From 3cd44d55a74672d6c032d1ba39314e0d9cc97cf1 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 5 Jun 2026 15:51:12 -0400 Subject: [PATCH 1/3] added new groups in adsorptionPt111 tree for vdWBidentates --- input/thermo/groups/adsorptionPt111.py | 117 +++++++++++++++++++++++++ 1 file changed, 117 insertions(+) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 028bf95d66..5624c3dd61 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -4661,6 +4661,120 @@ facet = "111", ) +entry( + index = 129, + label = "RXvdWBidentate", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {3,vdW} +3 R!H u0 px c0 {1,S} {5,[S,D]} +4 R!H u0 px c0 {2,vdW} {5,D} +5 R!H u0 px cx {3,[S,D]} {4,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-0.661, 1.496, 2.636, 3.252, 3.8, 3.999, 4.13], 'J/(mol*K)'), + H298=(-199.357, 'kJ/mol'), + S298=(-165.516, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XOC(OH)XO', 'XOCHXO', 'XONXO', 'XONOXO']""", +longDesc=u""" Calculated by Kirk Badger at Brown University using statistical mechanics +methods implemented in Franklin Goldsmith's thermo_kinetics_scripts repository +in the new_workflow folder: https://github.com/franklingoldsmith/thermo_kinetic +s_scripts/tree/main/new_workflow DFT calculations were performed with Quantum +Espresso using PAW pseudopotentals and the BEEF-vdW functional for an optimized +3x3x4 supercell with the bottom 2 layers fixed. The following settings were +applied: kpoints=5x5x1, ecutwfc=50 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", +) + +entry( + index = 130, + label = "XOCRXO", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {3,vdW} +3 O u0 p2 c0 {1,S} {5,S} +4 O u0 p2 c0 {2,vdW} {5,D} +5 C u0 p0 c0 {3,S} {4,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([2.365, 4.644, 5.906, 6.652, 7.422, 7.775, 8.101], 'J/(mol*K)'), + H298=(-231.878, 'kJ/mol'), + S298=(-198.718, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XOC(OH)XO', 'XOCHXO']""", +longDesc=u""" Calculated by Kirk Badger at Brown University using statistical mechanics +methods implemented in Franklin Goldsmith's thermo_kinetics_scripts repository +in the new_workflow folder: https://github.com/franklingoldsmith/thermo_kinetic +s_scripts/tree/main/new_workflow DFT calculations were performed with Quantum +Espresso using PAW pseudopotentals and the BEEF-vdW functional for an optimized +3x3x4 supercell with the bottom 2 layers fixed. The following settings were +applied: kpoints=5x5x1, ecutwfc=50 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 O + | : +*********** +""", + metal = "Pt", + facet = "111", +) + +entry( + index = 131, + label = "XONXO", + group= +""" +1 * X u0 p0 c0 {3,S} +2 X u0 p0 c0 {3,vdW} +3 O u0 p2 c0 {1,S} {5,S} +4 O u0 p2 c0 {2,vdW} {5,D} +5 N u0 px cx {3,S} {4,D} +""", + thermo=ThermoData( + Tdata=([300, 400, 500, 600, 800, 1000, 1500], 'K'), + Cpdata=([-3.686, -1.653, -0.634, -0.147, 0.177, 0.222, 0.159], 'J/(mol*K)'), + H298=(-166.836, 'kJ/mol'), + S298=(-132.313, 'J/(mol*K)'), + ), +shortDesc=u"""Averaged from: ['XONXO', 'XONOXO']""", +longDesc=u""" Calculated by Kirk Badger at Brown University using statistical mechanics +methods implemented in Franklin Goldsmith's thermo_kinetics_scripts repository +in the new_workflow folder: https://github.com/franklingoldsmith/thermo_kinetic +s_scripts/tree/main/new_workflow DFT calculations were performed with Quantum +Espresso using PAW pseudopotentals and the BEEF-vdW functional for an optimized +3x3x4 supercell with the bottom 2 layers fixed. The following settings were +applied: kpoints=5x5x1, ecutwfc=50 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 O + | : +*********** +""", + metal = "Pt", + facet = "111", +) + tree( """ L1: RX @@ -4791,5 +4905,8 @@ L5: (ONOR)X L3: (OR2)X L4: (OROR)X + L2: RXvdWBidentate + L3: XOCRXO + L3: XONXO """, ) From 239738ff29320606cae41d999642b465ecf288e6 Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 5 Jun 2026 16:30:02 -0400 Subject: [PATCH 2/3] fixing group connectivity strings --- 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 5624c3dd61..18637c3e24 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -4667,7 +4667,7 @@ group= """ 1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {3,vdW} +2 X u0 p0 c0 {4,vdW} 3 R!H u0 px c0 {1,S} {5,[S,D]} 4 R!H u0 px c0 {2,vdW} {5,D} 5 R!H u0 px cx {3,[S,D]} {4,D} @@ -4705,7 +4705,7 @@ group= """ 1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {3,vdW} +2 X u0 p0 c0 {4,vdW} 3 O u0 p2 c0 {1,S} {5,S} 4 O u0 p2 c0 {2,vdW} {5,D} 5 C u0 p0 c0 {3,S} {4,D} @@ -4743,7 +4743,7 @@ group= """ 1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {3,vdW} +2 X u0 p0 c0 {4,vdW} 3 O u0 p2 c0 {1,S} {5,S} 4 O u0 p2 c0 {2,vdW} {5,D} 5 N u0 px cx {3,S} {4,D} From 06964d2673b16c9d7010c791d666864501cea64e Mon Sep 17 00:00:00 2001 From: Kirk Badger Date: Fri, 5 Jun 2026 17:13:34 -0400 Subject: [PATCH 3/3] trying to dag the vdW surface site --- input/thermo/groups/adsorptionPt111.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/input/thermo/groups/adsorptionPt111.py b/input/thermo/groups/adsorptionPt111.py index 18637c3e24..4849448777 100644 --- a/input/thermo/groups/adsorptionPt111.py +++ b/input/thermo/groups/adsorptionPt111.py @@ -4666,8 +4666,8 @@ label = "RXvdWBidentate", group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,vdW} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,vdW} 3 R!H u0 px c0 {1,S} {5,[S,D]} 4 R!H u0 px c0 {2,vdW} {5,D} 5 R!H u0 px cx {3,[S,D]} {4,D} @@ -4704,8 +4704,8 @@ label = "XOCRXO", group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,vdW} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,vdW} 3 O u0 p2 c0 {1,S} {5,S} 4 O u0 p2 c0 {2,vdW} {5,D} 5 C u0 p0 c0 {3,S} {4,D} @@ -4742,8 +4742,8 @@ label = "XONXO", group= """ -1 * X u0 p0 c0 {3,S} -2 X u0 p0 c0 {4,vdW} +1 X u0 p0 c0 {3,S} +2 * X u0 p0 c0 {4,vdW} 3 O u0 p2 c0 {1,S} {5,S} 4 O u0 p2 c0 {2,vdW} {5,D} 5 N u0 px cx {3,S} {4,D}