Added recommended_libraries.yml #712
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| # Recommended RMG libraries per chemistry type. | ||
| # Used by RMG's 'auto' library selection mode. | ||
| # Each set maps to thermo, kinetics, and transport library lists. | ||
| # Kinetics entries can be plain strings or dicts of {name: str, seed: bool}. | ||
| # | ||
| # CH pyrolysis is split into two sets: | ||
| # CH_pyrolysis_core — fundamental high-T C/H chemistry (acetylene initiation, | ||
| # alkane cracking, small radical thermo). Auto-included when | ||
| # C present, T >= 800 K, and no O in species. | ||
| # PAH_formation — first ring formation, naphthalene pathways (CPD + HACA), | ||
| # second ring growth, larger PAH chemistry, alkyl-aromatics. | ||
| # Only auto-included when no O in species; otherwise requires | ||
| # the explicit <PAH_libs> keyword in the input file. | ||
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| primary: | ||
| thermo: | ||
| - primaryThermoLibrary | ||
| - BurkeH2O2 # H/O | ||
| - Spiekermann_refining_elementary_reactions # RMG's own high-level calculations for small species | ||
| - thermo_DFT_CCSDTF12_BAC # Trusted thermo library | ||
| - DFT_QCI_thermo # Trusted thermo library | ||
| - CBS_QB3_1dHR # Trusted thermo library | ||
| kinetics: | ||
| - name: primaryH2O2 # H/O seed | ||
| seed: true | ||
| transport: | ||
| - PrimaryTransportLibrary | ||
| - OneDMinN2 | ||
| - NOx2018 | ||
| - GRI-Mech | ||
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| oxidation: | ||
| thermo: | ||
| - FFCM1(-) # H2/CO/C1 reaction model | ||
| - FormicAcid # C1 oxidation pathways, inc. HOCO and HOCHO PESs | ||
| - NOx2018 # C1/C1/C-N/N | ||
| kinetics: | ||
| - FormicAcid # C1 oxidation pathways, inc. HOCO and HOCHO PESs | ||
| - FFCM1(-) # H2/CO/C1 reaction model | ||
| - NOx2018 # C1/C1/C-N/N | ||
| - 2005_Senosiain_OH_C2H2 # OH + acetylene surface reactions | ||
| transport: [] | ||
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| nitrogen: | ||
| thermo: | ||
| - NH3 # foundational NH3 thermo | ||
| - NOx2018 # C1/C1/C-N/N | ||
| - NitrogenCurran # computations for nitrogen-containing compounds | ||
| - CHON_G4 # CHON small molecule G4 | ||
| kinetics: | ||
| - primaryNitrogenLibrary # foundational nitrogen kinetics in combustion | ||
| - NOx2018 # C1/C1/C-N/N | ||
| - HydrazinePDep # well-skipping pressure-dependent reactions on the N3H5 and N4H6 PESs | ||
| - Ethylamine | ||
| transport: [] | ||
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| sulfur: | ||
| thermo: | ||
| - SulfurLibrary | ||
| kinetics: | ||
| - primarySulfurLibrary | ||
| - Sulfur/DMDS | ||
| - Sulfur/DMS | ||
| transport: [] | ||
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| # Core high-T C/H chemistry: acetylene initiation, alkane cracking, fundamental radicals | ||
| CH_pyrolysis_core: | ||
| thermo: | ||
| - NOx2018 # C1/C1/C-N/N | ||
| - Butadiene_Dimerization | ||
| - Chernov | ||
| - heavy_oil_ccsdtf12_1dHR | ||
| - Klippenstein_Glarborg2016 | ||
| kinetics: | ||
| - C2H2_init | ||
| - Klippenstein_Glarborg2016 | ||
| - Chernov | ||
| transport: [] | ||
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| # PAH formation and growth: first ring, naphthalene, polycyclic aromatics, alkyl-aromatics | ||
| PAH_formation: | ||
| thermo: | ||
| - Butadiene_Dimerization | ||
| - C10H11 | ||
| - s3_5_7_ane | ||
| - Fulvene_H | ||
| - naphthalene_H | ||
| - vinylCPD_H | ||
| - Lai_Hexylbenzene | ||
| - Narayanaswamy | ||
| - SABIC_aromatics_1dHR_extended | ||
| - SABIC_aromatics_1dHR | ||
| - SABIC_aromatics | ||
| - bio_oil | ||
| kinetics: | ||
| # First aromatic ring formation | ||
| - 2001_Tokmakov_H_Toluene_to_CH3_Benzene | ||
| - 2003_Miller_Propargyl_Recomb_High_P | ||
| - 2009_Sharma_C5H5_CH3_highP | ||
| - 2015_Buras_C2H3_C4H6_highP | ||
| - fascella | ||
| - kislovB | ||
| # Naphthalene pathways (CPD route + HACA) | ||
| - Butadiene_Dimerization | ||
| - C10H11 | ||
| - Fulvene_H | ||
| - biCPD_H_shift | ||
| - naphthalene_H | ||
| - vinylCPD_H | ||
| - Mebel_C6H5_C2H2 | ||
| - Mebel_Naphthyl | ||
| # Larger aromatics and PAH growth | ||
| - C6H5_C4H4_Mebel | ||
| - C12H11_pdep | ||
| - c-C5H5_CH3_Sharma | ||
| - Lai_Hexylbenzene | ||
| - Narayanaswamy | ||
| # First-to-second aromatic ring sub-libraries | ||
| - First_to_Second_Aromatic_Ring/2005_Ismail_C6H5_C4H6_highP | ||
| - First_to_Second_Aromatic_Ring/2012_Matsugi_C3H3_C7H7_highP | ||
| - First_to_Second_Aromatic_Ring/2016_Mebel_C10H9_highP | ||
| - First_to_Second_Aromatic_Ring/2016_Mebel_C9H9_highP | ||
| - First_to_Second_Aromatic_Ring/2016_Mebel_Indene_CH3_highP | ||
| - First_to_Second_Aromatic_Ring/2017_Buras_C6H5_C3H6_highP | ||
| - First_to_Second_Aromatic_Ring/2017_Mebel_C6H4C2H_C2H2_highP | ||
| - First_to_Second_Aromatic_Ring/2017_Mebel_C6H5C2H2_C2H2_highP | ||
| - First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C2H2_highP | ||
| - First_to_Second_Aromatic_Ring/2017_Mebel_C6H5_C4H4_highP | ||
| - First_to_Second_Aromatic_Ring/phenyl_diacetylene_effective | ||
| # Aromatics high pressure PES libraries | ||
| - Aromatics_high_pressure/C10H10_1 | ||
| - Aromatics_high_pressure/C10H10_2 | ||
| - Aromatics_high_pressure/C10H10_H_abstraction | ||
| - Aromatics_high_pressure/C10H11_1 | ||
| - Aromatics_high_pressure/C10H11_2 | ||
| - Aromatics_high_pressure/C10H11_3 | ||
| - Aromatics_high_pressure/C10H11_4 | ||
| - Aromatics_high_pressure/C10H7 | ||
| - Aromatics_high_pressure/C10H8_H_abstraction_H_recomb | ||
| - Aromatics_high_pressure/C10H9_1 | ||
| - Aromatics_high_pressure/C10H9_2 | ||
| - Aromatics_high_pressure/C10H9_3 | ||
| - Aromatics_high_pressure/C10H9_4 | ||
| - Aromatics_high_pressure/C12H10_1 | ||
| - Aromatics_high_pressure/C12H10_2 | ||
| - Aromatics_high_pressure/C12H10_H_abstraction | ||
| - Aromatics_high_pressure/C12H11 | ||
| - Aromatics_high_pressure/C12H8_H_abstraction | ||
| - Aromatics_high_pressure/C12H9 | ||
| - Aromatics_high_pressure/C14H10_H_abstraction_H_recomb | ||
| - Aromatics_high_pressure/C14H11_1 | ||
| - Aromatics_high_pressure/C14H11_2 | ||
| - Aromatics_high_pressure/C14H11_3 | ||
| - Aromatics_high_pressure/C14H11_4 | ||
| - Aromatics_high_pressure/C14H9 | ||
| - Aromatics_high_pressure/C16H11 | ||
| - Aromatics_high_pressure/C7H8 | ||
| - Aromatics_high_pressure/C7H8_H_abstraction | ||
| - Aromatics_high_pressure/C7H9 | ||
| - Aromatics_high_pressure/C8H6_H_abstraction | ||
| - Aromatics_high_pressure/C8H7 | ||
| - Aromatics_high_pressure/C8H8_H_abstraction | ||
| - Aromatics_high_pressure/C8H9 | ||
| - Aromatics_high_pressure/C9H10_H_abstraction | ||
| - Aromatics_high_pressure/C9H11 | ||
| - Aromatics_high_pressure/C9H7 | ||
| - Aromatics_high_pressure/C9H8_1 | ||
| - Aromatics_high_pressure/C9H8_2 | ||
| - Aromatics_high_pressure/C9H8_H_abstraction | ||
| - Aromatics_high_pressure/C9H9_1 | ||
| - Aromatics_high_pressure/C9H9_2 | ||
| transport: [] | ||
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| liquid_oxidation: | ||
| thermo: [] | ||
| kinetics: | ||
| - Chung_solvation_corrections | ||
| transport: [] | ||
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| surface: | ||
| thermo: | ||
| - surfaceThermoPt111 | ||
| kinetics: | ||
| - name: Surface/CPOX_Pt/Deutschmann2006_adjusted | ||
|
Contributor
There was a problem hiding this comment. Do we think these surface kinetics libraries are safe enough to put in our recommendations?
Contributor
There was a problem hiding this comment. Yeah, I don't think so. Initially, I thought there is no harm in just adding them to the recommended list. However, this would suggest that we actually believe that the kinetic data from these microkinetic models is better or more accurate than anything that is out there. Of course, this is not true, but it might appear so to new users. There is nothing wrong with any of these microkinetic models. They were created in very different ways and have different parameters, which will change the generated mechanisms. Honestly, I would not recommend any of them, but instead advise the users to work with them at their own risk or create their own library. What do others think @mjohnson541 @kirkbadger18 @rwest @cfgoldsmith ? If we definitely want to add one of the libraries as a recommendation, I would add all to not discriminate against any of these studies.
Contributor
There was a problem hiding this comment. I agree, if there are BEP rules then those are probably good enough for a first pass mechanism, I doubt there will be real additional gains by using previous results with a mix of functionals/settings. There are some reactions however, like O2 adsorption, which I believe BEP rules do not work for, and are always added as a library value.
Contributor
There was a problem hiding this comment. I agree with what Bjarne and Kirk have said. Also, like Kirk mentioned, RMG cannot currently find O2 dissociative adsorption by itself (or CO adsorption) because it lacks the families. I think at least one of these libraries (or a dedicated O2 + CO library) is needed as a seed to build a reasonable mechanism, specifically to include O2 and CO adsorption. I think the easiest thing would be to pick Deutschmann_adjusted as the seed (it's already the one used in RMG's official catalysis example), keep all libraries in to avoid showing favoritism, and mention in a comment that BEP rules probably work better but you have to put O2 and CO adsorption in your seed or RMG won't find them. Alternatively, @bjkreitz and @kirkbadger18 , if either of you have favorite/trusted O2 and CO adsorption reactions to use as a seed, we could add that and recommend it instead? |
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| seed: false | ||
| # BEP rules probably work better, but you have to put O2 and CO adsorption in your seed or RMG won't find them | ||
| - Surface/Methane/Vlachos_Pt111 | ||
| - Surface/Methane/Vlachos_Rh | ||
| - Surface/Methane/Deutschmann_Ni | ||
| - Surface/DOC/Arevalo_Pt111 | ||
| - Surface/DOC/Ishikawa_Rh111 | ||
| - Surface/DOC/Mhadeshwar_Pt111 | ||
| transport: [] | ||
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alongd marked this conversation as resolved.
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| surface_nitrogen: | ||
| thermo: [] | ||
| kinetics: | ||
| # Ammonia decomposition / oxidation on various facets | ||
| - Surface/Ammonia/Schneider_Pt111 | ||
| - Surface/Ammonia/Schneider_Pt211 | ||
| - Surface/Ammonia/Schneider_Rh111 | ||
| - Surface/Ammonia/Schneider_Rh211 | ||
| - Surface/Ammonia/Schneider_Pd111 | ||
| - Surface/Ammonia/Schneider_Pd211 | ||
| - Surface/Ammonia/Novell_Pt111 | ||
| - Surface/Ammonia/Novell_Rh111 | ||
| - Surface/Ammonia/Novell_Pd111 | ||
| - Surface/Ammonia/Duan_Ni111 | ||
| - Surface/Ammonia/Duan_Ni211 | ||
| - Surface/Ammonia/Vlachos_Ru0001 | ||
| - Surface/Ammonia/Roldan_Ru0001 | ||
| - Surface/Ammonia/Popa_Rh111 | ||
| - Surface/Ammonia/Offermans_Pt111 | ||
| - Surface/Ammonia/Kraehnert_Pt111 | ||
| - Surface/Ammonia/Rebrov_Pt111 | ||
| - Surface/Ammonia/Scheuer_Pt | ||
| # Hydrazine decomposition | ||
| - Surface/Hydrazine/Roldan_Cu111 | ||
| - Surface/Hydrazine/Roldan_Ir111 | ||
| # Nitrogen-specific DOC reactions | ||
| - Surface/DOC/Nitrogen | ||
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alongd marked this conversation as resolved.
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| transport: [] | ||
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| halogens: | ||
| thermo: | ||
| - Chlorinated_Hydrocarbons #Chlorinated hydrocarbons used to fit/validate Cl GAV's and non-NNI's | ||
| - Chlorination #chlorinated species from many sources (CBS-QB3, Burcat, etc.), recommended as a secondary library for Chlorine models | ||
| - CHOBr_G4 #non-cyclic and cyclic closed & radical small molecules with at least 1 Br & C, H, O. G4 method. | ||
| - CHOClBr_G4 # non-cyclic, closed/radical, at least 1 Cl and 1 Br & C, H, O. G4 method. | ||
| - CHOCl_G4 # non-cyclic/cyclic, closed/radical, at least 1 Cl & C, H, O. G4 method. | ||
| - CHOFBr_G4 # non-cyclic, closed/radical, at least 1 F and 1 Br & C, H, O. G4 method. | ||
| - CHOFClBr_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl, 1 Br & C, H, O. G4 method. | ||
| - CHOFCl_G4 # non-cyclic closed/radical, at least 1 F, 1 Cl & C, H, O. G4 method. | ||
| - CHOF_G4 # non-cyclic/cyclic closed/radical, at least 1 F & C, H, O. G4 method. | ||
| - Fluorine #thermo to pair with "NIST_Fluorine" kinetic library | ||
| - halogens #to be used for F/Cl/Br-containing systems, various sources (i.e. G4/RRHO, ATcT) | ||
| - iodinated_Hydrocarbons | ||
| - 2-BTP_G4 #to pair with the 2-BTP thermo library. F- and Br-containing species, G4 level of theory, RRHO approx. | ||
| - 2-BTP #to use with "2-BTP" kinetic library. Computed with G3MP2B3 & G3B3 composite ab initio methods; Geometries, vib. freq.,and ZPE calculated at B3LYP/6–31G(d) level of theory. | ||
| kinetics: | ||
| - 2-BTP #flame suppression chemistry for 2-bromo-3,3,3-trifluoropropene | ||
| - CH3Cl #chloromethane pyrolysis/oxidation and relevant H-abstraction reactions, combined with CRECK C1-C3 mechanism | ||
| - CF2BrCl # suppression chemistry of Halon 1211 (CF2BrCl) + light hydrocarbon (CH4, C2H4, and C3H8) chemistry | ||
| - DTU_mech_CH3Cl # pyrolysis/oxidation of methyl chloride | ||
| - NIST_Fluorine # C1-C2 hydrofluorocarbon combustion of refrigerants | ||
| - Iodine-R_recombination | ||
| - YF #combustion of the refrigerant HFO-1234yf (2,3,3,3-tetrafluroropropene, YF) | ||
| transport: | ||
| - NIST_Fluorine | ||
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| electrochem: | ||
| thermo: | ||
| - LithiumPrimaryThermo | ||
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Contributor
There was a problem hiding this comment. I need to check these thermo libraries in more detail. |
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| - LithiumPrimaryThermo2 | ||
| - LithiumAdditionalThermo | ||
| - computationalLithiumElectrode | ||
| - electrocatThermo | ||
| - electrocatLiThermo | ||
| - LithiumSurface | ||
| - surfaceThermoLi | ||
| kinetics: | ||
| - LithiumPrimaryKinetics | ||
| - LithiumPrimaryKinetics2 | ||
| - LithiumPrimaryChargedKinetics | ||
| - LithiumAnalogyKinetics | ||
| - LithiumSurface | ||
| - LithiumSurfaceAnalogy | ||
| transport: [] | ||
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If we're running on Pt111 is RMG smart enough to ignore surfaceThermoLi?
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I have no idea re surface libs, @rwest, could you please comment?
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I tried this out and no, RMG does not ignore surfaceThermoLi.
I think we should remove surfaceThermoLi from this list because surfaceThermoLi only contains a vacant site.
Even though both vacant sites are all zeros, I think it would confuse users if they try to build a mechanism and see the vacant site coming from Li and all the other thermo based on Pt.