Adding surface libraries

[Tingchenlee]

• Purpose:
  Adding more surface reactions into kinetic libraries

• Description:
  A separated PR from Add training reactions and enlarge the nodes in the tree for some surface reaction families  #479
  Separating previous one into three PRs: "adding libraries", "adding tree nodes", and "adding training data"

• Notice:
  Roldan_Cu111 and Roldan_Ir111 libraries include some bidentate species, need further discussion

[davidfarinajr]

Thanks for these additions Ting-Chen! I didn't check very carefully but the tests pass and there is a lot here to check by hand. I think one thing we could do on this PR is come up with a new organization scheme for the kinetics libraries surface folder. Because we are adding a bunch of new ones in this PR, it's hard for someone to know which libraries they should use in the Surface folder. Perhaps we could organize it this way?

Surface -> chemistry -> metal -> author

which might looks like

- Surface
    - cpox
         - Pt
              - default (combo from papers we think are best)
              - model1_facet
              - model2_facet
    - nitrogen
          - Pt
               - default
               - model1_facet
               - model2_facet
           - Ni
           - Cu

Maybe we could add 1 commit here that reorganizes this folder

[Tingchenlee]

I feel that the reaction rates really varied depending on the metallic facets. From the above picture, it seems like the data of ammonia decomposition on Pt111 from other research groups are close to each other. Maybe we can just organize the libraries with the metal? Some libraries include not only nitrogen reactions but also carbon related (e.g. the automotive exhaust gases system)

[Tingchenlee]

And the original rate estimation is a kind of too fast

[Tingchenlee]

The Vlachos_Ru0001 library includes the coverage_dependence feature.

[rwest]

The Vlachos_Ru0001 library includes the coverage_dependence feature.

Great! Please put in order a, m, E, and when there is more than one, merge into a single dictionary. Thanks

[Tingchenlee]

I reorganized surface libraries to Methane, Ammonia, DOC, and Hydrazine folders.
Then added coverage_dependence into Mhadeshwar_Pt111, Nitrogen, Vlachos_Pt111 , Vlachos_Rh , and Vlachos_Ru0001 libraries.
Run the database test on RMG-Py cde branch and passed.
I think this PR is ready to be reviewed.

[Tingchenlee]

Run some tests for coverage dependence and the models completed:
RMG-Py:cde
RMG-database:add_surface_libraries

database(
    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','CHON_G4','NOx2018', 'GRI-Mech3.0-N', 'NitrogenCurran','DFT_QCI_thermo'],
    reactionLibraries =['Surface/DOC/Nitrogen','Surface/DOC/Mhadeshwar_Pt111','Surface/Methane/Vlachos_Pt111'],
    seedMechanisms = [],
    kineticsDepositories = ['training'],
    kineticsFamilies = ['surface'],
    kineticsEstimator = 'rate rules',
)

catalystProperties(
    metal = 'Pt111'
)

generatedSpeciesConstraints(
    allowed=['input species','seed mechanisms','reaction libraries'],
    maximumCarbonAtoms=2,
    maximumOxygenAtoms=2,
    maximumNitrogenAtoms=2,
    maximumSurfaceSites=2,
    maximumRadicalElectrons=2,
)

# List of species
species(
    label='X',
    reactive=True,
    structure=adjacencyList("1 X u0"),
)

species(
    label='O2',
    reactive=True,
    structure=adjacencyList(
"""
multiplicity 3
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
"""),
)

species(
    label='NH3',
    reactive=True,
    structure=adjacencyList(
"""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
"""),
)

species(
    label='CH4',
    reactive=True,
    structure=SMILES("[CH4]"),
)

#-------------

surfaceReactor(  
    temperature=[(500,'K'),(1500,'K')],
    initialPressure=(1.0, 'bar'),
    nSims=6,
    initialGasMoleFractions={
        "NH3": 0.15,
        "O2": 0.8,
        "CH4":0.05,
    },
    initialSurfaceCoverages={
        "X": 1.0,
    },
    surfaceVolumeRatio=(2.3832928e4, 'm^-1'),
    terminationConversion = {"NH3":0.9,},
    terminationTime=(10, 's'),
)

simulator( 
    atol=1e-22, 
    rtol=1e-12, 
)

model( 
    toleranceKeepInEdge=0.05,
    toleranceMoveToCore=0.5, 
    toleranceInterruptSimulation=1e6, 
    maximumEdgeSpecies=5000, 
    minCoreSizeForPrune=50,
    toleranceThermoKeepSpeciesInEdge=0.5, 
    minSpeciesExistIterationsForPrune=2, 
)

options(
    units='si',
    saveRestartPeriod=None,
    generateOutputHTML=True,
    generatePlots=True, 
    saveEdgeSpecies=True,
    saveSimulationProfiles=True,
)

MODEL GENERATION COMPLETED

The final model core has 51 species and 257 reactions
The final model edge has 419 species and 1216 reactions

---

database(
    thermoLibraries=['surfaceThermoPt111', 'primaryThermoLibrary', 'thermo_DFT_CCSDTF12_BAC','CHON_G4','NOx2018', 'GRI-Mech3.0-N', 'NitrogenCurran','DFT_QCI_thermo'],
    reactionLibraries =[],
    seedMechanisms = ['Surface/Ammonia/Vlachos_Ru0001'],
    kineticsDepositories = ['training'],
    kineticsFamilies = ['surface'],
    kineticsEstimator = 'rate rules',
)

catalystProperties(
    metal = 'Ru0001'
)

generatedSpeciesConstraints(
    allowed=['input species','seed mechanisms','reaction libraries'],
    maximumCarbonAtoms=0,
    maximumOxygenAtoms=2,
    maximumNitrogenAtoms=2,
    maximumSurfaceSites=2,
    maximumRadicalElectrons=2,
)

# List of species
species(
    label='X',
    reactive=True,
    structure=adjacencyList("1 X u0"),
)

species(
    label='O2',
    reactive=True,
    structure=adjacencyList(
"""
multiplicity 3
1 O u1 p2 c0 {2,S}
2 O u1 p2 c0 {1,S}
"""),
)

species(
    label='NH3',
    reactive=True,
    structure=adjacencyList(
"""
1 N u0 p1 c0 {2,S} {3,S} {4,S}
2 H u0 p0 c0 {1,S}
3 H u0 p0 c0 {1,S}
4 H u0 p0 c0 {1,S}
"""),
)

#-------------

surfaceReactor(  
    temperature=[(500,'K'),(1500,'K')],
    initialPressure=(1.0, 'bar'),
    nSims=6,
    initialGasMoleFractions={
        "NH3": 0.2,
        "O2": 0.8,
    },
    initialSurfaceCoverages={
        "X": 1.0,
    },
    surfaceVolumeRatio=(2.3832928e4, 'm^-1'),
    terminationConversion = {"NH3":0.9,},
    terminationTime=(10, 's'),
)

simulator( 
    atol=1e-22, 
    rtol=1e-12, 
)

model( 
    toleranceKeepInEdge=0.05,
    toleranceMoveToCore=0.5, 
    toleranceInterruptSimulation=1e6, 
    maximumEdgeSpecies=5000, 
    minCoreSizeForPrune=50,
    toleranceThermoKeepSpeciesInEdge=0.5, 
    minSpeciesExistIterationsForPrune=2, 
)

options(
    units='si',
    saveRestartPeriod=None,
    generateOutputHTML=True,
    generatePlots=True, 
    saveEdgeSpecies=True,
    saveSimulationProfiles=True,
)

MODEL GENERATION COMPLETED

The final model core has 16 species and 18 reactions
The final model edge has 11 species and 20 reactions

---

The coverage_dependence reactions in Vlachos_Rh library are all in the reverse reactions (and there are commented out)

[ChrisBNEU]

The reorganizing of the libraries is straightforward and helpful, and the coverage dependent parameters that you added in are all fine. I only skimmed the other reactions, but they have all been used repeatedly so far so I am confident they work. I have also used the schneider pt111 and roldan ir111 libraries for HAN, and it has built the model.

I vote that this is ready to be merged, once we have merged coverage dependence.