From 98cee2d8167ff28f627452f9509a7e456497be4c Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 20:13:51 -0800 Subject: [PATCH 1/7] feat: add docs for GaN-Mg tutorial --- .../defect-point-pair-gallium-nitride.md | 126 ++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md new file mode 100644 index 00000000..f3fd84c4 --- /dev/null +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -0,0 +1,126 @@ +--- +# 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 FIG. 1. +Specifically, the material from FIG. 1. b) of the paper: + + +![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") + + +## 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. + +## 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 = [[3, 0, 0], [0, 3, 0], [0, 0, 2]] + +# List of dictionaries with defect parameters +PRIMARY_DEFECT_CONFIG = { + "defect_type": "substitution", + "approximate_coordinate": [0.5, 0.5, 0.5], + "chemical_element": "Mg", +} + +SECONDARY_DEFECT_CONFIG = { + "defect_type": "vacancy", + "approximate_coordinate": [0.5, 0.5, 0.65], +} +``` + +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 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 material with substitution defects in the current Materials Designer environment and save it. + +![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp "N-doped 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`, `impurities`, `doped-semiconductors`, `substitutional`, `point-defects`, `nitrogen`, `GaN` From 81618712a7df03d949f4c76933bf986cad622d79 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 20:15:06 -0800 Subject: [PATCH 2/7] update: mkdocs --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) 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 From e44bb9cb17c94f7b7dec66b428dfcf6c9e09346d Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 21:02:33 -0800 Subject: [PATCH 3/7] update: add corrections --- .../defect-point-pair-gallium-nitride.md | 26 +++++++++++-------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md index f3fd84c4..9d33bf53 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -21,27 +21,29 @@ We will focus on creating GaN-nitrogen structures from FIG. 1. Specifically, the material from FIG. 1. b) of the paper: -![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") +![Point Pair Defects: Mg Substitution and Vacancy in GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.png "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") +![Standata GaN Import](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.png "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") +![Supercell Creation for GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.png "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") +![3D Editor](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.png "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. @@ -50,7 +52,7 @@ For the defect creation, we will use the [JupyterLite](../../../jupyterlite/over 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") +![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.png "JupyterLite Dialog") ### 3.2. Open `create_point_defect_pair.ipynb` notebook @@ -63,24 +65,26 @@ Next, edit `create_point_defect_pair.ipynb` notebook to modify the parameters by Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: ```python -SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 2]] +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": [0.5, 0.5, 0.5], + "approximate_coordinate": [1.608, 4.642, 5.240], "chemical_element": "Mg", + "use_cartesian_coordinates": True, } SECONDARY_DEFECT_CONFIG = { "defect_type": "vacancy", - "approximate_coordinate": [0.5, 0.5, 0.65], + "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") +![Notebook setup](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.png "Notebook setup") ## 4. Run the Notebook @@ -92,13 +96,13 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook, the user will be able to visualize the structure of GaN with substitution defects. -![Review the Results](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp "Review the Results") +![Review the Results](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.png "Review the Results") ## 6. Pass the Material to Materials Designer The user can pass the material with substitution defects in the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp "N-doped GaN") +![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.png "N-doped GaN") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. From b25f4774f9a15152c8a6b2198eaef93e019c3228 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 21:04:36 -0800 Subject: [PATCH 4/7] update: add all the images --- .../0-figure-from-manuscript.webp | 3 +++ .../defect_point_pair_gallium_nitride/1-standata-GaN.webp | 3 +++ .../2-advanced-supercell.webp | 3 +++ .../4-threejs-editor-coordinates.webp | 3 +++ .../defects/defect_point_pair_gallium_nitride/5-jl-setup.webp | 3 +++ .../defect_point_pair_gallium_nitride/6-jl-result-preview.webp | 3 +++ .../defect_point_pair_gallium_nitride/7-wave-result.webp | 3 +++ 7 files changed, 21 insertions(+) create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp create mode 100644 images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp new file mode 100644 index 00000000..fb26e0ff --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:6a970c4f94491de99a09bedbd78ca8d11b996e6a301a58d9a8f50be7516f9d35 +size 68642 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp new file mode 100644 index 00000000..918bc90f --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/1-standata-GaN.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a8e8f6663f119b056e387b14eaa48de7009340cc4c794efb04b0d1bb46a2feda +size 14566 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp new file mode 100644 index 00000000..5e01be7b --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e5d1ef2f584b81121e877a41881081afa36c5aee76e5158b43e5482b0cad9dd4 +size 17658 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.webp new file mode 100644 index 00000000..8b19ef50 --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/4-threejs-editor-coordinates.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:996813cb8c291f0e1c019893c922f93d99c62bfa29b2512c46a34a298d7eed3f +size 66834 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp new file mode 100644 index 00000000..66c4a044 --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:62ae546aaca218b9aca3a6a7604d8a1e50d68b0233487ca40afe3da63af4246a +size 47366 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp new file mode 100644 index 00000000..4f1e8f17 --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f1204dd177bc9021b706a78002e99c64d62392b862f7d67080bc791373e7d7a1 +size 52312 diff --git a/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp new file mode 100644 index 00000000..d8d3d7cb --- /dev/null +++ b/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:07a456a00439c579a0099b0d7c0081bcb7b374c6d15d39a758f1ce00f9bc6298 +size 27962 From e62cc9779f3281b49db15b3c0473795349a50721 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 21:04:47 -0800 Subject: [PATCH 5/7] chore: use webp --- .../defect-point-pair-gallium-nitride.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md index 9d33bf53..22e68cb9 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -21,24 +21,24 @@ We will focus on creating GaN-nitrogen structures from FIG. 1. Specifically, the material from FIG. 1. b) of the paper: -![Point Pair Defects: Mg Substitution and Vacancy in GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/0-figure-from-manuscript.png "Point Defect Pair: Substitution, Vacancy in GaN, FIG. 2.") +![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.png "Standata GaN Import") +![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.png "Supercell GaN") +![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.png "3D Editor") +![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. @@ -52,7 +52,7 @@ For the defect creation, we will use the [JupyterLite](../../../jupyterlite/over 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.png "JupyterLite Dialog") +![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") ### 3.2. Open `create_point_defect_pair.ipynb` notebook @@ -84,7 +84,7 @@ SECONDARY_DEFECT_CONFIG = { Here's the visual of the updated content: -![Notebook setup](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.png "Notebook setup") +![Notebook setup](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp "Notebook setup") ## 4. Run the Notebook @@ -96,13 +96,13 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook, the user will be able to visualize the structure of GaN with substitution defects. -![Review the Results](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/6-jl-result-preview.png "Review the Results") +![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 material with substitution defects in the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.png "N-doped GaN") +![Final Material](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/7-wave-result.webp "N-doped GaN") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. From 116a28a2772824c24ff6474c550d3c1c2c4e9db1 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 26 Nov 2024 21:06:56 -0800 Subject: [PATCH 6/7] chore: correct explanations --- .../specific/defect-point-pair-gallium-nitride.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md index 22e68cb9..2084ee38 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -18,7 +18,7 @@ This tutorial demonstrates the process of creating material with nitrogen vacanc 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 FIG. 1. -Specifically, the material from FIG. 1. b) of the paper: +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.") @@ -94,15 +94,15 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and ## 5. Analyze the Results -After running the notebook, the user will be able to visualize the structure of GaN with substitution defects. +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 material with substitution defects in the current Materials Designer environment and save it. +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 "N-doped GaN") +![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. From 19b4da82eebca41472cdf16b7ec6424414a6a6fa Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 27 Nov 2024 19:18:35 -0800 Subject: [PATCH 7/7] udapte: fix tags --- .../materials/specific/defect-point-pair-gallium-nitride.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md index 2084ee38..7fe8333b 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md @@ -17,7 +17,7 @@ This tutorial demonstrates the process of creating material with nitrogen vacanc 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 FIG. 1. +We will focus on creating GaN-nitrogen structures from the publication. Specifically, the material from FIG. 2. c) of the manuscript: @@ -127,4 +127,4 @@ The following JupyterLite notebook demonstrates the process of creating material ## Tags -`defects`, `impurities`, `doped-semiconductors`, `substitutional`, `point-defects`, `nitrogen`, `GaN` +`defects`, `defect pair`, `substitutional`, `vacancy`, `point defects`, `impurities`, `doped semiconductors`, `nitrogen`, `GaN`, `gallium nitride`