New style adjacency list and multiplicity label

examples/cantherm/networks/acetyl+O2/input.py

@@ -16,6 +16,7 @@
 
 species(
     label = 'acetylperoxy',
+    multiplicity = 2,
     structure = SMILES('CC(=O)O[O]'),
     E0 = (-34.6,'kcal/mol'),
     modes = [
@@ -38,6 +39,7 @@
 
 species(
     label = 'hydroperoxylvinoxy',
+    multiplicity = 2,
     structure = SMILES('[CH2]C(=O)OO'),
     E0 = (-32.4,'kcal/mol'),
     modes = [
@@ -61,6 +63,7 @@
 
 species(
     label = 'acetyl',
+    multiplicity = 2,
     structure = SMILES('C[C]=O'),
     E0 = (0.0,'kcal/mol'),  #(-20.5205,"kJ/mol")
     modes = [
@@ -75,6 +78,7 @@
 
 species(
     label = 'oxygen',
+    multiplicity = 3,
     structure = SMILES('[O][O]'),
     E0 = (0.0,'kcal/mol'),  #(-5.74557,"kJ/mol")
     modes = [
@@ -88,6 +92,7 @@
 
 species(
     label = 'ketene',
+    multiplicity = 1,
     structure = SMILES('C=C=O'),
     E0 = (-6.6,'kcal/mol'),
     #modes = [
@@ -101,6 +106,7 @@
 
 species(
     label = 'lactone',
+    multiplicity = 1,
     structure = SMILES('C1OC1(=O)'),
     E0 = (-30.8,'kcal/mol'),
     #modes = [
@@ -116,6 +122,7 @@
 
 species(
     label = 'hydroxyl',
+    multiplicity = 2,
     structure = SMILES('[OH]'),
     E0 = (0.0,'kcal/mol'),
     #modes = [
@@ -129,6 +136,7 @@
 
 species(
     label = 'hydroperoxyl',
+    multiplicity = 2,
     structure = SMILES('O[O]'),
     E0 = (0.0,'kcal/mol'),
     #modes = [
@@ -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')),

examples/cantherm/networks/n-butanol/input.py

@@ -15,6 +15,7 @@
 
 species(
     label = 'n-C4H10',
+    multiplicity = 1,
     structure = SMILES('CCCCO'),
     E0 = (-317.807,'kJ/mol'),
     modes = [
@@ -35,6 +36,7 @@
 
 species(
     label = 'C4H8',
+    multiplicity = 1,
     structure = SMILES('C=CCC'),
     E0 = (-17.8832,'kJ/mol'),
     modes = [
@@ -50,6 +52,7 @@
 
 species(
     label = 'H2O',
+    multiplicity = 1,
     structure = SMILES('O'),
     E0 = (-269.598,'kJ/mol'),
     modes = [
@@ -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")),

examples/generateReactions/input.py

@@ -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"),
 )

examples/measure/acetylO2/input.py

@@ -16,6 +16,7 @@
 
 species(
     label='acetylperoxy',
+    multiplicity = 2,
     SMILES='CC(=O)O[O]',
     E0=(-34.6,'kcal/mol'),
     states=States(
@@ -39,6 +40,7 @@
 
 species(
     label='hydroperoxylvinoxy',
+    multiplicity = 2,
     SMILES='[CH2]C(=O)OO',
     E0=(-32.4,'kcal/mol'),
     states=States(
@@ -63,6 +65,7 @@
 
 species(
     label='acetyl',
+    multiplicity = 1,
     SMILES='C[C]=O',
     E0=(0.0,'kcal/mol'),
     states=States(
@@ -84,6 +87,7 @@
 
 species(
     label='oxygen',
+    multiplicity = 3,
     SMILES='[O][O]',
     E0=(0.0,'kcal/mol'),
     states=States(
@@ -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(

examples/rmg/1,3-hexadiene/input.py

@@ -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"),
 )

examples/rmg/TEOS/input.py

@@ -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"),
 )

examples/rmg/c3h4/input.py

@@ -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"),
 )

examples/rmg/ch3no2/input.py

@@ -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}
         """),
 )
 

examples/rmg/diesel/input.py

@@ -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