Electrochemistry! (finally) a.k.a. RMG-electrocat

.github/workflows/CI.yml

@@ -175,7 +175,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
 
       - name: Install Q2DTor
         run: echo "" | make q2dtor
@@ -296,7 +296,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-core.log"
+            cat "$regr_test-core.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
             echo "<details>"
             if python-jl scripts/checkModels.py \
@@ -313,7 +313,7 @@ jobs:
               export FAILED=Yes
             fi
             echo "" # blank line so next block is interpreted as markdown
-            cat "$regr_test-edge.log"
+            cat "$regr_test-edge.log" || (echo "Dumping the whole log failed, please download it from GitHub actions. Here are the first 100 lines:" && head -n100 "$regr_test-core.log")
             echo "</details>"
 
             # Check for Regression between Reference and Dynamic (skip superminimal)
@@ -405,3 +405,5 @@ jobs:
         with:
           push: true
           tags: reactionmechanismgenerator/rmg:latest
+          build-args: |
+            RMS_Branch=for_rmg

.github/workflows/docs.yml

@@ -64,7 +64,7 @@ jobs:
         timeout-minutes: 120 # this usually takes 20-45 minutes (or hangs for 6+ hours).
         run: |
           python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator'
+          julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator'
 
       - name: Checkout gh-pages Branch
         uses: actions/checkout@v2

arkane/encorr/ae.py

@@ -73,7 +73,10 @@
     'Methane',
     'Methyl',
     'Ammonia',
-    'Chloromethane'
+    'Chloromethane',
+    # Lithium species shall be uncommented after we reconcile the difference in AECs and BACs
+    # 'Lithium Hydride',
+    # 'Lithium Fluoride'
 ]
 
 

arkane/encorr/bac.py

@@ -241,7 +241,7 @@ class BAC:
     ref_databases = {}
     atom_spins = {
         'H': 0.5, 'C': 1.0, 'N': 1.5, 'O': 1.0, 'F': 0.5,
-        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5
+        'Si': 1.0, 'P': 1.5, 'S': 1.0, 'Cl': 0.5, 'Br': 0.5, 'I': 0.5, 'Li': 0.5,
     }
     exp_coeff = 3.0  # Melius-type parameter (Angstrom^-1)
 

documentation/source/users/rmg/installation/anacondaDeveloper.rst

@@ -117,7 +117,7 @@ Installation by Source Using Anaconda Environment for Unix-based Systems: Linux
 
 #. Install and Link Julia dependencies: ::
 
-     julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
+     julia -e 'using Pkg; Pkg.add("PyCall");Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="for_rmg")); using ReactionMechanismSimulator;'
 
      python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 

examples/rmg/CO2RR/input.py

@@ -0,0 +1,317 @@
+# Data sources
+database(
+    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','DFT_QCI_thermo', 'electrocatThermo', 
+    # 'CO2RR_Adsorbates_Ag111'
+    ],
+    reactionLibraries = [('Surface/CPOX_Pt/Deutschmann2006_adjusted', False)],
+    seedMechanisms = [],
+    kineticsDepositories = ['training'],
+    kineticsFamilies = ['electrochem', 
+                        # 'surface',
+                        'Surface_Abstraction',
+                        'Surface_Abstraction_vdW',
+                        'Surface_Abstraction_Single_vdW',
+                        'Surface_Abstraction_Beta_double_vdW',
+                        'Surface_Adsorption_Dissociative',
+                        'Surface_Adsorption_Dissociative_Double',
+                        'Surface_Adsorption_vdW',
+                        'Surface_Dissociation',
+                        'Surface_Dissociation_Double_vdW',
+                        'Surface_Dissociation_vdW',
+                        'Surface_EleyRideal_Addition_Multiple_Bond',
+                        'Surface_Migration',
+                        ],
+    kineticsEstimator = 'rate rules',
+
+)
+
+catalystProperties(
+    metal = 'Ag111'
+)
+
+# List of species
+species(
+    label='CO2',
+    reactive=True,
+    structure=adjacencyList(
+        """
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,D}
+3 O u0 p2 c0 {2,D}
+"""),
+)
+
+
+species(
+   label='proton',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 H u0 p0 c+1
+"""),
+)
+
+species(
+    label='vacantX',
+    reactive=True,
+    structure=adjacencyList("1 X u0"),
+)
+
+species(
+   label='H',
+   reactive=True,
+   structure=adjacencyList(
+       """
+1 H u1 p0 c0
+"""),
+)
+
+species(
+    label='CO2X',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {3,D}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,D} {2,D}
+4 X u0 p0 c0
+"""),
+)
+
+species(
+    label='CHO2X',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 X u0 p0 c0 {1,S}
+"""),
+)
+
+species(
+    label='CO2HX',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {2,S} {4,S}
+2 C u0 p0 c0 {1,S} {3,D} {5,S}
+3 O u0 p2 c0 {2,D}
+4 H u0 p0 c0 {1,S}
+5 X u0 p0 c0 {2,S}
+
+"""),
+)
+
+species(
+    label='OCX',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {2,D} 
+2 C u0 p0 c0 {1,D} {3,D}
+3 X u0 p0 c0 {2,D}
+"""),
+)
+
+species(
+    label='OX',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {2,D} 
+2 X u0 p0 c0 {1,D}
+"""),
+)
+
+species(
+    label='CH2O2X',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {3,S} {5,S}
+2 O u0 p2 c0 {3,D}
+3 C u0 p0 c0 {1,S} {2,D} {4,S}
+4 H u0 p0 c0 {3,S}
+5 H u0 p0 c0 {1,S}
+6 X u0 p0 c0
+"""),
+)
+
+species(
+    label='CHOX',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 X u0 p0 c0 {2,S}
+"""),
+)
+
+species(
+    label='CH2OX',
+    reactive=True,
+    structure=adjacencyList("""
+1 O u0 p2 c0 {2,D}
+2 C u0 p0 c0 {1,D} {3,S} {4,S}
+3 H u0 p0 c0 {2,S}
+4 H u0 p0 c0 {2,S}
+5 X u0 p0 c0
+"""),
+)
+
+
+forbidden(
+        label='CO2-bidentate',
+        structure=adjacencyList(
+                """
+                1 O u0 p2 c0 {2,D}
+                2 C u0 p0 c0 {1,D} {3,S} {4,S}
+                3 X u0 p0 c0 {2,S}
+                4 O u0 p2 c0 {2,S} {5,S}
+                5 X u0 p0 c0 {4,S}
+                """
+        )
+)
+
+liquidSurfaceReactor(
+    temperature=(300,'K'),
+    liqPotential=(0,'V'),
+    surfPotential=(-2.0,'V'),
+    initialConcentrations={
+        "CO2": (1e-3,'mol/cm^3'),
+        "proton": (1e-4,'mol/m^3'),
+    },
+	initialSurfaceCoverages={
+        # "HX": 0.5,
+        # # "CXO2": 0.0,
+        "CHO2X": 0.1,
+        "CO2HX": 0.1,
+        "vacantX": 0.1,
+        "CO2X": 0.4,
+        'OX': 0.1,
+        'OCX': 0.1,
+        'CH2O2X': 0.05,
+        'CHOX': 0.04,
+        'CH2OX': 0.01
+    },
+    surfaceVolumeRatio=(1.0e5, 'm^-1'),
+    terminationTime=(1.0e3,'sec'),
+    # terminationConversion={'CO2': 0.90},
+    # constantSpecies=["proton"],
+ )
+
+liquidSurfaceReactor(
+    temperature=(300,'K'),
+    liqPotential=(0,'V'),
+    surfPotential=(-1.5,'V'),
+    initialConcentrations={
+        "CO2": (1e-3,'mol/cm^3'),
+        "proton": (1e-4,'mol/m^3'),
+    },
+	initialSurfaceCoverages={
+        # "HX": 0.5,
+        # # "CXO2": 0.0,
+        "CHO2X": 0.1,
+        "CO2HX": 0.1,
+        "vacantX": 0.1,
+        "CO2X": 0.4,
+        'OX': 0.1,
+        'OCX': 0.1,
+        'CH2O2X': 0.05,
+        'CHOX': 0.04,
+        'CH2OX': 0.01
+    },
+    surfaceVolumeRatio=(1.0e5, 'm^-1'),
+    terminationTime=(1.0e3,'sec'),
+    # terminationConversion={'CO2': 0.90},
+    # constantSpecies=["proton"],
+ )
+
+liquidSurfaceReactor(
+    temperature=(300,'K'),
+    liqPotential=(0,'V'),
+    surfPotential=(-1.0,'V'),
+    initialConcentrations={
+        "CO2": (1e-3,'mol/cm^3'),
+        "proton": (1e-4,'mol/m^3'),
+    },
+	initialSurfaceCoverages={
+        # "HX": 0.5,
+        # # "CXO2": 0.0,
+        "CHO2X": 0.1,
+        "CO2HX": 0.1,
+        "vacantX": 0.1,
+        "CO2X": 0.4,
+        'OX': 0.1,
+        'OCX': 0.1,
+        'CH2O2X': 0.05,
+        'CHOX': 0.04,
+        'CH2OX': 0.01
+    },
+    surfaceVolumeRatio=(1.0e5, 'm^-1'),
+    terminationTime=(1.0e3,'sec'),
+    # terminationConversion={'CO2': 0.90},
+    # constantSpecies=["proton"],
+ )
+
+# liquidSurfaceReactor(
+#     temperature=(300,'K'),
+#     liqPotential=(0,'V'),
+#     surfPotential=(-0.5,'V'),
+#     initialConcentrations={
+#         "CO2": (1e-3,'mol/cm^3'),
+#         "proton": (1e-4,'mol/m^3'),
+#     },
+# 	initialSurfaceCoverages={
+#         # "HX": 0.5,
+#         # # "CXO2": 0.0,
+#         "CHO2X": 0.1,
+#         "CO2HX": 0.1,
+#         "vacantX": 0.1,
+#         "CO2X": 0.4,
+#         'OX': 0.1,
+#         'OCX': 0.1,
+#         'CH2O2X': 0.05,
+#         'CHOX': 0.04,
+#         'CH2OX': 0.01
+#     },
+#     surfaceVolumeRatio=(1.0e5, 'm^-1'),
+#     terminationTime=(1.0e3,'sec'),
+#     # terminationConversion={'CO2': 0.90},
+#     # constantSpecies=["proton"],
+#  )
+
+solvation(
+	solvent='water'
+)
+
+simulator(
+    atol=1e-16,
+    rtol=1e-8,
+)
+
+model(
+    toleranceKeepInEdge=1E-16,
+    toleranceMoveToCore=1E-3,
+    toleranceRadMoveToCore=1E-6,
+    toleranceInterruptSimulation=1E6,
+    filterReactions=False,
+    maximumEdgeSpecies=5000,
+    toleranceBranchReactionToCore=1E-6,
+    branchingIndex=0.5,
+    branchingRatioMax=1.0,
+)
+
+options(
+    units='si',
+    generateOutputHTML=True,
+    generatePlots=True,
+    saveEdgeSpecies=True,
+    saveSimulationProfiles=False,
+)
+
+generatedSpeciesConstraints(
+    allowed=['input species','reaction libraries'],
+    maximumSurfaceSites=2,
+    maximumCarbonAtoms=3,
+    maximumOxygenAtoms=2,
+    maximumRadicalElectrons=1,
+)