Merge pull request #310 from Exabyte-io/feature/SOF-7509

feature/SOF-7509 Gr/Ni optimize tutorial

Author: VsevolodX

images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/0-figure-from-manuscript.webp

@@ -0,0 +1,160 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Graphene/Ni(111) Interface Optimization
+
+## Introduction
+
+This tutorial demonstrates how to create and optimize a Graphene/Ni(111) interface structure following the experimental observations presented in the literature. We will focus on finding the most energetically favorable position of graphene on the Ni(111) surface.
+
+!!!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){:target='_blank'}.
+
+We will recreate the interface structure and optimize the film position to match the experimental findings shown in the figure below:
+
+![Gr/Ni Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)")
+
+## 1. Create Interface Structure
+
+### 1.1. Load Base Materials
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and import both graphene and nickel materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+![Import Graphene and Ni](/images/materials-designer/import/import_from_standata.webp "Import Gr and Ni from Standata")
+
+### 1.2. Launch JupyterLite Session
+
+Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment.
+
+### 1.3. Open `create_interface_with_min_strain_zsl.ipynb` notebook
+
+Find and open the `create_interface_with_min_strain_zsl.ipynb` notebook. This notebook will help us create the initial interface structure.
+
+### 1.4. Set up interface parameters
+
+Edit the notebook parameters to create the Gr/Ni(111) interface:
+
+```python
+# Material selection
+SUBSTRATE_NAME = "Nickel"
+FILM_NAME = "Graphene"
+
+# Slab parameters
+SUBSTRATE_MILLER_INDICES = (1, 1, 1)
+SUBSTRATE_THICKNESS = 4  # in atomic layers
+FILM_THICKNESS = 1  # in atomic layers
+
+# Interface parameters
+MAX_AREA = 50  # in Angstrom^2
+INTERFACE_DISTANCE = 2.58  # in Angstrom from literature
+INTERFACE_VACUUM = 20.0  # in Angstrom
+```
+
+![Interface Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)")
+
+### 1.5. Run interface creation
+
+Run the notebook using "Run > Run All Cells". This will:
+
+1. Create slabs from both materials
+2. Find the optimal lattice matching using the ZSL algorithm
+3. Generate the initial interface structure
+
+## 2. Optimize Film Position
+
+### 2.1. Open `optimize_film_position.ipynb` notebook
+
+Find and open the `optimize_film_position.ipynb` notebook which will help us find the optimal position of the graphene layer.
+
+### 2.2. Set optimization parameters
+
+Configure the optimization parameters:
+
+```python
+# Grid parameters
+GRID_SIZE = (20, 20)  # Resolution of the x-y grid
+GRID_RANGE_X = (-0.5, 0.5)  # Range in crystal coordinates
+GRID_RANGE_Y = (-0.5, 0.5)
+USE_CARTESIAN = False  # Use crystal coordinates
+
+# Visualization parameters
+STRUCTURE_REPETITIONS = [3, 3, 1]
+```
+
+Key parameters explained:
+- `GRID_SIZE`: Controls the resolution of position sampling
+- `GRID_RANGE`: Search range in crystal coordinates
+- `USE_CARTESIAN`: Set to False for hexagonal systems
+
+![Optimization Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)")
+
+### 2.3. Run optimization
+
+Run all cells in the notebook. The optimization will:
+
+1. Calculate energy landscape across different positions
+2. Find the global minimum energy position
+3. Generate visualizations of the results
+
+![Energy Landscape](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/4-energy-landscape.webp "Energy landscape of film positions")
+
+![Energy Heatmap](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/5-energy-heatmap.webp "Energy heatmap of film positions")
+
+## 3. Analyze Results
+
+Compare the original and optimized interface structures to see the difference in the graphene position.
+
+![Initial and optimized interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/6-jl-result-preview-compare.webp "Initial and optimized interface structures")
+
+![Final Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/7-wave-result-final.webp "Optimized Gr/Ni Interface")
+
+
+## 4. Save Optimized Structure
+
+The optimized interface structure will be automatically passed back to Materials Designer where you can:
+1. Save it in the workspace
+2. Export it in various formats (JSON, POSCAR, etc.)
+3. Use it for further calculations
+
+## Interactive JupyterLite Notebook
+
+The following JupyterLite notebook demonstrates the complete process. Select "Run" > "Run All Cells".
+
+{% with origin_url=config.extra.jupyterlite.origin_url %}
+{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
+{% with notebook_name='specific_examples/optimize_film_position_graphene_nickel_interface.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## Parameter Fine-tuning
+
+To adjust the interface optimization:
+
+1. Interface Creation:
+   - Adjust `SUBSTRATE_THICKNESS` for more Ni layers
+   - Modify `MAX_AREA` to control supercell size
+   - Change `INTERFACE_DISTANCE` if needed
+
+2. Position Optimization:
+   - Increase `GRID_SIZE` for finer sampling
+   - Adjust `GRID_RANGE` to search different areas
+   - Enable 3D visualization with `SHOW_3D_LANDSCAPE = True`
+
+## References
+
+1. Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. Nanoscale, 6(5), 2548-2562. [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f)
+
+2. Gamo, Y., Nagashima, A., Wakabayashi, M., Terai, M., & Oshima, C. (1997). Atomic structure of monolayer graphite formed on Ni(111). Surface Science, 374(1-3), 61-64. [DOI: 10.1016/S0039-6028(96)01307-3](https://www.sciencedirect.com/science/article/abs/pii/S0039602896007856)
+
+3. Bertoni, G., Calmels, L., Altibelli, A., & Serin, V. (2004). First-principles calculation of the electronic structure and EELS spectra at the graphene/Ni(111) interface. Physical Review B, 71(7). [DOI: 10.1103/PhysRevB.71.075402](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402)
+
+## Tags
+
+`graphene`, `nickel`, `interface`, `optimization`, `2D materials`, `surface science`, `Gr/Ni(111)`, `C`, `Ni`

images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/2-jl-setup-nb-interface.webp

@@ -238,6 +238,7 @@ nav:
                 - Ripple perturbation of a Graphene sheet:                               tutorials/materials/specific/perturbation-ripples-graphene.md
                 - Grain Boundary in FCC Metals (Copper):                                tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md
                 - Grain Boundary (2D) in h-BN:                                   tutorials/materials/specific/grain-boundary-2d-boron-nitride.md
+                - Gr/Ni(111) Interface Optimization:                                     tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md
 
 # COMMON UI COMPONENTS
     - Interface Components: