Merge pull request #303 from Exabyte-io/feature/SOF-7526

feature/SOF 7526

lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md

@@ -0,0 +1,134 @@
+---
+# YAML header
+render_macros: true
+---
+
+
+# Interfaces between 2D and 3D Materials: Graphene on SiO2 (alpha-quartz).
+
+## Introduction.
+
+This tutorial demonstrates the process of creating interfaces between 2D and 3D materials, specifically graphene and silicon dioxide (SiO<sub>2</sub>), based on the work presented in the following manuscript, where the electronic properties of graphene on SiO<sub>2</sub> are studied.
+
+!!!note "Manuscript"
+    **Yong-Ju Kang, Joongoo Kang, and K. J. Chang**
+    "Electronic structure of graphene and doping effect on SiO2"
+    Physical Review B 78, 115404 (2008)
+    [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404)
+
+We use the [Materials Designer](../../../materials-designer/overview.md) to create interfaces between graphene and silicon dioxide with oxygen termination, as shown in the manuscript.
+
+We will focus on replicating the material from FIG. 1. (b) -- with Graphene on O-terminated SiO<sub>2</sub>. The material (a) requires relaxation to correctly reproduce the structure, which is not covered in this tutorial.
+
+![Graphene on Silicon Dioxide](/images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/0-figure-from-manuscript.webp "Graphene on Silicon Dioxide, FIG. 1(b)")
+
+## 1. Load and Preview Materials.
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and import graphene and silicon dioxide materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+Then use the [JupyterLite](../../../jupyterlite/overview.md) environment to create the target structures.
+
+## 2. Create Interface Between Graphene and Silicon Dioxide.
+
+### 2.1 Launch JupyterLite Session.
+
+Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment.
+
+![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog")
+
+### 2.2 Open and Modify the Notebook.
+
+Select the input materials with the first being the substrate (SiO₂) and the second being the film (graphene).
+
+Open the `create_interface_with_min_strain_zsl.ipynb` notebook and modify the parameters as follows:
+
+- Miller indices: `(0, 0, 1)` for both materials
+- Thickness: `1` layer for graphene, `7` layers for SiO₂ (resulting in 14 bilayers as specified in the manuscript)
+- Interface distance: `2.58` Å (as stated in the manuscript)
+- Interface vacuum: `20.0` Å (as specified in the manuscript)
+
+Let's set `MAX_AREA=150` Ų to allow for a larger search area for the superlattice search algorithm.
+
+`TERMINATION_PAIR_INDICES` will be set to `[1]` to get the O-terminated interface as shown in the manuscript.
+
+Adjust the "1.1. Set up slab parameters" cell as shown:
+
+```python
+# Enable interactive selection of terminations via UI prompt
+IS_TERMINATIONS_SELECTION_INTERACTIVE = False
+
+FILM_INDEX = 1  # Index in the list of materials, to access as materials[FILM_INDEX]
+FILM_MILLER_INDICES = (0, 0, 1)
+FILM_THICKNESS = 1  # in atomic layers
+FILM_VACUUM = 0.0  # in angstroms
+FILM_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]
+FILM_USE_ORTHOGONAL_Z = True
+
+SUBSTRATE_INDEX = 0
+SUBSTRATE_MILLER_INDICES = (0, 0, 1)
+SUBSTRATE_THICKNESS = 7  # in atomic layers (for 14 bilayers -- from manuscript)
+SUBSTRATE_VACUUM = 0.0  # in angstroms
+SUBSTRATE_XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]
+SUBSTRATE_USE_ORTHOGONAL_Z = True
+
+# Maximum area for the superlattice search algorithm
+MAX_AREA = 150  # in Angstrom^2
+# Set the termination pair indices
+TERMINATION_PAIR_INDICES = [1]  # For O-terminated
+INTERFACE_DISTANCE = 2.58  # in Angstrom -- from manuscript
+INTERFACE_VACUUM = 20.0  # in Angstrom -- from manuscript
+```
+
+![Notebook Setup](/images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/2-jl-setup-notebook.webp "Notebook Setup")
+
+### 2.3 Run the Notebook
+
+Run the notebook to generate the interface structure between graphene and silicon dioxide with oxygen termination.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+### 2.4. View Results.
+
+The generation might take some time.
+After that, the user can pass the material to the Materials Designer for further analysis.
+
+![Gr/SiO2 Interface](/images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/3-jl-result-preview.webp "Gr/SiO2 Interface")
+
+## 3. Pass the Material to Materials Designer.
+
+After generating the interface structure, pass the material to the Materials Designer for further analysis.
+
+The interface between graphene and silicon dioxide with oxygen termination is shown below.
+
+![Gr/SiO2 Interface](/images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/4-wave-result-material.webp "Gr/SiO2 Interface")
+
+## Interactive JupyterLite Notebook.
+
+
+The interactive JupyterLite notebook for creating interfaces between graphene and silicon dioxide is embedded below. To run the notebook, click on the "Run All" button.
+
+
+{% with origin_url=config.extra.jupyterlite.origin_url %}
+{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
+{% with notebook_name='specific_examples/interface_3d_2d_graphene_silicon_dioxide.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References.
+
+1. **Yong-Ju Kang, Joongoo Kang, and K. J. Chang**
+    "Electronic structure of graphene and doping effect on SiO2"
+    Physical Review B 78, 115404 (2008)
+    [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404)
+
+
+2. **Arjun Dahala  and  Matthias Batzill**
+    "Graphene–nickel interfaces: a review"
+    Nanoscale 6, 2548-2562 (2014)
+    [DOI: 10.1039/C3NR05279F](https://doi.org/10.1039/C3NR05279F)
+
+## Tags.
+
+`graphene`, `silicon dioxide`, `interface`, `2D`,`3D`, `oxygen`, `termination`

mkdocs.yml

@@ -30,7 +30,7 @@ extra_javascript:
 copyright: <a target="_blank" href="https://mat3ra.com">Exabyte Inc</a>. All rights reserved. | <a target="_blank" href="https://platform.mat3ra.com">Back to platform</a>
 
 extra:
-    version: "2024.10.17"
+    version: "2024.12.19"
     preload_javascript:
         - /extra/js/preload_hotjar.js
         - /extra/js/preload.js
@@ -231,6 +231,7 @@ nav:
                 - SrTiO3 Slab:                                                  tutorials/materials/specific/slab-strontium-titanate.md
                 - Interface between Graphene and hBN:                          tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md
                 - Interface between Copper and SiO2 (Cristobalite):                  tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md
+                - Interface between Graphene and SiO2 (alpha-quartz):                tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md
 
 # COMMON UI COMPONENTS
     - Interface Components: