diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 72a10e1a78..7b7af02fad 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -10,12 +10,16 @@ The calculation of the adsorption corrections is explained in detail in the SI. If you use these adsorption corrections database in your work, please cite the publications mentioned above. -TODO: Update adsorption corrections for N containing molecules. +-Update: Kirk Badger at Brown University added many nitrogen containing adsorbates to the Pt(111) thermolibrary and integrated +this data with the data from Kreitz to retrain every level of the adsorption correction tree. There were a few bugs that were resolved +from the prior scripts. The prior scripts were misidentifying linear species in some cases, and were using the same function to assign +thermo for the gas species as for the surface species, this meant that enthalpy was accidentally set equal to internal energy, and the +constant pressure heat capacity was set equal to the cosntant volume heat capacity. This is fixed as of 2026. """ entry( index = 1, - label = "R*", + label = "RX", group= """ 1 R ux @@ -24,111 +28,76 @@ thermo=None, shortDesc=u"""Anything adsorbed anyhow.""", longDesc=u""" - R - X -*********** -This node should be empty, ensuring that one of the nodes below is used. - - -The group could well be defined as: - - 1 R ux - 2 * Xux - -but then it is identical with the R*vdW node, and the database tests -do not like that. It should be OK, because things would check the -tree in order, and if there *was* a bond it would match either -R*bidentate or R*single_chemisorbed and thus not R*vdW. -""", - metal = "Pt", - facet = "111", -) - -#entry( -# index = 1, -# label = "R-*", -# group = -#""" -#1 * X u0 p0 c0 {2,S} -#2 R u0 p0 c0 {1,S} -#""", -# thermo=ThermoData( -# Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), -# Cpdata=([-2.46, -1.45, -0.78, -0.33, 0.18, 0.46, 0.74], 'cal/(mol*K)'), -# H298=(-58.54, 'kcal/mol'), -# S298=(-26.39, 'cal/(mol*K)'), -# ), -# shortDesc=u"""Came from H single-bonded on Pt(111)""", -# longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -# DFT binding energy: -2.479 eV. -# Linear scaling parameters: ref_adatom_H = -2.479 eV, psi = 0.00000 eV, gamma_H(X) = 1.000. -# -# R -# | -#*********** -# -#""", -# metal = "Pt", -# facet = "111", -#) - -### This doesn't have a place in the tree, so I'm commenting it out. -- RHW -# entry( -# index = 2, -# label = "(R2)*", -# group = -# """ -# 1 * X u0 p0 c0 -# 2 R u0 p0 c0 {3,S} -# 3 R u0 p0 c0 {2,S} -# """, -# thermo=ThermoData( -# Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), -# Cpdata=([0.92, 0.95, 0.97, 0.98, 0.98, 0.99, 0.99], 'cal/(mol*K)'), -# H298=(-1.45, 'kcal/mol'), -# S298=(-7.73, 'cal/(mol*K)'), -# ), -# shortDesc=u"""Came from H2 physisorbed on Pt(111)""", -# longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -# DFT binding energy: -0.054 eV. -# Linear scaling parameters: ref_adatom_H = -2.479 eV, psi = -0.05448 eV, gamma_H(X) = 0.000. -# The two lowest frequencies, 14.0 and 24.4 cm-1, where replaced by the 2D gas model. -# -# R-R -# : -# *********** -#""", -# metal = "Pt", -# facet = "111", -# ) +""", + metal = "Pt", + facet = "111", +) entry( - index = 3, - label = "(OR2)*", - group = + index = 2, + label = "RXbidentate", + group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,S} -3 R u0 px c0 {2,S} -4 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,[S,D,T]} +2 X u0 p0 c0 {4,[S,D,T]} +3 R!H u0 {1,[S,D,T]} {4,[S,D,T]} +4 R!H u0 {2,[S,D,T]} {3,[S,D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([7.39, 8.41, 8.91, 9.16, 9.4, 9.51, 9.6], 'J/(mol*K)'), - H298=(-49.08, 'kJ/mol'), - S298=(-123.53, 'J/(mol*K)'), + Cpdata=([-4.795, -0.607, 1.915, 3.432, 4.915, 5.495, 5.873], 'J/(mol*K)'), + H298=(-230.789, 'kJ/mol'), + S298=(-186.344, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged H2OX, HOOHX, CH3OHX, HCOOHX, CH3CH2OHX, CH3OCH3X, CH3OCH2OHX on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. +shortDesc=u"""Averaged from: ['XCXCCH2', 'XCXCH2', 'XCXCHCH3', 'XCXCCH3', 'XCXC', 'XCH2XCCH2', +'XCH2XCH2', 'CH3XCHXCH2', 'XCH2XCH', 'XCH2XCOH', 'XCHXCHCH3', 'XCHXCCH3', +'XCHXC', 'XCHXCO', 'XCHXCH', 'XCH2XNH', 'XCH2XN', 'XCHXN', 'NHXCXNH', 'XNHXCO', +'XNXCO', 'XNXCNH', 'XCHXNH', 'OHXCXNH', 'XCHXN', 'XNXCOH', 'XCH2XO', 'XOXCNH', +'XCHXO', 'XCH2XNH', 'XCH2XN', 'XCHXN', 'NHXCXNH', 'XNHXCO', 'XNXCO', 'XNXCNH', +'XCHXNH', 'OHXCXNH', 'XCHXN', 'XNXCOH', 'XNHXNH', 'CH3XNXNOH', 'XNHXN', +'XNXNCH3', 'XOXNH', 'XOXNO', 'XOXO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) - RO-R - : -*********** +entry( + index = 3, + label = "CXCX", + group= +""" +1 * X u0 p0 c0 {3,[S,D,T]} +2 X u0 p0 c0 {4,[S,D,T]} +3 C u0 {1,[S,D,T]} {4,[S,D,T]} +4 C u0 {2,[S,D,T]} {3,[S,D,T]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-8.884, -3.936, -0.796, 1.195, 3.346, 4.351, 5.233], 'J/(mol*K)'), + H298=(-344.237, 'kJ/mol'), + S298=(-195.899, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCXCCH2', 'XCXCH2', 'XCXCHCH3', 'XCXCCH3', 'XCXC', 'XCH2XCCH2', +'XCH2XCH2', 'CH3XCHXCH2', 'XCH2XCH', 'XCH2XCOH', 'XCHXCHCH3', 'XCHXCCH3', +'XCHXC', 'XCHXCO', 'XCHXCH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -136,32 +105,31 @@ entry( index = 4, - label = "O-*R", - group = + label = "C#XC-XR", + group= """ -1 * X u0 p0 c0 {2,S} -2 O u0 p2 c0 {1,S} {3,S} -3 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,T} {4,S} +4 C u0 p0 c0 {2,S} {3,S} {5,D} +5 R!H u0 px c0 {4,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.67, 8.28, 9.16, 9.7, 10.33, 10.68, 11.17], 'J/(mol*K)'), - H298=(-194.2, 'kJ/mol'), - S298=(-157.49, 'J/(mol*K)'), + Cpdata=([-5.908, -0.012, 3.286, 5.159, 6.913, 7.592, 8.093], 'J/(mol*K)'), + H298=(-442.76, 'kJ/mol'), + S298=(-204.353, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XOCH3, XOH, XOCH2CH3, HOC(O)XO, HC(O)XO, XOCHCH2, XOOH, XOCH2OH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - O - | -*********** +shortDesc=u"""Averaged from: ['XCXCCH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -169,34 +137,32 @@ entry( index = 5, - label = "(OROR)*", - group = + label = "C#XC-XR2", + group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {3,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,T} {4,S} +4 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} +5 R u0 px c0 {4,S} +6 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.32, 7.23, 7.68, 7.95, 8.29, 8.51, 8.71], 'J/(mol*K)'), - H298=(-63.01, 'kJ/mol'), - S298=(-110.35, 'J/(mol*K)'), + Cpdata=([-9.216, -3.734, -0.103, 2.279, 4.931, 6.215, 7.45], 'J/(mol*K)'), + H298=(-438.941, 'kJ/mol'), + S298=(-201.882, 'J/(mol*K)'), ), - shortDesc=u"""Came from HOOHX physisorbed on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - - The two lowest frequencies, 12.0 and 47.7 cm-1, where replaced by the 2D gas model. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - RO-OR - : -*********** +shortDesc=u"""Averaged from: ['XCXCH2', 'XCXCHCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -204,31 +170,31 @@ entry( index = 6, - label = "O*O*", - group = + label = "C#XC=XR", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 O u0 p2 c0 {1,S} {4,S} -4 O u0 p2 c0 {2,S} {3,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,T} {4,S} +4 C u0 p0 c0 {2,D} {3,S} {5,S} +5 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([8.69, 12.02, 13.4, 13.87, 13.89, 13.63, 13.13], 'J/(mol*K)'), - H298=(-107.21, 'kJ/mol'), - S298=(-167.43, 'J/(mol*K)'), + Cpdata=([-10.312, -7.023, -5.043, -3.772, -2.346, -1.624, -0.832], 'J/(mol*K)'), + H298=(-491.004, 'kJ/mol'), + S298=(-152.622, 'J/(mol*K)'), ), - shortDesc=u"""Came from XOXO, twice single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - O--O - | | -***** ***** +shortDesc=u"""Averaged from: ['XCXCCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -236,33 +202,30 @@ entry( index = 7, - label = "O-*OR", - group = + label = "C-XC-X", + group= """ -1 * X u0 p0 c0 {2,S} -2 O u0 p2 c0 {1,S} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 px c0 {3,S} +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,D} +4 C u0 p0 c0 {2,D} {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([10.21, 11.38, 11.38, 11.02, 10.19, 9.56, 8.77], 'J/(mol*K)'), - H298=(-134.04, 'kJ/mol'), - S298=(-120.71, 'J/(mol*K)'), + Cpdata=([-9.162, -5.09, -2.937, -1.762, -0.711, -0.328, -0.071], 'J/(mol*K)'), + H298=(-617.066, 'kJ/mol'), + S298=(-172.682, 'J/(mol*K)'), ), - shortDesc=u"""Came from XOOH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - OR - | - O - | -*********** +shortDesc=u"""Averaged from: ['XCXC']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -270,29 +233,33 @@ entry( index = 8, - label = "O=*", - group = + label = "C-XR2C-XR", + group= """ -1 * X u0 p0 c0 {2,D} -2 O u0 p2 c0 {1,D} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 C u0 p0 c0 {2,S} {3,S} {7,D} +5 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} +7 R!H u0 px c0 {4,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-2.44, 0.14, 1.49, 2.26, 3.07, 3.45, 3.84], 'J/(mol*K)'), - H298=(-382.56, 'kJ/mol'), - S298=(-140.6, 'J/(mol*K)'), + Cpdata=([-2.136, 2.224, 4.826, 6.423, 8.025, 8.636, 8.889], 'J/(mol*K)'), + H298=(-182.472, 'kJ/mol'), + S298=(-191.92, 'J/(mol*K)'), ), - shortDesc=u"""Came from XO double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - O - || -*********** +shortDesc=u"""Averaged from: ['XCH2XCCH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -300,31 +267,34 @@ entry( index = 9, - label = "O-*NR2", - group = + label = "C-XR2C-XR2", + group= """ 1 * X u0 p0 c0 {3,S} -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 O u0 p2 c0 {1,S} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S} +5 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {4,S} +8 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.24, 2.94, 3.33, 3.56, 3.78, 3.87, 3.95], 'cal/(mol*K)'), - H298=(-30.61, 'kcal/mol'), - S298=(-35.75, 'cal/(mol*K)'), + Cpdata=([-2.371, 2.407, 5.145, 6.72, 8.221, 8.788, 9.01], 'J/(mol*K)'), + H298=(-126.568, 'kJ/mol'), + S298=(-192.345, 'J/(mol*K)'), ), - shortDesc=u"""Came from XONH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.698 eV. - Linear scaling parameters: ref_adatom_O = -3.586 eV, psi = 1.09537 eV, gamma_O(X) = 0.500. - - NR2 - | - O - | -*********** +shortDesc=u"""Averaged from: ['XCH2XCH2', 'CH3XCHXCH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -332,35 +302,33 @@ entry( index = 10, - label = "O-*CR3", - group = + label = "C-XR2C=XR", + group= """ 1 * X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 O u0 p2 c0 {1,S} {2,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} +2 X u0 p0 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 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.44, 2.24, 2.93, 3.54, 4.49, 5.18, 6.35], 'J/(mol*K)'), - H298=(-182.55, 'kJ/mol'), - S298=(-149.81, 'J/(mol*K)'), + Cpdata=([-7.577, -2.139, 1.344, 3.558, 5.964, 7.098, 8.08], 'J/(mol*K)'), + H298=(-333.29, 'kJ/mol'), + S298=(-214.968, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XOCH3, XOCH2CH3, and XOCH2OH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR3 - | - O - | -*********** +shortDesc=u"""Averaged from: ['XCH2XCH', 'XCH2XCOH', 'XCHXCHCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -368,29 +336,32 @@ entry( index = 11, - label = "(NR3)*", - group = + label = "C-XRC-XR", + group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 R u0 px c0 {2,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,S} {3,D} {6,S} +5 R u0 px c0 {3,S} +6 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.0, 1.92, 2.51, 2.9, 3.35, 3.59, 3.83], 'cal/(mol*K)'), - H298=(-16.11, 'kcal/mol'), - S298=(-32.0, 'cal/(mol*K)'), + Cpdata=([-10.114, -6.494, -3.657, -1.632, 0.897, 2.463, 4.797], 'J/(mol*K)'), + H298=(-230.06, 'kJ/mol'), + S298=(-194.29, 'J/(mol*K)'), ), - shortDesc=u"""Came from NH3X physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.673 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.67337 eV, gamma_N(X) = 0.000. - - R2N-R - : -*********** +shortDesc=u"""Averaged from: ['XCHXCCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -398,27 +369,31 @@ entry( index = 12, - label = "N-*R2", - group = + label = "C-XRC=X", + group= """ -1 * X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,[S,D]} -3 R u0 px c0 {2,[S,D]} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,D} {5,S} +4 C u0 p0 c0 {2,D} {3,D} +5 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.86, 0.72, 1.69, 2.29, 2.94, 3.25, 3.59], 'cal/(mol*K)'), - H298=(-53.39, 'kcal/mol'), - S298=(-47.88, 'cal/(mol*K)'), + Cpdata=([-14.003, -9.238, -6.324, -4.491, -2.471, -1.479, -0.526], 'J/(mol*K)'), + H298=(-444.24, 'kJ/mol'), + S298=(-193.307, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -2.030 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.58258 eV, gamma_N(X) = 0.333. - - NR2 - | -*********** +shortDesc=u"""Averaged from: ['XCHXC']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -426,27 +401,32 @@ entry( index = 13, - label = "N=*R", - group = + label = "C=XRC-XR", + group= """ -1 * X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 C u0 p0 c0 {2,S} {3,S} {6,D} +5 R u0 px c0 {3,S} +6 R!H u0 px c0 {4,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.74, -0.24, 0.7, 1.29, 1.93, 2.25, 2.6], 'cal/(mol*K)'), - H298=(-88.28, 'kcal/mol'), - S298=(-40.72, 'cal/(mol*K)'), + Cpdata=([-17.837, -11.801, -7.788, -5.157, -2.221, -0.843, 0.222], 'J/(mol*K)'), + H298=(-400.07, 'kJ/mol'), + S298=(-211.081, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNH double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -3.440 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.54193 eV, gamma_N(X) = 0.667. - - NR - || -*********** +shortDesc=u"""Averaged from: ['XCHXCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -454,26 +434,32 @@ entry( index = 14, - label = "N#*", - group = + label = "C=XRC=XR", + group= """ -1 * X u0 p0 c0 {2,T} -2 N u0 p1 c0 {1,T} +1 * X u0 p0 c0 {3,D} +2 X u0 p0 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 R u0 px c0 {3,S} +6 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.93, -0.2, 0.19, 0.42, 0.66, 0.78, 0.9], 'cal/(mol*K)'), - H298=(-103.33, 'kcal/mol'), - S298=(-32.92, 'cal/(mol*K)'), + Cpdata=([-17.882, -12.533, -8.423, -5.514, -2.095, -0.445, 0.766], 'J/(mol*K)'), + H298=(-224.989, 'kJ/mol'), + S298=(-184.879, 'J/(mol*K)'), ), - shortDesc=u"""Came from XN triple-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -4.352 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 0.00000 eV, gamma_N(X) = 1.000. - - N - ||| -*********** +shortDesc=u"""Averaged from: ['XCHXCH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -481,31 +467,31 @@ entry( index = 15, - label = "(NR2OR)*", - group = + label = "CXNX", + group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 O u0 p2 c0 {2,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} +1 X u0 p0 c0 {3,[S,D,T]} +2 * X u0 p0 c0 {4,[S,D]} +3 C u0 p0 c0 {1,[S,D,T]} {4,[S,D]} +4 N u0 p1 c0 {2,[S,D]} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.36, 0.16, 0.59, 0.93, 1.37, 1.64, 1.92], 'cal/(mol*K)'), - H298=(-18.16, 'kcal/mol'), - S298=(-32.2, 'cal/(mol*K)'), + Cpdata=([-3.501, 0.376, 2.717, 4.144, 5.537, 6.052, 6.303], 'J/(mol*K)'), + H298=(-190.892, 'kJ/mol'), + S298=(-186.3, 'J/(mol*K)'), ), - shortDesc=u"""Came from H2XNOH physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.654 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.65407 eV, gamma_N(X) = 0.000. - The two lowest frequencies, 17.1 and 68.9 cm-1, where replaced by the 2D gas model. - - R2N-OR - : -*********** +shortDesc=u"""Averaged from: ['XCH2XNH', 'XCH2XN', 'XCHXN', 'NHXCXNH', 'XNHXCO', 'XNXCO', +'XNXCNH', 'XCHXNH', 'OHXCXNH', 'XCHXN', 'XNXCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -513,28 +499,33 @@ entry( index = 16, - label = "(NRO)*", - group = + label = "C-XR2N-XR", + group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 O u0 p2 c0 {2,D} -4 R u0 p0 c0 {2,S} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 N u0 p1 c0 {2,S} {3,S} {7,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {3,S} +7 R u0 p0 c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.74, 2.63, 3.12, 3.38, 3.6, 3.67, 3.76], 'cal/(mol*K)'), - H298=(-39.84, 'kcal/mol'), - S298=(-37.88, 'cal/(mol*K)'), + Cpdata=([-1.909, 4.606, 7.698, 9.056, 9.742, 9.635, 9.11], 'J/(mol*K)'), + H298=(-108.027, 'kJ/mol'), + S298=(-197.829, 'J/(mol*K)'), ), - shortDesc=u"""Came from HNOX physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.270 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -1.26632 eV, gamma_N(X) = 0.000. - - RN=O - : -*********** +shortDesc=u"""Averaged from: ['XCH2XNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -542,29 +533,32 @@ entry( index = 17, - label = "N-*ROR", - group = + label = "C-XR2N=X", + group= """ -1 * X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 p0 c0 {2,S} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 N u0 p1 c0 {2,D} {3,S} 5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.82, 2.71, 3.18, 3.44, 3.72, 3.86, 3.98], 'cal/(mol*K)'), - H298=(-44.41, 'kcal/mol'), - S298=(-45.51, 'cal/(mol*K)'), + Cpdata=([-4.645, 0.277, 3.104, 4.734, 6.251, 6.853, 7.449], 'J/(mol*K)'), + H298=(-217.964, 'kJ/mol'), + S298=(-193.314, 'J/(mol*K)'), ), - shortDesc=u"""Came from HXNOH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.370 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 0.08004 eV, gamma_N(X) = 0.333. - - R-N-OR - | -*********** +shortDesc=u"""Averaged from: ['XCH2XN']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -572,29 +566,31 @@ entry( index = 18, - label = "N-*O", - group = + label = "C-XRN-X", + group= """ -1 * X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,D} -3 O u0 p2 c0 {2,D} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 R u0 px c0 {3,S} +5 N u0 p1 c0 {2,S} {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.48, 2.2, 2.6, 2.83, 3.02, 3.07, 3.06], 'cal/(mol*K)'), - H298=(-47.5, 'kcal/mol'), - S298=(-40.63, 'cal/(mol*K)'), + Cpdata=([-8.92, -5.628, -3.376, -1.842, -0.146, 0.563, 0.869], 'J/(mol*K)'), + H298=(-99.595, 'kJ/mol'), + S298=(-171.411, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNO single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.580 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.13417 eV, gamma_N(X) = 0.333. - - O - || - N - | -*********** +shortDesc=u"""Averaged from: ['XCHXN']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -602,28 +598,32 @@ entry( index = 19, - label = "N=*O-*", - group = + label = "C-XRN-XR", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,S} -3 N u0 p1 c0 {1,D} {4,S} -4 O u0 p2 c0 {2,S} {3,S} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 N u0 p1 c0 {2,S} {3,S} {6,S} +5 R!H u0 px c0 {3,D} +6 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.99, 2.43, 2.68, 2.82, 2.96, 3.00, 3.01], 'cal/(mol*K)'), - H298=(-42.57, 'kcal/mol'), - S298=(-35.43, 'cal/(mol*K)'), + Cpdata=([-1.172, 2.134, 4.468, 6.071, 7.829, 8.56, 8.932], 'J/(mol*K)'), + H298=(-127.548, 'kJ/mol'), + S298=(-183.708, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNXO bidentate, double- and single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.390 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 1.51181 eV, gamma_N(X) = 0.667. - - N--O - || | -*********** +shortDesc=u"""Averaged from: ['NHXCXNH', 'XNHXCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -631,30 +631,31 @@ entry( index = 20, - label = "N=*OR", - group = + label = "C-XRN=X", + group= """ -1 * X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 p0 c0 {3,S} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 N u0 p1 c0 {2,D} {3,S} +5 R!H u0 px c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.16, 3.09, 3.5, 3.66, 3.71, 3.67, 3.65], 'cal/(mol*K)'), - H298=(-70.93, 'kcal/mol'), - S298=(-44.7, 'cal/(mol*K)'), + Cpdata=([-2.472, 0.885, 2.64, 3.556, 4.264, 4.422, 4.376], 'J/(mol*K)'), + H298=(-263.944, 'kJ/mol'), + S298=(-188.758, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNOH double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -3.260 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.35381 eV, gamma_N(X) = 0.667. - - OR - | - N - || -*********** +shortDesc=u"""Averaged from: ['XNXCO', 'XNXCNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -662,32 +663,32 @@ entry( index = 21, - label = "(NR2NR2)*", - group = + label = "C=XRN-XR", + group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 N u0 p1 c0 {2,S} {6,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {3,S} +1 X u0 p0 c0 {3,D} +2 * X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 N u0 p1 c0 {2,S} {3,S} {6,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.1, 0.6, 0.94, 1.19, 1.5, 1.68, 1.88], 'cal/(mol*K)'), - H298=(-26.81, 'kcal/mol'), - S298=(-31.95, 'cal/(mol*K)'), + Cpdata=([-3.55, 0.349, 2.796, 4.377, 6.094, 6.89, 7.649], 'J/(mol*K)'), + H298=(-316.863, 'kJ/mol'), + S298=(-195.23, 'J/(mol*K)'), ), - shortDesc=u"""Came from NH2NH2X physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.977 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.97746 eV, gamma_N(X) = 0.000. - The two lowest frequencies, 6.9 and 79.2 cm-1, where replaced by the 2D gas model. - - R2N-NR2 - : -*********** +shortDesc=u"""Averaged from: ['XCHXNH', 'OHXCXNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -695,980 +696,981 @@ entry( index = 22, - label = "(NRNR)*", - group = + label = "C=XRN=X", + group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 N u0 p1 c0 {2,D} {5,S} -4 R u0 p0 c0 {2,S} +1 X u0 p0 c0 {3,D} +2 * X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 N u0 p1 c0 {2,D} {3,S} 5 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.62, 3.77, 4.27, 4.45, 4.43, 4.3, 4.09], 'cal/(mol*K)'), - H298=(-24.31, 'kcal/mol'), - S298=(-42.07, 'cal/(mol*K)'), + Cpdata=([-4.321, -0.928, 1.329, 2.814, 4.344, 4.892, 4.999], 'J/(mol*K)'), + H298=(-128.754, 'kJ/mol'), + S298=(-175.675, 'J/(mol*K)'), ), - shortDesc=u"""Came from NHNHX physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.676 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.67607 eV, gamma_N(X) = 0.000. - - RN=NR - : -*********** +shortDesc=u"""Averaged from: ['XCHXN', 'XNXCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) - -#entry( -# index = 23, -# label = "(NN)*", -# group = -#""" -#1 * X u0 p0 c0 -#3 N u0 p1 c0 {3,T} -#4 N u0 p1 c0 {2,T} -#""", -# thermo=ThermoData( -# Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), -# Cpdata=([2.62, 3.77, 4.27, 4.45, 4.43, 4.3, 4.09], 'cal/(mol*K)'), -# H298=(-6.31, 'kcal/mol'), -# S298=(-15.27, 'cal/(mol*K)'), -# ), -# shortDesc=u"""Came from NN physisorbed on Pt(111)""", -# longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -# DFT binding energy: -0.109 eV. -# Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.10949 eV, gamma_N(X) = 0.000. -# The two lowest frequencies, 6.3 and 24.2 cm-1, where replaced by the 2D gas model. -# -# N#N -# : -#*********** -#""" -#) - entry( - index = 24, - label = "N-*RNR2", - group = + index = 23, + label = "CXOX", + group= """ -1 * X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,S} {4,S} -3 N u0 p1 c0 {2,S} {5,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,[S,D,T]} +2 X u0 p0 c0 {4,S} +3 C u0 {1,[S,D,T]} {4,S} +4 O u0 p2 {2,S} {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.57, 2.38, 2.87, 3.19, 3.55, 3.73, 3.91], 'cal/(mol*K)'), - H298=(-40.74, 'kcal/mol'), - S298=(-45.43, 'cal/(mol*K)'), + Cpdata=([0.188, 4.19, 6.483, 7.719, 8.646, 8.809, 8.678], 'J/(mol*K)'), + H298=(-118.315, 'kJ/mol'), + S298=(-170.773, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNHNH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.270 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 0.18029 eV, gamma_N(X) = 0.333. - - R-N-NR2 - | -*********** +shortDesc=u"""Averaged from: ['XCH2XO', 'XOXCNH', 'XCHXO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 25, - label = "N-*NR", - group = + index = 24, + label = "C-XR2O-X", + group= """ -1 * X u0 p0 c0 {2,S} -2 N u0 p1 c0 {1,S} {3,D} -3 N u0 p1 c0 {2,D} {4,S} -4 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 O u0 p2 c0 {2,S} {3,S} +5 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.42, 2.37, 2.9, 3.21, 3.47, 3.57, 3.69], 'cal/(mol*K)'), - H298=(-37.65, 'kcal/mol'), - S298=(-43.45, 'cal/(mol*K)'), + Cpdata=([0.468, 5.286, 7.754, 8.883, 9.435, 9.309, 8.847], 'J/(mol*K)'), + H298=(-63.513, 'kJ/mol'), + S298=(-170.273, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNNH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.060 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 0.39360 eV, gamma_N(X) = 0.333. - - NR - || - N - | -*********** +shortDesc=u"""Averaged from: ['XCH2XO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 26, - label = "N=*NR2", - group = + index = 25, + label = "C-XRO-X", + group= """ -1 * X u0 p0 c0 {2,D} -2 N u0 p1 c0 {1,D} {3,S} -3 N u0 p1 c0 {2,S} {4,S} {5,S} -4 R u0 p0 c0 {3,S} -5 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 O u0 p2 c0 {2,S} {3,S} +5 R!H u0 px c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.71, 3.72, 4.13, 4.24, 4.1, 3.91, 3.71], 'cal/(mol*K)'), - H298=(-59.44, 'kcal/mol'), - S298=(-43.17, 'cal/(mol*K)'), + Cpdata=([2.502, 5.33, 7.166, 8.314, 9.366, 9.623, 9.407], 'J/(mol*K)'), + H298=(-50.787, 'kJ/mol'), + S298=(-174.316, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNNH2 double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -2.040 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = 0.86160 eV, gamma_N(X) = 0.667. - - NR2 - | - N - || -*********** +shortDesc=u"""Averaged from: ['XOXCNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 27, - label = "N-*RN-*R", - group = + index = 26, + label = "C=XRO-X", + group= """ -1 * X u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,D} 2 X u0 p0 c0 {4,S} -3 N u0 p1 c0 {1,S} {4,S} {5,S} -4 N u0 p1 c0 {2,S} {3,S} {6,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 O u0 p2 c0 {2,S} {3,S} +5 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.06, 3.29, 3.9, 4.17, 4.27, 4.22, 4.08], 'cal/(mol*K)'), - H298=(-27.1, 'kcal/mol'), - S298=(-42.53, 'cal/(mol*K)'), + Cpdata=([-2.405, 1.953, 4.528, 5.96, 7.136, 7.494, 7.781], 'J/(mol*K)'), + H298=(-240.645, 'kJ/mol'), + S298=(-167.729, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNHXNH bidentate, twice single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.982 eV. - Linear scaling parameters: ref_adatom_N1 = -4.352 eV, ref_adatom_N2 = -4.352 eV, psi = 1.91976 eV, gamma_N1(X) = 0.333, gamma_N2(X) = 0.333. - - RN--NR - | | -*********** +shortDesc=u"""Averaged from: ['XCHXO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 28, - label = "N-*RCR3", - group = + index = 27, + label = "NXCX", + group= """ -1 * X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {1,S} {2,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,[S,D,T]} +2 X u0 p0 c0 {4,[S,D]} +3 C u0 p0 c0 {1,[S,D,T]} {4,[S,D]} +4 N u0 p1 c0 {2,[S,D]} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.96, 1.81, 2.36, 2.72, 3.14, 3.36, 3.63], 'cal/(mol*K)'), - H298=(-51.48, 'kcal/mol'), - S298=(-46.63, 'cal/(mol*K)'), + Cpdata=([-3.501, 0.376, 2.717, 4.144, 5.537, 6.052, 6.303], 'J/(mol*K)'), + H298=(-190.892, 'kJ/mol'), + S298=(-186.3, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNHCH3 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.850 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.40192 eV, gamma_N(X) = 0.333. - - R-N-CR3 - | -*********** +shortDesc=u"""Averaged from: ['XCH2XNH', 'XCH2XN', 'XCHXN', 'NHXCXNH', 'XNHXCO', 'XNXCO', +'XNXCNH', 'XCHXNH', 'OHXCXNH', 'XCHXN', 'XNXCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 29, - label = "N-*CR2", - group = + index = 28, + label = "inv(C-XR2N-XR)", + group= """ 1 * X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 N u0 p1 c0 {1,S} {2,D} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 N u0 p1 c0 {2,S} {3,S} {7,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {3,S} +7 R u0 p0 c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.62, 2.41, 2.85, 3.12, 3.4, 3.53, 3.7], 'cal/(mol*K)'), - H298=(-50.13, 'kcal/mol'), - S298=(-44.16, 'cal/(mol*K)'), + Cpdata=([-1.909, 4.606, 7.698, 9.056, 9.742, 9.635, 9.11], 'J/(mol*K)'), + H298=(-108.027, 'kJ/mol'), + S298=(-197.829, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNCH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.660 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.21342 eV, gamma_N(X) = 0.333. - - CR2 - || - N - | -*********** +shortDesc=u"""Averaged from: ['XCH2XNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 30, - label = "N=*CR3", - group = -""" -1 * X u0 p0 c0 {3,D} -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {1,D} {2,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.92, 1.54, 1.98, 2.29, 2.68, 2.93, 3.32], 'cal/(mol*K)'), - H298=(-84.35, 'kcal/mol'), - S298=(-47.17, 'cal/(mol*K)'), - ), - shortDesc=u"""Came from XNCH3 double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -3.050 eV. - Linear scaling parameters: ref_adatom_N = -4.352 eV, psi = -0.14794 eV, gamma_N(X) = 0.667. - - CR3 - | - N - || -*********** -""", - metal = "Pt", - facet = "111", -) - -### Leads to AtomTypeError: Unable to determine atom type for atom O-, which has 3 single bonds, 0 double bonds to C, 0 double bonds to O, 0 double bonds to S, 0 triple bonds, 0 benzene bonds, 0 lone pairs, and 2 charge. -### And is not in the tree anyway, so commenting out. RHW -# entry( -# index = 31, -# label = "N-*O2", -# group = -# """ -# 1 * X u0 p0 c0 {2,S} -# 2 N u0 p0 c+1 {1,S} {3,S} {4,D} -# 3 O u0 p2 c-1 {2,S} -# 4 O u0 p2 c0 {2,D} -# """, -# thermo=ThermoData( -# Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), -# Cpdata=([1.92, 2.12, 2.17, 2.17, 2.13, 2.09, 2.04], 'cal/(mol*K)'), -# H298=(34.56, 'kcal/mol'), -# S298=(-33.93, 'cal/(mol*K)'), -# ), -# shortDesc=u"""Came from ON-O single-bonded on Pt(111)""", -# longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -# Linear scaling parameters: ref_adatom_N = 0.525 eV, psi = -0.86302 eV, gamma_N(X) = 0.333. -# The two lowest frequencies, -33.2 and 55.1 cm-1, where replaced by the 2D gas model. -# -# O-N=O -# | -# *********** -# """, -# metal = "Pt", -# facet = "111", -# ) - -entry( - index = 32, - label = "Cq*", - group = + index = 29, + label = "inv(C-XR2N=X)", + group= """ -1 * X u0 p0 c0 {2,Q} -2 C u0 p0 c0 {1,Q} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} +4 N u0 p1 c0 {2,D} {3,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-7.34, -3.34, -1.0, 0.42, 1.97, 2.73, 3.51], 'J/(mol*K)'), - H298=(-657.91, 'kJ/mol'), - S298=(-133.84, 'J/(mol*K)'), + Cpdata=([-4.645, 0.277, 3.104, 4.734, 6.251, 6.853, 7.449], 'J/(mol*K)'), + H298=(-217.964, 'kJ/mol'), + S298=(-193.314, 'J/(mol*K)'), ), - shortDesc=u"""Came from XC quadruple-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - C - |||| -*********** +shortDesc=u"""Averaged from: ['XCH2XN']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 33, - label = "C-*C-*", - group = + index = 30, + label = "inv(C-XRN-X)", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,D} -3 C u0 p0 c0 {1,D} {4,D} -4 C u0 p0 c0 {2,D} {3,D} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 R u0 px c0 {3,S} +5 N u0 p1 c0 {2,S} {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.31, 7.38, 9.53, 10.71, 11.76, 12.14, 12.4], 'J/(mol*K)'), - H298=(-613.35, 'kJ/mol'), - S298=(-163.77, 'J/(mol*K)'), + Cpdata=([-8.92, -5.628, -3.376, -1.842, -0.146, 0.563, 0.869], 'J/(mol*K)'), + H298=(-99.595, 'kJ/mol'), + S298=(-171.411, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCXC double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - C==C - || || -*********** +shortDesc=u"""Averaged from: ['XCHXN']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 34, - label = "C=*(=R)", - group = + index = 31, + label = "inv(C-XRN-XR)", + group= """ -1 * X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 R!H u0 px c0 {2,D} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 N u0 p1 c0 {2,S} {3,S} {6,S} +5 R!H u0 px c0 {3,D} +6 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.94, 6.26, 8.08, 9.18, 10.4, 11.04, 11.77], 'J/(mol*K)'), - H298=(-429.79, 'kJ/mol'), - S298=(-168.79, 'J/(mol*K)'), + Cpdata=([-1.172, 2.134, 4.468, 6.071, 7.829, 8.56, 8.932], 'J/(mol*K)'), + H298=(-127.548, 'kJ/mol'), + S298=(-183.708, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCCH2, XCCCH2, XCCO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - || - C - || -*********** - -Because the C atom bonded to the surface only has one ligand -not two, it is not a child of the C=*R2 node +shortDesc=u"""Averaged from: ['NHXCXNH', 'XNHXCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 35, - label = "C#*CR3", - group = + index = 32, + label = "inv(C-XRN=X)", + group= """ -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 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,D} +3 C u0 p0 c0 {1,S} {4,S} {5,D} +4 N u0 p1 c0 {2,D} {3,S} +5 R!H u0 px c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.91, 1.58, 4.18, 6.07, 8.47, 9.86, 11.63], 'J/(mol*K)'), - H298=(-594.9, 'kJ/mol'), - S298=(-174.23, 'J/(mol*K)'), + Cpdata=([-2.472, 0.885, 2.64, 3.556, 4.264, 4.422, 4.376], 'J/(mol*K)'), + H298=(-263.944, 'kJ/mol'), + S298=(-188.758, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCCH3, XCCH2CH3, XCCH2OH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR3 - | - C - ||| -*********** +shortDesc=u"""Averaged from: ['XNXCO', 'XNXCNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 36, - label = "C#*R", - group = + index = 33, + label = "inv(C=XRN-XR)", + group= """ -1 * X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {4,S} +3 C u0 p0 c0 {1,D} {4,S} {5,S} +4 N u0 p1 c0 {2,S} {3,S} {6,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.12, 2.73, 5.33, 7.1, 9.21, 10.37, 11.81], 'J/(mol*K)'), - H298=(-571.12, 'kJ/mol'), - S298=(-176.66, 'J/(mol*K)'), + Cpdata=([-3.55, 0.349, 2.796, 4.377, 6.094, 6.89, 7.649], 'J/(mol*K)'), + H298=(-316.863, 'kJ/mol'), + S298=(-195.23, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH, XCCH3, XCOH, XCCHCH2, XCCH2CH3, XCCHO, XCCH2OH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - C - ||| -*********** +shortDesc=u"""Averaged from: ['XCHXNH', 'OHXCXNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 37, - label = "C=*RC=*R", - group = + index = 34, + label = "inv(C=XRN=X)", + group= """ 1 * X u0 p0 c0 {3,D} 2 X u0 p0 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 R u0 px c0 {3,S} -6 R u0 px c0 {4,S} +4 N u0 p1 c0 {2,D} {3,S} +5 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-5.41, -0.06, 4.05, 6.96, 10.38, 12.03, 13.24], 'J/(mol*K)'), - H298=(-221.27, 'kJ/mol'), - S298=(-175.96, 'J/(mol*K)'), + Cpdata=([-4.321, -0.928, 1.329, 2.814, 4.344, 4.892, 4.999], 'J/(mol*K)'), + H298=(-128.754, 'kJ/mol'), + S298=(-175.675, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXCH double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R-C--C-R - || || -*********** +shortDesc=u"""Averaged from: ['XCHXN', 'XNXCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 38, - label = "C=*R2", - group = + index = 35, + label = "NXNX", + group= """ -1 * X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 R u0 px c0 {2,S} -4 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,[S,D]} +2 X u0 p0 c0 {4,[S,D]} +3 N u0 {1,[S,D]} {4,[S,D]} +4 N u0 {2,[S,D]} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.24, 3.87, 6.15, 7.64, 9.38, 10.32, 11.42], 'J/(mol*K)'), - H298=(-370.06, 'kJ/mol'), - S298=(-174.19, 'J/(mol*K)'), + Cpdata=([-1.208, 2.257, 4.13, 5.109, 5.838, 5.997, 6.042], 'J/(mol*K)'), + H298=(-159.633, 'kJ/mol'), + S298=(-177.885, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH2, CH3XCCH3, CH3XCOH, XCHCH2CH3, XCHCH3, XCHCHCH2, XCHCHO, XCHOH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R-C-R - || -*********** +shortDesc=u"""Averaged from: ['XNHXNH', 'CH3XNXNOH', 'XNHXN', 'XNXNCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 39, - label = "C-*R2C-*R2", - group = + index = 36, + label = "N-XRN-XR", + group= """ 1 * X u0 p0 c0 {3,S} 2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 C u0 p0 c0 {2,S} {3,S} {7,S} {8,S} -5 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {4,S} -8 R u0 px c0 {4,S} +3 N u0 p1 c0 {1,S} {4,S} {5,S} +4 N u0 p1 c0 {2,S} {3,S} {6,S} +5 R u0 p0 c0 {3,S} +6 R u0 p0 c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([5.94, 10.72, 13.46, 15.04, 16.54, 17.1, 17.33], 'J/(mol*K)'), - H298=(-124.09, 'kJ/mol'), - S298=(-192.34, 'J/(mol*K)'), + Cpdata=([0.311, 3.352, 4.726, 5.245, 5.299, 5.042, 4.566], 'J/(mol*K)'), + H298=(-124.415, 'kJ/mol'), + S298=(-159.55, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH2XCH2 and CH3XCHXCH2 on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R2C--CR2 - | | -*********** +shortDesc=u"""Averaged from: ['XNHXNH', 'CH3XNXNOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 40, - label = "C-*R3", - group = + index = 37, + label = "N-XRN=X", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 R u0 px c0 {2,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,D} +3 N u0 p1 c0 {1,S} {4,S} {5,S} +4 N u0 p1 c0 {2,D} {3,S} +5 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.16, 2.29, 4.74, 6.49, 8.69, 9.93, 11.24], 'J/(mol*K)'), - H298=(-212.02, 'kJ/mol'), - S298=(-176.19, 'J/(mol*K)'), + Cpdata=([-2.727, 1.161, 3.532, 4.973, 6.377, 6.953, 7.518], 'J/(mol*K)'), + H298=(-194.851, 'kJ/mol'), + S298=(-196.22, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH2CH2CH3, XCH2CH2OH, XCH2CH3, XCH2CHCH2, XCH2CHO, XCH3, CH3XCHCH3, CH3XCHOH, XCH2OH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR3 - | -*********** +shortDesc=u"""Averaged from: ['XNHXN', 'XNXNCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 41, - label = "(CR3CR3)*", - group = + index = 38, + label = "NXOX", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 C u0 p0 c0 {2,S} {7,S} {8,S} {9,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} -7 R u0 px c0 {3,S} -8 R u0 px c0 {3,S} -9 R u0 px c0 {3,S} +1 * X u0 p0 c0 {3,[S,D]} +2 X u0 p0 c0 {4,S} +3 N u0 px cx {1,[S,D]} {4,[S,D]} +4 O u0 p2 c0 {2,S} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([9.04, 9.93, 10.39, 10.67, 10.97, 11.11, 11.2], 'J/(mol*K)'), - H298=(-29.6, 'kJ/mol'), - S298=(-137.34, 'J/(mol*K)'), + Cpdata=([-3.488, 0.667, 2.757, 3.716, 4.224, 4.19, 4.019], 'J/(mol*K)'), + H298=(-187.602, 'kJ/mol'), + S298=(-164.124, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH3CH3X, CH3CH2CH3X, CH3CH2OHX on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R3C-CR3 - : -*********** +shortDesc=u"""Averaged from: ['XOXNH', 'XOXNO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 42, - label = "(CR4)*", - group = + index = 39, + label = "N-XRO-X", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 R u0 px c0 {2,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 N u0 p1 c0 {1,S} {4,S} {5,S} +4 O u0 p2 c0 {2,S} {3,S} +5 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([8.55, 9.48, 9.93, 10.16, 10.36, 10.44, 10.48], 'J/(mol*K)'), - H298=(-41.27, 'kJ/mol'), - S298=(-125.91, 'J/(mol*K)'), + Cpdata=([-2.407, 3.152, 6.018, 7.336, 8.0, 7.929, 7.745], 'J/(mol*K)'), + H298=(-158.346, 'kJ/mol'), + S298=(-186.753, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH4X, CH3CH3X, CH3CH2CH3X, CH3CH2OHX, CH3OHX, CH3OCH3X, CH3OCH2OHX on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R3C-R - : -*********** +shortDesc=u"""Averaged from: ['XOXNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 43, - label = "C=*N-*", - group = + index = 40, + label = "N[+]=XR[-]O-X", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,D} {4,D} -4 N u0 p1 c0 {2,S} {3,D} +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {4,S} +3 N u0 p0 c+1 {1,D} {4,S} {5,S} +4 O u0 p2 c0 {2,S} {3,S} +5 R!H u0 p[1,2,3] c-1 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.44, 2.71, 2.86, 2.96, 3.05, 3.07, 3.05], 'cal/(mol*K)'), - H298=(-88.23, 'kcal/mol'), - S298=(-34.98, 'cal/(mol*K)'), + Cpdata=([-4.568, -1.818, -0.504, 0.096, 0.447, 0.451, 0.292], 'J/(mol*K)'), + H298=(-216.857, 'kJ/mol'), + S298=(-141.494, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCXN bidentate, double- and single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -3.340 eV. - Linear scaling parameters: ref_adatom_C1 = -6.750 eV, ref_adatom_N2 = 0.525 eV, psi = -0.13303 eV, gamma_C1(X) = 0.500, gamma_N2(X) = 0.333. - - C==N - || | -*********** +shortDesc=u"""Averaged from: ['XOXNO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 44, - label = "C=*(=NR)", - group = + index = 41, + label = "OXOX", + group= """ -1 * X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 N u0 p1 c0 {2,D} {4,S} -4 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 O u0 p2 c0 {1,S} {4,S} +4 O u0 p2 c0 {2,S} {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.15, 2.88, 3.33, 3.62, 3.93, 4.05, 4.11], 'cal/(mol*K)'), - H298=(-48.26, 'kcal/mol'), - S298=(-30.68, 'cal/(mol*K)'), + Cpdata=([-3.845, -0.672, 0.701, 1.206, 1.284, 1.068, 0.608], 'J/(mol*K)'), + H298=(-115.224, 'kJ/mol'), + S298=(-168.993, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCNH double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.740 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = 1.63638 eV, gamma_C(X) = 0.500. - - NR - || - C - || -*********** +shortDesc=u"""Averaged from: ['XOXO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 45, - label = "C#*NR2", - group = + index = 42, + label = "RXbridgedBidentate", + group= """ -1 * X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 N u0 p1 c0 {2,S} {4,S} {5,S} -4 R u0 p0 c0 {3,S} -5 R u0 p0 c0 {3,S} +1 * X u0 {3,[S,D,T]} +2 X u0 {4,[S,D,T]} +3 R!H ux {1,[S,D,T]} {5,[S,D,T]} +4 R!H ux {2,[S,D,T]} {5,[S,D,T]} +5 R!H ux {3,[S,D,T]} {4,[S,D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.76, 3.37, 3.63, 3.74, 3.79, 3.77, 3.75], 'cal/(mol*K)'), - H298=(-106.38, 'kcal/mol'), - S298=(-49.82, 'cal/(mol*K)'), + Cpdata=([-7.399, -2.681, 0.326, 2.287, 4.517, 5.632, 6.689], 'J/(mol*K)'), + H298=(-448.964, 'kJ/mol'), + S298=(-205.343, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCNH2 triple-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -4.060 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = 1.00119 eV, gamma_C(X) = 0.750. - - NR2 - | - C - ||| -*********** +shortDesc=u"""Averaged from: ['XCCH2XC', 'XCCH2XCH2', 'XCHCH2XC', 'XCHCHXC', 'XCCHXCH2', +'XCH2CH2XCH2', 'XCHCHXCH2', 'XCHCXCH', 'XCHCXC', 'XCHCH2XCH2', 'XCHCH2XCH', +'XCHCHXCH', 'XCHCHXO', 'XOC(O)XO', 'H2C(XO)XO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) - -## Not present in the tree -# entry( -# index = 46, -# label = "C=*O", -# group = -# """ -# 1 * X u0 p0 c0 {2,D} -# 2 C u0 p0 c0 {1,D} {3,D} -# 3 O u0 p2 c0 {2,D} -# """, -# thermo=ThermoData( -# Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), -# Cpdata=([1.81, 2.37, 2.68, 2.88, 3.05, 3.1, 3.08], 'cal/(mol*K)'), -# H298=(-41.06, 'kcal/mol'), -# S298=(-38.09, 'cal/(mol*K)'), -# ), -# shortDesc=u"""Came from CO-f double-bonded on Pt(111)""", -# longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. -# DFT binding energy: -1.480 eV. -# Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = 1.89529 eV, gamma_C(X) = 0.500. -# -# O -# || -# C -# || -# *********** -# """, -# metal = "Pt", -# facet = "111", -# ) - entry( - index = 47, - label = "C#*OR", - group = + index = 43, + label = "CXRCX", + group= """ -1 * X u0 p0 c0 {2,T} -2 C u0 p0 c0 {1,T} {3,S} -3 O u0 p2 c0 {2,S} {4,S} -4 R u0 px c0 {3,S} +1 * X u0 {3,[S,D,T]} +2 X u0 {4,[S,D,T]} +3 C u0 {1,[S,D,T]} {5,[S,D,T]} +4 C u0 {2,[S,D,T]} {5,[S,D,T]} +5 R!H u0 {3,[S,D,T]} {4,[S,D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([5.83, 9.83, 11.9, 12.95, 13.69, 13.91, 14.43], 'J/(mol*K)'), - H298=(-463.49, 'kJ/mol'), - S298=(-187.54, 'J/(mol*K)'), + Cpdata=([-7.956, -2.886, 0.364, 2.487, 4.895, 6.087, 7.184], 'J/(mol*K)'), + H298=(-464.276, 'kJ/mol'), + S298=(-209.129, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCOH triple-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - OR - | - C - ||| -*********** +shortDesc=u"""Averaged from: ['XCCH2XC', 'XCCH2XCH2', 'XCHCH2XC', 'XCHCHXC', 'XCCHXCH2', +'XCH2CH2XCH2', 'XCHCHXCH2', 'XCHCXCH', 'XCHCXC', 'XCHCH2XCH2', 'XCHCH2XCH', +'XCHCHXCH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 48, - label = "C-*R2C=*R", - group = + index = 44, + label = "C#X-R-C#X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 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 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {4,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {5,T} +3 C u0 p0 c0 {1,T} {4,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,T} {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.74, 6.17, 9.66, 11.87, 14.28, 15.41, 16.39], 'J/(mol*K)'), - H298=(-330.81, 'kJ/mol'), - S298=(-214.97, 'J/(mol*K)'), + Cpdata=([-13.199, -3.559, 1.86, 4.867, 7.501, 8.36, 8.712], 'J/(mol*K)'), + H298=(-673.643, 'kJ/mol'), + S298=(-243.646, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCHXCH2, XCH2XCOH, XCHXCHCH3 on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R2C--CR - | || -*********** +shortDesc=u"""Averaged from: ['XCCH2XC']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 49, - label = "C-*R2CR3", - group = + index = 45, + label = "C#X-R-C-XR2", + group= """ -1 * X u0 p0 c0 {2,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 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {3,S} -8 R u0 px c0 {3,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,T} {4,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} +6 R u0 px c0 {5,S} +7 R u0 px c0 {5,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.39, 3.93, 6.35, 8.02, 10.07, 11.2, 12.43], 'J/(mol*K)'), - H298=(-214.46, 'kJ/mol'), - S298=(-192.28, 'J/(mol*K)'), + Cpdata=([-8.845, -4.501, -1.425, 0.824, 3.748, 5.415, 7.189], 'J/(mol*K)'), + H298=(-479.679, 'kJ/mol'), + S298=(-200.61, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH2CH2CH3, XCH2CH2OH, XCH2CH3, CH3XCHCH3, CH3XCHOH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - R-C-CR3 - | -*********** +shortDesc=u"""Averaged from: ['XCCH2XCH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 50, - label = "(CR2NR)*", - group = + index = 46, + label = "C#X-R-C=XR", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 N u0 p1 c0 {2,D} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {5,D} +3 C u0 p0 c0 {1,T} {4,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,D} {4,S} {6,S} +6 R u0 p0 c0 {5,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.5, 1.37, 1.81, 2.02, 2.14, 2.13, 2.08], 'cal/(mol*K)'), - H298=(-12.55, 'kcal/mol'), - S298=(-33.14, 'cal/(mol*K)'), + Cpdata=([-8.318, -2.551, 1.217, 3.663, 6.362, 7.614, 8.562], 'J/(mol*K)'), + H298=(-459.783, 'kJ/mol'), + S298=(-222.487, 'J/(mol*K)'), ), - shortDesc=u"""Came from H2CNHX physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.228 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = -0.22807 eV, gamma_C(X) = 0.000. - The two lowest frequencies, 46.0 and 79.7 cm-1, where replaced by the 2D gas model. - - R2C=NR - : -*********** +shortDesc=u"""Averaged from: ['XCHCH2XC']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 51, - label = "C-*R2NR2", - group = + index = 47, + label = "C#X-R=C-XR", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 N u0 p1 c0 {2,S} {6,S} {7,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {3,T} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,T} {4,S} +4 R!H u0 px c0 {3,S} {5,D} +5 C u0 p0 c0 {2,S} {4,D} {6,S} +6 R u0 px c0 {5,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.1, 1.76, 2.28, 2.67, 3.19, 3.48, 3.79], 'cal/(mol*K)'), - H298=(-53.29, 'kcal/mol'), - S298=(-39.03, 'cal/(mol*K)'), + Cpdata=([-1.515, 3.089, 5.355, 6.567, 7.69, 8.134, 8.428], 'J/(mol*K)'), + H298=(-404.809, 'kJ/mol'), + S298=(-202.293, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2NH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.980 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = -0.29283 eV, gamma_C(X) = 0.250. - - R - | - R-C-NR2 - | -*********** +shortDesc=u"""Averaged from: ['XCHCHXC']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 48, + label = "C=X=R-C-XR2", + group= +""" +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,D} {4,D} +4 R!H u0 px c0 {3,D} {5,S} +5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} +6 R u0 px c0 {5,S} +7 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-11.329, -5.473, -1.47, 1.186, 4.182, 5.673, 7.181], 'J/(mol*K)'), + H298=(-545.726, 'kJ/mol'), + S298=(-217.923, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCCHXCH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 49, + label = "R2C-X-R-C-XR2", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,S} {8,S} {9,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} +6 R u0 px c0 {5,S} +7 R u0 px c0 {5,S} +8 R u0 px c0 {3,S} +9 R u0 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-9.338, -4.702, -1.218, 1.353, 4.674, 6.506, 8.194], 'J/(mol*K)'), + H298=(-391.619, 'kJ/mol'), + S298=(-209.34, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCH2CH2XCH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 50, + label = "RC-X=R-C-XR2", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,D} {6,S} +4 R!H u0 px c0 {3,D} {5,S} +5 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {5,S} +8 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-8.191, -2.267, 1.229, 3.323, 5.462, 6.44, 7.415], 'J/(mol*K)'), + H298=(-429.229, 'kJ/mol'), + S298=(-227.783, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCHXCH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 51, + label = "RC-X=R=C-XR", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,D} {6,S} +4 R!H u0 p0 c0 {3,D} {5,D} +5 C u0 p0 c0 {2,S} {4,D} {7,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-5.301, -0.66, 2.211, 4.009, 5.941, 6.852, 7.716], 'J/(mol*K)'), + H298=(-373.265, 'kJ/mol'), + S298=(-196.347, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCXCH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", @@ -1676,2138 +1678,2703 @@ entry( index = 52, - label = "(CR2O)*", - group = + label = "RC-X=R=C=X", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,D} +3 C u0 p0 c0 {1,S} {4,D} {6,S} +4 R!H u0 p0 c0 {3,D} {5,D} +5 C u0 p0 c0 {2,D} {4,D} +6 R u0 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-11.663, -8.592, -6.236, -4.529, -2.431, -1.331, -0.302], 'J/(mol*K)'), + H298=(-436.651, 'kJ/mol'), + S298=(-188.069, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCXC']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 53, + label = "RC=X-R-C-XR2", + group= +""" +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,D} {4,S} {6,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {5,S} +8 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-0.988, 1.684, 3.396, 4.662, 6.389, 7.386, 8.308], 'J/(mol*K)'), + H298=(-529.006, 'kJ/mol'), + S298=(-196.129, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCH2XCH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 54, + label = "RC=X-R-C=XR", + group= +""" +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {5,D} +3 C u0 p0 c0 {1,D} {4,S} {6,S} +4 R!H u0 px c0 {3,S} {5,S} +5 C u0 p0 c0 {2,D} {4,S} {7,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-2.417, 2.316, 5.02, 6.669, 8.422, 9.172, 9.482], 'J/(mol*K)'), + H298=(-232.503, 'kJ/mol'), + S298=(-203.938, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCH2XCH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 55, + label = "RC=X-R=C-XR", + group= +""" +1 * X u0 p0 c0 {3,D} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,D} {4,S} {6,S} +4 R!H u0 px c0 {3,S} {5,D} +5 C u0 p0 c0 {2,S} {4,D} {7,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {5,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-14.372, -9.417, -5.572, -2.749, 0.804, 2.822, 5.317], 'J/(mol*K)'), + H298=(-615.396, 'kJ/mol'), + S298=(-200.988, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCHXCH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 56, + label = "CXROX", + group= +""" +1 * X u0 {3,[S,D,T]} +2 X u0 {4,S} +3 C u0 {1,[S,D,T]} {5,[S,D,T]} +4 O u0 p2 {2,S} {5,S} +5 R!H u0 px {3,[S,D,T]} {4,S} + +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-5.542, -1.627, 1.088, 2.965, 5.232, 6.433, 7.636], 'J/(mol*K)'), + H298=(-448.966, 'kJ/mol'), + S298=(-211.148, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCHXO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 57, + label = "RC-X=R-O-X", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 C u0 p0 c0 {1,S} {4,D} {6,S} +4 R!H u0 px c0 {3,D} {5,S} +5 O u0 p2 c0 {2,S} {4,S} +6 R u0 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-5.542, -1.627, 1.088, 2.965, 5.232, 6.433, 7.636], 'J/(mol*K)'), + H298=(-448.966, 'kJ/mol'), + S298=(-211.148, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHCHXO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 58, + label = "OXROX", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {4,S} +3 O u0 p2 c0 {1,S} {5,S} +4 O u0 p2 c0 {2,S} {5,S} +5 R!H u0 px c0 {3,S} {4,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-4.984, -1.979, -0.285, 0.747, 1.892, 2.502, 3.249], 'J/(mol*K)'), + H298=(-357.096, 'kJ/mol'), + S298=(-179.723, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XOC(O)XO', 'H2C(XO)XO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 59, + label = "O-X-C-O-X", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {5,S} +3 O u0 p2 c0 {1,S} {4,S} +4 C u0 p0 c0 {3,S} {5,S} +5 O u0 p2 c0 {2,S} {4,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-4.984, -1.979, -0.285, 0.747, 1.892, 2.502, 3.249], 'J/(mol*K)'), + H298=(-357.096, 'kJ/mol'), + S298=(-179.723, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XOC(O)XO', 'H2C(XO)XO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 60, + label = "RXsingleChemisorbed", + group= +""" +1 * X u0 {2,[S,D,T,Q]} +2 R ux {1,[S,D,T,Q]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-6.58, -3.581, -1.74, -0.565, 0.753, 1.432, 2.201], 'J/(mol*K)'), + H298=(-304.926, 'kJ/mol'), + S298=(-167.92, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCN', 'XCH', 'XCCHCH2', 'XCCHO', 'XCCH3', 'XCCH2CH3', +'XCCH2OH', 'XCNO', 'XCNH2', 'XCOH', 'CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', +'XCHCHCH3', 'OXCNH2', 'NH2XCNH', 'XCHNH', 'OHXCNH', 'NH2XCNH', 'XCHO', 'XCOOH', +'CH3XCO', 'XCCHO', 'CH3CH2XCO', 'XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', +'CH3XCHCH3', 'CH3XCHOH', 'XCH2NH2', 'XCH2OH', 'CH3XCHOH', 'XCCO', 'XCCCH2', +'XCCH2', 'XCNH', 'XCH2', 'XCHCHCH2', 'XCHCHO', 'CH3XCCH3', 'CH3XCOH', +'XCHCH2CH3', 'XCHCH3', 'XCHNH2', 'OHXCNH2', 'NH2XCNH2', 'XCHOH', 'CH3XCOH', +'XNO', 'XNCNH', 'XNCO', 'XNCH2', 'XNNH', 'XNNCH3', 'XNH2', 'XNHCHO', 'XNHCH3', +'XNHNO', 'XNHNH2', 'XNHOH', 'XNO2', 'OXNNH', 'HXNO', 'CH3NXNOH', 'CH3XNNOH', +'XNH', 'XNCN', 'XNCH3', 'XNNH2', 'XNOH', 'XOH', 'XOCHCH2', 'HC(O)XO', +'XOC(OH)O', 'XOCH3', 'XOCH2CH3', 'XOCH2OH', 'XONH2', 'XOOH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 61, + label = "CX", + group= +""" +1 * X u0 {2,[S,D,T,Q]} +2 C ux {1,[S,D,T,Q]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-8.123, -4.992, -2.977, -1.644, -0.099, 0.71, 1.593], 'J/(mol*K)'), + H298=(-354.324, 'kJ/mol'), + S298=(-169.986, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCN', 'XCH', 'XCCHCH2', 'XCCHO', 'XCCH3', 'XCCH2CH3', +'XCCH2OH', 'XCNO', 'XCNH2', 'XCOH', 'CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', +'XCHCHCH3', 'OXCNH2', 'NH2XCNH', 'XCHNH', 'OHXCNH', 'NH2XCNH', 'XCHO', 'XCOOH', +'CH3XCO', 'XCCHO', 'CH3CH2XCO', 'XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', +'CH3XCHCH3', 'CH3XCHOH', 'XCH2NH2', 'XCH2OH', 'CH3XCHOH', 'XCCO', 'XCCCH2', +'XCCH2', 'XCNH', 'XCH2', 'XCHCHCH2', 'XCHCHO', 'CH3XCCH3', 'CH3XCOH', +'XCHCH2CH3', 'XCHCH3', 'XCHNH2', 'OHXCNH2', 'NH2XCNH2', 'XCHOH', 'CH3XCOH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 62, + label = "C#XR", + group= +""" +1 * X u0 p0 c0 {2,T} +2 C u0 p0 c0 {1,T} {3,S} +3 R u0 px c0 {2,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-9.675, -6.277, -4.07, -2.601, -0.892, 0.029, 1.183], 'J/(mol*K)'), + H298=(-541.868, 'kJ/mol'), + S298=(-177.049, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCH', 'XCCHCH2', 'XCCHO', 'XCCH3', 'XCCH2CH3', 'XCCH2OH', +'XCNO', 'XCNH2', 'XCOH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 63, + label = "C#XCR2", + group= +""" +1 * X u0 p0 c0 {3,T} +2 C u0 p0 c0 {3,S} {4,S} {5,D} +3 C u0 p0 c0 {1,T} {2,S} +4 R u0 px c0 {2,S} +5 R!H u0 px c0 {2,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-12.369, -9.501, -7.368, -5.786, -3.722, -2.526, -1.16], 'J/(mol*K)'), + H298=(-568.221, 'kJ/mol'), + S298=(-183.565, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCCHCH2', 'XCCHO']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 64, + label = "C#XCR3", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 O u0 p2 c0 {2,D} +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 R u0 px c0 {2,S} 5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.0, 6.87, 7.39, 7.72, 8.09, 8.27, 8.39], 'J/(mol*K)'), - H298=(-73.08, 'kJ/mol'), - S298=(-122.36, 'J/(mol*K)'), + Cpdata=([-10.246, -6.744, -4.142, -2.248, 0.153, 1.544, 3.315], 'J/(mol*K)'), + H298=(-597.493, 'kJ/mol'), + S298=(-180.123, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged H2COX, HCOOHX, CH3CHOX, OCO2H2X, CH2COX on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R2C=O - : -*********** +shortDesc=u"""Averaged from: ['XCCH3', 'XCCH2CH3', 'XCCH2OH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 53, - label = "C-*R2OR", - group = + index = 65, + label = "C#XN", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} -3 O u0 p2 c0 {2,S} {6,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {3,S} +1 * X u0 p0 c0 {2,T} +2 C u0 p0 c0 {1,T} {3,S} +3 N u0 p1 c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-3.14, 0.0, 2.2, 3.74, 5.64, 6.69, 7.8], 'J/(mol*K)'), - H298=(-225.57, 'kJ/mol'), - S298=(-157.56, 'J/(mol*K)'), + Cpdata=([-4.802, -2.782, -1.842, -1.37, -1.0, -0.884, -0.705], 'J/(mol*K)'), + H298=(-429.444, 'kJ/mol'), + S298=(-161.835, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCH2OH, CH3XCHOH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - R-C-OR - | -*********** +shortDesc=u"""Averaged from: ['XCNO', 'XCNH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 54, - label = "(CR3NR2)*", - group = + index = 66, + label = "C#XOR", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 N u0 p1 c0 {2,S} {7,S} {8,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {2,S} -6 R u0 p0 c0 {2,S} -7 R u0 p0 c0 {3,S} -8 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {2,T} +2 C u0 p0 c0 {1,T} {3,S} +3 O u0 p2 c0 {2,S} {4,S} +4 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.08, 0.64, 1.01, 1.25, 1.53, 1.68, 1.84], 'cal/(mol*K)'), - H298=(-23.1, 'kcal/mol'), - S298=(-33.73, 'cal/(mol*K)'), + Cpdata=([-2.481, 1.519, 3.59, 4.636, 5.376, 5.591, 6.114], 'J/(mol*K)'), + H298=(-465.97, 'kJ/mol'), + S298=(-187.544, 'J/(mol*K)'), ), - shortDesc=u"""Came from CH3NH2X physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.879 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = -0.87925 eV, gamma_C(X) = 0.000. - The two lowest frequencies, 16.6 and 84.5 cm-1, where replaced by the 2D gas model. - - R3C-NR2 - : -*********** +shortDesc=u"""Averaged from: ['XCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 55, - label = "(CR3OR)*", - group = + index = 67, + label = "C-XR2", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} -3 O u0 p2 c0 {2,S} {7,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} -7 R u0 px c0 {3,S} +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,D} {4,S} +3 R!H u0 px c0 {2,D} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([8.44, 9.53, 10.02, 10.25, 10.41, 10.45, 10.47], 'J/(mol*K)'), - H298=(-57.56, 'kJ/mol'), - S298=(-139.36, 'J/(mol*K)'), + Cpdata=([-8.007, -4.999, -3.006, -1.685, -0.197, 0.529, 1.224], 'J/(mol*K)'), + H298=(-306.661, 'kJ/mol'), + S298=(-166.429, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH3OHX, CH3OCH3X, H2CO2H2X, CH3OCH2OHX on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R3C-OR - : -*********** +shortDesc=u"""Averaged from: ['CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3', +'OXCNH2', 'NH2XCNH', 'XCHNH', 'OHXCNH', 'NH2XCNH', 'XCHO', 'XCOOH', 'CH3XCO', +'XCCHO', 'CH3CH2XCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 56, - label = "C-*RC=*", - group = + index = 68, + label = "C-XRCR2", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,D} -3 C u0 p0 c0 {1,S} {4,D} {5,S} -4 C u0 p0 c0 {2,D} {3,D} +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,D} {4,S} +3 C u0 p0 c0 {2,D} {5,S} {6,S} +4 R u0 px c0 {2,S} 5 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.53, 3.23, 6.15, 7.98, 10.0, 10.99, 11.95], 'J/(mol*K)'), - H298=(-440.52, 'kJ/mol'), - S298=(-184.43, 'J/(mol*K)'), + Cpdata=([-7.024, -3.455, -0.964, 0.723, 2.651, 3.602, 4.504], 'J/(mol*K)'), + H298=(-290.648, 'kJ/mol'), + S298=(-182.514, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXC single- and double bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - RC--C - | || -*********** +shortDesc=u"""Averaged from: ['CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) +entry( + index = 69, + label = "C-XRN", + group= +""" +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {4,D} {3,S} +3 N u0 p1 c0 {2,S} +4 R!H u0 p[1,2,3] c0 {2,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-6.998, -4.5, -2.956, -1.997, -1.04, -0.66, -0.35], 'J/(mol*K)'), + H298=(-299.043, 'kJ/mol'), + S298=(-153.59, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['OXCNH2', 'NH2XCNH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) entry( - index = 57, - label = "C-*RCR2", - group = + index = 70, + label = "C-XRNR", + group= """ 1 * X u0 p0 c0 {2,S} 2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 C u0 p0 c0 {2,D} {5,S} {6,S} +3 N u0 p1 c0 {2,D} {5,S} 4 R u0 px c0 {2,S} 5 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.29, 4.86, 7.35, 9.04, 10.97, 11.92, 12.82], 'J/(mol*K)'), - H298=(-288.17, 'kJ/mol'), - S298=(-182.51, 'J/(mol*K)'), + Cpdata=([-8.453, -5.685, -3.912, -2.763, -1.518, -0.942, -0.403], 'J/(mol*K)'), + H298=(-288.87, 'kJ/mol'), + S298=(-151.565, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH2XCCH3, CH2XCOH, XCHCCH2, XCHCH2, XCHCHCH3 on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. +shortDesc=u"""Averaged from: ['XCHNH', 'OHXCNH', 'NH2XCNH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) - CR2 - || - C-R - | -*********** +entry( + index = 71, + label = "C-XRO", + group= +""" +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,D} {4,S} +3 O u0 p2 c0 {2,D} +4 R u0 px c0 {2,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-9.126, -6.33, -4.525, -3.32, -1.915, -1.187, -0.452], 'J/(mol*K)'), + H298=(-336.396, 'kJ/mol'), + S298=(-164.4, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCHO', 'XCOOH', 'CH3XCO', 'XCCHO', 'CH3CH2XCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 58, - label = "C=*RCR3", - group = + index = 72, + label = "C-XR3", + group= """ -1 * X u0 p0 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} +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 R u0 px c0 {2,S} 4 R u0 px c0 {2,S} 5 R u0 px c0 {2,S} -6 R u0 px c0 {2,S} -7 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.78, 4.72, 6.6, 7.86, 9.39, 10.26, 11.34], 'J/(mol*K)'), - H298=(-372.23, 'kJ/mol'), - S298=(-179.04, 'J/(mol*K)'), + Cpdata=([-9.256, -5.928, -3.602, -1.974, 0.039, 1.155, 2.354], 'J/(mol*K)'), + H298=(-221.516, 'kJ/mol'), + S298=(-177.467, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH3XCCH3, CH3XCOH, XCHCH2CH3, XCHCH3 on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR3 - | - C-R - || -*********** +shortDesc=u"""Averaged from: ['XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', 'CH3XCHCH3', 'CH3XCHOH', +'XCH2NH2', 'XCH2OH', 'CH3XCHOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 59, - label = "(CRN)*", - group = + index = 73, + label = "C-XR2CR3", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,T} {4,S} -3 N u0 p1 c0 {2,T} -4 R u0 p0 c0 {2,S} +1 * X u0 p0 c0 {2,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 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {3,S} +7 R u0 px c0 {3,S} +8 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.02, 0.68, 1.15, 1.46, 1.81, 1.96, 2.06], 'cal/(mol*K)'), - H298=(-7.52, 'kcal/mol'), - S298=(-22.92, 'cal/(mol*K)'), + Cpdata=([-7.927, -4.391, -1.968, -0.293, 1.756, 2.884, 4.113], 'J/(mol*K)'), + H298=(-216.941, 'kJ/mol'), + S298=(-192.287, 'J/(mol*K)'), ), - shortDesc=u"""Came from HCNX physisorbed on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.010 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = -0.00995 eV, gamma_C(X) = 0.000. - The two lowest frequencies, 51.9 and 72.8 cm-1, where replaced by the 2D gas model. - - RC#N - : -*********** +shortDesc=u"""Averaged from: ['XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', 'CH3XCHCH3', 'CH3XCHOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 60, - label = "C=*RN=*", - group = + index = 74, + label = "C-XR2N", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,D} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 N u0 p1 c0 {2,D} {3,S} -5 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 N u0 p1 c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.59, 1.77, 2.56, 3.08, 3.67, 3.93, 4.1], 'cal/(mol*K)'), - H298=(-22.54, 'kcal/mol'), - S298=(-35.76, 'cal/(mol*K)'), + Cpdata=([-11.501, -8.834, -6.746, -5.175, -3.118, -1.943, -0.697], 'J/(mol*K)'), + H298=(-231.326, 'kJ/mol'), + S298=(-143.176, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCXNH, twice double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.650 eV. - Linear scaling parameters: ref_adatom_C1 = -6.750 eV, ref_adatom_N2 = 0.525 eV, psi = 2.37733 eV, gamma_C1(X) = 0.500, gamma_N2(X) = 0.667. - - R - | - C--N - || || -*********** +shortDesc=u"""Averaged from: ['XCH2NH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 61, - label = "C-*RNR", - group = + index = 75, + label = "C-XR2OR", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 N u0 p1 c0 {2,D} {5,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {2,S} +2 C u0 p0 c0 {1,S} {3,S} {4,S} {5,S} +3 O u0 p2 c0 {2,S} {6,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.74, 2.48, 2.93, 3.22, 3.53, 3.67, 3.82], 'cal/(mol*K)'), - H298=(-63.07, 'kcal/mol'), - S298=(-38.15, 'cal/(mol*K)'), + Cpdata=([-11.456, -8.317, -6.115, -4.578, -2.676, -1.621, -0.516], 'J/(mol*K)'), + H298=(-228.049, 'kJ/mol'), + S298=(-157.564, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHNH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -2.220 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = -0.52691 eV, gamma_C(X) = 0.250. +shortDesc=u"""Averaged from: ['XCH2OH', 'CH3XCHOH']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) - NR - || - C-R - | -*********** +entry( + index = 76, + label = "C=X(=R)", + group= +""" +1 * X u0 p0 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 R!H u0 px c0 {2,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-6.678, -3.549, -1.767, -0.677, 0.517, 1.114, 1.713], 'J/(mol*K)'), + H298=(-376.101, 'kJ/mol'), + S298=(-170.526, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCCO', 'XCCCH2', 'XCCH2', 'XCNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 62, - label = "C=*RN-*R", - group = + index = 77, + label = "C=X(=C)", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 N u0 p1 c0 {2,S} {3,S} {6,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {4,S} +1 * X u0 p0 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 C u0 p0 c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.89, 2.02, 2.67, 3.07, 3.47, 3.65, 3.81], 'cal/(mol*K)'), - H298=(-70.06, 'kcal/mol'), - S298=(-46.17, 'cal/(mol*K)'), + Cpdata=([-6.756, -3.436, -1.616, -0.523, 0.693, 1.335, 2.065], 'J/(mol*K)'), + H298=(-432.678, 'kJ/mol'), + S298=(-171.763, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXNH, double- and single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -2.490 eV. - Linear scaling parameters: ref_adatom_C1 = -6.750 eV, ref_adatom_N2 = 0.525 eV, psi = 0.71054 eV, gamma_C1(X) = 0.500, gamma_N2(X) = 0.333. +shortDesc=u"""Averaged from: ['XCCO', 'XCCCH2', 'XCCH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) - RC--NR - || | -*********** +entry( + index = 78, + label = "C=X(=NR)", + group= +""" +1 * X u0 p0 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,D} +3 N u0 p1 c0 {2,D} {4,S} +4 R u0 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-6.443, -3.888, -2.219, -1.141, -0.01, 0.449, 0.658], 'J/(mol*K)'), + H298=(-206.367, 'kJ/mol'), + S298=(-166.816, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCNH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 63, - label = "C=*RNR2", - group = + index = 79, + label = "C=XR2", + group= """ 1 * X u0 p0 c0 {2,D} 2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 N u0 p1 c0 {2,S} {5,S} {6,S} -4 R u0 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} +3 R u0 px c0 {2,S} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.34, 3.12, 3.49, 3.66, 3.79, 3.81, 3.84], 'cal/(mol*K)'), - H298=(-69.75, 'kcal/mol'), - S298=(-37.75, 'cal/(mol*K)'), + Cpdata=([-7.263, -4.167, -2.297, -1.096, 0.291, 1.044, 1.921], 'J/(mol*K)'), + H298=(-352.634, 'kJ/mol'), + S298=(-164.709, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHNH2 double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -2.670 eV. - Linear scaling parameters: ref_adatom_C = -6.750 eV, psi = 0.70666 eV, gamma_C(X) = 0.500. - - NR2 - | - C-R - || -*********** +shortDesc=u"""Averaged from: ['XCH2', 'XCHCHCH2', 'XCHCHO', 'CH3XCCH3', 'CH3XCOH', +'XCHCH2CH3', 'XCHCH3', 'XCHNH2', 'OHXCNH2', 'NH2XCNH2', 'XCHOH', 'CH3XCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 64, - label = "C-*RO", - group = + index = 80, + label = "C=XRCR2", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 O u0 p2 c0 {2,D} -4 R u0 px c0 {2,S} +1 * X u0 p0 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {5,D} +3 C u0 p0 c0 {1,D} {2,S} {6,S} +4 R u0 px c0 {2,S} +5 R!H u0 px c0 {2,D} +6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.65, 2.4, 4.38, 5.69, 7.2, 7.95, 8.71], 'J/(mol*K)'), - H298=(-282.27, 'kJ/mol'), - S298=(-161.1, 'J/(mol*K)'), + Cpdata=([-7.502, -4.231, -2.08, -0.611, 1.184, 2.171, 3.256], 'J/(mol*K)'), + H298=(-381.649, 'kJ/mol'), + S298=(-179.047, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged HXCO, OXCOH, CH3XCO, CHXCO, CH3CH2XCO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - C=O - | -*********** +shortDesc=u"""Averaged from: ['XCHCHCH2', 'XCHCHO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 65, - label = "C=*RO-*", - group = + index = 81, + label = "C=XRCR3", + group= """ 1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 O u0 p2 c0 {2,S} {3,S} -5 R u0 px c0 {3,S} +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 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} +7 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([5.91, 10.27, 12.84, 14.27, 15.45, 15.81, 16.1], 'J/(mol*K)'), - H298=(-238.17, 'kJ/mol'), - S298=(-167.73, 'J/(mol*K)'), + Cpdata=([-6.536, -3.596, -1.716, -0.454, 1.074, 1.948, 3.03], 'J/(mol*K)'), + H298=(-374.707, 'kJ/mol'), + S298=(-179.041, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXO double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R - | - C--O - || | -*********** +shortDesc=u"""Averaged from: ['CH3XCCH3', 'CH3XCOH', 'XCHCH2CH3', 'XCHCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 66, - label = "C=*ROR", - group = + index = 82, + label = "C=XRN", + group= """ 1 * X u0 p0 c0 {2,D} 2 C u0 p0 c0 {1,D} {3,S} {4,S} -3 O u0 p2 c0 {2,S} {5,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {3,S} +3 N u0 p1 c0 {2,S} +4 R u0 p0 c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.05, 2.82, 4.47, 5.52, 6.78, 7.48, 8.24], 'J/(mol*K)'), - H298=(-325.89, 'kJ/mol'), - S298=(-146.57, 'J/(mol*K)'), + Cpdata=([-5.314, -3.237, -2.228, -1.679, -1.161, -0.928, -0.62], 'J/(mol*K)'), + H298=(-306.517, 'kJ/mol'), + S298=(-144.277, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCHOH and CH3XCOH on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - OR - | - C-R - || -*********** +shortDesc=u"""Averaged from: ['XCHNH2', 'OHXCNH2', 'NH2XCNH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 67, - label = "C*", - group = + index = 83, + label = "C=XROR", + group= """ -1 * X u0 {2,[S,D,T,Q]} -2 C ux {1,[S,D,T,Q]} +1 * X u0 p0 c0 {2,D} +2 C u0 p0 c0 {1,D} {3,S} {4,S} +3 O u0 p2 c0 {2,S} {5,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.31, 3.22, 5.55, 7.13, 8.99, 9.99, 11.1], 'J/(mol*K)'), - H298=(-359.63, 'kJ/mol'), - S298=(-173.0, 'J/(mol*K)'), + Cpdata=([-8.363, -5.498, -3.838, -2.79, -1.538, -0.826, -0.079], 'J/(mol*K)'), + H298=(-328.365, 'kJ/mol'), + S298=(-146.569, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XCHOH', 'CH3XCOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 68, - label = "N*", - group = + index = 84, + label = "NX", + group= """ 1 * X u0 {2,[S,D,T]} -2 N ux {1,[S,D,T]} +2 N u0 {1,[S,D,T]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-4.245, -1.035, 0.763, 1.813, 2.873, 3.381, 4.003], 'J/(mol*K)'), + H298=(-241.467, 'kJ/mol'), + S298=(-168.306, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNO', 'XNCNH', 'XNCO', 'XNCH2', 'XNNH', 'XNNCH3', 'XNH2', +'XNHCHO', 'XNHCH3', 'XNHNO', 'XNHNH2', 'XNHOH', 'XNO2', 'OXNNH', 'HXNO', +'CH3NXNOH', 'CH3XNNOH', 'XNH', 'XNCN', 'XNCH3', 'XNNH2', 'XNOH']""", +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_kinetic +s_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. """, - thermo=u'N-*R2', - longDesc=u"""Thermo is currently for N-*R2. Maybe should average all the children instead?""", + metal = "Pt", + facet = "111", ) entry( - index = 69, - label = "O*", - group = + index = 85, + label = "N-XR", + group= """ -1 * X u0 {2,[S,D]} -2 O ux {1,[S,D]} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,D} +3 R!H u0 px c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([5.66, 7.38, 8.31, 8.88, 9.52, 9.88, 10.36], 'J/(mol*K)'), - H298=(-215.12, 'kJ/mol'), - S298=(-155.61, 'J/(mol*K)'), + Cpdata=([-5.514, -2.968, -1.574, -0.768, 0.034, 0.402, 0.82], 'J/(mol*K)'), + H298=(-215.369, 'kJ/mol'), + S298=(-163.05, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNO', 'XNCNH', 'XNCO', 'XNCH2', 'XNNH', 'XNNCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 70, - label = "R*single-chemisorbed", - group = + index = 86, + label = "N-XCR", + group= """ -1 * X u0 {2,[S,D,T,Q]} -2 R ux {1,[S,D,T,Q]} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,D} +3 C u0 p0 c0 {2,D} {4,D} +4 R!H u0 px c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.84, 4.02, 6.08, 7.46, 9.09, 9.97, 10.96], 'J/(mol*K)'), - H298=(-331.96, 'kJ/mol'), - S298=(-169.67, 'J/(mol*K)'), + Cpdata=([-8.735, -7.168, -6.454, -6.084, -5.664, -5.378, -4.904], 'J/(mol*K)'), + H298=(-272.152, 'kJ/mol'), + S298=(-145.417, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNCNH', 'XNCO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 71, - label = "C*C*", - group = + index = 87, + label = "N-XCR2", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,[S,D,T]} -3 C u0 {1,[S,D,T]} {4,[S,D,T]} -4 C u0 {2,[S,D,T]} {3,[S,D,T]} +1 * X u0 p0 c0 {3,S} +2 C u0 p0 c0 {3,D} {4,S} {5,S} +3 N u0 p1 c0 {1,S} {2,D} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.88, 5.67, 8.7, 10.62, 12.69, 13.65, 14.5], 'J/(mol*K)'), - H298=(-353.37, 'kJ/mol'), - S298=(-192.89, 'J/(mol*K)'), + Cpdata=([-1.707, 1.64, 3.521, 4.671, 5.896, 6.505, 7.246], 'J/(mol*K)'), + H298=(-213.18, 'kJ/mol'), + S298=(-180.636, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNCH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 72, - label = "C*N*", - group = -""" -1 * X u0 {3,[S,D]} -2 X u0 {4,[S,D,T]} -3 C u0 {1,[S,D]} {4,[S,D,T]} -4 N u0 {2,[S,D,T]} {3,[S,D,T]} -""", - thermo=u'C=*RN-*R', - longDesc=u"""Thermo is currently for C=*RN-*R. Maybe should average all the children instead?""", -) - -#Changed the adjacency list because O can only have a single bond to the surface and another atom. -#Always 2 free electron pairs. BK 2023/1/10 -entry( - index = 73, - label = "C*O*", - group = + index = 88, + label = "N-XNR", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,S} -3 C u0 {1,[S,D,T]} {4,S} -4 O u0 p2 {2,S} {3,S} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,D} +3 N u0 p1 c0 {2,D} {4,S} +4 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([7.34, 11.93, 14.46, 15.74, 16.6, 16.72, 16.63], 'J/(mol*K)'), - H298=(-149.6, 'kJ/mol'), - S298=(-169.0, 'J/(mol*K)'), + Cpdata=([-3.854, -0.981, 0.698, 1.7, 2.689, 3.114, 3.559], 'J/(mol*K)'), + H298=(-169.315, 'kJ/mol'), + S298=(-164.071, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all child nodes on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNNH', 'XNNCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 74, - label = "N*N*", - group = + index = 89, + label = "N-XR2", + group= """ -1 * X u0 {3,[S,D]} -2 X u0 {4,[S,D]} -3 N u0 {1,[S,D]} {4,[S,D]} -4 N u0 {2,[S,D]} {3,[S,D]} +1 * X u0 p0 c0 {2,[S,D]} +2 N u0 px cx {1,[S,D]} {3,[S,D]} {4,[S,D]} +3 R!H u0 px cx {2,[S,D]} +4 R u0 px c0 {2,[S,D]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-2.47, 0.767, 2.688, 3.875, 5.176, 5.85, 6.65], 'J/(mol*K)'), + H298=(-220.012, 'kJ/mol'), + S298=(-171.136, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNH2', 'XNHCHO', 'XNHCH3', 'XNHNO', 'XNHNH2', 'XNHOH', 'XNO2', +'OXNNH', 'HXNO', 'CH3NXNOH', 'CH3XNNOH']""", +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_kinetic +s_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. """, - thermo=u'N-*RN-*R', - longDesc=u"""Thermo is currently for N-*RN-*R. Maybe should average all the children instead?""", + metal = "Pt", + facet = "111", ) entry( - index = 75, - label = "R*bidentate", - group = + index = 90, + label = "N-XRCR", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,[S,D,T]} -3 R!H ux {1,[S,D,T]} {4,[S,D,T]} -4 R!H ux {2,[S,D,T]} {3,[S,D,T]} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,S} {4,S} +3 C u0 p0 c0 {2,S} {5,D} +4 R u0 px c0 {2,S} +5 R!H u0 px c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.59, 6.37, 9.34, 11.19, 13.12, 13.99, 14.74], 'J/(mol*K)'), - H298=(-330.73, 'kJ/mol'), - S298=(-190.23, 'J/(mol*K)'), + Cpdata=([-4.328, -0.938, 1.222, 2.693, 4.463, 5.437, 6.648], 'J/(mol*K)'), + H298=(-334.011, 'kJ/mol'), + S298=(-216.907, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all child nodes on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNHCHO']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 76, - label = "R*vdW", - group = + index = 91, + label = "N-XRCR3", + group= """ -1 * X u0 -2 R u0 +1 * X u0 p0 c0 {3,S} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 N u0 p1 c0 {1,S} {2,S} {7,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} +7 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([7.25, 8.33, 8.9, 9.23, 9.56, 9.7, 9.8], 'J/(mol*K)'), - H298=(-56.05, 'kJ/mol'), - S298=(-125.18, 'J/(mol*K)'), + Cpdata=([3.994, 8.661, 12.118, 14.767, 18.588, 21.339, 25.873], 'J/(mol*K)'), + H298=(-356.67, 'kJ/mol'), + S298=(-167.995, 'J/(mol*K)'), ), - shortDesc=u"""Averaged of (CR4)*, (CR3)*, and (OR2)* (nitrogen is not included) on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNHCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 77, - label = "N*O*", - group = -""" -1 * X u0 p0 c0 {3,[S,D]} -2 X u0 p0 c0 {4,[S,D]} -3 N u0 p1 c0 {1,[S,D]} {4,[S,D]} -4 O u0 p2 c0 {2,[S,D]} {3,[S,D]} -""", - thermo=u'N=*O-*', - longDesc=u"""Is there really any way to do N*O* besides N=*O-* ?""", - metal = "Pt", - facet = "111", -) - -#entry( -# index = 78, -# label = "O*O*", -# group = -#""" -#1 * X u0 p0 c0 {3,S} -#2 * X u0 p0 c0 {4,S} -#3 O u0 p2 c0 {1,S} {4,S} -#4 O u0 p2 c0 {2,S} {3,S} -#""", -# thermo=u'O-*O-*', -# longDesc=u"""Is there really any way to do O*O* besides O-*O-* ?""", -# metal = "Pt", -# facet = "111", -#) - -###Have not been able to find any examples of when N is triple bonded to the surface and -###has an R group attached. Redid for no R group below. --EM -#entry( -# index = 79, -# label = "N#*R", -# group = -#""" -#1 * X u0 c-1 {2,T} -#2 N u0 c+1 {1,T} {3,S} -#3 R u0 c0 {2,S} -#""", -# thermo=u'N*', -# metal = "Pt", -# facet = "111", -#) - -entry( - index = 79, - label = "N#*", - group = + index = 92, + label = "N-XRNR", + group= """ -1 * X u0 p0 {2,T} -2 N u0 p1 {1,T} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,S} {4,S} +3 N u0 p1 c0 {2,S} {5,D} +4 R u0 px c0 {2,S} +5 R!H u0 px c0 {3,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([2.584, 5.55, 7.122, 7.922, 8.483, 8.562, 8.462], 'J/(mol*K)'), + H298=(-271.605, 'kJ/mol'), + S298=(-189.56, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNHNO']""", +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_kinetic +s_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. """, - thermo=u'N*', metal = "Pt", facet = "111", ) + entry( - index = 80, - label = "(CR3)*", - group = + index = 93, + label = "N-XRNR2", + group= """ -1 * X u0 -2 C u0 {3,D} {4,S} {5,S} -3 R!H u0 {2,D} -4 R u0 {2,S} -5 R u0 {2,S} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,S} {4,S} +3 N u0 p1 c0 {2,S} {5,S} {6,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {3,S} +6 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.54, 7.68, 8.34, 8.74, 9.14, 9.32, 9.44], 'J/(mol*K)'), - H298=(-74.45, 'kJ/mol'), - S298=(-130.43, 'J/(mol*K)'), + Cpdata=([-1.185, 2.056, 4.018, 5.261, 6.661, 7.372, 8.062], 'J/(mol*K)'), + H298=(-172.993, 'kJ/mol'), + S298=(-188.5, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['XNHNH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 81, - label = "(CR2)*", - group = + index = 94, + label = "N-XROR", + group= """ -1 * X u0 -2 C u0 {3,T} {4,S} -3 R!H u0 {2,T} -4 R u0 {2,S} +1 * X u0 p0 c0 {2,S} +2 N u0 p1 c0 {1,S} {3,S} {4,S} +3 O u0 p2 c0 {2,S} {5,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-0.228, 3.377, 5.253, 6.315, 7.409, 7.934, 8.402], 'J/(mol*K)'), + H298=(-184.483, 'kJ/mol'), + S298=(-189.451, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNHOH']""", +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_kinetic +s_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. """, - thermo=u'(CRCR)*', metal = "Pt", facet = "111", ) entry( - index = 82, - label = "(N=[O,N]R)*", - group = + index = 95, + label = "N[+]-XR[-]R", + group= """ -1 * X u0 -2 N u0 {3,D} {4,S} -3 [N,O] u0 {2,D} -4 R u0 {2,S} +1 * X u0 p0 c0 {2,S} +2 N u0 p0 c+1 {1,S} {3,S} {4,D} +3 R!H u0 p[1,2,3] c-1 {2,S} +4 R!H u0 px c0 {2,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-1.078, 1.553, 2.933, 3.648, 4.201, 4.335, 4.328], 'J/(mol*K)'), + H298=(-218.965, 'kJ/mol'), + S298=(-163.298, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNO2', 'OXNNH']""", +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_kinetic +s_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. """, - thermo=u'(NRO)*', - longDesc=u"""Parent of (RN=O)* and (RN=NR)*. Should it be an average?""", metal = "Pt", facet = "111", ) entry( - index = 83, - label = "N-*RN=*", - group = + index = 96, + label = "N[+]=XR[-]R", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,D} -3 N u0 p1 c0 {1,S} {4,S} {5,S} -4 N u0 p1 c0 {2,D} {3,S} -5 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {2,D} +2 N u0 p0 c+1 {1,D} {3,S} {4,S} +3 R!H u0 p[1,2,3] c-1 {2,S} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.83, 2.02, 2.69, 3.08, 3.41, 3.53, 3.66], 'cal/(mol*K)'), - H298=(-43.06, 'kcal/mol'), - S298=(-45.85, 'cal/(mol*K)'), + Cpdata=([-4.586, -2.627, -1.537, -0.917, -0.317, -0.061, 0.133], 'J/(mol*K)'), + H298=(-147.529, 'kJ/mol'), + S298=(-143.039, 'J/(mol*K)'), ), - shortDesc=u"""Came from XNHXN single- and double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.280 eV. - Linear scaling parameters: ref_adatom_N1 = -4.352 eV, ref_adatom_N2 = -4.352 eV, psi = 3.07184 eV, gamma_N1(X) = 0.333, gamma_N2(X) = 0.667. - - RN--N - | | -*********** +shortDesc=u"""Averaged from: ['HXNO', 'CH3NXNOH', 'CH3XNNOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 84, - label = "(CRCR)*", - group = + index = 97, + label = "N=XR", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,T} {4,S} -3 C u0 p0 c0 {2,T} {5,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {3,S} +1 * X u0 p0 c0 {2,D} +2 N u0 p1 c0 {1,D} {3,S} +3 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.69, 1.89, 2.02, 2.13, 2.46, 2.9, 3.96], 'J/(mol*K)'), - H298=(-59.58, 'kJ/mol'), - S298=(-115.19, 'J/(mol*K)'), + Cpdata=([-6.626, -2.68, -0.666, 0.371, 1.212, 1.524, 1.998], 'J/(mol*K)'), + H298=(-319.988, 'kJ/mol'), + S298=(-168.387, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CHCHX and CHCCH3X on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - RC#CR - : -*********** +shortDesc=u"""Averaged from: ['XNH', 'XNCN', 'XNCH3', 'XNNH2', 'XNOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 85, - label = "C-*R2N=*", - group = + index = 98, + label = "N=XC#R", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,D} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 N u0 p1 c0 {2,D} {3,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} +1 * X u0 p0 c0 {2,D} +2 N u0 p1 c0 {1,D} {3,S} +3 C u0 p0 c0 {2,S} {4,T} +4 R!H u0 px c0 {3,T} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.01, 2.14, 2.79, 3.16, 3.5, 3.63, 3.76], 'cal/(mol*K)'), - H298=(-51.5, 'kcal/mol'), - S298=(-47.12, 'cal/(mol*K)'), + Cpdata=([-15.304, -12.918, -11.895, -11.386, -10.762, -10.276, -9.457], 'J/(mol*K)'), + H298=(-332.074, 'kJ/mol'), + S298=(-142.031, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2XN bidentate, single- and double-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -1.710 eV. - Linear scaling parameters: ref_adatom_C1 = -6.750 eV, ref_adatom_N2 = 0.525 eV, psi = -0.37462 eV, gamma_C1(X) = 0.250, gamma_N2(X) = 0.667. - - R2C--N - | || -*********** +shortDesc=u"""Averaged from: ['XNCN']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 86, - label = "C-*R2N-*R", - group = + index = 99, + label = "N=XC-R", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 N u0 p1 c0 {2,S} {3,S} {7,S} -5 R u0 p0 c0 {3,S} -6 R u0 p0 c0 {3,S} -7 R u0 p0 c0 {4,S} +1 * X u0 p0 c0 {3,D} +2 C u0 p0 c0 {3,S} {4,S} +3 N u0 p1 c0 {1,D} {2,S} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.41, 3.0, 3.77, 4.11, 4.29, 4.28, 4.16], 'cal/(mol*K)'), - H298=(-25.1, 'kcal/mol'), - S298=(-47.43, 'cal/(mol*K)'), + Cpdata=([-1.701, 1.153, 2.807, 3.883, 5.154, 5.877, 6.86], 'J/(mol*K)'), + H298=(-353.431, 'kJ/mol'), + S298=(-176.565, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2XNH twice single-bonded on Pt(111)""", - longDesc=u"""Calculated by Katrin Blondal at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). Based on DFT calculations by Jelena Jelic at KIT. - DFT binding energy: -0.756 eV. - Linear scaling parameters: ref_adatom_C1 = -6.750 eV, ref_adatom_N2 = 0.525 eV, psi = 0.75753 eV, gamma_C1(X) = 0.250, gamma_N2(X) = 0.333. - - R2C--NR - | | -*********** +shortDesc=u"""Averaged from: ['XNCH3']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 87, - label = "C=*(=C)", - group = + index = 100, + label = "N=XN", + group= """ -1 * X u0 p0 c0 {2,D} -2 C u0 p0 c0 {1,D} {3,D} -3 C u0 p0 c0 {2,D} +1 * X u0 p0 c0 {2,D} +2 N u0 p1 c0 {1,D} {3,S} +3 N u0 p1 c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.94, 6.26, 8.08, 9.18, 10.4, 11.04, 11.77], 'J/(mol*K)'), - H298=(-429.79, 'kJ/mol'), - S298=(-168.79, 'J/(mol*K)'), + Cpdata=([2.988, 7.107, 8.778, 9.2, 8.654, 7.878, 7.118], 'J/(mol*K)'), + H298=(-250.227, 'kJ/mol'), + S298=(-174.51, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCCH2, XCCCH2, XCCO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - C - || - C - || -*********** - -Because the C atom bonded to the surface only has one ligand -not two, it is not a child of the C=*R2 node +shortDesc=u"""Averaged from: ['XNNH2']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 88, - label = "C-*R2O-*", - group = + index = 101, + label = "N=XOR", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 O u0 p2 c0 {2,S} {3,S} -5 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} +1 * X u0 p0 c0 {2,D} +2 N u0 p1 c0 {1,D} {3,S} +3 O u0 p2 c0 {2,S} {4,S} +4 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([8.78, 13.6, 16.07, 17.2, 17.75, 17.62, 17.16], 'J/(mol*K)'), - H298=(-61.03, 'kJ/mol'), - S298=(-170.27, 'J/(mol*K)'), + Cpdata=([0.702, 4.715, 6.511, 7.217, 7.378, 7.177, 7.067], 'J/(mol*K)'), + H298=(-294.53, 'kJ/mol'), + S298=(-178.708, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2XO single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - R2C--O - | | -*********** +shortDesc=u"""Averaged from: ['XNOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 89, - label = "(CR2CR)*", - group = + index = 102, + label = "OX", + group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,S} -3 C u0 p0 c0 {2,D} {6,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} -6 R u0 px c0 {3,S} +1 * X u0 {2,[S,D]} +2 O ux {1,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([7.43, 9.04, 9.92, 10.43, 10.9, 11.07, 11.17], 'J/(mol*K)'), - H298=(-76.74, 'kJ/mol'), - S298=(-143.86, 'J/(mol*K)'), + Cpdata=([-3.886, -2.127, -1.125, -0.5, 0.209, 0.597, 1.11], 'J/(mol*K)'), + H298=(-191.097, 'kJ/mol'), + S298=(-155.727, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged CH2CH2X, CH3CHCH2X, CH2CCH2X on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - R2C=CR - : -*********** +shortDesc=u"""Averaged from: ['XOH', 'XOCHCH2', 'HC(O)XO', 'XOC(OH)O', 'XOCH3', 'XOCH2CH3', +'XOCH2OH', 'XONH2', 'XOOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) - entry( - index = 90, - label = "C=*RC-*R", - group = + index = 103, + label = "O-XR", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,D} {4,S} {5,S} -4 C u0 p0 c0 {2,S} {3,S} {6,D} -5 R u0 px c0 {3,S} -6 R!H u0 px c0 {4,D} +1 * X u0 p0 c0 {2,S} +2 O u0 p2 c0 {1,S} {3,S} +3 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-5.37, 0.67, 4.68, 7.31, 10.25, 11.63, 12.69], 'J/(mol*K)'), - H298=(-396.35, 'kJ/mol'), - S298=(-202.17, 'J/(mol*K)'), + Cpdata=([-3.886, -2.127, -1.125, -0.5, 0.209, 0.597, 1.11], 'J/(mol*K)'), + H298=(-191.097, 'kJ/mol'), + S298=(-155.727, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXCO double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC---C=R - || | -*********** +shortDesc=u"""Averaged from: ['XOH', 'XOCHCH2', 'HC(O)XO', 'XOC(OH)O', 'XOCH3', 'XOCH2CH3', +'XOCH2OH', 'XONH2', 'XOOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 91, - label = "C#*C-*R", - group = + index = 104, + label = "O-XCR2", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,T} {4,S} -4 C u0 p0 c0 {2,S} {3,S} {5,D} -5 R!H u0 px c0 {4,D} +1 * X u0 p0 c0 {3,S} +2 C u0 p0 c0 {3,S} {4,S} {5,D} +3 O u0 p2 c0 {1,S} {2,S} +4 R u0 px c0 {2,S} +5 R!H u0 px c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.41, 8.3, 11.6, 13.47, 15.23, 15.91, 16.41], 'J/(mol*K)'), - H298=(-440.28, 'kJ/mol'), - S298=(-204.35, 'J/(mol*K)'), + Cpdata=([2.854, 5.052, 6.224, 6.899, 7.592, 7.912, 8.196], 'J/(mol*K)'), + H298=(-230.516, 'kJ/mol'), + S298=(-194.234, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCXCCH2 twice single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C---C=R - ||| | -*********** +shortDesc=u"""Averaged from: ['XOCHCH2', 'HC(O)XO', 'XOC(OH)O']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 92, - label = "C#*C-*R2", - group = + index = 105, + label = "O-XCR3", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,T} {4,S} -4 C u0 p0 c0 {2,S} {3,S} {5,S} {6,S} -5 R u0 px c0 {4,S} -6 R u0 px c0 {4,S} +1 * X u0 p0 c0 {3,S} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 O u0 p2 c0 {1,S} {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.9, 4.58, 8.22, 10.59, 13.24, 14.53, 15.76], 'J/(mol*K)'), - H298=(-436.46, 'kJ/mol'), - S298=(-201.88, 'J/(mol*K)'), + Cpdata=([-6.87, -6.074, -5.389, -4.777, -3.825, -3.13, -1.969], 'J/(mol*K)'), + H298=(-185.03, 'kJ/mol'), + S298=(-149.812, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCXCH2 and XCXCHCH3 on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C---CR2 - ||| | -*********** +shortDesc=u"""Averaged from: ['XOCH3', 'XOCH2CH3', 'XOCH2OH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) - entry( - index = 93, - label = "C-*R2C-*R", - group = + index = 106, + label = "O-XN", + group= """ 1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,S} {4,S} {5,S} {6,S} -4 C u0 p0 c0 {2,S} {3,S} {7,D} -5 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} -7 R!H u0 px c0 {4,D} +2 N u0 p1 c0 {3,S} +3 O u0 p2 c0 {1,S} {2,S} + +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-7.084, -4.161, -2.544, -1.628, -0.739, -0.36, -0.052], 'J/(mol*K)'), + H298=(-130.622, 'kJ/mol'), + S298=(-134.71, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XONH2']""", +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_kinetic +s_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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 107, + label = "O-XOR", + group= +""" +1 * X u0 p0 c0 {2,S} +2 O u0 p2 c0 {1,S} {3,S} +3 O u0 p2 c0 {2,S} {4,S} +4 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.18, 10.54, 13.14, 14.74, 16.34, 16.95, 17.2], 'J/(mol*K)'), - H298=(-179.99, 'kJ/mol'), - S298=(-191.92, 'J/(mol*K)'), + Cpdata=([1.892, 3.068, 3.066, 2.708, 1.879, 1.245, 0.455], 'J/(mol*K)'), + H298=(-136.519, 'kJ/mol'), + S298=(-120.712, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2CXCH2 single and single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - R2C--C=R - | | -*********** +shortDesc=u"""Averaged from: ['XOOH']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 95, - label = "C-*RC-*R", - group = + index = 108, + label = "RXvdW", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 C u0 p0 c0 {1,S} {4,D} {5,S} -4 C u0 p0 c0 {2,S} {3,D} {6,S} -5 R u0 px c0 {3,S} -6 R u0 px c0 {4,S} +1 X u0 +2 * R u0 """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.8, 1.82, 4.66, 6.68, 9.21, 10.78, 13.11], 'J/(mol*K)'), - H298=(-227.58, 'kJ/mol'), - S298=(-194.29, 'J/(mol*K)'), + Cpdata=([-2.697, -1.427, -0.713, -0.282, 0.19, 0.43, 0.673], 'J/(mol*K)'), + H298=(-78.192, 'kJ/mol'), + S298=(-128.976, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHXCCH3 single and single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC==CR - | | -*********** +shortDesc=u"""Averaged from: ['CHCHX', 'CHCCH3X', 'NCOHX', 'CH2CH2X', 'CH3CHCH2X', 'CH2CCH2X', +'CH2NHX', 'CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX', 'CH4X', +'CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX', 'CH3NH2X', 'CH3OHX', 'CH3OCH3X', +'CH3OCH2OHX', 'H2C(OH)OHX', 'OCNHX', 'NHCNHX', 'NH3X', 'OCHNH2X', 'NH2NH2X', +'NH2NCH3CH3X', 'H2NOHX', 'ONNH2X', 'ONNCH3CH3X', 'ONOHX', 'H2OX', 'HOOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 96, - label = "C#*C=*R", - group = + index = 109, + label = "(CR2)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {4,D} -3 C u0 p0 c0 {1,T} {4,S} -4 C u0 p0 c0 {2,D} {3,S} {5,S} -5 R u0 px c0 {4,S} +1 X u0 +2 * C u0 {3,T} {4,S} +3 R!H u0 {2,T} +4 R u0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-2.0, 1.29, 3.27, 4.54, 5.97, 6.69, 7.48], 'J/(mol*K)'), - H298=(-488.53, 'kJ/mol'), - S298=(-158.38, 'J/(mol*K)'), + Cpdata=([-6.11, -5.831, -5.665, -5.52, -5.191, -4.827, -4.063], 'J/(mol*K)'), + H298=(-75.082, 'kJ/mol'), + S298=(-120.514, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCXCCH3 triple and double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C--CR - ||| || -*********** +shortDesc=u"""Averaged from: ['CHCHX', 'CHCCH3X', 'NCOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 97, - label = "C=*=R-C-*R2", - group = + index = 110, + label = "(CRCR)X", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,D} {4,D} -4 R!H u0 px c0 {3,D} {5,S} -5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} -6 R u0 px c0 {5,S} -7 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,T} {4,S} +3 C u0 p0 c0 {2,T} {5,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-3.01, 2.84, 6.84, 9.5, 12.5, 13.99, 15.5], 'J/(mol*K)'), - H298=(-543.25, 'kJ/mol'), - S298=(-229.45, 'J/(mol*K)'), + Cpdata=([-8.706, -8.504, -8.378, -8.256, -7.93, -7.499, -6.43], 'J/(mol*K)'), + H298=(-62.68, 'kJ/mol'), + S298=(-119.645, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCCHXCH2 double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C=R--CR2 - || | -*********** +shortDesc=u"""Averaged from: ['CHCHX', 'CHCCH3X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 98, - label = "R2C-*-R-C-*R2", - group = + index = 111, + label = "(CRN)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,S} {4,S} {8,S} {9,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} -6 R u0 px c0 {5,S} -7 R u0 px c0 {5,S} -8 R u0 px c0 {3,S} -9 R u0 px c0 {3,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,T} {4,S} +3 N u0 p1 c0 {2,T} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.02, 3.61, 7.1, 9.67, 12.99, 14.82, 16.51], 'J/(mol*K)'), - H298=(-389.14, 'kJ/mol'), - S298=(-209.34, 'J/(mol*K)'), + Cpdata=([-0.92, -0.483, -0.241, -0.047, 0.285, 0.517, 0.671], 'J/(mol*K)'), + H298=(-99.884, 'kJ/mol'), + S298=(-122.254, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCH2CH2XCH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - R2C--R--CR2 - | | -*********** +shortDesc=u"""Averaged from: ['NCOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 99, - label = "RC=*-R=C-*R", - group = + index = 112, + label = "(CR3)X", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,D} {4,S} {6,S} -4 R!H u0 px c0 {3,S} {5,D} -5 C u0 p0 c0 {2,S} {4,D} {7,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {5,S} +1 X u0 +2 * C u0 {3,D} {4,S} {5,S} +3 R!H u0 {2,D} +4 R u0 {2,S} +5 R u0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-6.06, -1.1, 2.74, 5.57, 9.12, 11.14, 13.63], 'J/(mol*K)'), - H298=(-612.92, 'kJ/mol'), - S298=(-200.99, 'J/(mol*K)'), + Cpdata=([-2.139, -0.779, -0.025, 0.403, 0.804, 0.953, 1.029], 'J/(mol*K)'), + H298=(-74.899, 'kJ/mol'), + S298=(-130.966, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCHXCH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC--R==CR - || | -*********** +shortDesc=u"""Averaged from: ['CH2CH2X', 'CH3CHCH2X', 'CH2CCH2X', 'CH2NHX', 'CH2COX', 'CH2OX', +'OC(OH)OHX', 'CH3CHOX', 'HCOOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 100, - label = "RC-*=R-C-*R2", - group = + index = 113, + label = "(CR2CR)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,S} {4,D} {6,S} -4 R!H u0 px c0 {3,D} {5,S} -5 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,D} {4,S} {5,S} +3 C u0 p0 c0 {2,D} {6,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} 6 R u0 px c0 {3,S} -7 R u0 px c0 {5,S} -8 R u0 px c0 {5,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.12, 6.05, 9.54, 11.64, 13.78, 14.75, 15.73], 'J/(mol*K)'), - H298=(-426.75, 'kJ/mol'), - S298=(-227.78, 'J/(mol*K)'), + Cpdata=([-0.886, 0.725, 1.607, 2.108, 2.582, 2.761, 2.858], 'J/(mol*K)'), + H298=(-79.219, 'kJ/mol'), + S298=(-143.863, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCHXCH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC==R--CR2 - | | -*********** +shortDesc=u"""Averaged from: ['CH2CH2X', 'CH3CHCH2X', 'CH2CCH2X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 101, - label = "RC=*-R-C-*R2", - group = + index = 114, + label = "(CR2N)X", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,D} {4,S} {6,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,S} {4,S} {7,S} {8,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {5,S} -8 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,D} {4,S} {5,S} +3 N u0 p1 c0 {2,D} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-7.57, -2.61, 1.61, 4.87, 9.19, 11.68, 14.45], 'J/(mol*K)'), - H298=(-529.03, 'kJ/mol'), - S298=(-222.29, 'J/(mol*K)'), + Cpdata=([-5.016, -1.971, -0.438, 0.26, 0.613, 0.552, 0.294], 'J/(mol*K)'), + H298=(-58.642, 'kJ/mol'), + S298=(-135.288, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCH2XCH2 single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC--R--CR2 - || | -*********** +shortDesc=u"""Averaged from: ['CH2NHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 102, - label = "RC-*=R=C-*R", - group = + index = 115, + label = "(CR2O)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,S} {4,D} {6,S} -4 R!H u0 p0 c0 {3,D} {5,D} -5 C u0 p0 c0 {2,S} {4,D} {7,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,D} {4,S} {5,S} +3 O u0 p2 c0 {2,D} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.01, 7.65, 10.53, 12.32, 14.26, 15.17, 16.03], 'J/(mol*K)'), - H298=(-370.79, 'kJ/mol'), - S298=(-196.35, 'J/(mol*K)'), + Cpdata=([-2.315, -1.443, -0.922, -0.592, -0.225, -0.051, 0.079], 'J/(mol*K)'), + H298=(-75.558, 'kJ/mol'), + S298=(-122.364, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCXCH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC==R==CR - | | -*********** +shortDesc=u"""Averaged from: ['CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 103, - label = "RC-*=R=C=*", - group = + index = 116, + label = "(CR4)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,D} -3 C u0 p0 c0 {1,S} {4,D} {6,S} -4 R!H u0 p0 c0 {3,D} {5,D} -5 C u0 p0 c0 {2,D} {4,D} -6 R u0 px c0 {3,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 R u0 px c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.81, 3.88, 6.24, 7.94, 10.04, 11.14, 12.17], 'J/(mol*K)'), - H298=(-432.93, 'kJ/mol'), - S298=(-179.15, 'J/(mol*K)'), + Cpdata=([-0.611, 0.464, 1.02, 1.329, 1.626, 1.755, 1.861], 'J/(mol*K)'), + H298=(-50.674, 'kJ/mol'), + S298=(-127.608, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCXC single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC==R==C - | || -*********** +shortDesc=u"""Averaged from: ['CH4X', 'CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX', 'CH3NH2X', +'CH3OHX', 'CH3OCH3X', 'CH3OCH2OHX', 'H2C(OH)OHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 104, - label = "O-*-C-O-*", - group = + index = 117, + label = "(CR3CR3)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,S} -3 O u0 p2 c0 {1,S} {4,S} -4 C u0 p0 c0 {3,S} {5,S} -5 O u0 p2 c0 {2,S} {4,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {2,S} {7,S} {8,S} {9,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} +7 R u0 px c0 {3,S} +8 R u0 px c0 {3,S} +9 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.33, 6.34, 8.03, 9.06, 10.2, 10.82, 11.57], 'J/(mol*K)'), - H298=(-354.62, 'kJ/mol'), - S298=(-179.72, 'J/(mol*K)'), + Cpdata=([0.725, 1.62, 2.083, 2.358, 2.656, 2.793, 2.88], 'J/(mol*K)'), + H298=(-32.083, 'kJ/mol'), + S298=(-137.338, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged OC(XO)XO and H2C(XO)XO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - O--R--O - | | -*********** +shortDesc=u"""Averaged from: ['CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 105, - label = "RC-*=R-O-*", - group = + index = 118, + label = "(CR3N)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,S} {4,D} {6,S} -4 R!H u0 px c0 {3,D} {5,S} -5 O u0 p2 c0 {2,S} {4,S} -6 R u0 px c0 {3,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 N u0 p1 c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.77, 6.69, 9.4, 11.28, 13.55, 14.75, 15.95], 'J/(mol*K)'), - H298=(-446.49, 'kJ/mol'), - S298=(-211.15, 'J/(mol*K)'), + Cpdata=([-7.383, -5.169, -3.741, -2.808, -1.758, -1.219, -0.61], 'J/(mol*K)'), + H298=(-106.092, 'kJ/mol'), + S298=(-141.215, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCHXO single and single -bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC==R--O - | | -*********** +shortDesc=u"""Averaged from: ['CH3NH2X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 106, - label = "C-*R2", - group = + index = 119, + label = "(CR3OR)X", + group= """ -1 * X u0 p0 c0 {2,S} -2 C u0 p0 c0 {1,S} {3,D} {4,S} -3 R!H u0 px c0 {2,D} -4 R u0 px c0 {2,S} +1 X u0 p0 c0 +2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 O u0 p2 c0 {2,S} {7,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} +6 R u0 px c0 {2,S} +7 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.32, 3.63, 5.87, 7.37, 9.08, 9.94, 10.77], 'J/(mol*K)'), - H298=(-285.22, 'kJ/mol'), - S298=(-171.81, 'J/(mol*K)'), + Cpdata=([0.121, 1.214, 1.71, 1.937, 2.093, 2.135, 2.153], 'J/(mol*K)'), + H298=(-60.04, 'kJ/mol'), + S298=(-139.363, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all children on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['CH3OHX', 'CH3OCH3X', 'CH3OCH2OHX', 'H2C(OH)OHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 107, - label = "C=*RCR2", - group = + index = 120, + label = "(NR2)X", + group= """ -1 * X u0 p0 c0 {3,D} -2 C u0 p0 c0 {3,S} {4,S} {5,D} -3 C u0 p0 c0 {1,D} {2,S} {6,S} -4 R u0 px c0 {2,S} -5 R!H u0 px c0 {2,D} -6 R u0 px c0 {3,S} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,D} {4,S} +3 R!H u0 px c0 {2,D} +4 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.82, 4.08, 6.24, 7.7, 9.5, 10.49, 11.57], 'J/(mol*K)'), - H298=(-379.17, 'kJ/mol'), - S298=(-179.05, 'J/(mol*K)'), + Cpdata=([-1.774, -1.224, -0.874, -0.625, -0.309, -0.136, 0.025], 'J/(mol*K)'), + H298=(-109.75, 'kJ/mol'), + S298=(-122.197, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XCHCHCH2 and XCHCHO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR2 - | - C-R - || -*********** +shortDesc=u"""Averaged from: ['OCNHX', 'NHCNHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 108, - label = "C#*CR2", - group = + index = 121, + label = "(N=C)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 C u0 p0 c0 {3,S} {4,S} {5,D} -3 C u0 p0 c0 {1,T} {2,S} -4 R u0 px c0 {2,S} -5 R!H u0 px c0 {2,D} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,D} {4,S} +3 C u0 p0 c0 {2,D} +4 R u0 p0 c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.45, 2.64, 4.89, 6.54, 8.67, 9.9, 11.29], 'J/(mol*K)'), - H298=(-565.15, 'kJ/mol'), - S298=(-180.28, 'J/(mol*K)'), + Cpdata=([-1.774, -1.224, -0.874, -0.625, -0.309, -0.136, 0.025], 'J/(mol*K)'), + H298=(-109.75, 'kJ/mol'), + S298=(-122.197, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCCHCH2 and XCCHO triple-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR2 - | - C - ||| -*********** +shortDesc=u"""Averaged from: ['OCNHX', 'NHCNHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 109, - label = "O-*CR2", - group = + index = 122, + label = "(NR3)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 C u0 p0 c0 {3,S} {4,S} {5,D} -3 O u0 p2 c0 {1,S} {2,S} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,S} {4,S} {5,S} +3 R u0 px c0 {2,S} 4 R u0 px c0 {2,S} -5 R!H u0 px c0 {2,D} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([11.17, 13.37, 14.54, 15.21, 15.91, 16.23, 16.51], 'J/(mol*K)'), - H298=(-228.04, 'kJ/mol'), - S298=(-194.23, 'J/(mol*K)'), + Cpdata=([-4.937, -2.682, -1.327, -0.473, 0.481, 0.961, 1.433], 'J/(mol*K)'), + H298=(-99.581, 'kJ/mol'), + S298=(-139.272, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged XOCHCH2, HOC(O)XO, HC(O)XO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - - CR2 - | - O - | -*********** +shortDesc=u"""Averaged from: ['NH3X', 'OCHNH2X', 'NH2NH2X', 'NH2NCH3CH3X', 'H2NOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 110, - label = "C*RC*", - group = + index = 123, + label = "(NC)X", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,[S,D,T]} -3 C u0 {1,[S,D,T]} {5,[S,D,T]} -4 C u0 {2,[S,D,T]} {5,[S,D,T]} -5 R!H u0 {3,[S,D,T]} {4,[S,D,T]} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,S} {4,S} {5,S} +3 C u0 p0 c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([0.71, 5.77, 9.02, 11.15, 13.56, 14.75, 15.84], 'J/(mol*K)'), - H298=(-461.69, 'kJ/mol'), - S298=(-209.35, 'J/(mol*K)'), + Cpdata=([-3.627, -2.282, -1.489, -0.985, -0.403, -0.095, 0.18], 'J/(mol*K)'), + H298=(-101.157, 'kJ/mol'), + S298=(-138.501, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all child nodes on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['OCHNH2X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 111, - label = "R*bridged-bidentate", - group = + index = 124, + label = "(NN)X", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,[S,D,T]} -3 R!H ux {1,[S,D,T]} {5,[S,D,T]} -4 R!H ux {2,[S,D,T]} {5,[S,D,T]} -5 R!H ux {3,[S,D,T]} {4,[S,D,T]} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,S} {4,S} {5,S} +3 N u0 p1 c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([1.19, 5.91, 8.92, 10.88, 13.11, 14.22, 15.28], 'J/(mol*K)'), - H298=(-446.4, 'kJ/mol'), - S298=(-205.52, 'J/(mol*K)'), + Cpdata=([-6.538, -4.302, -2.97, -2.136, -1.218, -0.762, -0.308], 'J/(mol*K)'), + H298=(-119.234, 'kJ/mol'), + S298=(-150.696, 'J/(mol*K)'), ), - shortDesc=u"""Averaged from all child nodes on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. -*********** +shortDesc=u"""Averaged from: ['NH2NH2X', 'NH2NCH3CH3X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 112, - label = "C*RO*", - group = + index = 125, + label = "(NO)X", + group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,S} -3 C u0 {1,[S,D,T]} {5,[S,D,T]} -4 O u0 p2 {2,S} {5,S} -5 R!H u0 px {3,[S,D,T]} {4,S} +1 X u0 p0 c0 +2 * N u0 p1 c0 {3,S} {4,S} {5,S} +3 O u0 p2 c0 {2,S} +4 R u0 px c0 {2,S} +5 R u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([2.77, 6.69, 9.4, 11.28, 13.55, 14.75, 15.95], 'J/(mol*K)'), - H298=(-446.49, 'kJ/mol'), - S298=(-211.15, 'J/(mol*K)'), + Cpdata=([-4.993, -3.162, -2.106, -1.465, -0.78, -0.451, -0.141], 'J/(mol*K)'), + H298=(-83.038, 'kJ/mol'), + S298=(-132.089, 'J/(mol*K)'), ), - shortDesc=u"""Same as child node RC-*=R-O-*""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. +shortDesc=u"""Averaged from: ['H2NOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 113, - label = "O*RO*", - group = + index = 126, + label = "(OR)X", + group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,S} -3 O u0 p2 c0 {1,S} {5,S} -4 O u0 p2 c0 {2,S} {5,S} -5 R!H u0 px c0 {3,S} {4,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,D} +3 R!H u0 p1 c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([3.33, 6.34, 8.03, 9.06, 10.2, 10.82, 11.57], 'J/(mol*K)'), - H298=(-354.62, 'kJ/mol'), - S298=(-179.72, 'J/(mol*K)'), + Cpdata=([-3.606, -2.304, -1.526, -1.013, -0.385, -0.041, 0.25], 'J/(mol*K)'), + H298=(-139.797, 'kJ/mol'), + S298=(-141.385, 'J/(mol*K)'), ), - shortDesc=u"""Came from averaged OC(XO)XO and H2C(XO)XO on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - O--R--O - | | -*********** +shortDesc=u"""Averaged from: ['ONNH2X', 'ONNCH3CH3X', 'ONOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 114, - label = "C#*-R-C-*R2", - group = + index = 127, + label = "(ONR)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,T} {4,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,S} {4,S} {6,S} {7,S} -6 R u0 px c0 {5,S} -7 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,D} +3 N u0 p1 c0 {2,D} {4,S} +4 R u0 px c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.53, 3.81, 6.89, 9.14, 12.06, 13.73, 15.5], 'J/(mol*K)'), - H298=(-477.2, 'kJ/mol'), - S298=(-200.61, 'J/(mol*K)'), + Cpdata=([-3.606, -2.304, -1.526, -1.013, -0.385, -0.041, 0.25], 'J/(mol*K)'), + H298=(-139.797, 'kJ/mol'), + S298=(-141.385, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCCH2XCH2 double-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C--R--CR2 - ||| | -*********** +shortDesc=u"""Averaged from: ['ONNH2X', 'ONNCH3CH3X', 'ONOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 115, - label = "C#*-R=C-*R", - group = + index = 128, + label = "(ONN)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {5,S} -3 C u0 p0 c0 {1,T} {4,S} -4 R!H u0 px c0 {3,S} {5,D} -5 C u0 p0 c0 {2,S} {4,D} {6,S} -6 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,D} +3 N u0 p1 c0 {2,D} {4,S} +4 N u0 p2 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([6.8, 11.4, 13.67, 14.88, 16.0, 16.45, 16.74], 'J/(mol*K)'), - H298=(-402.33, 'kJ/mol'), - S298=(-202.29, 'J/(mol*K)'), + Cpdata=([-2.633, -1.581, -1.003, -0.651, -0.264, -0.073, 0.086], 'J/(mol*K)'), + H298=(-143.729, 'kJ/mol'), + S298=(-139.884, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCHXC single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C--R==CR - ||| | -*********** +shortDesc=u"""Averaged from: ['ONNH2X', 'ONNCH3CH3X']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 116, - label = "C#*-R-C#*", - group = + index = 129, + label = "(ONOR)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {5,T} -3 C u0 p0 c0 {1,T} {4,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,T} {4,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,D} +3 N u0 p1 c0 {2,D} {4,S} +4 O u0 p2 c0 {3,S} {5,S} +5 R u0 px c0 {4,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-4.88, 4.76, 10.17, 13.18, 15.82, 16.67, 17.03], 'J/(mol*K)'), - H298=(-671.16, 'kJ/mol'), - S298=(-243.65, 'J/(mol*K)'), + Cpdata=([-5.553, -3.751, -2.573, -1.736, -0.625, 0.024, 0.577], 'J/(mol*K)'), + H298=(-131.932, 'kJ/mol'), + S298=(-144.387, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCCH2XC single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C--R--C - ||| ||| -*********** +shortDesc=u"""Averaged from: ['ONOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 117, - label = "RC=*-R-C=*R", - group = + index = 130, + label = "(OR2)X", + group= """ -1 * X u0 p0 c0 {3,D} -2 X u0 p0 c0 {5,D} -3 C u0 p0 c0 {1,D} {4,S} {6,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,D} {4,S} {7,S} -6 R u0 px c0 {3,S} -7 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,S} {4,S} +3 R u0 p[0,1,2] c0 {2,S} +4 R u0 p[0,1,2] c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([5.9, 10.63, 13.33, 14.98, 16.74, 17.49, 17.8], 'J/(mol*K)'), - H298=(-230.02, 'kJ/mol'), - S298=(-203.94, 'J/(mol*K)'), + Cpdata=([-3.434, -2.005, -1.266, -0.832, -0.334, -0.054, 0.209], 'J/(mol*K)'), + H298=(-44.072, 'kJ/mol'), + S298=(-101.295, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCH2XCH single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - RC--R--CR - || || -*********** +shortDesc=u"""Averaged from: ['H2OX', 'HOOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) entry( - index = 118, - label = "C#*-R-C=*R", - group = + index = 131, + label = "(OROR)X", + group= """ -1 * X u0 p0 c0 {3,T} -2 X u0 p0 c0 {5,D} -3 C u0 p0 c0 {1,T} {4,S} -4 R!H u0 px c0 {3,S} {5,S} -5 C u0 p0 c0 {2,D} {4,S} {6,S} -6 R u0 px c0 {5,S} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,S} {4,S} +3 O u0 p2 c0 {2,S} {5,S} +4 R u0 p0 c0 {2,S} +5 R u0 p0 c0 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.0, 5.76, 9.53, 11.98, 14.68, 15.93, 16.88], 'J/(mol*K)'), - H298=(-457.3, 'kJ/mol'), - S298=(-222.49, 'J/(mol*K)'), + Cpdata=([-1.999, -1.084, -0.634, -0.367, -0.023, 0.197, 0.393], 'J/(mol*K)'), + H298=(-65.492, 'kJ/mol'), + S298=(-110.352, 'J/(mol*K)'), ), - shortDesc=u"""Came from XCHCH2XC single-bonded on Pt(111)""", - longDesc=u"""Calculated by Bjarne Kreitz at Brown University using statistical mechanics (files: compute_NASA_for_Pt-adsorbates.ipynb and compute_NASA_for_Pt-gas_phase.ipynb). - Based on DFT calculations by Bjarne Kreitz from Brown University. DFT calculations were performed with Quantum Espresso - using PAW pseudopotentials and the BEEF-vdW functional for an optimized 3x3 supercell (1/9ML coverage) - following the procedure outlined by Blondal et al (DOI:10.1021/acs.iecr.9b01464). The following settings were applied: - kpoints=(5x5x1), 4 layers (2 bottom layers fixed), ecutwfc=60 Ry, smearing='mazari-vanderbilt', mixing_mode='local-TF',fmax=2.5e-2. - See Kreitz et al. 2023 (DOI:10.1021/acscatal.2c03378) for details on the DFT method. - C--R--CR - ||| || -*********** +shortDesc=u"""Averaged from: ['HOOHX']""", +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_kinetic +s_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. """, metal = "Pt", facet = "111", ) - tree( """ -L1: R* - L2: R*bridged-bidentate - L3: C*RC* - L4: C=*=R-C-*R2 - L4: R2C-*-R-C-*R2 - L4: RC=*-R=C-*R - L4: RC-*=R-C-*R2 - L4: RC=*-R-C-*R2 - L4: RC-*=R=C-*R - L4: RC-*=R=C=* - L4: C#*-R-C-*R2 - L4: C#*-R=C-*R - L4: C#*-R-C#* - L4: RC=*-R-C=*R - L4: C#*-R-C=*R - L3: C*RO* - L4: RC-*=R-O-* - L3: O*RO* - L4: O-*-C-O-* - L2: R*bidentate - L3: C*C* - L4: C-*C-* - L4: C=*RC=*R - L4: C-*R2C-*R2 - L4: C-*R2C=*R - L4: C-*RC=* - L4: C=*RC-*R - L4: C#*C-*R - L4: C#*C-*R2 - L4: C#*C=*R - L4: C-*R2C-*R - L4: C-*RC-*R - L3: C*N* - L4: C-*R2N=* - L4: C-*R2N-*R - L4: C=*N-* - L4: C=*RN=* - L4: C=*RN-*R - L3: C*O* - L4: C=*RO-* - L4: C-*R2O-* - L3: N*N* - L4: N-*RN-*R - L4: N-*RN=* - L3: N*O* - L4: N=*O-* - L3: O*O* - L2: R*single-chemisorbed - L3: C* - L4: Cq* - L4: C#*R - L5: C#*CR3 - L5: C#*NR2 - L5: C#*OR - L5: C#*CR2 - L4: C=*R2 - L5: C=*RCR3 - L5: C=*RNR2 - L5: C=*ROR - L5: C=*RCR2 - L4: C=*(=R) - L5: C=*(=C) - L5: C=*(=NR) - L4: C-*R3 - L5: C-*R2CR3 - L5: C-*R2NR2 - L5: C-*R2OR - L4: C-*R2 - L5: C-*RO - L5: C-*RCR2 - L5: C-*RNR - L3: N* - L4: N#* - L4: N=*R - L5: N=*CR3 - L5: N=*NR2 - L5: N=*OR - L4: N-*R2 - L5: N-*RCR3 - L5: N-*RNR2 - L5: N-*ROR - L5: N-*CR2 - L5: N-*NR - L5: N-*O - L3: O* - L4: O=* - L4: O-*R - L5: O-*CR3 - L5: O-*CR2 - L5: O-*NR2 - L5: O-*OR - L2: R*vdW - L3: (CR4)* - L4: (CR3CR3)* - L4: (CR3NR2)* - L4: (CR3OR)* - L3: (CR3)* - L4: (CR2NR)* - L4: (CR2CR)* - L4: (CR2O)* - L3: (CR2)* - L4: (CRN)* - L4: (CRCR)* - L3: (NR3)* - L4: (NR2NR2)* - L4: (NR2OR)* - L3: (N=[O,N]R)* - L4: (NRO)* - L4: (NRNR)* - L3: (OR2)* - L4: (OROR)* +L1: RX + L2: RXbidentate + L3: CXCX + L4: C#XC-XR + L4: C#XC-XR2 + L4: C#XC=XR + L4: C-XC-X + L4: C-XR2C-XR + L4: C-XR2C-XR2 + L4: C-XR2C=XR + L4: C-XRC-XR + L4: C-XRC=X + L4: C=XRC-XR + L4: C=XRC=XR + L3: CXNX + L4: C-XR2N-XR + L4: C-XR2N=X + L4: C-XRN-X + L4: C-XRN-XR + L4: C-XRN=X + L4: C=XRN-XR + L4: C=XRN=X + L3: CXOX + L4: C-XR2O-X + L4: C-XRO-X + L4: C=XRO-X + L3: NXCX + L4: inv(C-XR2N-XR) + L4: inv(C-XR2N=X) + L4: inv(C-XRN-X) + L4: inv(C-XRN-XR) + L4: inv(C-XRN=X) + L4: inv(C=XRN-XR) + L4: inv(C=XRN=X) + L3: NXNX + L4: N-XRN-XR + L4: N-XRN=X + L3: NXOX + L4: N-XRO-X + L4: N[+]=XR[-]O-X + L3: OXOX + L2: RXbridgedBidentate + L3: CXRCX + L4: C#X-R-C#X + L4: C#X-R-C-XR2 + L4: C#X-R-C=XR + L4: C#X-R=C-XR + L4: C=X=R-C-XR2 + L4: R2C-X-R-C-XR2 + L4: RC-X=R-C-XR2 + L4: RC-X=R=C-XR + L4: RC-X=R=C=X + L4: RC=X-R-C-XR2 + L4: RC=X-R-C=XR + L4: RC=X-R=C-XR + L3: CXROX + L4: RC-X=R-O-X + L3: OXROX + L4: O-X-C-O-X + L2: RXsingleChemisorbed + L3: CX + L4: C#XR + L5: C#XCR2 + L5: C#XCR3 + L5: C#XN + L5: C#XOR + L4: C-XR2 + L5: C-XRCR2 + L5: C-XRN + L5: C-XRNR + L5: C-XRO + L4: C-XR3 + L5: C-XR2CR3 + L5: C-XR2N + L5: C-XR2OR + L4: C=X(=R) + L5: C=X(=C) + L5: C=X(=NR) + L4: C=XR2 + L5: C=XRCR2 + L5: C=XRCR3 + L5: C=XRN + L5: C=XROR + L3: NX + L4: N-XR + L5: N-XCR + L5: N-XCR2 + L5: N-XNR + L4: N-XR2 + L5: N-XRCR + L5: N-XRCR3 + L5: N-XRNR + L5: N-XRNR2 + L5: N-XROR + L5: N[+]-XR[-]R + L5: N[+]=XR[-]R + L4: N=XR + L5: N=XC#R + L5: N=XC-R + L5: N=XN + L5: N=XOR + L3: OX + L4: O-XR + L5: O-XCR2 + L5: O-XCR3 + L5: O-XN + L5: O-XOR + L2: RXvdW + L3: (CR2)X + L4: (CRCR)X + L4: (CRN)X + L3: (CR3)X + L4: (CR2CR)X + L4: (CR2N)X + L4: (CR2O)X + L3: (CR4)X + L4: (CR3CR3)X + L4: (CR3N)X + L4: (CR3OR)X + L3: (NR2)X + L4: (N=C)X + L3: (NR3)X + L4: (NC)X + L4: (NN)X + L4: (NO)X + L3: (OR)X + L4: (ONR)X + L5: (ONN)X + L5: (ONOR)X + L3: (OR2)X + L4: (OROR)X """, )