diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index 7b4f3fea1..325edf5a6 100644 --- a/lang/en/docs/includes/references.bib +++ b/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}, diff --git a/lang/en/docs/index-guide.md b/lang/en/docs/index-guide.md index 0a59279f8..f0cd103ed 100644 --- a/lang/en/docs/index-guide.md +++ b/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) | diff --git a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-simulation.md new file mode 100644 index 000000000..c2b6d1246 --- /dev/null +++ b/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 diff --git a/mkdocs-guide.yml b/mkdocs-guide.yml index 31c6c13cd..feb48b988 100644 --- a/mkdocs-guide.yml +++ b/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 diff --git a/mkdocs.yml b/mkdocs.yml index 17e81bb45..90b1c3d37 100644 --- a/mkdocs.yml +++ b/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