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+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` diff --git a/mkdocs.yml b/mkdocs.yml index ac5035bb..2476ac10 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -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