Merge pull request #305 from Exabyte-io/feature/SOF-7524

feature/SOF-7524 Vacancy in hBN tutorial

lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md

@@ -0,0 +1,138 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Vacancy Point Defects in Hexagonal Boron Nitride.
+
+## Introduction.
+
+This tutorial demonstrates the process of creating materials with vacancy point defects, based on the work presented in the following manuscript:
+
+!!!note "Manuscript"
+    Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen, "Quantum point defects in 2D materials - the QPOD database", Nature, 2022. [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w){:target='_blank'}.
+
+We use the [Materials Designer](../../../materials-designer/overview.md) and JupyterLite environment to create a nanoribbon of hexagonal boron nitride (h-BN) and introduce vacancy defects. The process combines the capabilities of nanoribbon creation and point defect introduction.
+
+We will focus on creating a structure similar to Figure 6 from the manuscript, which demonstrates boron vacancy defects in hexagonal boron nitride:
+
+![Vacancy in h-BN](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/0-figure-from-manuscript.webp "Vacancy in h-BN")
+
+## 1. Import Base Material.
+
+First, we need to import the hexagonal boron nitride (h-BN) material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md) database.
+
+### 1.1. Open Materials Designer.
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and click on the "Input/Output" menu.
+
+### 1.2. Import from Standata.
+
+1. Select "Import from Standata" in the Input/Output menu
+2. In the search box, enter "Boron Nitride"
+4. Click on the h-BN material to import it
+
+![Standata h-BN Import](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata h-BN Import")
+
+## 2. Create h-BN Nanoribbon.
+
+Next, we'll create a nanoribbon structure using the JupyterLite environment.
+
+### 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 Configure Nanoribbon Notebook.
+
+Find and open `create_nanoribbon.ipynb` in the list of notebooks. Edit the nanoribbon parameters in section 1.1 of the notebook:
+
+```python
+WIDTH = 3  # in number of unit cells
+LENGTH = 6  # in number of unit cells
+VACUUM_WIDTH = 0  # in number of unit cells
+VACUUM_LENGTH = 0 # in number of unit cells
+EDGE_TYPE = "zigzag"  # "zigzag" or "armchair"
+```
+
+![Nanoribbon Parameters](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/2-jl-nb-setup-nanoribbon.webp "Nanoribbon Parameters")
+
+### 2.3. Run the Notebook.
+
+Run the notebook by clicking `Run` > `Run All` in the top menu. This will create a nanoribbon structure from the imported h-BN material.
+
+### 2.4. Review Nanoribbon in Materials Designer.
+
+After the notebook completes:
+
+1. The nanoribbon structure will be passed back to Materials Designer
+2. User can view the structure in the 3D editor
+3. Verify the nanoribbon dimensions and edge type
+
+![Nanoribbon Preview](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/3-wave-preview-nanoribbon.webp "Nanoribbon Preview")
+
+
+## 3. Create the Vacancy Defect.
+
+After creating the nanoribbon, we'll introduce the vacancy defect using the point defect notebook.
+
+### 3.1. Open Point Defect Notebook.
+
+Open `create_point_defect.ipynb` and modify the defect configuration parameters:
+
+```python
+SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+DEFECT_CONFIGS = [
+    {
+        "defect_type": "vacancy",
+        "approximate_coordinate": [0.5, 0.5, 0.5],
+        "use_cartesian_coordinates": False
+    }
+]
+```
+
+The configuration specifies:
+
+- `defect_type`: "vacancy" for removing an atom
+- `approximate_coordinate`: Position in crystal coordinates where the vacancy will be created
+- `use_cartesian_coordinates`: False to use fractional coordinates
+
+![Point Defect Parameters](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/4-jl-nb-setup-point-defect.webp "Point Defect Parameters")
+
+### 3.2. Run the Notebook.
+
+Click `Run` > `Run All` in the top menu to run the notebook and preview the results.
+
+![Review the Results](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/5-jl-result-preview.webp "Review the Results")
+
+## 4. Save the Material.
+
+After running both notebooks, user can visualize the structure of h-BN with the vacancy defect in the Materials Designer 3D viewer.
+
+![Vacancy in h-BN](/images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/6-wave-result.webp "Vacancy in h-BN")
+
+
+[Save or download](../../../materials-designer/header-menu/input-output.md) in Material JSON format
+
+## Interactive JupyterLite Notebook.
+
+The following JupyterLite notebooks demonstrate 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/defect_point_vacancy_boron_nitride.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References.
+
+1. Fabian Bertoldo, Sajid Ali, Simone Manti & Kristian S. Thygesen, "Quantum point defects in 2D materials - the QPOD database", Nature, 2022. [DOI:10.1038/s41524-022-00730-w](https://doi.org/10.1038/s41524-022-00730-w){:target='_blank'}.
+
+2. Kohan A. F., Ceder G., Morgan D., Van de Walle C. G. (2000). First-principles study of native point defects in h-BN. Physical Review B, 61(23), 15019-15027. [DOI:10.1103/PhysRevB.61.15019](https://doi.org/10.1103/PhysRevB.61.15019){:target='_blank'}.
+
+## Tags.
+
+`defects`, `vacancy`, `point-defects`, `h-BN`, `boron-nitride`, `2D-materials`

mkdocs.yml

@@ -222,6 +222,7 @@ nav:
             - Specific:
                 - Substitutional Point Defects in Graphene:                   tutorials/materials/specific/defect-point-substitution-graphene.md
                 - Vacancy-Substitution Pair Defects in GaN:                   tutorials/materials/specific/defect-point-pair-gallium-nitride.md
+                - Vacancy Point Defect in h-BN:                                       tutorials/materials/specific/defect-point-vacancy-boron-nitride.md
                 - Island Surface Defect Formation in TiN:                     tutorials/materials/specific/defect-surface-island-titanium-nitride.md
                 - Twisted Bilayer h-BN nanoribbons:                       tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md
                 - Twisted Bilayer MoS2 commensurate lattices:                tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md