Merge pull request #295 from Exabyte-io/feature/SOF-7507

Feature/SOF-7507 feature: Vacancy and Substitution Pair defect tutorial

Author: VsevolodX

images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp

@@ -0,0 +1,130 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Nitrogen vacancy and Mg substitution in GaN
+
+## Introduction
+
+This tutorial demonstrates the process of creating material with nitrogen vacancies and magnesium substitution defects in GaN.
+
+
+!!!note "Manuscript"
+    **Giacomo Miceli, Alfredo Pasquarello**,
+    "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016.
+    [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}.
+
+We use the [Materials Designer](../../../materials-designer/overview.md) to create a supercell of GaN, identify the crystal site positions for defects, and introduce nitrogen atoms and vacancies accordingly.
+
+We will focus on creating GaN-nitrogen structures from the publication.
+Specifically, the material from FIG. 2. c) of the manuscript: 
+
+
+![Point Pair Defects: Mg Substitution and Vacancy in GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp "Point Defect Pair: Substitution, Vacancy in GaN, FIG. 2.")
+
+
+## 1. Create GaN Supercell
+
+First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the GaN material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+![Standata GaN Import](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp "Standata GaN Import")
+
+We then use the [Advanced](../../../materials-designer/header-menu/advanced/supercell.md) menu to create a supercell of GaN with a size of 4x4x1.
+
+![Supercell Creation for GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp "Supercell GaN")
+
+## 2. Identify Defect Sites
+
+Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to identify the crystal site positions for the defects.
+
+![3D Editor](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.webp "3D Editor")
+
+Hover over the atoms to get the coordinates of the atoms to replace. Then copy/paste these coordinates into a text file for later use.
+
+`[1.608, 4.642, 5.240]` for the Mg substitution defect and `[1.608, 4.642, 7.210]` for the nitrogen vacancy.
+
+## 3. Create Nitrogen Defects and Vacancies
+
+For the defect creation, we will use the [JupyterLite](../../../jupyterlite/overview.md) environment with the corresponding notebook.
+
+### 3.1. 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")
+
+### 3.2. Open `create_point_defect_pair.ipynb` notebook
+
+Find `create_point_defect_pair.ipynb` in the list of notebooks and click/double-click open it.
+
+### 3.3. Open and modify the notebook
+
+Next, edit `create_point_defect_pair.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L257) containing the approximate coordinates of the atoms to replace.
+
+Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows:
+
+```python
+SUPERCELL_MATRIX = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+
+# List of dictionaries with defect parameters
+PRIMARY_DEFECT_CONFIG = {
+    "defect_type": "substitution",
+    "approximate_coordinate": [1.608, 4.642, 5.240],
+    "chemical_element": "Mg",
+    "use_cartesian_coordinates": True,
+}
+
+SECONDARY_DEFECT_CONFIG = {
+    "defect_type": "vacancy",
+    "approximate_coordinate": [1.608, 4.642, 7.210],
+    "use_cartesian_coordinates": True,
+}
+```
+
+Here's the visual of the updated content:
+
+![Notebook setup](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp "Notebook setup")
+
+## 4. Run the Notebook
+
+Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and wait for the results to appear.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+## 5. Analyze the Results
+
+After running the notebook, the user will be able to visualize the structure of GaN with substitution and vacancy defects.
+
+![Review the Results](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp "Review the Results")
+
+## 6. Pass the Material to Materials Designer
+
+The user can pass the resulting material in the current Materials Designer environment and save it.
+
+![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp "Vacancy and Mg Substitution in GaN")
+
+Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format.
+
+
+## Interactive JupyterLite Notebook
+
+The following JupyterLite notebook demonstrates the process of creating materials with substitution defects in GaN. 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_substitution_gallium_nitride.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. **Giacomo Miceli, Alfredo Pasquarello**,
+   "Self-compensation due to point defects in Mg-doped GaN", Physical Review B, 2016.
+   [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}.
+
+## Tags
+
+`defects`, `defect pair`, `substitutional`, `vacancy`, `point defects`, `impurities`, `doped semiconductors`,  `nitrogen`, `GaN`, `gallium nitride`

images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp

@@ -221,6 +221,7 @@ 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
                 - 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