From bcfabec80e064302b175ffe3ffc78cd390afc3ab Mon Sep 17 00:00:00 2001 From: ssun30 Date: Fri, 1 May 2026 11:39:22 -0400 Subject: [PATCH] Fixed CO2RR Ag111 library descriptions --- .../libraries/CO2RR_Adsorbates_Ag111.py | 41 +++++++++++-------- 1 file changed, 25 insertions(+), 16 deletions(-) diff --git a/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py b/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py index 6796cf3878..03346c5115 100644 --- a/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py +++ b/input/thermo/libraries/CO2RR_Adsorbates_Ag111.py @@ -5,24 +5,33 @@ solvent = "water" shortDesc = u"CO2RR adsorbate thermochemistry on Ag(111) from DFT" longDesc = u""" -NASA polynomial thermochemistry for C1 and C2 adsorbate intermediates -relevant to electrochemical CO2 reduction (CO2RR) on Ag(111). -Adsorbates are labeled with a trailing or interleaved 'X' to indicate -surface binding sites, per RMG conventions. +This library contains NASA polynomial thermochemistry for adsorbate +intermediates relevant to electrochemical CO2 reduction (CO2RR) on the +Ag(111) surface. All adsorbates are denoted with a trailing 'X' (or +interleaved 'X' for bidentate species) to indicate surface binding sites, +consistent with RMG conventions. -DFT (Manish Kumar Kothakonda, Northeastern): VASP with PBE + Grimme D3 -zero-damping (IVDW = 12) and PAW pseudopotentials. -A two-stage protocol was used: -Initial geometries were pre-optimized at ENCUT = 400 eV with a 3x3x1 -Monkhorst-Pack k-mesh, then fully re-relaxed to force convergence at -tighter settings of ENCUT = 500 eV and 4x4x1 k-mesh (IBRION = 2, -EDIFFG = -0.03 eV/A). All final energies - adsorbate slabs, bare-slab -reference, and vibrational frequencies - were computed at the tight -settings. +DFT calculations were performed by Manish Kumar Kothakonda (Northeastern University). +Geometry optimization of adsorbates on a periodic Ag(111) slab. +Calculations used VASP 6.3.1 with the PBE exchange-correlation functional, +Grimme D3 zero-damping dispersion correction (IVDW = 12), and PAW +pseudopotentials. Plane-wave cutoff ENCUT = 500 eV; 3x3x1 Gamma-centered +Monkhorst-Pack k-point mesh; Methfessel-Paxton smearing (ISMEAR = 1, +SIGMA = 0.10 eV); spin-polarized (ISPIN = 2); SCF convergence +EDIFF = 1E-6 eV; ionic force convergence EDIFFG = -0.03 eV/A +(IBRION = 2). The slab is a hexagonal Ag(111) supercell with lattice +parameters a = b = 11.506 A, c = 31.046 A (cell volume 3559.27 A^3), +containing 64 Ag atoms arranged in 4 atomic layers; the bottom 3 layers +were held fixed (F F F) while the top layer plus adsorbate atoms were +allowed to relax (T T T). Implicit solvation in water was applied via +VASPsol. Harmonic vibrational frequencies were computed using finite-difference +displacements (IBRION = 5, NFREE = 2, POTIM = 0.015 A) on the relaxed +atoms (adsorbate plus top slab layer). -Post-processing and thermo (Su Sun) via the Westgroup pipeline -(adapted from input_generator.py and compute_NASA_for_adsorbates): VASP -outputs converted to ASE .traj and inspected; vibrational frequencies +Post-processing and stat thermo calculations were performed by +Su Sun (Northeastern University) via the Westgroup pipeline +(adapted from input_generator.py and compute_NASA_for_adsorbates): +VASP outputs converted to ASE .traj and inspected; vibrational frequencies and ZPEs consolidated into per-species zpe_log_.txt files; imaginary modes replaced with 12 cm^-1. Heat of formation at 0 K was computed from a thermochemical cycle against CH4, H2O, and H2 references