
Update RMG example ch3no2 with multiplicity label
bbuesser Mar 14, 2014
7406845
Update RMG example diesel with multiplicity label
bbuesser Mar 14, 2014
141803d
Update RMG example e85 with multiplicity label
bbuesser Mar 14, 2014
a536e37
Update RMG example liquid_phase with multiplicity label
bbuesser Mar 14, 2014
8a5f90c
Update RMG example methylformate with multiplicity label
bbuesser Mar 14, 2014
44b86f6
Update RMG example minimal with multiplicity label
bbuesser Mar 14, 2014
bab0769
Update RMG example minimal_sensitivity with multiplicity label
bbuesser Mar 14, 2014
b7b4725
Update RMG example TEOS with multiplicity label
bbuesser Mar 14, 2014
795b41b
Add multiplicity label to loadEntry for transport libraries
bbuesser Mar 14, 2014
2239906
Add multiplicity label to loadEntry for thermo libraries and groups
bbuesser Mar 14, 2014
ab77c8a
Add multiplicity label to loadEntry for statmech depository
bbuesser Mar 14, 2014
f67bab4
Add multiplicity label to class Entry and loadEntry for forbidden
bbuesser Mar 14, 2014
9e6ac85
Add multiplicity label to loadEntry for kinetics depository
bbuesser Mar 14, 2014
09fc652
Add multiplicity label to loadEntry for kinetic groups
bbuesser Mar 14, 2014
00db033
Add multiplicity label in loadEntry for kinetic libraries
bbuesser Mar 14, 2014
f1572c0
Add multiplicity label to group.py
bbuesser Mar 14, 2014
a58ba69
Add printMultiplicity=True to toAdjacencyList() in
bbuesser Mar 14, 2014
b260eb5
Add multiplicity label to molecule.py
bbuesser Mar 14, 2014
d723666
Update to- and fromAdjacencyList() for multiplicity in Molecule instead
bbuesser Mar 14, 2014
13a5393
Use new molecule.multiplicity attribute in qm.molecule
bbuesser Mar 14, 2014
b84567d
Add multiplicity to read input file
bbuesser Mar 14, 2014
ed1b8c7
Add copy() to reaction.py to make deep copies of reaction objects
bbuesser Mar 14, 2014
4b7d957
Add multiplicity attribute to Species.py
bbuesser Mar 14, 2014
871c712
Add species multiplicity model.py
bbuesser Mar 14, 2014
2f4d651
Update family.py for new species multiplicity and search for spin
bbuesser Mar 14, 2014
712fecb
Change toAdjacencyList() to new adjacency list style
bbuesser Apr 25, 2014
d4e0ce4
Add multiplicity label to saveEntry() for transport libraries.
bbuesser May 16, 2014
c36551b
Add multiplicity label to saveEntry() for thermo libraries.
bbuesser May 16, 2014
a73f602
Add multiplicity label to saveEntry() for forbiddenstructures.py
bbuesser May 16, 2014
2faa10c
Replace strip() with split() to read adjacency lists in kinetics library
bbuesser May 16, 2014
8aedab8
Set printMultiplicity label in toAdjacencyList() explicitely to True
bbuesser May 16, 2014
d714d75
Define type of maxMultiplicity in fromAdjacencyList()
bbuesser May 16, 2014
154eb1c
Prepare molecule.py for new adjacency list style
bbuesser May 16, 2014
af961ac
Remove maxMultiplicity argument
bbuesser May 16, 2014
49bd3dd
Modify adjlist.py to read and write the new-style adjacency list.
bbuesser May 16, 2014
8db74f9
Updating examples with new adjacency list style
bbuesser May 16, 2014
5b2145c
Updating existing unit tests for new adjacency list style
bbuesser May 19, 2014
16a0cea
Remove maxMultiplicity argument
bbuesser May 19, 2014
31322a5
Updating existing unit test for new adjacency list style
bbuesser May 19, 2014
ca65b4d
Update fromRDKitMol() for the new adjacency list style
bbuesser May 19, 2014
d4dd500
Change treatment of missing lone pair card
bbuesser May 19, 2014
5be8ba1
Update existing unit test for new adjacency list style
bbuesser May 19, 2014
a37b47d
Prevent species generation from crashing if molecule is None and add
bbuesser May 19, 2014
472b828
Update existing unit tests for the new adjacency list style
bbuesser May 19, 2014
6ac5b9c
Remove merge conflicts
bbuesser May 19, 2014
c2199b9
Add write multiplicity label to kinetics groups
bbuesser May 19, 2014
cb0e868
Add multiplicity and lone pairs to functions required for pickling
bbuesser May 20, 2014
b999f1b
Add additional unit test for handling the new adjacency list styles
bbuesser May 20, 2014
ce3c8d7
Prevent species creation from crashing of molecule is an empty vector
bbuesser May 20, 2014
19f7502
Add multiplicity to species unit test for pickling species
bbuesser May 20, 2014
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9 changes: 9 additions & 0 deletions examples/cantherm/networks/acetyl+O2/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

species(
label = 'acetylperoxy',
multiplicity = 2,
structure = SMILES('CC(=O)O[O]'),
E0 = (-34.6,'kcal/mol'),
modes = [
Expand All @@ -38,6 +39,7 @@

species(
label = 'hydroperoxylvinoxy',
multiplicity = 2,
structure = SMILES('[CH2]C(=O)OO'),
E0 = (-32.4,'kcal/mol'),
modes = [
Expand All @@ -61,6 +63,7 @@

species(
label = 'acetyl',
multiplicity = 2,
structure = SMILES('C[C]=O'),
E0 = (0.0,'kcal/mol'), #(-20.5205,"kJ/mol")
modes = [
Expand All @@ -75,6 +78,7 @@

species(
label = 'oxygen',
multiplicity = 3,
structure = SMILES('[O][O]'),
E0 = (0.0,'kcal/mol'), #(-5.74557,"kJ/mol")
modes = [
Expand All @@ -88,6 +92,7 @@

species(
label = 'ketene',
multiplicity = 1,
structure = SMILES('C=C=O'),
E0 = (-6.6,'kcal/mol'),
#modes = [
Expand All @@ -101,6 +106,7 @@

species(
label = 'lactone',
multiplicity = 1,
structure = SMILES('C1OC1(=O)'),
E0 = (-30.8,'kcal/mol'),
#modes = [
Expand All @@ -116,6 +122,7 @@

species(
label = 'hydroxyl',
multiplicity = 2,
structure = SMILES('[OH]'),
E0 = (0.0,'kcal/mol'),
#modes = [
Expand All @@ -129,6 +136,7 @@

species(
label = 'hydroperoxyl',
multiplicity = 2,
structure = SMILES('O[O]'),
E0 = (0.0,'kcal/mol'),
#modes = [
Expand All @@ -142,6 +150,7 @@

species(
label = 'nitrogen',
multiplicity = 1,
structure = SMILES('N#N'),
molecularWeight = (28.04,"g/mol"),
collisionModel = TransportData(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
Expand Down
4 changes: 4 additions & 0 deletions examples/cantherm/networks/n-butanol/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@

species(
label = 'n-C4H10',
multiplicity = 1,
structure = SMILES('CCCCO'),
E0 = (-317.807,'kJ/mol'),
modes = [
Expand All @@ -35,6 +36,7 @@

species(
label = 'C4H8',
multiplicity = 1,
structure = SMILES('C=CCC'),
E0 = (-17.8832,'kJ/mol'),
modes = [
Expand All @@ -50,6 +52,7 @@

species(
label = 'H2O',
multiplicity = 1,
structure = SMILES('O'),
E0 = (-269.598,'kJ/mol'),
modes = [
Expand All @@ -63,6 +66,7 @@

species(
label = "bath_gas",
multiplicity = 1,
E0 = (0,'kJ/mol'),
molecularWeight = (28.04,"g/mol"),
collisionModel = TransportData(sigma=(3.41,"angstrom"), epsilon=(124,"K")),
Expand Down
3 changes: 3 additions & 0 deletions examples/generateReactions/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,18 +11,21 @@
# List of species
species(
label='ethane',
multiplicity = 1,
reactive=True,
structure=SMILES("CC"),
)

species(
label='H',
multiplicity = 2,
reactive=True,
structure=SMILES("[H]"),
)

species(
label='butane',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCC"),
)
Expand Down
9 changes: 9 additions & 0 deletions examples/measure/acetylO2/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@

species(
label='acetylperoxy',
multiplicity = 2,
SMILES='CC(=O)O[O]',
E0=(-34.6,'kcal/mol'),
states=States(
Expand All @@ -39,6 +40,7 @@

species(
label='hydroperoxylvinoxy',
multiplicity = 2,
SMILES='[CH2]C(=O)OO',
E0=(-32.4,'kcal/mol'),
states=States(
Expand All @@ -63,6 +65,7 @@

species(
label='acetyl',
multiplicity = 1,
SMILES='C[C]=O',
E0=(0.0,'kcal/mol'),
states=States(
Expand All @@ -84,6 +87,7 @@

species(
label='oxygen',
multiplicity = 3,
SMILES='[O][O]',
E0=(0.0,'kcal/mol'),
states=States(
Expand All @@ -102,30 +106,35 @@

species(
label='ketene',
multiplicity = 1,
SMILES='C=C=O',
E0=(-6.6,'kcal/mol'),
)

species(
label='lactone',
multiplicity = 1,
SMILES='C1OC1(=O)',
E0=(-30.8,'kcal/mol'),
)

species(
label='hydroxyl',
multiplicity = 2,
SMILES='[OH]',
E0=(0.0,'kcal/mol'),
)

species(
label='hydroperoxyl',
multiplicity = 2,
SMILES='O[O]',
E0=(0.0,'kcal/mol'),
)

species(
label='nitrogen',
multiplicity = 1,
SMILES='N#N',
lennardJones=LennardJones(sigma=(3.70,'angstrom'), epsilon=(94.9,'K')),
collisionModel = SingleExponentialDown(
Expand Down
13 changes: 11 additions & 2 deletions examples/rmg/1,3-hexadiene/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,28 +8,37 @@
kineticsEstimator = 'rate rules',
)

# Constraints on generated species
generatedSpeciesConstraints(
maximumRadicalElectrons = 2,
)

# List of species
species(
label='HXD13',
multiplicity = 1,
reactive=True,
structure=SMILES("C=CC=CCC"),
)
species(
label='CH4',
multiplicity = 1,
reactive=True,
structure=SMILES("C"),
)
species(
label='H2',
multiplicity = 1,
reactive=True,
structure=adjacencyList(
"""
1 H 0 {2,S}
2 H 0 {1,S}
1 H U0 L0 {2,S}
2 H U0 L0 {1,S}
"""),
)
species(
label='N2',
multiplicity = 1,
reactive=False,
structure=InChI("InChI=1/N2/c1-2"),
)
Expand Down
3 changes: 3 additions & 0 deletions examples/rmg/TEOS/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,16 +11,19 @@
# List of species
species(
label='TEOS',
multiplicity = 1,
reactive=True,
structure=InChI("InChI=1/C8H20O4Si/c1-5-9-13(10-6-2,11-7-3)12-8-4/h5-8H2,1-4H3"),
)
species(
label='EtOH',
multiplicity = 1,
reactive=True,
structure=InChI("InChI=1/C2H6O/c1-2-3/h3H,2H2,1H3"),
)
species(
label='Ar',
multiplicity = 1,
reactive=False,
structure=InChI("InChI=1/Ar"),
)
Expand Down
7 changes: 7 additions & 0 deletions examples/rmg/c3h4/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,19 +8,26 @@
kineticsEstimator = 'rate rules',
)

generatedSpeciesConstraints(
maximumRadicalElectrons = 4,
)

# List of species
species(
label='CH2',
reactive=True,
multiplicity = 3,
structure=SMILES("[CH2]"),
)
species(
label='C2H2',
multiplicity = 1,
reactive=True,
structure=SMILES("C#C"),
)
species(
label='N2',
multiplicity = 1,
reactive=False,
structure=InChI("InChI=1/N2/c1-2"),
)
Expand Down
25 changes: 14 additions & 11 deletions examples/rmg/ch3no2/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,36 +23,39 @@
# List of species
species(
label='CH3NO2',
multiplicity = 1,
reactive=True,
structure=adjacencyList(
"""
1 C 0 0 {2,S} {3,S} {4,S} {5,S}
2 H 0 0 {1,S}
3 H 0 0 {1,S}
4 H 0 0 {1,S}
5 N 0 0 {1,S} {6,D} {7,S}
6 O 0 2 {5,D}
7 O 0 3 {5,S}
1 C U0 L0 {2,S} {3,S} {4,S} {5,S}
2 H U0 L0 {1,S}
3 H U0 L0 {1,S}
4 H U0 L0 {1,S}
5 N U0 L0 {1,S} {6,D} {7,S}
6 O U0 L2 {5,D}
7 O U0 L3 {5,S}
"""),
)

species(
label='O2',
multiplicity = 3,
reactive=True,
structure=adjacencyList(
"""
1 O 1 2 {2,S}
2 O 1 2 {1,S}
1 O U1 L2 {2,S}
2 O U1 L2 {1,S}
"""),
)

species(
label='N2',
multiplicity = 1,
reactive=True,
structure=adjacencyList(
"""
1 N 1 1 {2,T}
2 N 1 1 {1,T}
1 N U0 L1 {2,T}
2 N U0 L1 {1,T}
"""),
)

Expand Down
10 changes: 9 additions & 1 deletion examples/rmg/diesel/input.py
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Expand Up @@ -11,43 +11,51 @@
# List of species
species(
label='n-decylbz',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCc1ccccc1"),
)
species(
label='n-C11',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCC"),
)
species(
label='n-C13',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCCCC"),
)
species(
label='n-C16',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCCCCCCC"),
)
species(
label='n-C19',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCCCCCCCCCC"),
)
species(
label='n-C21',
multiplicity = 1,
reactive=True,
structure=SMILES("CCCCCCCCCCCCCCCCCCCCC"),
)
species(
label='1M-napthalene',
multiplicity = 1,
reactive=True,
structure=SMILES("Cc1cccc2ccccc12"),
)
species(
label='O2',
multiplicity = 3,
reactive=True,
structure=SMILES("O=O"),
structure=SMILES("[O][O]"),
)

# Reaction systems
Expand Down
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