diff --git a/families/images/Surface_Proton_Electron_Reduction_Alpha.png b/families/images/Surface_Proton_Electron_Reduction_Alpha.png new file mode 100644 index 0000000000..231eb221f9 Binary files /dev/null and b/families/images/Surface_Proton_Electron_Reduction_Alpha.png differ diff --git a/families/images/Surface_Proton_Electron_Reduction_Alpha_vdW.png b/families/images/Surface_Proton_Electron_Reduction_Alpha_vdW.png new file mode 100644 index 0000000000..bdd293a1b6 Binary files /dev/null and b/families/images/Surface_Proton_Electron_Reduction_Alpha_vdW.png differ diff --git a/families/images/Surface_Proton_Electron_Reduction_Beta.png b/families/images/Surface_Proton_Electron_Reduction_Beta.png new file mode 100644 index 0000000000..50904c8588 Binary files /dev/null and b/families/images/Surface_Proton_Electron_Reduction_Beta.png differ diff --git a/families/images/Surface_Proton_Electron_Reduction_Beta_Dissociation.png b/families/images/Surface_Proton_Electron_Reduction_Beta_Dissociation.png new file mode 100644 index 0000000000..c60fb6168d Binary files /dev/null and b/families/images/Surface_Proton_Electron_Reduction_Beta_Dissociation.png differ diff --git a/families/images/Surface_Proton_Electron_Reduction_Beta_vdW.png b/families/images/Surface_Proton_Electron_Reduction_Beta_vdW.png new file mode 100644 index 0000000000..65d3895c99 Binary files /dev/null and b/families/images/Surface_Proton_Electron_Reduction_Beta_vdW.png differ diff --git a/input/kinetics/families/recommended.py b/input/kinetics/families/recommended.py index ae3e50700e..d93797667b 100644 --- a/input/kinetics/families/recommended.py +++ b/input/kinetics/families/recommended.py @@ -116,7 +116,7 @@ 'Surface_Adsorption_Bidentate', 'Surface_Bidentate_Dissociation', 'Surface_Monodentate_to_Bidentate', - 'Surface_Dissociation_to_Bidentate', + 'Surface_Dissociation_to_Bidentate', 'Surface_vdW_to_Bidentate', 'Surface_Adsorption_Dissociative_Double', 'Surface_Abstraction_Beta', @@ -152,7 +152,7 @@ 'Surface_Migration', } -# Electrochemical families! +# Electrochemical families. electrochem = { 'Surface_Proton_Electron_Reduction_Alpha', 'Surface_Proton_Electron_Reduction_Alpha_vdW', @@ -170,3 +170,24 @@ 'Li_Abstraction', 'R_Addition_MultipleBond_Disprop', } + +# Electrocatalytic CO2 Reduction families. +surface_CO2 = { + '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', + 'Surface_Proton_Electron_Reduction_Alpha', + 'Surface_Proton_Electron_Reduction_Alpha_vdW', + 'Surface_Proton_Electron_Reduction_Beta', + 'Surface_Proton_Electron_Reduction_Beta_vdW', + 'Surface_Proton_Electron_Reduction_Beta_Dissociation', +} diff --git a/input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt b/input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt new file mode 100644 index 0000000000..1e622a904f --- /dev/null +++ b/input/kinetics/libraries/CO2RR_DFT_Ag111/dictionary.txt @@ -0,0 +1,81 @@ + +X +1 X u0 p0 c0 + +proton +1 H u0 p0 c+1 + +e +1 e u0 p0 c-1 + +H2O +1 O u0 p2 c0 {2,S} {3,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} + +CO2X +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 O u0 p2 c0 {2,D} +4 X u0 p0 c0 + +CO2HX +1 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {5,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {3,S} + +CHO2X +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} + +OCX +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 X u0 p0 c0 {2,D} + +HCOOHX +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 + +CHOX +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} + +XCHOH +1 O u0 p2 c0 {2,S} {4,S} +2 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {2,D} + +CH2OX +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 + +XCH2OH +1 O u0 p2 c0 {2,S} {3,S} +2 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 X u0 p0 c0 {2,S} + +XCH2 +1 H u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,S} {4,D} +3 H u0 p0 c0 {2,S} +4 X u0 p0 c0 {2,D} diff --git a/input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py b/input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py new file mode 100644 index 0000000000..2f09e8a61c --- /dev/null +++ b/input/kinetics/libraries/CO2RR_DFT_Ag111/reactions.py @@ -0,0 +1,181 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "CO2RR_DFT_Ag111" +shortDesc = u"Calculated by Manish Kumar Kothakonda at Northeastern University" +longDesc = u""" +Place holder for long description +""" + + +entry( + index = 1, + label = "CO2X + proton <=> CO2HX", + degeneracy = 1, + kinetics = SurfaceChargeTransfer( + alpha = 0.62, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (0.75, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 2, + label = "CO2X + proton <=> CHO2X", + kinetics = SurfaceChargeTransfer( + alpha = 0.46, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (1.25, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 3, + label = "CO2HX + proton <=> OCX + H2O", + kinetics = SurfaceChargeTransfer( + alpha = 0.36, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (0.25, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 4, + label = "CO2HX + proton <=> HCOOHX", + kinetics = SurfaceChargeTransfer( + alpha = 0.62, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (2.40, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 5, + label = "CHO2X + proton <=> HCOOHX", + kinetics = SurfaceChargeTransfer( + alpha = 0.12, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (2.64, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 6, + label = "OCX + proton <=> CHOX", + kinetics = SurfaceChargeTransfer( + alpha = 0.49, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (0.45, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 7, + label = "CHOX + proton <=> XCHOH", + kinetics = SurfaceChargeTransfer( + alpha = 0.71, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (2.14, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 8, + label = "CHOX + proton <=> CH2OX", + kinetics = SurfaceChargeTransfer( + alpha = 0.36, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (2.60, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) + +entry( + index = 9, + label = "XCH2OH + proton <=> XCH2 + H2O", + kinetics = SurfaceChargeTransfer( + alpha = 0.19, # charge transfer coeff + A = (2.5e10, 'm^3/(mol*s)'), # pre-exponential factor estimate 10^11 s^-1 * 2.5e5 m^2/mol / 1000 m^3/mol H+ + n = 0, # temperature coeff + V0 = (-0.0, 'V'), # reference potential + Ea = (0.79, 'eV/molecule'), # activation energy + Tmin = (298, 'K'), + Tmax = (3000, 'K'), + electrons = 1, # electron stochiometric coeff + ), + shortDesc = u"""CO2RR_Ag111""", + longDesc = u"""Calculated by Manish Kumar Kothakonda""", + metal = "Ag", + facet = "111", +) diff --git a/input/recommended_libraries.yml b/input/recommended_libraries.yml index 235802a25e..7ef7ee2504 100644 --- a/input/recommended_libraries.yml +++ b/input/recommended_libraries.yml @@ -225,18 +225,18 @@ 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. + - 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. + - 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 @@ -265,4 +265,9 @@ electrochem: - LithiumAnalogyKinetics - LithiumSurface - LithiumSurfaceAnalogy + - Surface_Proton_Electron_Reduction_Alpha + - Surface_Proton_Electron_Reduction_Alpha_vdW + - Surface_Proton_Electron_Reduction_Beta + - Surface_Proton_Electron_Reduction_Beta_vdW + - Surface_Proton_Electron_Reduction_Beta_Dissociation transport: [] diff --git a/input/surface/libraries/metal.py b/input/surface/libraries/metal.py index bf512c5077..75cd0e1305 100644 --- a/input/surface/libraries/metal.py +++ b/input/surface/libraries/metal.py @@ -429,3 +429,22 @@ Lattice constant using PW91 is a=2.85 Angstrom. """, ) + +entry( + index = 22, + label = "Cu3Sn0001", + bindingEnergies = { + 'H': (-2.3766, 'eV/molecule'), + 'C': (-4.2480, 'eV/molecule'), + 'N': (-3.3060, 'eV/molecule'), + 'O': (-4.1415, 'eV/molecule'), + }, + surfaceSiteDensity = (1.4319e-09, 'mol/cm^2'), + facet = "0001", + metal = "Cu3Sn", + shortDesc = """Cu3Sn(0001)""", + longDesc = +""" +Calculated by Colin Gallagher and Su Sun at Northeastern University. Only Cu sites considered as active adsorption sites from thermodynamics analysis. +""", +) diff --git a/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py b/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py new file mode 100644 index 0000000000..6796cf3878 --- /dev/null +++ b/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py @@ -0,0 +1,371 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "CO2RR_Adsorbates_Ag111" +solvent = "water" +shortDesc = u"CO2RR adsorbate thermochemistry on Ag(111) from DFT" +longDesc = u""" +NASA polynomial thermochemistry for C1 and C2 adsorbate intermediates +relevant to electrochemical CO2 reduction (CO2RR) on Ag(111). +Adsorbates are labeled with a trailing or interleaved 'X' to indicate +surface binding sites, per RMG conventions. + +DFT (Manish Kumar Kothakonda, Northeastern): VASP with PBE + Grimme D3 +zero-damping (IVDW = 12) and PAW pseudopotentials. +A two-stage protocol was used: +Initial geometries were pre-optimized at ENCUT = 400 eV with a 3x3x1 +Monkhorst-Pack k-mesh, then fully re-relaxed to force convergence at +tighter settings of ENCUT = 500 eV and 4x4x1 k-mesh (IBRION = 2, +EDIFFG = -0.03 eV/A). All final energies - adsorbate slabs, bare-slab +reference, and vibrational frequencies - were computed at the tight +settings. + +Post-processing and thermo (Su Sun) via the Westgroup pipeline +(adapted from input_generator.py and compute_NASA_for_adsorbates): VASP +outputs converted to ASE .traj and inspected; vibrational frequencies +and ZPEs consolidated into per-species zpe_log_.txt files; +imaginary modes replaced with 12 cm^-1. Heat of formation at 0 K was +computed from a thermochemical cycle against CH4, H2O, and H2 references +(ATcT: h0_CH4 = -66.556 kJ/mol, h0_H2O = -238.938 kJ/mol, +h0_H2 = 0.0 kJ/mol). Reference gas electronic energies were read from the +final frame of each gas's ads_vib.traj at the same PBE+D3 level as the +slabs (displaced rather than relaxed geometries, a systematic ~1 kJ/mol +offset shared across all species); hard-coded ZPEs ZPE_CH4 = 1.196 eV, +ZPE_H2 = 0.277 eV, ZPE_H2O = 0.609 eV were used. Partition functions +were evaluated over 298.15-2000 K with the harmonic oscillator +approximation; when an adsorbate's two lowest modes fall below 100 cm^-1 +they are replaced by a 2D-gas translational model. +NASA polynomials were fit in two ranges (298-1000 K, 1000-2000 K) by +least-squares regression of Cp/R with enthalpy and entropy +matched at 298.15 K and continuity enforced at 1000 K. Heats of formation +were corrected from 0 K to 298 K using tabulated atomic H(298)-H(0) increments. +""" + +entry( + index = 0, + label = "CHX", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,T} +2 H u0 p0 c0 {1,S} +3 X u0 p0 c0 {1,T} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.266342243, 0.0255005593, -4.67302907e-05, 3.94631134e-08, -1.2647867e-11, 31227.7542, -4.07584264], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[5.83835547, -0.000550143917, 1.04877997e-06, -5.97825593e-10, 1.12691258e-13, 30217.8588, -30.2412718], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHX""", + longDesc = +u""" +""", +) + + +entry( + index = 1, + label = "COX", + molecule = +""" +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[4.76251327, 0.00111269978, -2.10966611e-06, 1.82404356e-09, -5.94635137e-13, -14561.0462, -12.3594921], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[4.99431896, -1.76936326e-05, 3.42262824e-08, -1.96003384e-11, 3.70408721e-15, -14601.0429, -13.4373387], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COX""", + longDesc = +u""" +""", +) + + +entry( + index = 2, + label = "HCOOH", + molecule = +""" +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 O u0 p2 c0 {2,S} {5,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[13.9828152, 8.07094773e-05, -1.53259344e-07, 1.32648986e-10, -4.32758868e-14, -50413.5699, -21.9105715], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.9995921, -1.26354032e-06, 2.44635089e-09, -1.40132815e-12, 2.64862147e-16, -50416.4578, -21.9885437], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""HCOOH""", + longDesc = +u""" +""", +) + + +entry( + index = 3, + label = "COHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {3,S} +2 C u0 p0 c0 {1,S} {4,T} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {2,T} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[7.90698765, 0.00510752439, -9.66734244e-06, 8.34878241e-09, -2.71941775e-12, 7452.81979, -31.9152917], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[8.97362495, -8.26142943e-05, 1.59656769e-07, -9.14041331e-11, 1.72709588e-14, 7268.29432, -36.8774988], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COHX""", + longDesc = +u""" +""", +) + + +entry( + index = 4, + label = "CHOHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {4,S} +2 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[10.4790225, 0.00244168743, -4.63031562e-06, 4.00396281e-09, -1.30541023e-12, -3872.00194, -32.829477], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.9875496, -3.87497326e-05, 7.49655069e-08, -4.29319322e-11, 8.11345985e-15, -3959.71854, -35.1938771], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHOHX""", + longDesc = +u""" +""", +) + + +entry( + index = 5, + label = "COOHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {5,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[10.986781, 6.20842133e-05, -1.17891803e-07, 1.02037681e-10, -3.32891347e-14, -44411.4442, -16.4053971], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.9996863, -9.71979115e-07, 1.88183405e-09, -1.07795624e-12, 2.03742017e-16, -44413.6656, -16.4653759], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COOHX""", + longDesc = +u""" +""", +) + + +entry( + index = 6, + label = "HCOOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[10.6983745, 0.00141493133, -2.68478436e-06, 2.32253402e-09, -7.57431101e-13, -54136.7261, -30.7077828], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.9928138, -2.2323418e-05, 4.3200796e-08, -2.47430431e-11, 4.6762909e-15, -54187.4686, -32.0765361], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""HCOOX""", + longDesc = +u""" +""", +) + + +entry( + index = 7, + label = "CX", + molecule = +""" +1 C u0 p0 c0 {2,Q} +2 X u0 p0 c0 {1,Q} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.208109795, 0.0141255843, -2.57114636e-05, 2.16103094e-08, -6.90214919e-12, 49419.1139, -0.591413039], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[2.90679495, -0.000321226726, 6.11116124e-07, -3.48106063e-10, 6.55928418e-14, 48849.4769, -15.2453553], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CX""", + longDesc = +u""" +""", +) + + +entry( + index = 8, + label = "CH3X", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[10.7907888, 0.000981788117, -1.86336377e-06, 1.61221374e-09, -5.25842614e-13, 2355.68713, -30.4031728], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.9950211, -1.54504782e-05, 2.99051637e-08, -1.71288833e-11, 3.23734262e-15, 2320.50412, -31.3525114], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH3X""", + longDesc = +u""" +""", +) + + +entry( + index = 9, + label = "CHOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[7.78973681, 0.000986354049, -1.87157965e-06, 1.61905637e-09, -5.28011849e-13, -9861.74615, -21.3183986], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.9949907, -1.55613972e-05, 3.01146711e-08, -1.72480167e-11, 3.25977367e-15, -9897.11865, -22.2725571], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHOX""", + longDesc = +u""" +""", +) + + +entry( + index = 10, + label = "CH4", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 H u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[13.9828152, 8.07094773e-05, -1.53259344e-07, 1.32648986e-10, -4.32758868e-14, -11094.9704, -22.9645165], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.9995921, -1.26354032e-06, 2.44635089e-09, -1.40132815e-12, 2.64862147e-16, -11097.8583, -23.0424887], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH4""", + longDesc = +u""" +""", +) + + +entry( + index = 11, + label = "CH2X", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,D} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {1,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[3.85100003, 0.0235194683, -4.38661963e-05, 3.75015562e-08, -1.21265551e-11, 19076.9562, -20.014004], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[8.86633631, -0.000437192952, 8.38897191e-07, -4.79205188e-10, 9.04376865e-14, 18190.0445, -43.4485995], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH2X""", + longDesc = +u""" +""", +) + + +entry( + index = 12, + label = "CH2OHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {1,S} +6 X u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[13.6992407, 0.00141127697, -2.6783469e-06, 2.31725865e-09, -7.55779555e-13, -15621.9329, -39.5967286], Tmin=(300.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.9928408, -2.22232177e-05, 4.3012071e-08, -2.46358334e-11, 4.65611636e-15, -15672.516, -40.9615025], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(300.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH2OHX""", + longDesc = +u""" +""", +) + diff --git a/input/thermo/libraries/CO2RR_Adsorbates_Cu111.py b/input/thermo/libraries/CO2RR_Adsorbates_Cu111.py new file mode 100644 index 0000000000..703db1a06c --- /dev/null +++ b/input/thermo/libraries/CO2RR_Adsorbates_Cu111.py @@ -0,0 +1,604 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "CO2RR_Adsorbates_Cu111" +solvent = "water" +shortDesc = "CO2RR adsorbate thermochemistry on Cu(111) from DFT" +longDesc = """ +NASA polynomial thermochemistry for C1 and C2 adsorbate intermediates +relevant to electrochemical CO2 reduction (CO2RR) on Cu(111). Species +include CHX, CH2X, CH3X, CHOX, CHOHX, CH2OHX, COX, COHX, COOHX, OCHOX, +COCHOX, OCHCHX, OCHCH2X, OCHCH3X, OCHCHOHX, OCHCH2OHX, OCHOCHX, OCH2CH3X, +and the C-C coupled XCOXCO dimer. Adsorbates are labeled with a trailing +or interleaved 'X' to indicate surface binding sites, per RMG conventions. + +DFT (Colin Gallagher, Northeastern): VASP with PBE + Grimme D3 zero-damping +(IVDW = 12) and PAW pseudopotentials. +A two-stage protocol was used: +Initial geometries were pre-optimized at ENCUT = 400 eV with a 3x3x1 +Monkhorst-Pack k-mesh, then fully re-relaxed to force convergence at +tighter settings of ENCUT = 500 eV and 4x4x1 k-mesh (IBRION = 2, +EDIFFG = -0.03 eV/A). All final energies - adsorbate slabs, bare-slab +reference, and vibrational frequencies - were computed at the tight +settings. +Other parameters: 1st order Methfessel-Paxton smearing +(ISMEAR = 1) with a smearing width of 0.1 eV, ISPIN = 2, +EDIFF = 1E-6 eV, no dipole correction. Slab: 4x4 Cu(111), 4 layers +(64 Cu), bottom 2 fixed and top 2 relaxed, in-plane area 86.32 A^2, +~18 A vacuum. Harmonic frequencies from finite differences (IBRION = 5, +NFREE = 2, POTIM = 0.015 A) on the free atoms (adsorbate + top 2 layers). + +Post-processing and thermo (Torrie Asifor) via the Westgroup pipeline +(adapted from input_generator.py and compute_NASA_for_adsorbates): VASP +outputs converted to ASE .traj and inspected; vibrational frequencies +and ZPEs consolidated into per-species zpe_log_.txt files; +imaginary modes replaced with 12 cm^-1. Heat of formation at 0 K was +computed from a thermochemical cycle against CH4, H2O, and H2 references +(ATcT: h0_CH4 = -66.556 kJ/mol, h0_H2O = -238.938 kJ/mol, +h0_H2 = 0.0 kJ/mol). Reference gas electronic energies were read from the +final frame of each gas's ads_vib.traj at the same PBE+D3 level as the +slabs (displaced rather than relaxed geometries, a systematic ~1 kJ/mol +offset shared across all species); hard-coded ZPEs ZPE_CH4 = 1.196 eV, +ZPE_H2 = 0.277 eV, ZPE_H2O = 0.609 eV were used. Partition functions +were evaluated over 298.15-2000 K with the harmonic oscillator +approximation; when an adsorbate's two lowest modes fall below 100 cm^-1 +they are replaced by a 2D-gas translational model using a legacy per-site +area of 6.90 A^2/site inherited from earlier 3x3 Cu(111) workflows (vs. +the actual 5.40 A^2/site for this 4x4 slab, a ~0.6 kJ/mol shift at 298 K). +NASA polynomials were fit in two ranges (298-1000 K, 1000-2000 K) by +least-squares regression of Cp/R with enthalpy and entropy matched at +298.15 K and continuity enforced at 1000 K. Heats of formation were +corrected from 0 K to 298 K using tabulated atomic H(298)-H(0) increments. + +Intended as a supporting thermo reference for RMG-generated CO2RR +mechanisms on Cu(111), where extensive benchmarks exist. Uncertainty is +consistent with typical PBE+D3 performance on transition-metal adsorbates +(~0.2 eV, ~20 kJ/mol per species). +""" + +entry( + index = 0, + label = "CH2OHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {5,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {6,S} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {1,S} +6 X u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.472735789, 0.0241008939, -2.46801184e-05, 1.37773161e-08, -3.0813789e-12, -21157.4578, 2.60923861], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.5681808, -0.00792065082, 1.40261804e-05, -7.39838131e-09, 1.31411936e-12, -23729.4054, -48.4995382], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH2OHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 1, + label = "CH2X", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,D} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {1,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.466416892, 0.0226076886, -3.69343557e-05, 3.09744704e-08, -9.99641342e-12, 8004.29404, -3.72629114], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.09877494, -0.00433095407, 7.66695886e-06, -4.02988705e-09, 7.12914077e-13, 6583.37634, -35.9122248], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH2X""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 2, + label = "CH3X", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 H u0 p0 c0 {1,S} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.797287316, 0.0196521154, -2.31595564e-05, 1.66221917e-08, -4.97799024e-12, -3111.00157, -4.77956538], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[8.91016513, -0.00741666648, 1.31686499e-05, -6.96776478e-09, 1.239664e-12, -5144.93228, -45.607756], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CH3X""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 3, + label = "CHOHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {4,S} +2 C u0 p0 c0 {1,S} {3,S} {5,D} +3 H u0 p0 c0 {2,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.41019307, 0.0224007435, -2.72300418e-05, 1.76532667e-08, -4.60273486e-12, -11957.2586, -6.3198189], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[9.6152098, -0.00536925487, 9.50116088e-06, -5.00366325e-09, 8.87974014e-13, -13954.9197, -47.4140367], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHOHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 4, + label = "CHOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.37863592, 0.012408481, -1.25801919e-05, 7.24790581e-09, -1.8141235e-12, -13935.0226, -9.04256939], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.62620563, -0.00385204041, 6.94355702e-06, -3.75812385e-09, 6.81108837e-13, -15307.787, -35.7479814], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHOX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 5, + label = "CHX", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,T} +2 H u0 p0 c0 {1,S} +3 X u0 p0 c0 {1,T} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-2.08855354, 0.0294663183, -5.2247455e-05, 4.3854041e-08, -1.3978891e-11, 15687.781, 6.79987743], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[4.98902907, -0.00223592875, 3.9741247e-06, -2.09265476e-09, 3.70889503e-13, 14337.5132, -26.7707539], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 6, + label = "COCHOX", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 C u0 p0 c0 {2,D} {3,S} {6,S} +5 H u0 p0 c0 {3,S} +6 X u0 p0 c0 {4,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.93949246, 0.0256383446, -2.77539412e-05, 1.63477437e-08, -4.11348733e-12, -34804.6135, -3.52046277], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[12.0315845, -0.00610743143, 1.11113129e-05, -6.09316938e-09, 1.11585568e-12, -37414.5425, -54.7480472], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COCHOX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 7, + label = "COHX", + molecule = +""" +1 O u0 p2 c0 {2,S} {3,S} +2 C u0 p0 c0 {1,S} {4,T} +3 H u0 p0 c0 {1,S} +4 X u0 p0 c0 {2,T} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.88601171, 0.0175443623, -2.3496585e-05, 1.60954951e-08, -4.3767108e-12, -10766.6389, -8.99891253], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.64233194, -0.00292695859, 5.17262432e-06, -2.71697657e-09, 4.81552239e-13, -12112.2365, -37.5691896], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 8, + label = "COOHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {5,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.05917125, 0.0219066236, -2.43200647e-05, 1.36437162e-08, -3.01907804e-12, -48232.3178, 0.75905578], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[9.25517481, -0.00446613856, 8.00866345e-06, -4.303982e-09, 7.76650481e-13, -50290.4042, -40.6148991], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COOHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 9, + label = "COX", + molecule = +""" +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[3.52678302, 0.00519878526, -6.77403179e-06, 5.45808928e-09, -1.86754692e-12, -22933.4167, -15.777435], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[5.53299166, -0.00147915536, 2.70209812e-06, -1.4866849e-09, 2.72829319e-13, -23451.2467, -25.9161271], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 10, + label = "OCH2CH3X", + molecule = +""" +1 O u0 p2 c0 {2,S} {9,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {3,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.526183454, 0.0258797543, -4.36025144e-06, -1.14542255e-08, 6.25217239e-12, -36161.4155, 3.24649437], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[16.8038419, -0.0159680235, 2.8516839e-05, -1.52454216e-08, 2.73639731e-12, -40823.2612, -81.6436784], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCH2CH3X""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 11, + label = "OCHCH2OHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {8,S} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 C u0 p0 c0 {2,D} {3,S} {7,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {3,S} +7 H u0 p0 c0 {4,S} +8 H u0 p0 c0 {1,S} +9 X u0 p0 c0 +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[3.09646829, 0.0237384116, -3.87127221e-06, -1.13323939e-08, 6.16656379e-12, -46953.0529, -4.1727781], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[17.7632799, -0.0135012658, 2.41421777e-05, -1.29323226e-08, 2.32590842e-12, -51169.7292, -80.7610976], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH2OHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 12, + label = "OCHCH2X", + molecule = +""" +1 O u0 p2 c0 {2,S} {7,S} +2 C u0 p0 c0 {1,S} {3,D} {4,S} +3 C u0 p0 c0 {2,D} {5,S} {6,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {3,S} +7 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.628328912, 0.0328527253, -3.1908806e-05, 1.59572749e-08, -3.05474396e-12, -23681.7878, 7.83815501], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.1893158, -0.00985950398, 1.76359697e-05, -9.44590688e-09, 1.69824677e-12, -27258.0458, -62.3914324], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH2X""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 13, + label = "OCHCH3X", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {1,D} {2,S} {7,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 X u0 p0 c0 +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.93148616, 0.0156994161, 5.27680207e-06, -1.57739035e-08, 6.86352711e-12, -27771.7175, -4.21488209], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[14.9647333, -0.0130728691, 2.33574302e-05, -1.24959647e-08, 2.24399815e-12, -31341.2771, -67.5434017], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH3X""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 14, + label = "OCHCHOHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {8,S} +2 O u0 p2 c0 {4,S} {7,S} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,S} {3,D} {6,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {4,S} +7 H u0 p0 c0 {2,S} +8 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.00911478161, 0.0397758564, -4.14240749e-05, 2.21262211e-08, -4.59902949e-12, -44975.5239, 5.06918604], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[15.8574169, -0.0102903723, 1.83673581e-05, -9.80550942e-09, 1.75919459e-12, -49009.9016, -75.1821401], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCHOHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 15, + label = "OCHCHX", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {6,D} +3 C u0 p0 c0 {1,D} {2,S} {5,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {3,S} +6 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.276809443, 0.0301374978, -3.16219676e-05, 1.72227608e-08, -3.75111053e-12, -18198.9697, -1.71302897], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[12.2388819, -0.00757866622, 1.36344476e-05, -7.36324538e-09, 1.33257199e-12, -21258.6668, -62.3317273], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 16, + label = "OCHOCHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {7,S} +2 O u0 p2 c0 {4,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,S} {3,D} {6,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {4,S} +7 X u0 p0 c0 {1,S} +8 X u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.188361028, 0.0359884107, -3.77327255e-05, 2.00961226e-08, -4.20161128e-12, -41417.7273, 5.73697635], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.933618, -0.00846409226, 1.52416698e-05, -8.24316109e-09, 1.493801e-12, -45025.8482, -65.8263189], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHOCHX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 17, + label = "OCHOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.6663831, 0.0145773007, -7.54839692e-06, -1.28850802e-09, 1.76379918e-12, -56459.297, -1.41903333], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[9.15358298, -0.00545271031, 9.86437499e-06, -5.37406014e-09, 9.79390495e-13, -58557.4789, -40.2571999], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHOX""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) + + +entry( + index = 18, + label = "XCOXCO", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 C u0 p0 c0 {2,D} {3,S} {6,S} +5 X u0 p0 c0 {3,S} +6 X u0 p0 c0 {4,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.49554898, 0.0242026474, -3.27700315e-05, 2.26836821e-08, -6.38929534e-12, -25528.1387, -6.08127138], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.2047191, -0.00286178768, 5.28404531e-06, -2.95345619e-09, 5.49031049e-13, -27368.1643, -44.4858043], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""XCOXCO""", + longDesc = +u""" +""", + metal = "Cu", + facet = "111", +) diff --git a/input/thermo/libraries/CO2RR_Adsorbates_Cu3Sn0001.py b/input/thermo/libraries/CO2RR_Adsorbates_Cu3Sn0001.py new file mode 100644 index 0000000000..867e628e6e --- /dev/null +++ b/input/thermo/libraries/CO2RR_Adsorbates_Cu3Sn0001.py @@ -0,0 +1,442 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "CO2RR_Adsorbates_Cu3Sn0001" +solvent = "water" +shortDesc = "CO2RR adsorbate thermochemistry on Cu3Sn(0001) from DFT" +longDesc = """ +NASA polynomial thermochemistry for C1 and C2 adsorbate intermediates +relevant to electrochemical CO2 reduction (CO2RR) on the Cu3Sn(0001) +surface of the epsilon-Cu3Sn intermetallic. Species include CHOX, COX, +COOHX, OCHOX, COCHOX, the C-C coupled XCOXCO dimer, and the C2 alkoxy +and enol intermediates OCHCHX, OCHCH2X, OCHCH3X, OCHCHOHX, OCHCH2OHX, +OCHOCHX, and OCH2CH3X. Adsorbates are labeled with a trailing or +interleaved 'X' to indicate surface binding sites, per RMG conventions. + +DFT (Colin Gallagher, Northeastern): VASP with PBE + Grimme D3 zero-damping +(IVDW = 12) and PAW pseudopotentials. +A two-stage protocol was used: +Initial geometries were pre-optimized at ENCUT = 400 eV with a 3x3x1 +Monkhorst-Pack k-mesh, then fully re-relaxed to force convergence at +tighter settings of ENCUT = 500 eV and 4x4x1 k-mesh (IBRION = 2, +EDIFFG = -0.03 eV/A). All final energies - adsorbate slabs, bare-slab +reference, and vibrational frequencies - were computed at the tight +settings. +Other parameters: 1st order Methfessel-Paxton smearing +(ISMEAR = 1) with a smearing width of 0.1 eV, ISPIN = 2, +EDIFF = 1E-6 eV, no dipole correction. Slab: hexagonal Cu3Sn(0001) +supercell with 48 Cu + 16 Sn across 5 layers (bottom 3 fixed, top 2 +relaxed), in-plane area 104.37 A^2, ~17 A vacuum. Harmonic frequencies +from finite differences (IBRION = 5, NFREE = 2, POTIM = 0.015 A) on the +free atoms (adsorbate + top 2 layers). + +Post-processing and thermo (Torrie Asifor) via the Westgroup pipeline +(adapted from input_generator.py and compute_NASA_for_adsorbates): VASP +outputs converted to ASE .traj and inspected; vibrational frequencies +and ZPEs consolidated into per-species zpe_log_.txt files; +imaginary modes replaced with 12 cm^-1. Heat of formation at 0 K was +computed from a thermochemical cycle against CH4, H2O, and H2 references +(ATcT: h0_CH4 = -66.556 kJ/mol, h0_H2O = -238.938 kJ/mol, +h0_H2 = 0.0 kJ/mol). Reference gas electronic energies were read from the +final frame of each gas's ads_vib.traj at the same PBE+D3 level as the +slabs (displaced rather than relaxed geometries, a systematic ~1 kJ/mol +offset shared across all species); hard-coded ZPEs ZPE_CH4 = 1.196 eV, +ZPE_H2 = 0.277 eV, ZPE_H2O = 0.609 eV were used. Partition functions +were evaluated over 298.15-2000 K with the harmonic oscillator +approximation; when an adsorbate's two lowest modes fall below 100 cm^-1 +they are replaced by a 2D-gas translational model using a legacy per-site +area of 6.90 A^2/site inherited from earlier 3x3 Cu(111) workflows (vs. +the actual 6.52 A^2/site for this Cu3Sn slab, a ~0.15 kJ/mol shift at +298 K). NASA polynomials were fit in two ranges (298-1000 K, +1000-2000 K) by least-squares regression of Cp/R with enthalpy and +entropy matched at 298.15 K and continuity enforced at 1000 K. Heats of +formation were corrected from 0 K to 298 K using tabulated atomic +H(298)-H(0) increments. + +Primary DFT-based thermo reference for RMG-generated CO2RR mechanisms on +Cu3Sn(0001) in the Westgroup automated microkinetic modeling pipeline. +Uncertainty is consistent with typical PBE+D3 performance on +transition-metal adsorbates (~0.2 eV, ~20 kJ/mol per species). +""" + +entry( + index = 0, + label = "CHOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.74349313, 0.0148300711, -1.65536121e-05, 1.03768953e-08, -2.77422703e-12, -14068.2838, -8.10961736], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.60674062, -0.00396066968, 7.15100332e-06, -3.87857554e-09, 7.04121665e-13, -15569.5014, -37.7908267], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""CHOX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 1, + label = "COCHOX", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 C u0 p0 c0 {2,D} {3,S} {6,S} +5 H u0 p0 c0 {3,S} +6 X u0 p0 c0 {4,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.51074428, 0.0220340273, -2.02688214e-05, 9.54750791e-09, -1.82176149e-12, -30765.8755, -4.81098828], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[11.9774317, -0.0061910143, 1.12437071e-05, -6.15372406e-09, 1.12529604e-12, -33288.3219, -53.2387915], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COCHOX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 2, + label = "COOHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {4,S} +2 O u0 p2 c0 {3,D} +3 C u0 p0 c0 {1,S} {2,D} {5,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.57291532, 0.0239770732, -2.79387799e-05, 1.65750947e-08, -3.92695945e-12, -48808.2078, -6.7526346], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[10.2432721, -0.0045092048, 8.09079692e-06, -4.35111478e-09, 7.85594402e-13, -50956.2429, -50.3765829], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COOHX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 3, + label = "COX", + molecule = +""" +1 O u0 p2 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.15374115, 0.00711964156, -1.13374895e-05, 1.00074377e-08, -3.47838511e-12, -19372.6808, -4.67420257], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[4.45424836, -0.00162230699, 2.9503086e-06, -1.61116576e-09, 2.93861513e-13, -19914.6116, -16.0376878], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""COX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 4, + label = "OCH2CH3X", + molecule = +""" +1 O u0 p2 c0 {2,S} {9,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 C u0 p0 c0 {2,S} {6,S} {7,S} {8,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {3,S} +7 H u0 p0 c0 {3,S} +8 H u0 p0 c0 {3,S} +9 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.788155367, 0.0249548897, -2.96759698e-06, -1.24467075e-08, 6.52723015e-12, -34237.4683, 2.48957937], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[16.8164772, -0.0159260566, 2.84392268e-05, -1.52019708e-08, 2.72829405e-12, -38845.6552, -81.1844559], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCH2CH3X""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 5, + label = "OCHCH2OHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {8,S} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 C u0 p0 c0 {2,D} {3,S} {7,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {3,S} +7 H u0 p0 c0 {4,S} +8 H u0 p0 c0 {1,S} +9 X u0 p0 c0 +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.97459822, 0.0242885566, -4.95324176e-06, -1.04154645e-08, 5.88135443e-12, -46058.3536, -4.8074186], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[17.7412996, -0.0135023109, 2.41363604e-05, -1.29228777e-08, 2.32333159e-12, -50287.6975, -81.8408018], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH2OHX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 6, + label = "OCHCH2X", + molecule = +""" +1 O u0 p2 c0 {2,S} {7,S} +2 C u0 p0 c0 {1,S} {3,D} {4,S} +3 C u0 p0 c0 {2,D} {5,S} {6,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {3,S} +7 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.163426185, 0.0309141687, -2.93377835e-05, 1.44116925e-08, -2.69761991e-12, -22710.7822, 5.99423326], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.0987573, -0.00985382394, 1.7589596e-05, -9.39193391e-09, 1.68443623e-12, -26156.9338, -61.4743534], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH2X""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 7, + label = "OCHCH3X", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {1,D} {2,S} {7,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +7 H u0 p0 c0 {3,S} +8 X u0 p0 c0 +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[3.00634079, 0.0152798875, 6.13476544e-06, -1.65540464e-08, 7.12691885e-12, -26918.8699, -4.30723606], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[14.9615622, -0.0130702141, 2.33503201e-05, -1.24906387e-08, 2.24283666e-12, -30476.5943, -67.2821044], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCH3X""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 8, + label = "OCHCHOHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {8,S} +2 O u0 p2 c0 {4,S} {7,S} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,S} {3,D} {6,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {4,S} +7 H u0 p0 c0 {2,S} +8 X u0 p0 c0 {1,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.31738489, 0.0337353549, -3.07765911e-05, 1.35163088e-08, -1.94956551e-12, -41257.9069, -0.331264019], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[15.8143526, -0.0101891781, 1.81561425e-05, -9.67051827e-09, 1.73209325e-12, -45043.1443, -74.2060751], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCHOHX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 9, + label = "OCHCHX", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {6,D} +3 C u0 p0 c0 {1,D} {2,S} {5,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {3,S} +6 X u0 p0 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.186083938, 0.0313033805, -3.31640683e-05, 1.83063923e-08, -4.06516487e-12, -16607.1771, -0.533154725], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[12.1682959, -0.00776604449, 1.39731944e-05, -7.54695754e-09, 1.3659676e-12, -19762.1543, -63.1133931], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHCHX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 10, + label = "OCHOCHX", + molecule = +""" +1 O u0 p2 c0 {3,S} {7,S} +2 O u0 p2 c0 {4,S} {8,S} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,S} {3,D} {6,S} +5 H u0 p0 c0 {3,S} +6 H u0 p0 c0 {4,S} +7 X u0 p0 c0 {1,S} +8 X u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.0579249054, 0.0344787757, -3.46894579e-05, 1.74808247e-08, -3.37110895e-12, -40845.0891, 4.97109633], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[13.9289506, -0.00853520745, 1.53752974e-05, -8.32061068e-09, 1.50852866e-12, -44422.9436, -65.4843799], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHOCHX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 11, + label = "OCHOX", + molecule = +""" +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} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.67220889, 0.0144593325, -7.37932862e-06, -1.33628765e-09, 1.74722736e-12, -57413.8836, -1.50759757], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[9.14577907, -0.00549354708, 9.94099598e-06, -5.41764493e-09, 9.87569455e-13, -59512.1847, -40.2901072], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""OCHOX""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +) + + +entry( + index = 12, + label = "XCOXCO", + molecule = +""" +1 O u0 p2 c0 {3,D} +2 O u0 p2 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 C u0 p0 c0 {2,D} {3,S} {6,S} +5 X u0 p0 c0 {3,S} +6 X u0 p0 c0 {4,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[2.41884657, 0.0278294959, -3.94623871e-05, 2.87941258e-08, -8.50641432e-12, -26978.4777, -12.375979], Tmin=(298.0, 'K'), Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[11.0515201, -0.00331790688, 6.11806441e-06, -3.41065788e-09, 6.32647174e-13, -29007.55, -55.2010354], Tmin=(1000.0, 'K'), Tmax=(2000.0, 'K')), + ], + Tmin=(298.0, 'K'), + Tmax=(2000.0, 'K'), +), + shortDesc = u"""XCOXCO""", + longDesc = +u""" +""", + metal = "Cu3Sn", + facet = "0001", +)