add pdd example using fully automated afm

Author: KEHANG

examples/pdd_chemistry/afm_one_sided/input.py

@@ -0,0 +1,122 @@
+database(
+    thermoLibraries = ['primaryThermoLibrary', 'SulfurLibrary','DFT_QCI_thermo'],
+    reactionLibraries = [],
+    seedMechanisms = [],
+    kineticsDepositories = 'default',
+    kineticsFamilies = ['H_Abstraction','R_Addition_MultipleBond','R_Recombination',
+    'Disproportionation'],
+    kineticsEstimator = 'rate rules',
+)
+
+generatedSpeciesConstraints(
+    maximumRadicalElectrons = 1,
+)
+
+species(
+    label='arccccr',
+    reactive=True,
+    structure=fragment_adj("""1  C u0 p0 c0 {2,S} {3,S} {11,S} {12,S}
+2  C u0 p0 c0 {1,S} {4,S} {13,S} {14,S}
+3  C u0 p0 c0 {1,S} {5,S} {15,S} {16,S}
+4  C u0 p0 c0 {2,S} {17,S} {18,S} {19,S}
+5  C u0 p0 c0 {3,S} {6,S} {7,D}
+6  C u0 p0 c0 {5,S} {8,D} {20,S}
+7  C u0 p0 c0 {5,D} {10,S} {24,S}
+8  C u0 p0 c0 {6,D} {9,S} {21,S}
+9  C u0 p0 c0 {8,S} {10,D} {22,S}
+10 C u0 p0 c0 {7,S} {9,D} {23,S}
+11 H u0 p0 c0 {1,S}
+12 H u0 p0 c0 {1,S}
+13 H u0 p0 c0 {2,S}
+14 H u0 p0 c0 {2,S}
+15 H u0 p0 c0 {3,S}
+16 H u0 p0 c0 {3,S}
+17 R u0 p0 c0 {4,S}
+18 H u0 p0 c0 {4,S}
+19 H u0 p0 c0 {4,S}
+20 H u0 p0 c0 {6,S}
+21 H u0 p0 c0 {8,S}
+22 H u0 p0 c0 {9,S}
+23 H u0 p0 c0 {10,S}
+24 H u0 p0 c0 {7,S}
+"""),
+)
+
+species(
+    label='rccccr',
+    reactive=True,
+    structure=fragment_adj("""1  C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
+2  C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
+3  C u0 p0 c0 {1,S} {9,S} {11,S} {12,S}
+4  C u0 p0 c0 {2,S} {10,S} {13,S} {14,S}
+5  H u0 p0 c0 {1,S}
+6  H u0 p0 c0 {1,S}
+7  H u0 p0 c0 {2,S}
+8  H u0 p0 c0 {2,S}
+9  R u0 p0 c0 {3,S}
+10 R u0 p0 c0 {4,S}
+11 H u0 p0 c0 {3,S}
+12 H u0 p0 c0 {3,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {4,S}
+"""),
+)
+
+species(
+    label='rcccc',
+    reactive=True,
+    structure=fragment_adj("""1  C u0 p0 c0 {2,S} {3,S} {5,S} {6,S}
+2  C u0 p0 c0 {1,S} {4,S} {7,S} {8,S}
+3  C u0 p0 c0 {1,S} {10,S} {11,S} {12,S}
+4  C u0 p0 c0 {2,S} {9,S} {13,S} {14,S}
+5  H u0 p0 c0 {1,S}
+6  H u0 p0 c0 {1,S}
+7  H u0 p0 c0 {2,S}
+8  H u0 p0 c0 {2,S}
+9  R u0 p0 c0 {4,S}
+10 H u0 p0 c0 {3,S}
+11 H u0 p0 c0 {3,S}
+12 H u0 p0 c0 {3,S}
+13 H u0 p0 c0 {4,S}
+14 H u0 p0 c0 {4,S}
+"""),
+)
+
+
+simpleReactor(
+    temperature = (623,"K"),  # 350 C
+    pressure = (1050,"bar"),
+    initialMoleFractions={
+        "arccccr": 1,
+        "rccccr": 1,
+        "rcccc": 1
+    },
+    terminationTime = (1000,"h"),
+    terminationConversion = {
+        "arccccr": 0.6,
+    },
+)
+
+simulator(
+    atol = 1e-16,
+    rtol = 1e-08,
+    sens_atol = 1e-06,
+    sens_rtol = 0.0001,
+)
+
+model(
+    toleranceKeepInEdge = 0.05,
+    toleranceMoveToCore = 0.2,
+    toleranceInterruptSimulation = 1000000000,
+    filterReactions=True,
+)
+
+options(
+    units = "si",
+    saveRestartPeriod = None,
+    generateOutputHTML = True,
+    generatePlots = False,
+    saveSimulationProfiles = False,
+    saveEdgeSpecies = True,
+    verboseComments = False,
+)

examples/pdd_chemistry/afm_one_sided/run.sh

@@ -0,0 +1,4 @@
+
+source activate afm_env
+rmg.py input.py
+source deactivate