diff --git a/input/thermo/libraries/surfaceThermoCovDepPt111.py b/input/thermo/libraries/surfaceThermoCovDepPt111.py deleted file mode 100644 index 62ffae8dc1..0000000000 --- a/input/thermo/libraries/surfaceThermoCovDepPt111.py +++ /dev/null @@ -1,79 +0,0 @@ -name = "Coverage Dependent Thermo for Pt(111)" -shortDesc = u"thermo with coverage dependence for Pt(111) surface species" -longDesc = u""" -COX coverage dependence as calculated by Jongyoon Bae, Bjarne Kreitz, Andrew A. Peterson, and C. Franklin Goldsmith -Journal of Chemical Information and Modeling 2025 65 (7), 3461-3476 -DOI: 10.1021/acs.jcim.4c02167 -Polynomial coeffients taken from global minimum Pt Table S3. See Supplemental Material. -""" - - -entry( - index = 1, - label = "X", - molecule = -""" -1 X u0 p0 c0 -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[0.0,0,0,0,0,0.0,0.0], Tmin=(298,'K'), Tmax=(1000,'K')), - NASAPolynomial(coeffs=[0.0,0,0,0,0,0.0,0.0], Tmin=(1000,'K'), Tmax=(2000,'K')), - ], - Tmin = (298,'K'), - Tmax = (2000,'K'), - ), - shortDesc = u"""library value for a vacant surface site""", - longDesc = u"""Zeros, by definition.""", - metal = "Pt", - facet = "111", -) - - -entry( - index = 2, - label = "XCO", - molecule = -""" -1 X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 O u0 p2 c0 {2,D} -""", - thermo = NASA( - polynomials = [ - NASAPolynomial(coeffs=[1.4289514345775818, 0.014037445912949231, -2.2117880511546713e-05, 1.7865950156490832e-08, -5.7147862830841945e-12, -34568.84870061009, -7.782662330904809], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), - NASAPolynomial(coeffs=[5.486566622473974, -0.0016811903234556856, 3.0903081182232816e-06, -1.7118686775497669e-09, 3.158649696949356e-13, -35481.550855606365, -27.6788563455022], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), - ], - Tmin = (298.0,'K'), - Tmax = (2000.0,'K'), - thermo_coverage_dependence = { - """ - 1 C u0 p0 {2,D} {3,D} - 2 O u0 p2 {1,D} - 3 X u0 p0 {1,D} - """: { - 'model': 'polynomial', - 'enthalpy-coefficients': [(0.312, 'eV/molecule'), (-0.323, 'eV/molecule'), (0.890, 'eV/molecule')], - 'entropy-coefficients': [(1.11e-4, 'eV/(molecule*K)'), (-6.48e-5, 'eV/(molecule*K)'), (-1.63e-4, 'eV/(molecule*K)')] - } - }, - ), - longDesc = u""" - Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in - Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: - - https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow - - DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW - functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings - were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), - smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. - - COX coverage dependence calculated by Jongyoon Bae, Bjarne Kreitz, Andrew A. Peterson, and C. Franklin Goldsmith - Journal of Chemical Information and Modeling 2025 65 (7), 3461-3476 - DOI: 10.1021/acs.jcim.4c02167 - Polynomial coeffients taken from global minimum Pt Table S3. See Supplemental Material. - """, - metal = "Pt", - facet = "111", -) diff --git a/input/thermo/libraries/surfaceThermoPt111_covdep.py b/input/thermo/libraries/surfaceThermoPt111_covdep.py new file mode 100644 index 0000000000..3109051712 --- /dev/null +++ b/input/thermo/libraries/surfaceThermoPt111_covdep.py @@ -0,0 +1,449 @@ +#!/usr/bin/env python +# encoding: utf-8 + +name = "SurfaceThermoPt111_covdep" +shortDesc = u"Surface adsorbates on Pt(111) with coverage-dependent thermo" +longDesc = u""" +Surface species adsorbed on Pt(111) with coverage-dependent thermo. The thermochemical +properties of the adsorbates are the same as in surfaceThermoPt111.py with the addition of polynomials +for the coverage-dependent enthalpy of formation of entropy. + +Details for the enthalpies of formation: +All species are computed with a consistent set of DFT settings in Quantum Espresso. +The reference species used are: *O, *CO, *NO, *H, *. Silbaugh and Campbell have reported the +heats of formation for these adsorbates with respect to elements in their +standard state at 298 K in https://doi.org/10.1021/acs.jpcc.6b06154. We apply +atomic corrections to get these heats of formation with respect to elements in +their standard state at 0 K as descibed by Ruscic and Bross in +https://www.sciencedirect.com/science/chapter/bookseries/abs/pii/B9780444640871000012 +We also correct the heat of formation ot the measured coverage down to 1/9 ML +for *O and *CO, and assume the heat of formation of a bare Pt(111) slab is 0. Our +heats of formation at 0 K are: + "XCO": -230.9, + "XH": -32.7, + "XNO": -20.24, + 'XO': -103.7, + "Pt": 0, +We then use these species and values as an anchor set to compute the heats +of formation for all adosrbates on Pt(111) as described by Kreitz et al. +https://pubs.rsc.org/en/content/articlelanding/2025/cs/d4cs00768a. +Lastly we correct the heats of formation back to being with respec to the +elements in their standard state at 298 K. This process is automated in +C. Franklin Goldsmith's thermo_kinetics_scripts repository in the +new_workflow folder: +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +Details for the notation: +Note: X indicates a bond to the surface. It is always on the left hand site of +an atom that is bonded to the surface e.g. XCO it means that C is bonded to +the surface. If the X is on the right hand side and at the end of a label, it +means that this species is physisorbed. + +Details for the coverage effects: +Coverage-dependent corrections to the enthalpy of formation and entropy are described +by polynomial models as a function of adsorbate surface coverage, following the approach +of Bae et al. (https://pubs.acs.org/doi/10.1021/acs.jcim.4c02167). +The order in the coefficients is: [(1st order), (2nd order), (3rd order)] +""" + +entry( + index = 1, + label = "XCO", + molecule = +""" +1 X u0 p0 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 O u0 p2 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.4289514345775818, 0.014037445912949231, -2.2117880511546713e-05, 1.7865950156490832e-08, -5.7147862830841945e-12, -34568.84870061009, -7.782662330904809], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[5.486566622473974, -0.0016811903234556856, 3.0903081182232816e-06, -1.7118686775497669e-09, 3.158649696949356e-13, -35481.550855606365, -27.6788563455022], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence = { + """ + 1 C u0 p0 {2,D} {3,D} + 2 O u0 p2 {1,D} + 3 X u0 p0 {1,D} + """: { + 'model': 'polynomial', + 'enthalpy-coefficients': [(0.312, 'eV/molecule'), (-0.323, 'eV/molecule'), (0.890, 'eV/molecule')], + 'entropy-coefficients': [(1.11e-4, 'eV/(molecule*K)'), (-6.48e-5, 'eV/(molecule*K)'), (-1.63e-4, 'eV/(molecule*K)')] + } + }, + ), + longDesc = u""" + Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in + Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + + https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + + DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW + functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings + were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), + smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + + COX coverage dependence calculated by Jongyoon Bae, Bjarne Kreitz, Andrew A. Peterson, and C. Franklin Goldsmith + Journal of Chemical Information and Modeling 2025 65 (7), 3461-3476 + DOI: 10.1021/acs.jcim.4c02167 + Polynomial coeffients taken from global minimum Pt Table S3. See Supplemental Material. + """, + metal = "Pt", + facet = "111", +) + +entry( + index = 2, + label = "XCH", + molecule = +""" +1 X u0 p0 c0 {2,T} +2 C u0 p0 c0 {1,T} {3,S} +3 H u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-2.668054071556987, 0.02906936052545507, -4.8265363884475096e-05, 3.875892627442114e-08, -1.1974939840756911e-11, -2202.5553595330853, 9.729432728113348], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[4.904296267990244, -0.0026386471764010657, 4.717289404373525e-06, -2.5126685290206794e-09, 4.49659036145192e-13, -3748.807352288421, -26.710780698175974], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence={ + """ + 1 X u0 p0 c0 {2,T} + 2 C u0 p0 c0 {1,T} {3,S} + 3 H u0 p0 c0 {2,S} + """: {'model': 'polynomial', + 'enthalpy-coefficients': [(62670, 'J/mol'), (0, 'J/mol'), (0, 'J/mol')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')]} + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + +Coverage dependence based on values in the Supporting Information of "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt" +Jonathan E. Sutton, Paraskevi Panagiotopoulou, Xenophon E. Verykios, and Dionisios G. Vlachos +The Journal of Physical Chemistry C 2013 117 (9), 4691-4706 +DOI: 10.1021/jp312593u +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 3, + label = "XCCH3", + molecule = +""" +1 X u0 p0 c0 {3,T} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {1,T} {2,S} +4 H u0 p0 c0 {2,S} +5 H u0 p0 c0 {2,S} +6 H u0 p0 c0 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[0.45723412880679587, 0.02222624102464355, -1.667214371225305e-05, 5.7213606113744865e-09, -3.993230911289944e-13, -11043.637207150816, -2.2732381499886802], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[11.307104591573854, -0.009366253405579311, 1.671500714924329e-05, -8.92182977096838e-09, 1.5993403971733366e-12, -13965.245844046643, -57.941171527260124], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence={ + """ + 1 X u0 p0 c0 {3,T} + 2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} + 3 C u0 p0 c0 {1,T} {2,S} + 4 H u0 p0 c0 {2,S} + 5 H u0 p0 c0 {2,S} + 6 H u0 p0 c0 {2,S} + """: {'model': 'polynomial', + 'enthalpy-coefficients': [(62670, 'J/mol'), (0, 'J/mol'), (0, 'J/mol')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')]}, + """ + 1 X u0 p0 c0 {2,T} + 2 C u0 p0 c0 {1,T} {3,S} + 3 H u0 p0 c0 {2,S} + """: {'model': 'polynomial', + 'enthalpy-coefficients': [(62670, 'J/mol'), (0, 'J/mol'), (0, 'J/mol')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')]}, + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + +Coverage dependence based on values in the Supporting Information of "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt" +Jonathan E. Sutton, Paraskevi Panagiotopoulou, Xenophon E. Verykios, and Dionisios G. Vlachos +The Journal of Physical Chemistry C 2013 117 (9), 4691-4706 +DOI: 10.1021/jp312593u +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 4, + label = "XO", + molecule = +""" +1 X u0 p0 c0 {2,D} +2 O u0 p2 c0 {1,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-0.29447758737461366, 0.014416268368780336, -2.6132274716597896e-05, 2.19005960702076e-08, -6.980197262178007e-12, -13066.562285947317, -0.1994364663449193], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[2.902441066530188, -0.00033857631003595914, 6.433642615608704e-07, -3.663229139884261e-10, 6.900876877074478e-14, -13654.383053304307, -15.255938164267217], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence = { + """ + 1 X u0 p0 c0 {2,D} + 2 O u0 p2 c0 {1,D} + """: { + 'model': 'polynomial', + 'enthalpy-coefficients': [(-0.043,'eV/molecule'), (1.042,'eV/molecule'), (0,'eV/molecule')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')] + } + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + +XO coverage dependence obtained from "Detailed Microkinetics for the Oxidation of Exhaust Gas Emissions +through Automated Mechanism Generation" by Bjarne Kreitz, Patrick Lott, Jongyoon Bae, Katrín Blöndal, +Sofia Angeli, Zachary W. Ulissi, Felix Studt, C. Franklin Goldsmith, and Olaf Deutschmann +ACS Catalysis 2022 12 (18), 11137-11151 +DOI: 10.1021/acscatal.2c03378 +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 5, + label = "CH3XCO", + 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 X u0 p0 c0 {3,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.2303812875933364, 0.021364197591551247, -1.0987964053318556e-05, -4.0854759822882103e-10, 1.7279200745627597e-12, -32282.401311062615, 0.4124679531891413], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[12.896110212786931, -0.010602930836050555, 1.8955766424558903e-05, -1.014588758269268e-08, 1.8229290835573665e-12, -35530.476320764086, -59.95424168175581], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence={""" + 1 C u0 p0 {2,D} {3,D} + 2 O u0 p2 {1,D} + 3 X u0 p0 {1,D} + """: {'model': 'polynomial', + 'enthalpy-coefficients': [(62670, 'J/mol'), (0, 'J/mol'), (0, 'J/mol')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')]} + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. +The two lowest frequencies, 23.8 and 88.9,where replaced by the 2D gas model. + +Coverage dependence based on values in the Supporting Information of "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt" +Jonathan E. Sutton, Paraskevi Panagiotopoulou, Xenophon E. Verykios, and Dionisios G. Vlachos +The Journal of Physical Chemistry C 2013 117 (9), 4691-4706 +DOI: 10.1021/jp312593u +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 6, + label = "XNO", + molecule = +""" +1 X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,D} +3 O u0 p2 c0 {2,D} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.861978139702, 0.012267712827676622, -1.7731771898190192e-05, 1.3155375661569419e-08, -3.940110211157303e-12, -6275.99064823019, -9.289679054876098], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[5.603255701316299, -0.0013940149474614871, 2.573609745219915e-06, -1.4363138871988452e-09, 2.6664790772466233e-13, -7148.294106663131, -27.81226494128604], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence = { + """ + 1 X u0 p0 c0 {2,S} + 2 N u0 p1 c0 {1,S} {3,D} + 3 O u0 p2 c0 {2,D} + """: { + 'model': 'polynomial', + 'enthalpy-coefficients': [(0.102,'eV/molecule'),(0.599,'eV/molecule'),(0,'eV/molecule')], + 'entropy-coefficients': [(0, 'kJ/(mol*K)'), (0, 'kJ/(mol*K)'), (0, 'kJ/(mol*K)')] + } + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + +XNO coverage dependence based on "Detailed Microkinetics for NOx-Inhibited Hydrocarbon Oxidation +through Automated Mechanism Generation within Correlated Uncertainty on Pt(111)", under review, +Kirk Badger, Bjarne Kreitz, Patrick Lott, and C. Franklin Goldsmith +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 7, + label = "XNO2", + molecule = +""" +1 X u0 p0 c0 {2,S} +2 N u0 p0 c+1 {1,S} {3,D} {4,S} +3 O u0 p2 c0 {2,D} +4 O u0 p3 c-1 {2,S} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[1.6007879331370871, 0.014704856571844503, -1.4669757091958005e-05, 6.819313569634828e-09, -1.147982283770417e-12, -12610.8227172237, -0.7662797899264149], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[7.295789997642349, -0.0025855481326240684, 4.764103709943176e-06, -2.6619174816996855e-09, 4.947906056262268e-13, -14096.822845174105, -29.782768933213145], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence = { + """ + 1 X u0 p0 c0 {2,S} + 2 N u0 p0 c+1 {1,S} {3,D} {4,S} + 3 O u0 p2 c0 {2,D} + 4 O u0 p3 c-1 {2,S} + """: { + 'model': 'polynomial', + 'enthalpy-coefficients': [(2.65,'eV/molecule'), (-14.2,'eV/molecule'), (18.1,'eV/molecule')], + 'entropy-coefficients': [(0, 'kJ/(mol*K)'), (0, 'kJ/(mol*K)'), (0, 'kJ/(mol*K)')] + } + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. +The two lowest frequencies, 31.35 and 43.35,where replaced by the 2D gas model. + +Coverage dependence based on "Detailed Microkinetics for NOx-Inhibited Hydrocarbon Oxidation through +Automated Mechanism Generation within Correlated Uncertainty on Pt(111)", under review, +Kirk Badger, Bjarne Kreitz, Patrick Lott, and C. Franklin Goldsmith. +Original 4th-order polynomials were refit to 3rd-order (maximum order compatible with current RMG version). +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 8, + label = "XCXCH2", + molecule = +""" +1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} +2 C u0 p0 c0 {1,S} {6,T} +3 H u0 p0 c0 {1,S} +4 H u0 p0 c0 {1,S} +5 X u0 p0 c0 {1,S} +6 X u0 p0 c0 {2,T} +""", + thermo = NASA( + polynomials = [ + NASAPolynomial(coeffs=[-1.7981611203722376, 0.032699651187770046, -4.2566267050901004e-05, 2.9154268374034755e-08, -8.035869472649143e-12, -981.598852018363, 5.8480974735541835], Tmin=(298.0,'K'),Tmax=(1000.0, 'K')), + NASAPolynomial(coeffs=[9.43020619567617, -0.006459541211980741, 1.1544864226387672e-05, -6.169040761124964e-09, 1.107133468924275e-12, -3665.1870318123556, -50.122403724130024], Tmin=(1000.0,'K'), Tmax=(2000.0, 'K')), + ], + Tmin = (298.0,'K'), + Tmax = (2000.0,'K'), + thermo_coverage_dependence = { + """ + 1 C u0 p0 c0 {2,S} {3,S} {4,S} {5,S} + 2 C u0 p0 c0 {1,S} {6,T} + 3 H u0 p0 c0 {1,S} + 4 H u0 p0 c0 {1,S} + 5 X u0 p0 c0 {1,S} + 6 X u0 p0 c0 {2,T} + """: { + 'model': 'polynomial', + 'enthalpy-coefficients': [(62670, 'J/mol'), (0, 'J/mol'), (0, 'J/mol')], + 'entropy-coefficients': [(0, 'J/(mol*K)'), (0, 'J/(mol*K)'), (0, 'J/(mol*K)')] + } + }, + ), +longDesc = u""" +Calculated by Kirk Badger at Brown University using statistical mechanics methods implemented in +Franklin Goldsmith's thermo_kinetics_scripts repository in the new_workflow folder: + +https://github.com/franklingoldsmith/thermo_kinetics_scripts/tree/main/new_workflow + +DFT calculations were performed with Quantum Espresso using PAW pseudopotentals and the BEEF-vdW +functional for an optimized 3x3x4 supercell with the bottom 2 layers fixed. The following settings +were applied: kpoints=5x5x1, ecutwfc=50 Ry (60 Ry single point evaluation after), +smearing='marzari-vanderbilt', degauss=0.02, mixing_mode='local-TF', conv_thr=1e-12, fmax=1e-3. + +Coverage dependence based on values in the Supporting Information of "Combined DFT, Microkinetic, and Experimental Study of Ethanol Steam Reforming on Pt" +Jonathan E. Sutton, Paraskevi Panagiotopoulou, Xenophon E. Verykios, and Dionisios G. Vlachos +The Journal of Physical Chemistry C 2013 117 (9), 4691-4706 +DOI: 10.1021/jp312593u +""", + metal = "Pt", + facet = "111", +)