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Merge pull request #2598 for electrochemistry a.k.a. RMG-electrocat
Electrochemistry! (finally) a.k.a. RMG-electrocat This brings in lots of electrochemistry work, both for CO2 reduction and for Lithium SEI work. See https://chemrxiv.org/engage/chemrxiv/article-details/6695ecaf5101a2ffa87f3953 for the Lithium stuff and https://doi.org/10.17760/D20467257}{10.17760/D20467257 for CO2 reduction. Many thanks to @davidfarinajr @mjohnson541 and @ssun30 Requires updated RMG-database at least at commit 0add9cdee2dd2e0677c765086dbcd471d1377cb4
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -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, | ||
| ) |
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