SOF-8043: Gr/Ni(111) registry and work of adhesion — tutorial

lang/en/docs/includes/references.bib

@@ -43,6 +43,17 @@ @doi =
     url = {https://link.aps.org/doi/10.1103/PhysRevB.78.115404}
 }
 
+@article{Lahiri2011,
+    title = {Graphene growth and stability at nickel surfaces},
+    author = {Lahiri, Jayeeta and Miller, Travis S. and Ross, Andrew J. and Adamska, Lyudmyla and Oleynik, Ivan I. and Batzill, Matthias},
+    journal = {New Journal of Physics},
+    volume = {13},
+    pages = {025001},
+    year = {2011},
+    doi = {10.1088/1367-2630/13/2/025001},
+    url = {https://doi.org/10.1088/1367-2630/13/2/025001}
+}
+
 @article{Dahal2014,
     title = {Graphene–nickel interfaces: a review},
     author = {Dahal, Arjun and Batzill, Matthias},

lang/en/docs/index-guide.md

@@ -45,7 +45,7 @@ Step-by-step recipes reproducing published work, one row per publication: the st
 | Jung et al. (2015)[^10]           | 2D–2D interface           | [Graphene / h-BN](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) |
 | Shan et al. (2011)[^11]           | 3D–3D interface           | [Cu / SiO2](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) |
 | Kang et al. (2008)[^12]           | 2D–3D interface           | [Graphene / SiO2](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) |
-| Dahal et al. (2014)[^13]          | Interface optimization    | [Graphene / Ni(111)](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) |
+| Dahal et al. (2014)[^13]          | Interface optimization    | [Graphene / Ni(111)](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | [Registry and work of adhesion](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md) |
 | Saidi et al. (2015)[^14]          | Adatom island             | [Pt on MoS2](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) |
 | Aradi et al. (2007)[^15]          | H-passivated nanowire     | [Si](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) |
 | Hansen et al. (1998)[^16]         | H-passivated surface      | [Si(100)](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) |

lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md

@@ -0,0 +1,246 @@
+---
+tags:
+  - graphene
+  - nickel
+  - interface
+  - registry
+  - adsorption
+  - work of adhesion
+  - relaxation
+  - machine-learned force field
+  - MACE
+  - C-2D-INT-Z
+
+hide:
+  - tags
+# YAML header
+render_macros: true
+---
+
+# Gr/Ni(111) Registry and Work of Adhesion
+
+## 1. Introduction
+
+This tutorial reproduces the structure and energetics of graphene on Ni(111) — which registry the
+film adopts, how far it sits above the surface, and the work of adhesion of each arrangement —
+using the interface created in the
+[structure creation tutorial](optimization-interface-film-xy-position-graphene-nickel.md).
+
+!!!note "Manuscript"
+    **Arjun Dahal, Matthias Batzill**,
+    "Graphene-nickel interfaces: a review" Nanoscale, 6(5), 2548 (2014)
+    [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f) [@Dahal2014]
+
+    Its computed values are from **Jayeeta Lahiri et al.**, "Graphene growth and stability at nickel
+    surfaces", New J. Phys. 13, 025001 (2011)
+    [DOI: 10.1088/1367-2630/13/2/025001](https://doi.org/10.1088/1367-2630/13/2/025001) [@Lahiri2011]
+
+### 1.1. What is being reproduced
+
+The review's computed values are from Lahiri *et al.* [@Lahiri2011] (New J. Phys. 13, 025001 (2011),
+open access), whose Table 1 is the quantitative target here:
+
+| interface | work of adhesion (J/m²) | separation (Å) |
+|---|---|---|
+| fcc (atop + fcc hollow) | 0.81 | 2.16 |
+| hcp (atop + hcp hollow) | 0.77 | 2.17 |
+| hollow (fcc + hcp hollows) | 0.31 | 3.26 |
+
+The bridge registry (Fig. 1d of the review) is not quantified in either paper and is computed as
+an extra point beyond the published set.
+
+![The four registries of graphene on a close-packed metal surface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Registries of graphene on a close-packed metal surface")
+
+## 2. Prerequisites
+
+Run the [structure creation tutorial](optimization-interface-film-xy-position-graphene-nickel.md)
+first. Its notebook builds the Gr/Ni(111) interface and saves it into the `uploads` folder as
+`Graphene_Nickel_interface`; the simulation notebook loads it back by exactly that name and stops
+if it is missing. The reduced cell is the 1×1 match: 2 carbon and 4 nickel atoms.
+
+## 3. Workflow overview
+
+Two tiers, both relaxed:
+
+1. **Fast tier (MACE-MP)** — each registry is placed on the substrate's own measured surface sites,
+   bracketed by a rigid separation scan, then relaxed with atomic positions free along z only and
+   the bottom substrate layers fixed.
+2. **Precise tier (LDA on the platform)** — one fixed-cell relaxation per selected registry,
+   starting from the MACE-relaxed geometry, at the paper's LDA functional.
+
+Both tiers also relax the same-cell references the work of adhesion needs — a bare Ni slab and a
+free-standing graphene layer — under the same constraint. The work of adhesion is:
+
+`W = [E(slab) + E(graphene) − E(interface)] / A`
+
+where `A` is the interface area.
+
+## 4. Calculation parameters
+
+The published method is LDA, spin-polarized, with geometry relaxation in which the bottom two of
+five substrate layers are held fixed. This tutorial's fast tier holds the bottom two layers fixed;
+the platform tier relaxes every atom.
+
+| | fast tier | precise tier | Lahiri et al. |
+|---|---|---|---|
+| Method | MACE-MP-0 (large, float64) + D3 | LDA (`pz`), GBRV ultrasoft | LDA, all-electron LCAO (DMol) |
+| Spin | via training data | collinear, moment started at 0.7 μB on Ni; graphene reference unpolarized | spin-polarized (bulk Ni: 0.56 μB) |
+| Relaxation | BFGS, z-only, bottom 2 Ni layers fixed | fixed-cell relaxation (`pw_relax`, `calculation = 'relax'`) | bottom 2 of 5 Ni layers fixed |
+| Cutoffs | — | 40 / 200 Ry (GBRV's published pair) | all-electron |
+| k-grid | — | 12×12×1 (multiple of 3, so K is on the mesh) | converged, not stated |
+| Smearing | — | Marzari-Vanderbilt cold, `degauss = 0.01` Ry | not stated |
+| Dispersion | D3 | none — matching the paper | none |
+
+Divergences from the published method:
+
+- 4 Ni layers, not 5.
+- 20 Å of vacuum, not 90.
+- Plane-wave pseudopotentials, not all-electron LCAO.
+- The platform tier relaxes every atom, where the paper held the bottom two layers fixed.
+
+## 5. Step-by-step instructions
+
+### 5.1. Open the notebook
+
+```
+other/materials_designer/specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb
+```
+
+### 5.2. Configure parameters
+
+The parameters cell sets the material and workflow parameters:
+
+```python
+# Material parameters
+FOLDER = "./uploads"
+BASE_MATERIAL_NAME = "Graphene_Nickel_interface"  # created by the companion structure notebook
+
+# Workflow parameters
+WORKFLOW_SEARCH_TERM = "fixed_cell_relaxation.json"
+APPLICATION_NAME = "espresso"
+MY_WORKFLOW_NAME = "Fixed-cell Relaxation (Gr/Ni registry)"
+```
+
+### 5.3. Set DFT parameters
+
+The same cell sets the method the precise tier submits:
+
+```python
+# Method parameters — the published setup (Lahiri et al., section 2.2) where the platform can
+# express it: LDA, spin-polarized, relaxed, no dispersion correction.
+PSEUDOPOTENTIAL_TYPE = "us"
+FUNCTIONAL = "pz"
+MODEL_SUBTYPE = "lda"
+ECUTWFC = 40   # GBRV's published pair
+ECUTRHO = 200
+SCF_KGRID = [12, 12, 1]  # multiple of 3 keeps K on the mesh; dense for a metal
+STARTING_MAGNETIZATION = {"Ni": 0.7}  # near the bulk moment
+
+# SCF settings for a spin-polarized metal slab
+SMEARING = "mv"
+DEGAUSS = 0.01  # Ry
+ADDITIONAL_PARAMETERS = {
+    "electrons": {
+        "mixing_mode": "local-TF",
+        "mixing_beta": 0.2,
+        "electron_maxstep": 200,
+    },
+}
+```
+
+### 5.4. Run the fast tier
+
+*Run* > *Run All Cells*. Sections 2–4 need no platform account: they load the interface, place
+each registry, relax it with MACE, and print the comparison against Lahiri Table 1.
+
+### 5.5. Run the precise tier
+
+Section 5 selects which registries submit to the platform. `DFT_REGISTRY_NAMES` ships with one
+registry active and three commented out:
+
+```python
+DFT_REGISTRY_NAMES = [
+    "atop_fcc",
+    # "atop_hcp",
+    # "hollow",
+    # "bridge",
+]
+```
+
+Running the rest of section 5 authenticates and submits a relaxation + total-energy job for each
+name in the list, plus the two reference jobs. Leaving `DFT_REGISTRY_NAMES` empty skips the
+platform tier; the automated test does exactly that, because relaxation jobs outlast what a
+browser test may wait for.
+
+### 5.6. Read the final table
+
+The final cell prints the computed values beside the published ones: work of adhesion, separation
+and buckling for each registry, in paper / MACE / DFT columns, with `—` wherever a tier did not run
+or the paper gives no value.
+
+## 6. Expected results
+
+The fast tier prints these values for the four registries, beside Lahiri et al.'s Table 1:
+
+| registry | MACE W_adh (J/m²) | MACE separation (Å) | MACE buckling (Å) | paper W_adh (J/m²) | paper separation (Å) |
+|---|---|---|---|---|---|
+| atop_fcc | 0.17 | 1.98 | −0.006 | 0.81 | 2.16 |
+| atop_hcp | 0.14 | 1.98 | −0.004 | 0.77 | 2.17 |
+| hollow | 0.30 | 4.08 | — | 0.31 | 3.26 |
+| bridge | 0.05 | 1.97 | — | — | — |
+
+A single precise-tier job, run on the platform for `atop_fcc`, gave a work of adhesion of
+1.01 J/m², a separation of 2.02 Å, and a buckling of +0.013 Å with the atop carbon outward; the
+registry was preserved.
+
+## 7. Customization options
+
+### 7.1. Submit more registries
+
+Uncomment additional entries in `DFT_REGISTRY_NAMES` to submit more precise-tier jobs:
+
+```python
+DFT_REGISTRY_NAMES = [
+    "atop_fcc",
+    "atop_hcp",
+    "hollow",
+    "bridge",
+]
+```
+
+### 7.2. Adjust computational resources
+
+Modify the compute parameters in the parameters cell:
+
+```python
+CLUSTER_NAME = None  # or a specific cluster name
+QUEUE_NAME = QueueName.OF
+PPN = 40
+TIME_LIMIT = "04:00:00"
+```
+
+### 7.3. Swap the MLFF model
+
+Change the fast-tier force field in the parameters cell:
+
+```python
+MACE_MODEL_FAMILY = "MACE-MP-0"
+MACE_MODEL = "large"
+MACE_DEFAULT_DTYPE = "float64"
+```
+
+## 8. Interactive JupyterLite notebook
+
+The notebook below runs the fast tier and, when registries are selected, the platform tier.
+Select *Run* > *Run All Cells*.
+
+{% with origin_url=config.extra.jupyterlite.origin_url_lab %}
+{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
+{% with notebook_name='specific_examples/optimization_interface_film_xy_position_graphene_nickel_SIMULATION.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+
+## 9. References

mkdocs-guide.yml

@@ -215,6 +215,7 @@ nav:
             - Grain Boundary in Cu (FCC):                                       tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md
             - Grain Boundary (2D) in h-BN:                                      tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md
             - Gr/Ni(111) Interface Optimization:                                tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md
+            - Gr/Ni(111) Registry and Work of Adhesion:                         tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md
             - Pt Adatoms Island on MoS2:                                        tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md
 
 # 2. Simulations

mkdocs.yml

@@ -175,6 +175,7 @@ nav:
             - Grain Boundary in FCC Metals (Copper):                        tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md
             - Grain Boundary (2D) in h-BN:                                  tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md
             - Gr/Ni(111) Interface Optimization:                            tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md
+            - Gr/Ni(111) Registry and Work of Adhesion:                     tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md
             - Pt Adatoms Island on MoS2:                                    tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md
 
 # COMMON UI COMPONENTS