From ae536ee387fef4909941ae5ffb3e1e6632466ef1 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Wed, 8 Apr 2026 16:27:24 -0400 Subject: [PATCH 01/17] updating all adsorption correction nodes to include new nitrogen chemistry and to resolve bugs in computing the values previously --- input/thermo/groups/adsorptionPt111.py | 5583 +++++++++++++----------- 1 file changed, 3077 insertions(+), 2506 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 72a10e1a78..d2ee5e2bba 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 {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]} +""", + 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', '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', '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', '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', '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', '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', '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 +302,34 @@ 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', '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 +337,32 @@ 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', '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 +370,31 @@ 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', '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 +402,32 @@ 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', '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 +435,32 @@ 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', '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 +468,31 @@ 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 p[0,1] c[0,+1] {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 +500,33 @@ 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', '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 +534,32 @@ 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', '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 +567,31 @@ 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 p2 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', '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 +599,32 @@ 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', '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 +632,31 @@ 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', '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 +664,32 @@ 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', '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", @@ -695,88 +697,95 @@ 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', '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 = 23, + label = "CXOX", + 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} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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 = 24, - label = "N-*RNR2", - group = + label = "C-XR2O-X", + 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} +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=([1.57, 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=([0.468, 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 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', '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", @@ -784,30 +793,31 @@ entry( index = 25, - label = "N-*NR", - group = + label = "C-XRO-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,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=([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=([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 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: ['XOXCNH', '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", @@ -815,31 +825,31 @@ entry( index = 26, - label = "N=*NR2", - group = + 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,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} """, 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=([-2.405, 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 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: ['XCHXO', '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", @@ -847,30 +857,31 @@ entry( index = 27, - label = "N-*RN-*R", - group = + label = "NXCX", + group= """ -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 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 {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 p[0,1] c[0,+1] {2,[S,D]} {3,[S,D]} """, 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=([-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 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: ['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", @@ -878,31 +889,33 @@ entry( index = 28, - label = "N-*RCR3", - group = + label = "inv(C-XR2N-XR)", + 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} +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=([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=([-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 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', '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", @@ -910,31 +923,32 @@ entry( index = 29, - label = "N-*CR2", - group = + label = "inv(C-XR2N=X)", + 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,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=([1.62, 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=([-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 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: ['XCH2XN', '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", @@ -942,125 +956,129 @@ entry( index = 30, - label = "N=*CR3", - group = + label = "inv(C-XRN-X)", + 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", -# ) +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 p2 c0 {2,S} {3,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""Averaged from: ['XCHXN', '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 = 32, - label = "Cq*", - group = + index = 31, + label = "inv(C-XRN-XR)", + 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,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=([-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=([-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 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: ['NHXCXNH', 'XNHXCO', '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 = 33, - label = "C-*C-*", - group = + index = 32, + label = "inv(C-XRN=X)", + group= """ -1 * X u0 p0 c0 {3,D} +1 * X u0 p0 c0 {3,S} 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} +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=([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=([-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 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. +shortDesc=u"""Averaged from: ['XNXCO', 'XNXCNH', '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", +) - C==C - || || -*********** +entry( + index = 33, + label = "inv(C=XRN-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 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=([-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"""Averaged from: ['XCHXNH', 'OHXCXNH', '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", @@ -1068,35 +1086,31 @@ entry( index = 34, - label = "C=*(=R)", - group = + label = "inv(C=XRN=X)", + 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,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=([2.94, 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=([-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 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: ['XCHXN', 'XNXCOH', '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", @@ -1104,35 +1118,30 @@ entry( index = 35, - label = "C#*CR3", - group = + label = "NXNX", + 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 {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]} """, 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=([-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 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: ['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", @@ -1140,32 +1149,32 @@ entry( index = 36, - label = "C#*R", - group = + label = "N-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,S} +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} """, 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=([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 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: ['XNHXNH', 'CH3XNXNOH', '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", @@ -1173,33 +1182,31 @@ entry( index = 37, - label = "C=*RC=*R", - group = + label = "N-XRN=X", + group= """ -1 * X u0 p0 c0 {3,D} +1 * X u0 p0 c0 {3,S} 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} +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=([-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=([-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 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: ['XNHXN', 'XNXNCH3', '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", @@ -1207,31 +1214,30 @@ entry( index = 38, - label = "C=*R2", - group = + label = "NXOX", + 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} +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=([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=([-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 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: ['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", @@ -1239,35 +1245,31 @@ entry( index = 39, - label = "C-*R2C-*R2", - group = + label = "N-XRO-X", + 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 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=([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=([-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 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: ['XOXNH', '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", @@ -1275,32 +1277,31 @@ entry( index = 40, - label = "C-*R3", - group = + label = "N[+]=XR[-]O-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,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 u0 px c-1 {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=([-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 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: ['XOXNO', '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", @@ -1308,36 +1309,30 @@ entry( index = 41, - label = "(CR3CR3)*", - group = + label = "OXOX", + 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} +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=([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=([-3.845, -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 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: ['XOXO', '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", @@ -1345,33 +1340,33 @@ entry( index = 42, - label = "(CR4)*", - group = + label = "RXbridgedBidentate", + 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 {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=([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=([-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 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: ['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", @@ -1379,28 +1374,33 @@ entry( index = 43, - label = "C=*N-*", - group = + label = "CXRCX", + 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 {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=([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=([-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 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: ['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", @@ -1408,30 +1408,31 @@ entry( index = 44, - label = "C=*(=NR)", - group = + label = "C#X-R-C#X", + 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,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=([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=([-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 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: ['XCCH2XC', '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", @@ -1439,170 +1440,169 @@ entry( index = 45, - label = "C#*NR2", - group = + label = "C#X-R-C-XR2", + 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 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=([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=([-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 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: ['XCCH2XCH2', '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", ) - -## 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 = 46, + label = "C#X-R-C=XR", + 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 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=([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=([-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 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: ['XCHCH2XC', '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 = 48, - label = "C-*R2C=*R", - group = + index = 47, + label = "C#X-R=C-XR", + 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,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=([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=([-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 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: ['XCHCHXC', '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 = 49, - label = "C-*R2CR3", - group = + index = 48, + 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,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=([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=([-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"""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. +shortDesc=u"""Averaged from: ['XCCHXCH2', '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", +) - R - | - R-C-CR3 - | -*********** +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', '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", @@ -1610,31 +1610,34 @@ entry( index = 50, - label = "(CR2NR)*", - group = + label = "RC-X=R-C-XR2", + 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,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=([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=([-8.191, -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"""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: ['XCHCHXCH2', '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", @@ -1642,33 +1645,33 @@ entry( index = 51, - label = "C-*R2NR2", - group = + label = "RC-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,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=([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=([-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"""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: ['XCHCXCH', '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", @@ -1676,32 +1679,32 @@ entry( index = 52, - label = "(CR2O)*", - group = + label = "RC-X=R=C=X", + group= """ -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} +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=([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=([-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"""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: ['XCHCXC', '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", @@ -1709,35 +1712,34 @@ entry( index = 53, - label = "C-*R2OR", - group = + label = "RC=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 O u0 p2 c0 {2,S} {6,S} -4 R u0 px c0 {2,S} -5 R u0 px c0 {2,S} +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=([-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=([-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"""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: ['XCHCH2XCH2', '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", @@ -1745,33 +1747,33 @@ entry( index = 54, - label = "(CR3NR2)*", - group = + label = "RC=X-R-C=XR", + 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 {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=([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=([-2.417, 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"""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: ['XCHCH2XCH', '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", @@ -1779,34 +1781,33 @@ entry( index = 55, - label = "(CR3OR)*", - group = + label = "RC=X-R=C-XR", + 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 {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=([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=([-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"""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: ['XCHCHXCH', '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", @@ -1814,69 +1815,65 @@ entry( index = 56, - label = "C-*RC=*", - group = + label = "CXROX", + 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} -5 R u0 px c0 {3,S} +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=([-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=([-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"""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: ['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 = "C-*RCR2", - group = + label = "RC-X=R-O-X", + 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} -4 R u0 px c0 {2,S} -5 R u0 px c0 {3,S} -6 R u0 px c0 {3,S} +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=([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=([-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"""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. - - CR2 - || - C-R - | -*********** +shortDesc=u"""Averaged from: ['XCHCHXO', '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", @@ -1884,36 +1881,31 @@ entry( index = 58, - label = "C=*RCR3", - group = + label = "OXROX", + 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} -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 {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=([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=([-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"""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: ['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", @@ -1921,29 +1913,31 @@ entry( index = 59, - label = "(CRN)*", - group = + label = "O-X-C-O-X", + 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 {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=([-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=([-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"""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: ['XOC(O)XO', 'H2C(XO)XO', '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", @@ -1951,31 +1945,38 @@ entry( index = 60, - label = "C=*RN=*", - group = + label = "RXsingleChemisorbed", + 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 {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=([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=([-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"""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: ['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", @@ -1983,31 +1984,34 @@ entry( index = 61, - label = "C-*RNR", - group = + label = "CX", + 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 {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=([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=([-8.018, -4.922, -2.931, -1.615, -0.092, 0.703, 1.567], 'J/(mol*K)'), + H298=(-354.778, 'kJ/mol'), + S298=(-169.809, '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. - - NR - || - C-R - | -*********** +shortDesc=u"""Averaged from: ['XCN', '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", @@ -2015,30 +2019,30 @@ entry( index = 62, - label = "C=*RN-*R", - group = + label = "C#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 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,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=([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=([-10.659, -6.972, -4.601, -3.041, -1.246, -0.288, 0.897], 'J/(mol*K)'), + H298=(-549.985, 'kJ/mol'), + S298=(-176.816, '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. - - RC--NR - || | -*********** +shortDesc=u"""Averaged from: ['XCH', '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", @@ -2046,32 +2050,31 @@ entry( index = 63, - label = "C=*RNR2", - group = + label = "C#XCR2", + 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} +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=([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=([-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"""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: ['XCCHCH2', 'XCCHO', '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", @@ -2079,33 +2082,32 @@ entry( index = 64, - label = "C-*RO", - group = + label = "C#XCR3", + 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,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=([-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=([-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 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: ['XCCH3', 'XCCH2CH3', 'XCCH2OH', '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", @@ -2113,34 +2115,29 @@ entry( index = 65, - label = "C=*RO-*", - group = + label = "C#XN", + 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} +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=([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=([-4.802, -2.781, -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 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: ['XCNO', 'XCNH2', '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", @@ -2148,34 +2145,30 @@ entry( index = 66, - label = "C=*ROR", - group = + label = "C#XOR", + 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} +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=([-0.05, 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=([-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 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: ['XCOH', '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", @@ -2183,26 +2176,32 @@ entry( index = 67, - label = "C*", - group = + label = "C-XR2", + group= """ -1 * X u0 {2,[S,D,T,Q]} -2 C ux {1,[S,D,T,Q]} +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=([-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=([-8.007, -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"""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: ['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", @@ -2210,38 +2209,64 @@ entry( index = 68, - label = "N*", - group = + label = "C-XRCR2", + group= """ -1 * X u0 {2,[S,D,T]} -2 N ux {1,[S,D,T]} +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=([-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"""Averaged from: ['CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3', +'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. """, - 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 = + label = "C-XRN", + group= """ -1 * X u0 {2,[S,D]} -2 O ux {1,[S,D]} +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 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=([-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 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: ['OXCNH2', 'NH2XCNH', '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", @@ -2249,26 +2274,31 @@ entry( index = 70, - label = "R*single-chemisorbed", - group = + label = "C-XRNR", + 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 C u0 p0 c0 {1,S} {3,D} {4,S} +3 N u0 p1 c0 {2,D} {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=([0.84, 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=([-8.453, -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"""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: ['XCHNH', 'OHXCNH', 'NH2XCNH', '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", @@ -2276,28 +2306,31 @@ entry( index = 71, - label = "C*C*", - group = + label = "C-XRO", + 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 {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=([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=([-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 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: ['XCHO', 'XCOOH', 'CH3XCO', 'XCCHO', 'CH3CH2XCO', '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", @@ -2305,44 +2338,68 @@ entry( index = 72, - label = "C*N*", - group = + label = "C-XR3", + 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]} +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} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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. """, - thermo=u'C=*RN-*R', - longDesc=u"""Thermo is currently for C=*RN-*R. Maybe should average all the children instead?""", + metal = "Pt", + facet = "111", ) -#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 = + label = "C-XR2CR3", + 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 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=([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=([-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"""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: ['XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', 'CH3XCHCH3', 'CH3XCHOH', +'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", @@ -2350,42 +2407,64 @@ entry( index = 74, - label = "N*N*", - group = + label = "C-XR2N", + 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} +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=([-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"""Averaged from: ['XCH2NH2', '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. """, - 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 = + label = "C-XR2OR", + 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 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=([1.59, 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=([-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"""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: ['XCH2OH', 'CH3XCHOH', '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", @@ -2393,26 +2472,29 @@ entry( index = 76, - label = "R*vdW", - group = + label = "C=X(=R)", + group= """ -1 * X u0 -2 R u0 +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=([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=([-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 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: ['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", @@ -2420,89 +2502,125 @@ entry( index = 77, - label = "N*O*", - group = + label = "C=X(=C)", + 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", -#) +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=([-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"""Averaged from: ['XCCO', 'XCCCH2', 'XCCH2', '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", +) + +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', '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 = 79, - label = "N#*", - group = + label = "C=XR2", + group= """ -1 * X u0 p0 {2,T} -2 N u0 p1 {1,T} +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} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-7.731, -4.344, -2.287, -0.973, 0.53, 1.334, 2.269], 'J/(mol*K)'), + H298=(-355.755, 'kJ/mol'), + S298=(-165.599, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XCH2', '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. """, - thermo=u'N*', metal = "Pt", facet = "111", ) + entry( index = 80, - label = "(CR3)*", - group = + label = "C=XRCR2", + 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 {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=([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=([-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"""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: ['XCHCHCH2', 'XCHCHO', '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", @@ -2510,60 +2628,98 @@ entry( index = 81, - label = "(CR2)*", - group = + label = "C=XRCR3", + 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 {3,D} +2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,S} +3 C u0 p0 c0 {1,D} {2,S} {7,S} +4 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=([-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"""Averaged from: ['CH3XCCH3', 'CH3XCOH', 'XCHCH2CH3', 'XCHCH3', '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. """, - thermo=u'(CRCR)*', metal = "Pt", facet = "111", ) entry( index = 82, - label = "(N=[O,N]R)*", - group = + label = "C=XRN", + 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,D} +2 C u0 p0 c0 {1,D} {3,S} {4,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=([-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"""Averaged from: ['XCHNH2', 'OHXCNH2', 'NH2XCNH2', '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. """, - 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 = + label = "C=XROR", + 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 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=([0.83, 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=([-8.363, -5.498, -3.838, -2.789, -1.537, -0.826, -0.079], 'J/(mol*K)'), + H298=(-328.365, 'kJ/mol'), + S298=(-146.569, '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: ['XCHOH', 'CH3XCOH', '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", @@ -2571,32 +2727,30 @@ entry( index = 84, - label = "(CRCR)*", - group = + label = "NX", + 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 {2,[S,D,T]} +2 N u0 {1,[S,D,T]} """, 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=([-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"""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: ['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. """, metal = "Pt", facet = "111", @@ -2604,30 +2758,29 @@ entry( index = 85, - label = "C-*R2N=*", - group = + label = "N-XR", + 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,S} +2 N u0 p1 c0 {1,S} {3,D} +3 R u0 px c0 {2,D} """, 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=([-5.612, -2.994, -1.557, -0.731, 0.066, 0.407, 0.755], 'J/(mol*K)'), + H298=(-212.616, 'kJ/mol'), + S298=(-165.284, '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: ['XNO', '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", @@ -2635,31 +2788,30 @@ entry( index = 86, - label = "C-*R2N-*R", - group = + label = "N-XCR", + 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 {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=([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=([-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"""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: ['XNCNH', 'XNCO', '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", @@ -2667,1147 +2819,1566 @@ entry( index = 87, - label = "C=*(=C)", - group = + label = "N-XCR2", + 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 {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=([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=([-1.707, 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"""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. +shortDesc=u"""Averaged from: ['XNCH2', '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", +) - C - || - C - || -*********** +entry( + index = 88, + label = "N-XNR", + 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 px c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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: ['XNNH', 'XNNCH3', '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", +) -Because the C atom bonded to the surface only has one ligand -not two, it is not a child of the C=*R2 node +entry( + index = 89, + label = "N-XR2", + group= +""" +1 * X u0 p0 c0 {2,[S,D]} +2 N u0 px cx {1,[S,D]} {3,[S,D]} {4,S} +3 R u0 px c0 {2,[S,D]} +4 R u0 px cx {2,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-3.272, 0.246, 2.345, 3.646, 5.068, 5.797, 6.65], 'J/(mol*K)'), + H298=(-219.998, 'kJ/mol'), + S298=(-171.405, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNH2', '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. """, metal = "Pt", facet = "111", ) entry( - index = 88, - label = "C-*R2O-*", - group = + index = 90, + label = "N-XRCR", + group= +""" +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=([-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: ['XNHCHO', '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 = 91, + label = "N-XRCR3", + 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} +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=([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 from: ['XNHCH3', '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 = 92, + label = "N-XRNR", + 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,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', '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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 93, + label = "N-XRNR2", + 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 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=([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=([-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"""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. +shortDesc=u"""Averaged from: ['XNHNH2', '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", +) - R2C--O - | | -*********** +entry( + index = 94, + label = "N-XROR", + 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 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', '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. """, metal = "Pt", facet = "111", ) entry( - index = 89, - label = "(CR2CR)*", - group = + index = 95, + label = "N[+]-XR[-]R", + 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} +1 * X u0 p0 c0 {2,S} +2 N u0 p0 c+1 {1,S} {3,S} {4,D} +3 R!H u0 px 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', '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. +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 96, + label = "N[+]=XR[-]R", + group= +""" +1 * X u0 p0 c0 {2,D} +2 N u0 p0 c+1 {1,D} {3,S} {4,S} +3 R!H u0 px c-1 {2,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=([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=([-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 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: ['HXNO', 'CH3NXNOH', 'CH3XNNOH', '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 = 97, + label = "N=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} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-8.824, -4.476, -2.143, -0.868, 0.283, 0.764, 1.399], 'J/(mol*K)'), + H298=(-328.269, 'kJ/mol'), + S298=(-168.676, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XNH', '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 = 90, - label = "C=*RC-*R", - group = + index = 98, + label = "N=XC#R", + group= +""" +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 u0 px c0 {3,T} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""Averaged from: ['XNCN', '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 = 99, + label = "N=XC-R", + 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} +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=([-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=([-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 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: ['XNCH3', '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 = 91, - label = "C#*C-*R", - group = + index = 100, + label = "N=XN", + 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 {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=([2.41, 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=([2.988, 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 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: ['XNNH2', '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 = 92, - label = "C#*C-*R2", - group = + index = 101, + label = "N=XOR", + 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 {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=([-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=([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 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: ['XNOH', '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 = 102, + label = "OX", + group= +""" +1 * X u0 {2,[S,D]} +2 O ux {1,[S,D]} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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 = 93, - label = "C-*R2C-*R", - group = + index = 103, + label = "O-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} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-5.27, -3.412, -2.328, -1.644, -0.868, -0.448, 0.09], 'J/(mol*K)'), + H298=(-192.597, 'kJ/mol'), + S298=(-151.553, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XOH', '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 = 104, + label = "O-XCR2", + 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 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=([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=([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 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: ['XOCHCH2', 'HC(O)XO', 'XOC(OH)O', '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 = 95, - label = "C-*RC-*R", - group = + index = 105, + label = "O-XCR3", + 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} +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=([-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=([-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 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: ['XOCH3', 'XOCH2CH3', 'XOCH2OH', '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 = 96, - label = "C#*C=*R", - group = + index = 106, + label = "O-XN", + 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 p0 c0 {3,S} +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=([-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=([-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"""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: ['XONH2', '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 = 97, - label = "C=*=R-C-*R2", - group = + 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=([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"""Averaged from: ['XOOH', '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 = 108, + label = "RXvdW", + group= +""" +1 * X u0 +2 R u0 +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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 = 109, + label = "(CR2)X", + group= +""" +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=([-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"""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 = 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, -7.929, -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', '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', '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', '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', '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', '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=([-0.627, 0.38, 0.901, 1.19, 1.469, 1.59, 1.685], 'J/(mol*K)'), + H298=(-46.964, 'kJ/mol'), + S298=(-118.627, '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', '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', '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', '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', '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} +3 C u0 p0 c0 {2,D} """, 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=([-1.773, -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', '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=([-4.613, -2.128, -0.623, 0.333, 1.405, 1.947, 2.484], 'J/(mol*K)'), + H298=(-95.524, 'kJ/mol'), + S298=(-136.79, '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', '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} +3 C u0 p0 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', '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} +3 N u0 p1 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', '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} +3 O u0 p2 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', '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 u0 px 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', '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', '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=([-3.913, -2.311, -1.477, -0.988, -0.437, -0.138, 0.148], 'J/(mol*K)'), + H298=(-36.933, 'kJ/mol'), + S298=(-98.276, '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', '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', '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 """, ) From 036e81b2b5fbe2fff4e3c7a2ca162b7596d9ec8d Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Wed, 8 Apr 2026 17:31:48 -0400 Subject: [PATCH 02/17] fixing duplication bug where species at the top level of a group/node were duplicated, but children were not --- input/thermo/groups/adsorptionPt111.py | 299 ++++++++++++------------- 1 file changed, 144 insertions(+), 155 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index d2ee5e2bba..b62384c89f 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -120,7 +120,7 @@ H298=(-442.76, 'kJ/mol'), S298=(-204.353, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCXCCH2', 'XCXCCH2']""", +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 @@ -153,7 +153,7 @@ H298=(-438.941, 'kJ/mol'), S298=(-201.882, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCXCH2', 'XCXCHCH3', 'XCXCH2', 'XCXCHCH3']""", +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 @@ -185,7 +185,7 @@ H298=(-491.004, 'kJ/mol'), S298=(-152.622, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCXCCH3', 'XCXCCH3']""", +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 @@ -216,7 +216,7 @@ H298=(-617.066, 'kJ/mol'), S298=(-172.682, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCXC', 'XCXC']""", +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 @@ -250,7 +250,7 @@ H298=(-182.472, 'kJ/mol'), S298=(-191.92, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XCCH2', 'XCH2XCCH2']""", +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 @@ -285,7 +285,7 @@ H298=(-126.568, 'kJ/mol'), S298=(-192.345, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XCH2', 'CH3XCHXCH2', 'XCH2XCH2', 'CH3XCHXCH2']""", +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 @@ -319,8 +319,7 @@ H298=(-333.29, 'kJ/mol'), S298=(-214.968, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XCH', 'XCH2XCOH', 'XCHXCHCH3', 'XCH2XCH', 'XCH2XCOH', -'XCHXCHCH3']""", +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 @@ -353,7 +352,7 @@ H298=(-230.06, 'kJ/mol'), S298=(-194.29, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXCCH3', 'XCHXCCH3']""", +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 @@ -385,7 +384,7 @@ H298=(-444.24, 'kJ/mol'), S298=(-193.307, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXC', 'XCHXC']""", +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 @@ -418,7 +417,7 @@ H298=(-400.07, 'kJ/mol'), S298=(-211.081, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXCO', 'XCHXCO']""", +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 @@ -451,7 +450,7 @@ H298=(-224.989, 'kJ/mol'), S298=(-184.879, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXCH', 'XCHXCH']""", +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 @@ -517,7 +516,7 @@ H298=(-108.027, 'kJ/mol'), S298=(-197.829, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XNH', 'XCH2XNH']""", +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 @@ -550,7 +549,7 @@ H298=(-217.964, 'kJ/mol'), S298=(-193.314, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XN', 'XCH2XN']""", +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 @@ -582,7 +581,7 @@ H298=(-99.595, 'kJ/mol'), S298=(-171.411, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXN', 'XCHXN']""", +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 @@ -615,7 +614,7 @@ H298=(-127.548, 'kJ/mol'), S298=(-183.708, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['NHXCXNH', 'XNHXCO', 'NHXCXNH', 'XNHXCO']""", +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 @@ -647,7 +646,7 @@ H298=(-263.944, 'kJ/mol'), S298=(-188.758, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNXCO', 'XNXCNH', 'XNXCO', 'XNXCNH']""", +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 @@ -680,7 +679,7 @@ H298=(-316.863, 'kJ/mol'), S298=(-195.23, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXNH', 'OHXCXNH', 'XCHXNH', 'OHXCXNH']""", +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 @@ -712,7 +711,7 @@ H298=(-128.754, 'kJ/mol'), S298=(-175.675, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXN', 'XNXCOH', 'XCHXN', 'XNXCOH']""", +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 @@ -776,7 +775,7 @@ H298=(-63.513, 'kJ/mol'), S298=(-170.273, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XO', 'XCH2XO']""", +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 @@ -808,7 +807,7 @@ H298=(-50.787, 'kJ/mol'), S298=(-174.316, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOXCNH', 'XOXCNH']""", +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 @@ -840,7 +839,7 @@ H298=(-240.645, 'kJ/mol'), S298=(-167.729, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXO', 'XCHXO']""", +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 @@ -906,7 +905,7 @@ H298=(-108.027, 'kJ/mol'), S298=(-197.829, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XNH', 'XCH2XNH']""", +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 @@ -939,7 +938,7 @@ H298=(-217.964, 'kJ/mol'), S298=(-193.314, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2XN', 'XCH2XN']""", +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 @@ -971,7 +970,7 @@ H298=(-99.595, 'kJ/mol'), S298=(-171.411, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXN', 'XCHXN']""", +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 @@ -1004,7 +1003,7 @@ H298=(-127.548, 'kJ/mol'), S298=(-183.708, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['NHXCXNH', 'XNHXCO', 'NHXCXNH', 'XNHXCO']""", +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 @@ -1036,7 +1035,7 @@ H298=(-263.944, 'kJ/mol'), S298=(-188.758, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNXCO', 'XNXCNH', 'XNXCO', 'XNXCNH']""", +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 @@ -1069,7 +1068,7 @@ H298=(-316.863, 'kJ/mol'), S298=(-195.23, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXNH', 'OHXCXNH', 'XCHXNH', 'OHXCXNH']""", +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 @@ -1101,7 +1100,7 @@ H298=(-128.754, 'kJ/mol'), S298=(-175.675, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHXN', 'XNXCOH', 'XCHXN', 'XNXCOH']""", +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 @@ -1165,7 +1164,7 @@ H298=(-124.415, 'kJ/mol'), S298=(-159.55, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHXNH', 'CH3XNXNOH', 'XNHXNH', 'CH3XNXNOH']""", +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 @@ -1197,7 +1196,7 @@ H298=(-194.851, 'kJ/mol'), S298=(-196.22, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHXN', 'XNXNCH3', 'XNHXN', 'XNXNCH3']""", +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 @@ -1260,7 +1259,7 @@ H298=(-158.346, 'kJ/mol'), S298=(-186.753, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOXNH', 'XOXNH']""", +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 @@ -1292,7 +1291,7 @@ H298=(-216.857, 'kJ/mol'), S298=(-141.494, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOXNO', 'XOXNO']""", +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 @@ -1323,7 +1322,7 @@ H298=(-115.224, 'kJ/mol'), S298=(-168.993, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOXO', 'XOXO']""", +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 @@ -1423,7 +1422,7 @@ H298=(-673.643, 'kJ/mol'), S298=(-243.646, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCH2XC', 'XCCH2XC']""", +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 @@ -1457,7 +1456,7 @@ H298=(-479.679, 'kJ/mol'), S298=(-200.61, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCH2XCH2', 'XCCH2XCH2']""", +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 @@ -1490,7 +1489,7 @@ H298=(-459.783, 'kJ/mol'), S298=(-222.487, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCH2XC', 'XCHCH2XC']""", +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 @@ -1523,7 +1522,7 @@ H298=(-404.809, 'kJ/mol'), S298=(-202.293, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCHXC', 'XCHCHXC']""", +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 @@ -1557,7 +1556,7 @@ H298=(-545.726, 'kJ/mol'), S298=(-217.923, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCHXCH2', 'XCCHXCH2']""", +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 @@ -1593,7 +1592,7 @@ H298=(-391.619, 'kJ/mol'), S298=(-209.34, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2CH2XCH2', 'XCH2CH2XCH2']""", +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 @@ -1628,7 +1627,7 @@ H298=(-429.229, 'kJ/mol'), S298=(-227.783, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCHXCH2', 'XCHCHXCH2']""", +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 @@ -1662,7 +1661,7 @@ H298=(-373.265, 'kJ/mol'), S298=(-196.347, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCXCH', 'XCHCXCH']""", +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 @@ -1695,7 +1694,7 @@ H298=(-436.651, 'kJ/mol'), S298=(-188.069, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCXC', 'XCHCXC']""", +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 @@ -1730,7 +1729,7 @@ H298=(-529.006, 'kJ/mol'), S298=(-196.129, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCH2XCH2', 'XCHCH2XCH2']""", +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 @@ -1764,7 +1763,7 @@ H298=(-232.503, 'kJ/mol'), S298=(-203.938, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCH2XCH', 'XCHCH2XCH']""", +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 @@ -1798,7 +1797,7 @@ H298=(-615.396, 'kJ/mol'), S298=(-200.988, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCHXCH', 'XCHCHXCH']""", +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 @@ -1864,7 +1863,7 @@ H298=(-448.966, 'kJ/mol'), S298=(-211.148, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCHXO', 'XCHCHXO']""", +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 @@ -1928,7 +1927,7 @@ H298=(-357.096, 'kJ/mol'), S298=(-179.723, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOC(O)XO', 'H2C(XO)XO', 'XOC(O)XO', 'H2C(XO)XO']""", +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 @@ -1992,11 +1991,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-8.018, -4.922, -2.931, -1.615, -0.092, 0.703, 1.567], 'J/(mol*K)'), - H298=(-354.778, 'kJ/mol'), - S298=(-169.809, 'J/(mol*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', 'XCN', 'XCH', 'XCCHCH2', 'XCCHO', 'XCCH3', 'XCCH2CH3', +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', @@ -2028,12 +2027,12 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-10.659, -6.972, -4.601, -3.041, -1.246, -0.288, 0.897], 'J/(mol*K)'), - H298=(-549.985, 'kJ/mol'), - S298=(-176.816, 'J/(mol*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', 'XCH', 'XCCHCH2', 'XCCHO', 'XCCH3', 'XCCH2CH3', -'XCCH2OH', 'XCNO', 'XCNH2', 'XCOH']""", +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 @@ -2065,7 +2064,7 @@ H298=(-568.221, 'kJ/mol'), S298=(-183.565, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCHCH2', 'XCCHO', 'XCCHCH2', 'XCCHO']""", +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 @@ -2098,7 +2097,7 @@ H298=(-597.493, 'kJ/mol'), S298=(-180.123, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCH3', 'XCCH2CH3', 'XCCH2OH', 'XCCH3', 'XCCH2CH3', 'XCCH2OH']""", +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 @@ -2124,11 +2123,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-4.802, -2.781, -1.842, -1.37, -1.0, -0.884, -0.705], '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"""Averaged from: ['XCNO', 'XCNH2', 'XCNO', 'XCNH2']""", +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 @@ -2159,7 +2158,7 @@ H298=(-465.97, 'kJ/mol'), S298=(-187.544, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCOH', 'XCOH']""", +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 @@ -2225,8 +2224,7 @@ H298=(-290.648, 'kJ/mol'), S298=(-182.514, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3', -'CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3']""", +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 @@ -2257,7 +2255,7 @@ H298=(-299.043, 'kJ/mol'), S298=(-153.59, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['OXCNH2', 'NH2XCNH', 'OXCNH2', 'NH2XCNH']""", +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 @@ -2289,7 +2287,7 @@ H298=(-288.87, 'kJ/mol'), S298=(-151.565, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHNH', 'OHXCNH', 'NH2XCNH', 'XCHNH', 'OHXCNH', 'NH2XCNH']""", +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 @@ -2320,8 +2318,7 @@ H298=(-336.396, 'kJ/mol'), S298=(-164.4, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHO', 'XCOOH', 'CH3XCO', 'XCCHO', 'CH3CH2XCO', 'XCHO', -'XCOOH', 'CH3XCO', 'XCCHO', 'CH3CH2XCO']""", +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 @@ -2389,8 +2386,7 @@ H298=(-216.941, 'kJ/mol'), S298=(-192.287, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', 'CH3XCHCH3', 'CH3XCHOH', -'XCH2CH2CH3', 'XCH2CH2OH', 'XCH2CH3', 'CH3XCHCH3', 'CH3XCHOH']""", +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 @@ -2422,7 +2418,7 @@ H298=(-231.326, 'kJ/mol'), S298=(-143.176, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2NH2', 'XCH2NH2']""", +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 @@ -2455,7 +2451,7 @@ H298=(-228.049, 'kJ/mol'), S298=(-157.564, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCH2OH', 'CH3XCHOH', 'XCH2OH', 'CH3XCHOH']""", +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 @@ -2515,7 +2511,7 @@ H298=(-432.678, 'kJ/mol'), S298=(-171.763, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCCO', 'XCCCH2', 'XCCH2', 'XCCO', 'XCCCH2', 'XCCH2']""", +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 @@ -2546,7 +2542,7 @@ H298=(-206.367, 'kJ/mol'), S298=(-166.816, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCNH', 'XCNH']""", +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 @@ -2573,11 +2569,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-7.731, -4.344, -2.287, -0.973, 0.53, 1.334, 2.269], 'J/(mol*K)'), - H298=(-355.755, 'kJ/mol'), - S298=(-165.599, 'J/(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"""Averaged from: ['XCH2', 'XCH2', 'XCHCHCH2', 'XCHCHO', 'CH3XCCH3', 'CH3XCOH', +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 @@ -2611,7 +2607,7 @@ H298=(-381.649, 'kJ/mol'), S298=(-179.047, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHCHCH2', 'XCHCHO', 'XCHCHCH2', 'XCHCHO']""", +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 @@ -2645,8 +2641,7 @@ H298=(-374.707, 'kJ/mol'), S298=(-179.041, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH3XCCH3', 'CH3XCOH', 'XCHCH2CH3', 'XCHCH3', 'CH3XCCH3', -'CH3XCOH', 'XCHCH2CH3', 'XCHCH3']""", +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 @@ -2677,8 +2672,7 @@ H298=(-306.517, 'kJ/mol'), S298=(-144.277, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHNH2', 'OHXCNH2', 'NH2XCNH2', 'XCHNH2', 'OHXCNH2', -'NH2XCNH2']""", +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 @@ -2706,11 +2700,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-8.363, -5.498, -3.838, -2.789, -1.537, -0.826, -0.079], '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: ['XCHOH', 'CH3XCOH', 'XCHOH', 'CH3XCOH']""", +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 @@ -2767,11 +2761,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-5.612, -2.994, -1.557, -0.731, 0.066, 0.407, 0.755], 'J/(mol*K)'), - H298=(-212.616, 'kJ/mol'), - S298=(-165.284, '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: ['XNO', 'XNO', 'XNCNH', 'XNCO', 'XNCH2', 'XNNH', 'XNNCH3']""", +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 @@ -2802,7 +2796,7 @@ H298=(-272.152, 'kJ/mol'), S298=(-145.417, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNCNH', 'XNCO', 'XNCNH', 'XNCO']""", +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 @@ -2834,7 +2828,7 @@ H298=(-213.18, 'kJ/mol'), S298=(-180.636, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNCH2', 'XNCH2']""", +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 @@ -2865,7 +2859,7 @@ H298=(-169.315, 'kJ/mol'), S298=(-164.071, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNNH', 'XNNCH3', 'XNNH', 'XNNCH3']""", +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 @@ -2892,12 +2886,12 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-3.272, 0.246, 2.345, 3.646, 5.068, 5.797, 6.65], 'J/(mol*K)'), - H298=(-219.998, 'kJ/mol'), - S298=(-171.405, 'J/(mol*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', 'XNH2', 'XNHCHO', 'XNHCH3', 'XNHNO', 'XNHNH2', 'XNHOH', -'XNO2', 'OXNNH', 'HXNO', 'CH3NXNOH', 'CH3XNNOH']""", +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 @@ -2929,7 +2923,7 @@ H298=(-334.011, 'kJ/mol'), S298=(-216.907, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHCHO', 'XNHCHO']""", +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 @@ -2963,7 +2957,7 @@ H298=(-356.67, 'kJ/mol'), S298=(-167.995, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHCH3', 'XNHCH3']""", +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 @@ -2995,7 +2989,7 @@ H298=(-271.605, 'kJ/mol'), S298=(-189.56, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHNO', 'XNHNO']""", +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 @@ -3028,7 +3022,7 @@ H298=(-172.993, 'kJ/mol'), S298=(-188.5, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHNH2', 'XNHNH2']""", +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 @@ -3060,7 +3054,7 @@ H298=(-184.483, 'kJ/mol'), S298=(-189.451, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNHOH', 'XNHOH']""", +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 @@ -3091,7 +3085,7 @@ H298=(-218.965, 'kJ/mol'), S298=(-163.298, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNO2', 'OXNNH', 'XNO2', 'OXNNH']""", +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 @@ -3122,7 +3116,7 @@ H298=(-147.529, 'kJ/mol'), S298=(-143.039, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['HXNO', 'CH3NXNOH', 'CH3XNNOH', 'HXNO', 'CH3NXNOH', 'CH3XNNOH']""", +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 @@ -3148,11 +3142,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-8.824, -4.476, -2.143, -0.868, 0.283, 0.764, 1.399], 'J/(mol*K)'), - H298=(-328.269, 'kJ/mol'), - S298=(-168.676, '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"""Averaged from: ['XNH', 'XNH', 'XNCN', 'XNCH3', 'XNNH2', 'XNOH']""", +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 @@ -3183,7 +3177,7 @@ H298=(-332.074, 'kJ/mol'), S298=(-142.031, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNCN', 'XNCN']""", +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 @@ -3214,7 +3208,7 @@ H298=(-353.431, 'kJ/mol'), S298=(-176.565, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNCH3', 'XNCH3']""", +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 @@ -3244,7 +3238,7 @@ H298=(-250.227, 'kJ/mol'), S298=(-174.51, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNNH2', 'XNNH2']""", +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 @@ -3275,7 +3269,7 @@ H298=(-294.53, 'kJ/mol'), S298=(-178.708, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XNOH', 'XNOH']""", +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 @@ -3331,12 +3325,12 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-5.27, -3.412, -2.328, -1.644, -0.868, -0.448, 0.09], 'J/(mol*K)'), - H298=(-192.597, 'kJ/mol'), - S298=(-151.553, '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"""Averaged from: ['XOH', 'XOH', 'XOCHCH2', 'HC(O)XO', 'XOC(OH)O', 'XOCH3', -'XOCH2CH3', 'XOCH2OH', 'XONH2', 'XOOH']""", +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 @@ -3368,8 +3362,7 @@ H298=(-230.516, 'kJ/mol'), S298=(-194.234, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOCHCH2', 'HC(O)XO', 'XOC(OH)O', 'XOCHCH2', 'HC(O)XO', -'XOC(OH)O']""", +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 @@ -3402,7 +3395,7 @@ H298=(-185.03, 'kJ/mol'), S298=(-149.812, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOCH3', 'XOCH2CH3', 'XOCH2OH', 'XOCH3', 'XOCH2CH3', 'XOCH2OH']""", +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 @@ -3433,7 +3426,7 @@ H298=(-130.622, 'kJ/mol'), S298=(-134.71, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XONH2', 'XONH2']""", +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 @@ -3464,7 +3457,7 @@ H298=(-136.519, 'kJ/mol'), S298=(-120.712, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XOOH', 'XOOH']""", +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 @@ -3556,11 +3549,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-8.706, -8.504, -8.378, -8.256, -7.929, -7.499, -6.43], '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"""Averaged from: ['CHCHX', 'CHCCH3X', 'CHCHX', 'CHCCH3X']""", +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 @@ -3591,7 +3584,7 @@ H298=(-99.884, 'kJ/mol'), S298=(-122.254, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['NCOHX', 'NCOHX']""", +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 @@ -3657,8 +3650,7 @@ H298=(-79.219, 'kJ/mol'), S298=(-143.863, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2CH2X', 'CH3CHCH2X', 'CH2CCH2X', 'CH2CH2X', 'CH3CHCH2X', -'CH2CCH2X']""", +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 @@ -3690,7 +3682,7 @@ H298=(-58.642, 'kJ/mol'), S298=(-135.288, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2NHX', 'CH2NHX']""", +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 @@ -3722,8 +3714,7 @@ H298=(-75.558, 'kJ/mol'), S298=(-122.364, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX', 'CH2COX', -'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX']""", +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 @@ -3752,11 +3743,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-0.627, 0.38, 0.901, 1.19, 1.469, 1.59, 1.685], 'J/(mol*K)'), - H298=(-46.964, 'kJ/mol'), - S298=(-118.627, '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"""Averaged from: ['CH4X', 'CH4X', 'CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX', 'CH3NH2X', +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 @@ -3793,8 +3784,7 @@ H298=(-32.083, 'kJ/mol'), S298=(-137.338, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX', 'CH3CH3X', 'CH3CH2CH3X', -'CH3CH2OHX']""", +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 @@ -3827,7 +3817,7 @@ H298=(-106.092, 'kJ/mol'), S298=(-141.215, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH3NH2X', 'CH3NH2X']""", +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 @@ -3861,8 +3851,7 @@ H298=(-60.04, 'kJ/mol'), S298=(-139.363, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH3OHX', 'CH3OCH3X', 'CH3OCH2OHX', 'H2C(OH)OHX', 'CH3OHX', -'CH3OCH3X', 'CH3OCH2OHX', 'H2C(OH)OHX']""", +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 @@ -3919,11 +3908,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-1.773, -1.224, -0.874, -0.625, -0.309, -0.136, 0.025], '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"""Averaged from: ['OCNHX', 'NHCNHX', 'OCNHX', 'NHCNHX']""", +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 @@ -3951,11 +3940,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-4.613, -2.128, -0.623, 0.333, 1.405, 1.947, 2.484], 'J/(mol*K)'), - H298=(-95.524, 'kJ/mol'), - S298=(-136.79, '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"""Averaged from: ['NH3X', 'NH3X', 'OCHNH2X', 'NH2NH2X', 'NH2NCH3CH3X', 'H2NOHX']""", +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 @@ -3985,7 +3974,7 @@ H298=(-101.157, 'kJ/mol'), S298=(-138.501, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['OCHNH2X', 'OCHNH2X']""", +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 @@ -4015,7 +4004,7 @@ H298=(-119.234, 'kJ/mol'), S298=(-150.696, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['NH2NH2X', 'NH2NCH3CH3X', 'NH2NH2X', 'NH2NCH3CH3X']""", +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 @@ -4045,7 +4034,7 @@ H298=(-83.038, 'kJ/mol'), S298=(-132.089, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['H2NOHX', 'H2NOHX']""", +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 @@ -4137,7 +4126,7 @@ H298=(-143.729, 'kJ/mol'), S298=(-139.884, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['ONNH2X', 'ONNCH3CH3X', 'ONNH2X', 'ONNCH3CH3X']""", +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 @@ -4169,7 +4158,7 @@ H298=(-131.932, 'kJ/mol'), S298=(-144.387, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['ONOHX', 'ONOHX']""", +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 @@ -4196,11 +4185,11 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), - Cpdata=([-3.913, -2.311, -1.477, -0.988, -0.437, -0.138, 0.148], 'J/(mol*K)'), - H298=(-36.933, 'kJ/mol'), - S298=(-98.276, '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"""Averaged from: ['H2OX', 'H2OX', 'HOOHX']""", +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 @@ -4232,7 +4221,7 @@ H298=(-65.492, 'kJ/mol'), S298=(-110.352, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['HOOHX', 'HOOHX']""", +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 From 7b868dd1679e3199a3c1826127f08e37c3a91d35 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 11:19:04 -0400 Subject: [PATCH 03/17] fixed some parents being more descriptive than children --- input/thermo/groups/adsorptionPt111.py | 21 ++++++++++++++------- 1 file changed, 14 insertions(+), 7 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index b62384c89f..124bddfa07 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -473,7 +473,7 @@ 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 p[0,1] c[0,+1] {2,[S,D]} {3,[S,D]} +4 N u0 p1 c0 {2,[S,D]} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -862,7 +862,7 @@ 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 p[0,1] c[0,+1] {2,[S,D]} {3,[S,D]} +4 N u0 p1 c0 {2,[S,D]} {3,[S,D]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -2247,7 +2247,7 @@ 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 u0 px c0 {2,D} +4 R!H u0 px c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3903,8 +3903,9 @@ group= """ 1 * X u0 p0 c0 -2 N u0 p1 c0 {3,D} +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'), @@ -3965,8 +3966,10 @@ group= """ 1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} +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'), @@ -3995,8 +3998,10 @@ group= """ 1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} +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'), @@ -4025,8 +4030,10 @@ group= """ 1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} +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'), From b52ee4fbd6d9739b4d9c615eb76a13e217df9b1e Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 13:19:44 -0400 Subject: [PATCH 04/17] switching p2 to p1 where it was in error --- input/thermo/groups/adsorptionPt111.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 124bddfa07..bf6e50b4a8 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -75,8 +75,8 @@ label = "CXCX", group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,[S,D,T]} +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]} """, @@ -573,7 +573,7 @@ 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 p2 c0 {2,S} {3,D} +5 N u0 p1 c0 {2,S} {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -731,8 +731,8 @@ label = "CXOX", group= """ -1 * X u0 {3,[S,D,T]} -2 X u0 {4,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} """, @@ -962,7 +962,7 @@ 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 p2 c0 {2,S} {3,D} +5 N u0 p1 c0 {2,S} {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -1120,8 +1120,8 @@ label = "NXNX", group= """ -1 * X u0 {3,[S,D]} -2 X u0 {4,[S,D]} +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]} """, From f9b6635b842b9e80df233687e24f0990350d1fa5 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 15:24:31 -0400 Subject: [PATCH 05/17] fixed mismatch of c-1 using R instead of RHmm I get -95.03 printed out from RMG --- input/thermo/groups/adsorptionPt111.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index bf6e50b4a8..2bbc635ce0 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -1283,7 +1283,7 @@ 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 u0 px c-1 {3,S} +5 R!H u0 px c-1 {3,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), From d0f096dc55f9279e566651e756f1dbe4e1f6685b Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 16:41:23 -0400 Subject: [PATCH 06/17] trying to fix charged carbon with p0 being found --- input/thermo/groups/adsorptionPt111.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 2bbc635ce0..1d13584930 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -1283,7 +1283,7 @@ 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 px c-1 {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'), From 35b6d158cf653f676c8878fe1acf797b16a4e33c Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 19:00:42 -0400 Subject: [PATCH 07/17] fixing R->RHmm I get -95.03 printed out from RMG for possibility of double or tripple bonds --- input/thermo/groups/adsorptionPt111.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 1d13584930..b5d466679a 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -2757,7 +2757,7 @@ """ 1 * X u0 p0 c0 {2,S} 2 N u0 p1 c0 {1,S} {3,D} -3 R u0 px c0 {2,D} +3 R!H u0 px c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -2881,7 +2881,7 @@ """ 1 * X u0 p0 c0 {2,[S,D]} 2 N u0 px cx {1,[S,D]} {3,[S,D]} {4,S} -3 R u0 px c0 {2,[S,D]} +3 R!H u0 px c0 {2,[S,D]} 4 R u0 px cx {2,S} """, thermo=ThermoData( @@ -3169,7 +3169,7 @@ 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 u0 px c0 {3,T} +4 R!H u0 px c0 {3,T} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -4063,7 +4063,7 @@ """ 1 * X u0 p0 c0 2 O u0 p2 c0 {3,D} -3 R u0 px c0 {2,D} +3 R!H u0 px c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), From 98920e299fadfac120a78e9bcf54680e99ce42ff Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Thu, 9 Apr 2026 22:23:44 -0400 Subject: [PATCH 08/17] fixing more of the issues making C p0 c-1 --- input/thermo/groups/adsorptionPt111.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index b5d466679a..618180146f 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3076,7 +3076,7 @@ """ 1 * X u0 p0 c0 {2,S} 2 N u0 p0 c+1 {1,S} {3,S} {4,D} -3 R!H u0 px c-1 {2,S} +3 R!H u0 p[1,2,3] c-1 {2,S} 4 R!H u0 px c0 {2,D} """, thermo=ThermoData( @@ -3107,7 +3107,7 @@ """ 1 * X u0 p0 c0 {2,D} 2 N u0 p0 c+1 {1,D} {3,S} {4,S} -3 R!H u0 px c-1 {2,S} +3 R!H u0 p[1,2,3] c-1 {2,S} 4 R u0 px c0 {2,S} """, thermo=ThermoData( From e30382d4bd45193a16996b381114b7d4cef9ccaa Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 10 Apr 2026 11:54:19 -0400 Subject: [PATCH 09/17] making some vdW correction groups more specific to prevent overlap between eachother --- input/thermo/groups/adsorptionPt111.py | 21 ++++++++++++--------- 1 file changed, 12 insertions(+), 9 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 618180146f..59010f4cda 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -2247,7 +2247,7 @@ 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 px c0 {2,D} +4 R!H u0 p[1,2,3] c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -2880,9 +2880,9 @@ group= """ 1 * X u0 p0 c0 {2,[S,D]} -2 N u0 px cx {1,[S,D]} {3,[S,D]} {4,S} -3 R!H u0 px c0 {2,[S,D]} -4 R u0 px cx {2,S} +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'), @@ -3873,8 +3873,9 @@ """ 1 * X u0 p0 c0 2 N u0 p1 c0 {3,D} {4,S} -3 R!H u0 px c0 {2,D} +3 R!H u0 px c0 {2,D} {5,[D,T]} 4 R u0 px c0 {2,S} +5 R u0 px c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3904,8 +3905,9 @@ """ 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} +3 C u0 p0 c0 {2,D} {5,[D,T]} +4 R u0 p0 c0 {2,S} +5 R!H u0 px c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3967,9 +3969,10 @@ """ 1 * X u0 p0 c0 2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 C u0 p0 c0 {2,S} +3 C u0 p0 c0 {2,S} {6,[D,T]} 4 R u0 px c0 {2,S} 5 R u0 px c0 {2,S} +6 R!H u0 px c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -4063,7 +4066,7 @@ """ 1 * X u0 p0 c0 2 O u0 p2 c0 {3,D} -3 R!H u0 px c0 {2,D} +3 R!H u0 p1 c0 {2,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), From 10d4fa04f224b3deb47c6263447848b30aae1fb1 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 10 Apr 2026 12:46:46 -0400 Subject: [PATCH 10/17] fixing R -> RHmm I get -95.03 printed out from RMG --- input/thermo/groups/adsorptionPt111.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 59010f4cda..d11ee71370 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3875,7 +3875,7 @@ 2 N u0 p1 c0 {3,D} {4,S} 3 R!H u0 px c0 {2,D} {5,[D,T]} 4 R u0 px c0 {2,S} -5 R u0 px c0 {3,[D,T]} +5 R!H u0 px c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), From 143ff89cb78ca27e0f58c3db9cdcdae38e3a841f Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 10 Apr 2026 13:36:03 -0400 Subject: [PATCH 11/17] adding more restrictions for vdW nodes --- input/thermo/groups/adsorptionPt111.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index d11ee71370..5312015386 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3875,7 +3875,7 @@ 2 N u0 p1 c0 {3,D} {4,S} 3 R!H u0 px c0 {2,D} {5,[D,T]} 4 R u0 px c0 {2,S} -5 R!H u0 px c0 {3,[D,T]} +5 R!H u0 p[1,2,3] c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3907,7 +3907,7 @@ 2 N u0 p1 c0 {3,D} {4,S} 3 C u0 p0 c0 {2,D} {5,[D,T]} 4 R u0 p0 c0 {2,S} -5 R!H u0 px c0 {3,[D,T]} +5 R!H u0 p[1,2,3] c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3972,7 +3972,7 @@ 3 C u0 p0 c0 {2,S} {6,[D,T]} 4 R u0 px c0 {2,S} 5 R u0 px c0 {2,S} -6 R!H u0 px c0 {3,[D,T]} +6 R!H u0 p[1,2,3] c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), From 1cabcb289455486dbd2d389c11308d68a678ad14 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 10 Apr 2026 14:51:35 -0400 Subject: [PATCH 12/17] trying putting the * on the central atom instead of surf for vdW --- input/thermo/groups/adsorptionPt111.py | 113 ++++++++++++------------- 1 file changed, 55 insertions(+), 58 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 5312015386..7b7af02fad 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3477,8 +3477,8 @@ label = "RXvdW", group= """ -1 * X u0 -2 R u0 +1 X u0 +2 * R u0 """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3510,8 +3510,8 @@ label = "(CR2)X", group= """ -1 * X u0 -2 C u0 {3,T} {4,S} +1 X u0 +2 * C u0 {3,T} {4,S} 3 R!H u0 {2,T} 4 R u0 {2,S} """, @@ -3541,11 +3541,11 @@ label = "(CRCR)X", 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 * 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'), @@ -3573,8 +3573,8 @@ label = "(CRN)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,T} {4,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} """, @@ -3604,8 +3604,8 @@ label = "(CR3)X", group= """ -1 * X u0 -2 C u0 {3,D} {4,S} {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} @@ -3637,8 +3637,8 @@ label = "(CR2CR)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {5,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} @@ -3670,8 +3670,8 @@ label = "(CR2N)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {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} @@ -3702,8 +3702,8 @@ label = "(CR2O)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,D} {4,S} {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} @@ -3734,8 +3734,8 @@ label = "(CR4)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3768,8 +3768,8 @@ label = "(CR3CR3)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3804,8 +3804,8 @@ label = "(CR3N)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3837,8 +3837,8 @@ label = "(CR3OR)X", group= """ -1 * X u0 p0 c0 -2 C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3871,11 +3871,10 @@ label = "(NR2)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 R!H u0 px c0 {2,D} {5,[D,T]} +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} -5 R!H u0 p[1,2,3] c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3903,11 +3902,10 @@ label = "(N=C)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,D} {4,S} -3 C u0 p0 c0 {2,D} {5,[D,T]} -4 R u0 p0 c0 {2,S} -5 R!H u0 p[1,2,3] c0 {3,[D,T]} +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'), @@ -3935,8 +3933,8 @@ label = "(NR3)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,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 u0 px c0 {2,S} @@ -3967,12 +3965,11 @@ label = "(NC)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} -3 C u0 p0 c0 {2,S} {6,[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} -6 R!H u0 p[1,2,3] c0 {3,[D,T]} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -4000,8 +3997,8 @@ label = "(NN)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,S} +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} @@ -4032,8 +4029,8 @@ label = "(NO)X", group= """ -1 * X u0 p0 c0 -2 N u0 p1 c0 {3,S} {4,S} {5,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} @@ -4064,8 +4061,8 @@ label = "(OR)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,D} +1 X u0 p0 c0 +2 * O u0 p2 c0 {3,D} 3 R!H u0 p1 c0 {2,D} """, thermo=ThermoData( @@ -4094,8 +4091,8 @@ label = "(ONR)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,D} +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} """, @@ -4125,8 +4122,8 @@ label = "(ONN)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,D} +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} """, @@ -4156,8 +4153,8 @@ label = "(ONOR)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,D} +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} @@ -4188,8 +4185,8 @@ label = "(OR2)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,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} """, @@ -4219,8 +4216,8 @@ label = "(OROR)X", group= """ -1 * X u0 p0 c0 -2 O u0 p2 c0 {3,S} {4,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} From ef042387d9e46ff4f16528e29f42e6b0c93dc43f Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Tue, 14 Apr 2026 10:57:07 -0400 Subject: [PATCH 13/17] reorganized vdw tree a little to prevent overelapping nodes --- input/thermo/groups/adsorptionPt111.py | 216 +++++++++---------------- 1 file changed, 76 insertions(+), 140 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 7b7af02fad..efc3fd217b 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -3477,8 +3477,8 @@ label = "RXvdW", group= """ -1 X u0 -2 * R u0 +1 * X u0 +2 R u0 """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3487,10 +3487,10 @@ S298=(-128.976, 'J/(mol*K)'), ), 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']""", +'CH2NHX', 'CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX', 'OCHNH2X', +'CH4X', 'CH3CH3X', 'CH3CH2CH3X', 'CH3CH2OHX', 'CH3NH2X', 'CH3OHX', 'CH3OCH3X', +'CH3OCH2OHX', 'H2C(OH)OHX', 'OCNHX', 'NHCNHX', 'NH3X', '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 @@ -3510,8 +3510,8 @@ label = "(CR2)X", group= """ -1 X u0 -2 * C u0 {3,T} {4,S} +1 * X u0 +2 C u0 {3,T} {4,S} 3 R!H u0 {2,T} 4 R u0 {2,S} """, @@ -3541,11 +3541,11 @@ label = "(CRCR)X", 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 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'), @@ -3573,8 +3573,8 @@ label = "(CRN)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,T} {4,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} """, @@ -3604,20 +3604,20 @@ label = "(CR3)X", group= """ -1 X u0 -2 * C u0 {3,D} {4,S} {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=([-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)'), + Cpdata=([-2.288, -0.929, -0.172, 0.264, 0.683, 0.849, 0.944], 'J/(mol*K)'), + H298=(-77.525, 'kJ/mol'), + S298=(-131.72, 'J/(mol*K)'), ), shortDesc=u"""Averaged from: ['CH2CH2X', 'CH3CHCH2X', 'CH2CCH2X', 'CH2NHX', 'CH2COX', 'CH2OX', -'OC(OH)OHX', 'CH3CHOX', 'HCOOHX']""", +'OC(OH)OHX', 'CH3CHOX', 'HCOOHX', '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 @@ -3637,8 +3637,8 @@ label = "(CR2CR)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,D} {4,S} {5,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} @@ -3670,8 +3670,8 @@ label = "(CR2N)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,D} {4,S} {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} @@ -3702,19 +3702,19 @@ label = "(CR2O)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,D} {4,S} {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=([-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)'), + Cpdata=([-2.534, -1.583, -1.016, -0.658, -0.255, -0.058, 0.095], 'J/(mol*K)'), + H298=(-79.824, 'kJ/mol'), + S298=(-125.054, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX']""", +shortDesc=u"""Averaged from: ['CH2COX', 'CH2OX', 'OC(OH)OHX', 'CH3CHOX', 'HCOOHX', '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 @@ -3734,8 +3734,8 @@ label = "(CR4)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3768,8 +3768,8 @@ label = "(CR3CR3)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3804,8 +3804,8 @@ label = "(CR3N)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3837,8 +3837,8 @@ label = "(CR3OR)X", group= """ -1 X u0 p0 c0 -2 * C u0 p0 c0 {3,S} {4,S} {5,S} {6,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} @@ -3868,44 +3868,14 @@ entry( index = 120, - label = "(NR2)X", - group= -""" -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=([-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"""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 = 121, label = "(N=C)X", group= """ -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} +1 * X u0 p0 c0 +2 N u0 p1 c0 {3,D} {4,S} +3 C u0 p0 c0 {2,D} {5,D} +4 R u0 p0 c0 {2,S} +5 R!H u0 p[1,2] c0 {3,D} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), @@ -3929,23 +3899,23 @@ ) entry( - index = 122, + index = 121, label = "(NR3)X", group= """ -1 X u0 p0 c0 -2 * N u0 p1 c0 {3,S} {4,S} {5,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 u0 px c0 {2,S} """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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)'), + Cpdata=([-5.265, -2.782, -1.287, -0.345, 0.702, 1.225, 1.746], 'J/(mol*K)'), + H298=(-99.186, 'kJ/mol'), + S298=(-139.465, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['NH3X', 'OCHNH2X', 'NH2NH2X', 'NH2NCH3CH3X', 'H2NOHX']""", +shortDesc=u"""Averaged from: ['NH3X', '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 @@ -3961,44 +3931,12 @@ ) entry( - index = 123, - label = "(NC)X", - group= -""" -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=([-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: ['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 = 124, + index = 122, label = "(NN)X", group= """ -1 X u0 p0 c0 -2 * N u0 p1 c0 {3,S} {4,S} {5,S} +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} @@ -4025,12 +3963,12 @@ ) entry( - index = 125, + index = 123, label = "(NO)X", group= """ -1 X u0 p0 c0 -2 * N u0 p1 c0 {3,S} {4,S} {5,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} @@ -4057,12 +3995,12 @@ ) entry( - index = 126, + index = 124, label = "(OR)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,D} +1 * X u0 p0 c0 +2 O u0 p2 c0 {3,D} 3 R!H u0 p1 c0 {2,D} """, thermo=ThermoData( @@ -4087,12 +4025,12 @@ ) entry( - index = 127, + index = 125, label = "(ONR)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,D} +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} """, @@ -4118,12 +4056,12 @@ ) entry( - index = 128, + index = 126, label = "(ONN)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,D} +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} """, @@ -4149,12 +4087,12 @@ ) entry( - index = 129, + index = 127, label = "(ONOR)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,D} +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} @@ -4181,12 +4119,12 @@ ) entry( - index = 130, + index = 128, label = "(OR2)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,S} {4,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} """, @@ -4212,12 +4150,12 @@ ) entry( - index = 131, + index = 129, label = "(OROR)X", group= """ -1 X u0 p0 c0 -2 * O u0 p2 c0 {3,S} {4,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} @@ -4364,10 +4302,8 @@ L4: (CR3CR3)X L4: (CR3N)X L4: (CR3OR)X - L3: (NR2)X - L4: (N=C)X + L3: (N=C)X L3: (NR3)X - L4: (NC)X L4: (NN)X L4: (NO)X L3: (OR)X From dd8f280bfbff9aeb473ffd610f372000412674bf Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 17 Apr 2026 09:35:16 -0400 Subject: [PATCH 14/17] added visuals for each group --- input/thermo/groups/adsorptionPt111.py | 515 +++++++++++++++++++++++++ 1 file changed, 515 insertions(+) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index efc3fd217b..3530beb382 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -28,6 +28,9 @@ thermo=None, shortDesc=u"""Anything adsorbed anyhow.""", longDesc=u""" + R + | +*********** """, metal = "Pt", facet = "111", @@ -65,6 +68,10 @@ 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. + + R---R + | | +*** *** """, metal = "Pt", facet = "111", @@ -98,6 +105,10 @@ 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. + + C-C + | | +*** *** """, metal = "Pt", facet = "111", @@ -130,6 +141,10 @@ 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. + + C---C=R + ||| | +*** *** """, metal = "Pt", facet = "111", @@ -163,6 +178,10 @@ 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. + + C---CR2 + ||| | +*** *** """, metal = "Pt", facet = "111", @@ -195,6 +214,10 @@ 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. + + C---C-R + ||| || +*** *** """, metal = "Pt", facet = "111", @@ -226,6 +249,10 @@ 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. + + C==C + || || +*** *** """, metal = "Pt", facet = "111", @@ -260,6 +287,10 @@ 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. + +R2C---C=R + | | +*** *** """, metal = "Pt", facet = "111", @@ -295,6 +326,10 @@ 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. + +R2C---CR2 + | | +*** *** """, metal = "Pt", facet = "111", @@ -329,6 +364,10 @@ 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. + +R2C---C-R + | || +*** *** """, metal = "Pt", facet = "111", @@ -362,6 +401,10 @@ 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. + + R-C=C-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -394,6 +437,10 @@ 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. + + R-C=C + | || +*** *** """, metal = "Pt", facet = "111", @@ -427,6 +474,10 @@ 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. + + R-C---C=R + || | +*** *** """, metal = "Pt", facet = "111", @@ -460,6 +511,10 @@ 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. + + R-C---C-R + || || +*** *** """, metal = "Pt", facet = "111", @@ -492,6 +547,10 @@ 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. + + C-N + | | +*** *** """, metal = "Pt", facet = "111", @@ -526,6 +585,10 @@ 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. + +R2C---N-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -559,6 +622,10 @@ 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. + +R2C---N + | || +*** *** """, metal = "Pt", facet = "111", @@ -591,6 +658,10 @@ 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. + + R-C=N + | | +*** *** """, metal = "Pt", facet = "111", @@ -624,6 +695,10 @@ 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. + + R=C---N-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -656,6 +731,10 @@ 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. + + R=C---N + | || +*** *** """, metal = "Pt", facet = "111", @@ -689,6 +768,10 @@ 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. + + R-C---N-R + || | +*** *** """, metal = "Pt", facet = "111", @@ -721,6 +804,10 @@ 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. + + R-C---N + || || +*** *** """, metal = "Pt", facet = "111", @@ -752,6 +839,10 @@ 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. + + C-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -785,6 +876,10 @@ 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. + +R2C---O + | | +*** *** """, metal = "Pt", facet = "111", @@ -817,6 +912,10 @@ 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. + + R=C---O + | | +*** *** """, metal = "Pt", facet = "111", @@ -849,6 +948,10 @@ 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. + + R-C---O + || | +*** *** """, metal = "Pt", facet = "111", @@ -881,6 +984,10 @@ 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. + + C-N + | | +*** *** """, metal = "Pt", facet = "111", @@ -915,6 +1022,10 @@ 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. + +R2C---N-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -948,6 +1059,10 @@ 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. + +R2C---N + | || +*** *** """, metal = "Pt", facet = "111", @@ -980,6 +1095,10 @@ 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. + + R-C=N + | | +*** *** """, metal = "Pt", facet = "111", @@ -1013,6 +1132,10 @@ 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. + + R=C---N-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -1045,6 +1168,10 @@ 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. + + R=C---N + | || +*** *** """, metal = "Pt", facet = "111", @@ -1078,6 +1205,10 @@ 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. + + R-C---N-R + || | +*** *** """, metal = "Pt", facet = "111", @@ -1110,6 +1241,10 @@ 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. + + R-C---N + || || +*** *** """, metal = "Pt", facet = "111", @@ -1141,6 +1276,10 @@ 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. + + N-N + | | +*** *** """, metal = "Pt", facet = "111", @@ -1174,6 +1313,10 @@ 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. + + R-N---N-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -1206,6 +1349,10 @@ 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. + + R-N---N + | || +*** *** """, metal = "Pt", facet = "111", @@ -1237,6 +1384,10 @@ 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. + + N-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1269,6 +1420,10 @@ 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. + + R-N---O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1301,6 +1456,10 @@ 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. + + R[-]-N[+]-O + || | + *** *** """, metal = "Pt", facet = "111", @@ -1332,6 +1491,10 @@ 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. + + O--O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1366,6 +1529,10 @@ 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. + + R-R-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -1400,6 +1567,10 @@ 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. + + C-R-C + | | +*** *** """, metal = "Pt", facet = "111", @@ -1432,6 +1603,10 @@ 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. + + C-R-C + ||| ||| +*** *** """, metal = "Pt", facet = "111", @@ -1466,6 +1641,10 @@ 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. + + C-R-CR2 + ||| | +*** *** """, metal = "Pt", facet = "111", @@ -1499,6 +1678,10 @@ 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. + + C-R-C-R + ||| || +*** *** """, metal = "Pt", facet = "111", @@ -1532,6 +1715,10 @@ 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. + + C-R=C-R + ||| | +*** *** """, metal = "Pt", facet = "111", @@ -1566,6 +1753,10 @@ 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. + + C=R-CR2 + || | +*** *** """, metal = "Pt", facet = "111", @@ -1602,6 +1793,10 @@ 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. + +R2C-R-CR2 + | | +*** *** """, metal = "Pt", facet = "111", @@ -1637,6 +1832,10 @@ 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. + + R-C=R-CR2 + | | +*** *** """, metal = "Pt", facet = "111", @@ -1671,6 +1870,10 @@ 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. + + R-C=R=C-R + | | +*** *** """, metal = "Pt", facet = "111", @@ -1704,6 +1907,10 @@ 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. + + R-C=R=C + | || +*** *** """, metal = "Pt", facet = "111", @@ -1739,6 +1946,10 @@ 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. + + R-C-R-CR2 + || | +*** *** """, metal = "Pt", facet = "111", @@ -1773,6 +1984,10 @@ 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. + + R-C-R-C-R + || || +*** *** """, metal = "Pt", facet = "111", @@ -1807,6 +2022,10 @@ 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. + + R-C-R=C-R + || | +*** *** """, metal = "Pt", facet = "111", @@ -1840,6 +2059,10 @@ 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. + + C-R-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1873,6 +2096,10 @@ 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. + + R-C=R-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1905,6 +2132,10 @@ 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. + + O-R-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1937,6 +2168,10 @@ 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. + + O-C-O + | | +*** *** """, metal = "Pt", facet = "111", @@ -1976,6 +2211,10 @@ 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. + + R + | +*********** """, metal = "Pt", facet = "111", @@ -2011,6 +2250,10 @@ 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. + + C + | +*********** """, metal = "Pt", facet = "111", @@ -2042,6 +2285,10 @@ 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. + + R-C + ||| +*********** """, metal = "Pt", facet = "111", @@ -2074,6 +2321,10 @@ 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. + + R=C-C + ||| +*********** """, metal = "Pt", facet = "111", @@ -2107,6 +2358,10 @@ 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. + + R3C-C + ||| +*********** """, metal = "Pt", facet = "111", @@ -2137,6 +2392,10 @@ 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. + + N-C + ||| +*********** """, metal = "Pt", facet = "111", @@ -2168,6 +2427,10 @@ 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. + + R-O-C + ||| +*********** """, metal = "Pt", facet = "111", @@ -2201,6 +2464,10 @@ 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. + + R=C-R + | +*********** """, metal = "Pt", facet = "111", @@ -2234,6 +2501,10 @@ 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. + + R-C=CR2 + | +*********** """, metal = "Pt", facet = "111", @@ -2265,6 +2536,10 @@ 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. + + N-C=R + | +*********** """, metal = "Pt", facet = "111", @@ -2297,6 +2572,10 @@ 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. + + R-C=N-R + | +*********** """, metal = "Pt", facet = "111", @@ -2328,6 +2607,10 @@ 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. + + R-C=O + | +*********** """, metal = "Pt", facet = "111", @@ -2361,6 +2644,10 @@ 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. + + R-CR2 + | +*********** """, metal = "Pt", facet = "111", @@ -2396,6 +2683,10 @@ 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. + + R2C-CR3 + | +*********** """, metal = "Pt", facet = "111", @@ -2428,6 +2719,10 @@ 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. + + R2C-N + | +*********** """, metal = "Pt", facet = "111", @@ -2461,6 +2756,10 @@ 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. + +R2C-OR + | +*********** """, metal = "Pt", facet = "111", @@ -2491,6 +2790,10 @@ 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. + + R=C + || +*********** """, metal = "Pt", facet = "111", @@ -2521,6 +2824,10 @@ 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. + + C=C + || +*********** """, metal = "Pt", facet = "111", @@ -2552,6 +2859,10 @@ 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. + + R-N=C + || +*********** """, metal = "Pt", facet = "111", @@ -2584,6 +2895,10 @@ 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. + + R-CR + || +*********** """, metal = "Pt", facet = "111", @@ -2617,6 +2932,10 @@ 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. + + R=C-C-R + || +*********** """, metal = "Pt", facet = "111", @@ -2651,6 +2970,10 @@ 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. + + R3C-C-R + || +*********** """, metal = "Pt", facet = "111", @@ -2682,6 +3005,10 @@ 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. + + N-C-R + || +*********** """, metal = "Pt", facet = "111", @@ -2714,6 +3041,10 @@ 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. + + R-O-C-R + || +*********** """, metal = "Pt", facet = "111", @@ -2745,6 +3076,10 @@ 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. + + N + | +*********** """, metal = "Pt", facet = "111", @@ -2775,6 +3110,10 @@ 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. + + R=N + | +*********** """, metal = "Pt", facet = "111", @@ -2806,6 +3145,10 @@ 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. + + R=C=N + | +*********** """, metal = "Pt", facet = "111", @@ -2838,6 +3181,10 @@ 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. + + R2C=N + | +*********** """, metal = "Pt", facet = "111", @@ -2869,6 +3216,10 @@ 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. + + R-N=N + | +*********** """, metal = "Pt", facet = "111", @@ -2901,6 +3252,10 @@ 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. + + R-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -2933,6 +3288,10 @@ 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. + + R=C-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -2967,6 +3326,10 @@ 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. + + R3C-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -2999,6 +3362,10 @@ 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. + + R=N-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -3032,6 +3399,10 @@ 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. + + R2N-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -3064,6 +3435,10 @@ 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. + + R-O-N-R + | +*********** """, metal = "Pt", facet = "111", @@ -3095,6 +3470,10 @@ 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. + + R=N[+]-R[-] + | +*********** """, metal = "Pt", facet = "111", @@ -3126,6 +3505,10 @@ 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. + + R[-]-N[+]-R + || +*********** """, metal = "Pt", facet = "111", @@ -3156,6 +3539,10 @@ 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. + + R-N + || +*********** """, metal = "Pt", facet = "111", @@ -3187,6 +3574,10 @@ 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. + + R≡C-N + || +*********** """, metal = "Pt", facet = "111", @@ -3218,6 +3609,10 @@ 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. + + R-C-N + || +*********** """, metal = "Pt", facet = "111", @@ -3248,6 +3643,10 @@ 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. + + N-N + || +*********** """, metal = "Pt", facet = "111", @@ -3279,6 +3678,10 @@ 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. + + R-O-N + || +*********** """, metal = "Pt", facet = "111", @@ -3309,6 +3712,10 @@ 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. + + O + | +*********** """, metal = "Pt", facet = "111", @@ -3340,6 +3747,10 @@ 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. + + R-O + | +*********** """, metal = "Pt", facet = "111", @@ -3372,6 +3783,10 @@ 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. + + R=C-O + | +*********** """, metal = "Pt", facet = "111", @@ -3405,6 +3820,10 @@ 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. + + R3C-O + | +*********** """, metal = "Pt", facet = "111", @@ -3436,6 +3855,10 @@ 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. + + N-O + | +*********** """, metal = "Pt", facet = "111", @@ -3467,6 +3890,10 @@ 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. + + R-O-O + | +*********** """, metal = "Pt", facet = "111", @@ -3500,6 +3927,10 @@ 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. + + R + : +*********** """, metal = "Pt", facet = "111", @@ -3531,6 +3962,10 @@ 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. + + R2C + : +*********** """, metal = "Pt", facet = "111", @@ -3563,6 +3998,10 @@ 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. + + R-C≡C-R + : +*********** """, metal = "Pt", facet = "111", @@ -3594,6 +4033,10 @@ 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. + + R-C≡N + : +*********** """, metal = "Pt", facet = "111", @@ -3627,6 +4070,10 @@ 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. + + R2C=R + : +*********** """, metal = "Pt", facet = "111", @@ -3660,6 +4107,10 @@ 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. + + R2C=C-R + : +*********** """, metal = "Pt", facet = "111", @@ -3692,6 +4143,10 @@ 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. + + R2C=N + : +*********** """, metal = "Pt", facet = "111", @@ -3724,6 +4179,10 @@ 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. + + R2C=O + : +*********** """, metal = "Pt", facet = "111", @@ -3758,6 +4217,10 @@ 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. + + CR4 + : +*********** """, metal = "Pt", facet = "111", @@ -3794,6 +4257,10 @@ 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. + + R3C-CR3 + : +*********** """, metal = "Pt", facet = "111", @@ -3827,6 +4294,10 @@ 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. + + R3C-N + : +*********** """, metal = "Pt", facet = "111", @@ -3861,6 +4332,10 @@ 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. + + R3C-O-R + : +*********** """, metal = "Pt", facet = "111", @@ -3893,6 +4368,10 @@ 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. + + R-N=C=R + : +*********** """, metal = "Pt", facet = "111", @@ -3925,6 +4404,10 @@ 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. + + R3N + : +*********** """, metal = "Pt", facet = "111", @@ -3957,6 +4440,10 @@ 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. + + R2N-N + : +*********** """, metal = "Pt", facet = "111", @@ -3989,6 +4476,10 @@ 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. + + R2N-O + : +*********** """, metal = "Pt", facet = "111", @@ -4019,6 +4510,10 @@ 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. + + R=O + : +*********** """, metal = "Pt", facet = "111", @@ -4050,6 +4545,10 @@ 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. + + R-N=O + : +*********** """, metal = "Pt", facet = "111", @@ -4081,6 +4580,10 @@ 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. + + N-N=O + : +*********** """, metal = "Pt", facet = "111", @@ -4113,6 +4616,10 @@ 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. + + R-O-N=O + : +*********** """, metal = "Pt", facet = "111", @@ -4144,6 +4651,10 @@ 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. + + R-O-R + : +*********** """, metal = "Pt", facet = "111", @@ -4176,6 +4687,10 @@ 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. + + R-O-O-R + : +*********** """, metal = "Pt", facet = "111", From 7e67289ac3df9772ca039b82efb84f0c6e014129 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 17 Apr 2026 09:42:33 -0400 Subject: [PATCH 15/17] removed OXOX group --- input/thermo/groups/adsorptionPt111.py | 121 +++++++++---------------- 1 file changed, 43 insertions(+), 78 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 3530beb382..a60a2cf178 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -1467,41 +1467,6 @@ entry( index = 41, - label = "OXOX", - 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=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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. - - O--O - | | -*** *** -""", - metal = "Pt", - facet = "111", -) - -entry( - index = 42, label = "RXbridgedBidentate", group= """ @@ -1539,7 +1504,7 @@ ) entry( - index = 43, + index = 42, label = "CXRCX", group= """ @@ -1577,7 +1542,7 @@ ) entry( - index = 44, + index = 43, label = "C#X-R-C#X", group= """ @@ -1613,7 +1578,7 @@ ) entry( - index = 45, + index = 44, label = "C#X-R-C-XR2", group= """ @@ -1651,7 +1616,7 @@ ) entry( - index = 46, + index = 45, label = "C#X-R-C=XR", group= """ @@ -1688,7 +1653,7 @@ ) entry( - index = 47, + index = 46, label = "C#X-R=C-XR", group= """ @@ -1725,7 +1690,7 @@ ) entry( - index = 48, + index = 47, label = "C=X=R-C-XR2", group= """ @@ -1763,7 +1728,7 @@ ) entry( - index = 49, + index = 48, label = "R2C-X-R-C-XR2", group= """ @@ -1802,6 +1767,42 @@ facet = "111", ) +entry( + index = 49, + label = "(OROR)X", + 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 p0 c0 {2,S} +5 R u0 p0 c0 {3,S} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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. + + R-O-O-R + : +*********** +""", + metal = "Pt", + facet = "111", +) + entry( index = 50, label = "RC-X=R-C-XR2", @@ -4660,42 +4661,6 @@ facet = "111", ) -entry( - index = 129, - label = "(OROR)X", - 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 p0 c0 {2,S} -5 R u0 p0 c0 {3,S} -""", - thermo=ThermoData( - Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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"""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. - - R-O-O-R - : -*********** -""", - metal = "Pt", - facet = "111", -) - tree( """ L1: RX From 0fa078d64e695de34eb7935b6c29f6fabe5db578 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 17 Apr 2026 13:27:28 -0400 Subject: [PATCH 16/17] moving XCHCO to the parrent node: C-XR2 --- input/thermo/groups/adsorptionPt111.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index a60a2cf178..51601f2fbb 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -2449,13 +2449,13 @@ """, thermo=ThermoData( Tdata=([300, 400, 500, 600, 800, 1000, 1500], '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)'), + Cpdata=([-8.229, -5.137, -3.085, -1.728, -0.209, 0.527, 1.229], 'J/(mol*K)'), + H298=(-289.527, 'kJ/mol'), + S298=(-165.923, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3', +shortDesc=u"""Averaged from: ['XCHCO', 'CH2XCCH3', 'CH2XCOH', 'XCHCCH2', 'XCHCH2', 'XCHCHCH3', 'OXCNH2', 'NH2XCNH', 'XCHNH', 'OHXCNH', 'NH2XCNH', 'XCHO', 'XCOOH', 'CH3XCO', -'XCCHO', 'CH3CH2XCO']""", +'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 @@ -2594,11 +2594,11 @@ """, 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)'), + Cpdata=([-6.986, -4.107, -2.256, -1.046, 0.308, 0.975, 1.636], 'J/(mol*K)'), + H298=(-279.216, 'kJ/mol'), + S298=(-163.124, 'J/(mol*K)'), ), -shortDesc=u"""Averaged from: ['XCHO', 'XCOOH', 'CH3XCO', 'XCCHO', 'CH3CH2XCO']""", +shortDesc=u"""Averaged from: ['XCHO', 'XCOOH', 'CH3XCO', '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 From b5576a15b8c3de75dbcfedaf8e494bfa36f9f6a7 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 17 Apr 2026 14:20:27 -0400 Subject: [PATCH 17/17] removing OXOX from the tree too --- input/thermo/groups/adsorptionPt111.py | 1 - 1 file changed, 1 deletion(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 51601f2fbb..fcbbefe988 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -4703,7 +4703,6 @@ L3: NXOX L4: N-XRO-X L4: N[+]=XR[-]O-X - L3: OXOX L2: RXbridgedBidentate L3: CXRCX L4: C#X-R-C#X