Skip to content

Commit 480b879

Browse files
Torrie01ssun30
Torrie01
authored and
ssun30
committed
[echem] Updated descriptions for CO2RR adsorbates
on Cu(111) and Cu3Sn(0001)
1 parent 2d87d3d commit 480b879

2 files changed

Lines changed: 133 additions & 40 deletions

File tree

‎input/thermo/libraries/CO2RR_Adsorbates_Cu111.py‎

Lines changed: 68 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,55 @@
22
# encoding: utf-8
33

44
name = "CO2RR_Adsorbates_Cu111"
5-
solvent = "water"
6-
shortDesc = u"Place holder for short description"
7-
longDesc = u"""
8-
Place holder for long description
5+
shortDesc = "CO2RR adsorbate thermochemistry on Cu(111) from DFT"
6+
longDesc = """
7+
NASA polynomial thermochemistry for C1 and C2 adsorbate intermediates
8+
relevant to electrochemical CO2 reduction (CO2RR) on Cu(111). Species
9+
include CHX, CH2X, CH3X, CHOX, CHOHX, CH2OHX, COX, COHX, COOHX, OCHOX,
10+
COCHOX, OCHCHX, OCHCH2X, OCHCH3X, OCHCHOHX, OCHCH2OHX, OCHOCHX, OCH2CH3X,
11+
and the C-C coupled XCOXCO dimer. Adsorbates are labeled with a trailing
12+
or interleaved 'X' to indicate surface binding sites, per RMG conventions.
13+
14+
DFT (Colin Gallagher, Northeastern): VASP with PBE + Grimme D3 zero-damping
15+
(IVDW = 12) and PAW pseudopotentials. A two-stage protocol was used:
16+
initial geometries were pre-optimized at ENCUT = 400 eV with a 3x3x1
17+
Monkhorst-Pack k-mesh, then fully re-relaxed to force convergence at
18+
tighter settings of ENCUT = 500 eV and 4x4x1 k-mesh (IBRION = 2,
19+
EDIFFG = -0.03 eV/A). All final energies - adsorbate slabs, bare-slab
20+
reference, and vibrational frequencies - were computed at the tight
21+
settings. Other parameters: 1st order Methfessel-Paxton smearing
22+
(ISMEAR = 1) with a smearing width of 0.1 eV, ISPIN = 2,
23+
EDIFF = 1E-6 eV, no dipole correction. Slab: 4x4 Cu(111), 4 layers
24+
(64 Cu), bottom 2 fixed and top 2 relaxed, in-plane area 86.32 A^2,
25+
~18 A vacuum. Harmonic frequencies from finite differences (IBRION = 5,
26+
NFREE = 2, POTIM = 0.015 A) on the free atoms (adsorbate + top 2 layers).
27+
28+
Post-processing and thermo (Torrie Asifor) via the Westgroup pipeline
29+
(adapted from input_generator.py and compute_NASA_for_adsorbates): VASP
30+
outputs converted to ASE .traj and inspected; vibrational frequencies
31+
and ZPEs consolidated into per-species zpe_log_<species>.txt files;
32+
imaginary modes replaced with 12 cm^-1. Heat of formation at 0 K was
33+
computed from a thermochemical cycle against CH4, H2O, and H2 references
34+
(ATcT: h0_CH4 = -66.556 kJ/mol, h0_H2O = -238.938 kJ/mol,
35+
h0_H2 = 0.0 kJ/mol). Reference gas electronic energies were read from the
36+
final frame of each gas's ads_vib.traj at the same PBE+D3 level as the
37+
slabs (displaced rather than relaxed geometries, a systematic ~1 kJ/mol
38+
offset shared across all species); hard-coded ZPEs ZPE_CH4 = 1.196 eV,
39+
ZPE_H2 = 0.277 eV, ZPE_H2O = 0.609 eV were used. Partition functions
40+
were evaluated over 298.15-2000 K with the harmonic oscillator
41+
approximation; when an adsorbate's two lowest modes fall below 100 cm^-1
42+
they are replaced by a 2D-gas translational model using a legacy per-site
43+
area of 6.90 A^2/site inherited from earlier 3x3 Cu(111) workflows (vs.
44+
the actual 5.40 A^2/site for this 4x4 slab, a ~0.6 kJ/mol shift at 298 K).
45+
NASA polynomials were fit in two ranges (298-1000 K, 1000-2000 K) by
46+
least-squares regression of Cp/R with enthalpy and entropy matched at
47+
298.15 K and continuity enforced at 1000 K. Heats of formation were
48+
corrected from 0 K to 298 K using tabulated atomic H(298)-H(0) increments.
49+
50+
Intended as a supporting thermo reference for RMG-generated CO2RR
51+
mechanisms on Cu(111), where extensive benchmarks exist. Uncertainty is
52+
consistent with typical PBE+D3 performance on transition-metal adsorbates
53+
(~0.2 eV, ~20 kJ/mol per species).
954
"""
1055

1156
entry(
@@ -30,7 +75,7 @@
3075
),
3176
shortDesc = u"""CH2OHX""",
3277
longDesc =
33-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
78+
u"""
3479
""",
3580
metal = "Cu",
3681
facet = "111",
@@ -57,7 +102,7 @@
57102
),
58103
shortDesc = u"""CH2X""",
59104
longDesc =
60-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
105+
u"""
61106
""",
62107
metal = "Cu",
63108
facet = "111",
@@ -85,7 +130,7 @@
85130
),
86131
shortDesc = u"""CH3X""",
87132
longDesc =
88-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
133+
u"""
89134
""",
90135
metal = "Cu",
91136
facet = "111",
@@ -113,7 +158,7 @@
113158
),
114159
shortDesc = u"""CHOHX""",
115160
longDesc =
116-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
161+
u"""
117162
""",
118163
metal = "Cu",
119164
facet = "111",
@@ -140,7 +185,7 @@
140185
),
141186
shortDesc = u"""CHOX""",
142187
longDesc =
143-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
188+
u"""
144189
""",
145190
metal = "Cu",
146191
facet = "111",
@@ -166,7 +211,7 @@
166211
),
167212
shortDesc = u"""CHX""",
168213
longDesc =
169-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
214+
u"""
170215
""",
171216
metal = "Cu",
172217
facet = "111",
@@ -195,7 +240,7 @@
195240
),
196241
shortDesc = u"""COCHOX""",
197242
longDesc =
198-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
243+
u"""
199244
""",
200245
metal = "Cu",
201246
facet = "111",
@@ -222,7 +267,7 @@
222267
),
223268
shortDesc = u"""COHX""",
224269
longDesc =
225-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
270+
u"""
226271
""",
227272
metal = "Cu",
228273
facet = "111",
@@ -250,7 +295,7 @@
250295
),
251296
shortDesc = u"""COOHX""",
252297
longDesc =
253-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
298+
u"""
254299
""",
255300
metal = "Cu",
256301
facet = "111",
@@ -276,7 +321,7 @@
276321
),
277322
shortDesc = u"""COX""",
278323
longDesc =
279-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
324+
u"""
280325
""",
281326
metal = "Cu",
282327
facet = "111",
@@ -308,7 +353,7 @@
308353
),
309354
shortDesc = u"""OCH2CH3X""",
310355
longDesc =
311-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
356+
u"""
312357
""",
313358
metal = "Cu",
314359
facet = "111",
@@ -340,7 +385,7 @@
340385
),
341386
shortDesc = u"""OCHCH2OHX""",
342387
longDesc =
343-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
388+
u"""
344389
""",
345390
metal = "Cu",
346391
facet = "111",
@@ -370,7 +415,7 @@
370415
),
371416
shortDesc = u"""OCHCH2X""",
372417
longDesc =
373-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
418+
u"""
374419
""",
375420
metal = "Cu",
376421
facet = "111",
@@ -401,7 +446,7 @@
401446
),
402447
shortDesc = u"""OCHCH3X""",
403448
longDesc =
404-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
449+
u"""
405450
""",
406451
metal = "Cu",
407452
facet = "111",
@@ -432,7 +477,7 @@
432477
),
433478
shortDesc = u"""OCHCHOHX""",
434479
longDesc =
435-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
480+
u"""
436481
""",
437482
metal = "Cu",
438483
facet = "111",
@@ -461,7 +506,7 @@
461506
),
462507
shortDesc = u"""OCHCHX""",
463508
longDesc =
464-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
509+
u"""
465510
""",
466511
metal = "Cu",
467512
facet = "111",
@@ -492,7 +537,7 @@
492537
),
493538
shortDesc = u"""OCHOCHX""",
494539
longDesc =
495-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
540+
u"""
496541
""",
497542
metal = "Cu",
498543
facet = "111",
@@ -520,7 +565,7 @@
520565
),
521566
shortDesc = u"""OCHOX""",
522567
longDesc =
523-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
568+
u"""
524569
""",
525570
metal = "Cu",
526571
facet = "111",
@@ -549,7 +594,7 @@
549594
),
550595
shortDesc = u"""XCOXCO""",
551596
longDesc =
552-
u"""Calculated by Torrie Asifor at Northeastern University using Statistical Mechanics. Based on DFT calculations by Colin Gallagher at Northeastern University
597+
u"""
553598
""",
554599
metal = "Cu",
555600
facet = "111",

0 commit comments

Comments
 (0)