From b2955be2e992fc0d0ceef23fe3b6a52f41fef853 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Thu, 2 Jan 2025 18:12:47 -0800 Subject: [PATCH 01/20] chore: add periods --- .../defect-point-interstitial-tin-oxide.md | 40 +++++++++---------- .../defect-point-pair-gallium-nitride.md | 28 ++++++------- .../defect-point-substitution-graphene.md | 28 ++++++------- .../defect-surface-adatom-graphene.md | 28 ++++++------- .../defect-surface-island-titanium-nitride.md | 34 ++++++++-------- .../grain-boundary-2d-boron-nitride.md | 30 +++++++------- .../grain-boundary-3d-fcc-metals-copper.md | 28 ++++++------- ...ioxide-hafnium-dioxide-titanium-nitride.md | 36 ++++++++--------- .../interface-2d-2d-graphene-boron-nitride.md | 24 +++++------ 9 files changed, 138 insertions(+), 138 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index 40ac6692..9a0fabb1 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -5,7 +5,7 @@ render_macros: true # Oxygen interstitial Defect(s) in SnO. -## Introduction +## Introduction. This tutorial demonstrates how to create an oxygen interstitial defect in tin monoxide (SnO), following the methodology described in the literature. @@ -19,42 +19,42 @@ We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [V ![SnO O-interstitial](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") -## 1. Prepare Base Structure +## 1. Prepare Base Structure. -### 1.1. Load Base Material +### 1.1. Load Base Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the SnO material from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md) using the search term "SnO". ![Original SnO](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp "SnO from Standata, 2x2x2 repetitions") -### 1.2. Launch JupyterLite Session +### 1.2. Launch JupyterLite Session. Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment. -### 1.3. Open `create_defect.ipynb` Notebook +### 1.3. Open `create_defect.ipynb` Notebook. Find and open the `create_defect.ipynb` notebook. Select "SnO" input material. We'll modify its parameters to create the Sn-vacancy O-interstitial defects according to the image above. -### 1.4. Set Defect Parameters +### 1.4. Set Defect Parameters. Replace the default parameters in section 1.1 with: ```python -# Supercell parameters +# Supercell parameters. SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 2]] -# Defect parameters +# Defect parameters. DEFECT_CONFIGS = [ { "defect_type": "vacancy", - # Coordiante will be resolved to nearest atom + # Coordiante will be resolved to nearest atom. "approximate_coordinate": [0.0, 0.25, 0.525], }, { "defect_type": "interstitial", - # Coordiante will be resolved to nearest Voronoi site + # Coordiante will be resolved to nearest Voronoi site. "coordinate": [0.0, 0.25, 0.35], "chemical_element": "O", "placement_method": "voronoi_site" @@ -77,9 +77,9 @@ Second defect: - `chemical_element`: "O" for oxygen interstitial - `placement_method`: "voronoi_site" to place atom at appropriate interstitial position -## 2. Create the Defect +## 2. Create the Defect. -### 2.1. Run Supercell Creation +### 2.1. Run Supercell Creation. Run the notebook by selecting "Run" > "Run All Cells". This will: @@ -87,25 +87,25 @@ Run the notebook by selecting "Run" > "Run All Cells". This will: 2. Create the O-interstitial at the specified position 3. Generate the final defect structure -## 3. Analyze Results +## 3. Analyze Results. After creating the defect, examine the structure to verify: ![SnO with O-interstitial defect](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/4-wave-result-material.webp "SnO with O-interstitial defect") -### 3.1. Defect Position +### 3.1. Defect Position. - O interstitial should be at (0.0, 0.5, 0.5) in crystal coordinates - Position should be in a void space between Sn-O layers - Verify symmetry of surrounding atoms -### 3.2. Local Structure +### 3.2. Local Structure. - Check distances to nearest Sn and O atoms - Verify no unrealistic atom overlaps - Confirm overall crystal structure is maintained -## 4. Save Defect Structure +## 4. Save Defect Structure. The defect structure will be automatically passed back to Materials Designer where you can: @@ -113,7 +113,7 @@ The defect structure will be automatically passed back to Materials Designer whe 2. Export it in various formats 3. Use it for further calculations -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells". @@ -126,7 +126,7 @@ The following embedded notebook demonstrates the complete process. Select "Run" {% endwith %} -## Parameter Fine-tuning +## Parameter Fine-tuning. To adjust the defect creation: @@ -141,10 +141,10 @@ To adjust the defect creation: - Change `SUPERCELL_MATRIX` for larger/smaller systems - Consider periodic boundary conditions effects -## References +## References. 1. Togo, A., Oba, F., & Tanaka, I. (2006). First-principles calculations of native defects in tin monoxide. Physical Review B, 74(19), 195128. -## Tags +## Tags. `SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O` 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 de09f10d..b93f0c32 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 @@ -3,9 +3,9 @@ render_macros: true --- -# Nitrogen vacancy and Mg substitution in GaN +# Nitrogen vacancy and Mg substitution in GaN. -## Introduction +## Introduction. This tutorial demonstrates the process of creating material with nitrogen vacancies and magnesium substitution defects in GaN. @@ -24,7 +24,7 @@ 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 +## 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). @@ -34,7 +34,7 @@ We then use the [Advanced](../../../materials-designer/header-menu/advanced/supe ![Supercell Creation for GaN](/images/tutorials/materials/defects/defect_point_pair_gallium_nitride/2-advanced-supercell.webp "Supercell GaN") -## 2. Identify Defect Sites +## 2. Identify Defect Sites. Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to identify the crystal site positions for the defects. @@ -44,21 +44,21 @@ Hover over the atoms to get the coordinates of the atoms to replace. Then copy/p `[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 +## 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 +### 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 +### 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 +### 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. @@ -86,19 +86,19 @@ 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 +## 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 +## 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 +## 6. Pass the Material to Materials Designer. The user can pass the resulting material in the current Materials Designer environment and save it. @@ -107,7 +107,7 @@ The user can pass the resulting material in the current Materials Designer envir 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 +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating materials with substitution defects in GaN. Select "Run" > "Run All Cells". @@ -119,12 +119,12 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} {% endwith %} -## References +## 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 +## Tags. `defects`, `defect pair`, `substitutional`, `vacancy`, `point defects`, `impurities`, `doped semiconductors`, `nitrogen`, `GaN`, `gallium nitride` diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 732bb613..15b6a97e 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -3,9 +3,9 @@ render_macros: true --- -# Substitutional Point Defects in Graphene +# Substitutional Point Defects in Graphene. -## Introduction +## Introduction. This tutorial demonstrates the process of creating materials with substitution defects, based on the work presented in the following manuscript, where nitrogen defects in graphene are studied. @@ -23,7 +23,7 @@ Specifically, the material from FIG. 1. b) of the paper: ![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") -## 1. Create Graphene Supercell +## 1. Create Graphene Supercell. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -33,7 +33,7 @@ We then use the [Advanced](../../../materials-designer/header-menu/advanced/supe ![Supercell Creation for Graphene](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/2-advanced-supercell.webp "Supercell Graphene") -## 2. Identify Defect Sites +## 2. Identify Defect Sites. Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to identify the crystal site positions for the defects. @@ -41,21 +41,21 @@ Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to ident 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 +## 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 +### 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.ipynb` notebook +### 3.2. Open `create_point_defect.ipynb` notebook. Find `create_point_defect.ipynb` in the list of notebooks and click/double-click open it. -### 3.3. Open and modify the notebook +### 3.3. Open and modify the notebook. Next, edit `create_point_defect.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#L32) containing the approximate coordinates of the atoms to replace. @@ -101,19 +101,19 @@ Here's the visual of the updated content: ![Notebook setup](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/5-jl-setup.webp "Notebook setup") -## 4. Run the Notebook +## 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 +## 5. Analyze the Results. After running the notebook, the user will be able to visualize the structure of Graphene with substitution defects. ![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results") -## 6. Pass the Material to Materials Designer +## 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. @@ -122,7 +122,7 @@ The user can pass the material with substitution defects in the current Material 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 +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating materials with substitution defects in graphene. Select "Run" > "Run All Cells". @@ -134,11 +134,11 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} {% endwith %} -## References +## References. 1. Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}. -## Tags +## Tags. `defects`, `graphene`, `substitutional`, `point-defects`, `nitrogen` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 1c63384d..88a89f63 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -3,9 +3,9 @@ render_macros: true --- -# Adatom on Graphene Surface +# Adatom on Graphene Surface. -## Introduction +## Introduction. This tutorial demonstrates the process of creating a graphene structure with an adatom on the surface based on the work presented in the following manuscript. @@ -20,7 +20,7 @@ The image shows the adatom on the graphene surface. ![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface") -## 1. Load and preview Graphene structure +## 1. Load and preview Graphene structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -28,15 +28,15 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a graphene structure with an adatom on the surface. -## 2. Add Li adatom +## 2. Add Li adatom. -### 2.1 Launch JupyterLite Session +### 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 +### 2.2. Open and modify the notebook. Next, edit `create_adatom_defect.ipynb` notebook to modify the parameters by changing values: @@ -69,13 +69,13 @@ VACUUM = 6 SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]] ``` -### 2.3. Run the notebook +### 2.3. Run the notebook. Run the notebook by selecting "Run > Run All Cells" from the menu. ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 2.4. Analyze the Results +### 2.4. Analyze the Results. After running the notebook, the Graphene structure with a Li adatom on the surface will be created. @@ -83,7 +83,7 @@ The user will be able to visualize the created structure and download the corres ![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-li.webp "Li Adatom on Graphene Surface") -### 2.5. Pass the Material to the Materials Designer +### 2.5. Pass the Material to the Materials Designer. After reviewing the results, the user can pass the material to Materials Designer for further analysis. @@ -91,9 +91,9 @@ After reviewing the results, the user can pass the material to Materials Designe Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. -## 3. Add other metal adatoms +## 3. Add other metal adatoms. -### 3.1. Repeat the steps above +### 3.1. Repeat the steps above. To create a Graphene structure with other metal adatoms, repeat the steps above by changing the `CHEMICAL_ELEMENT`, `APPORXIMATE_POSITION_ON_SURFACE`, and `DISTANCE_Z` parameters according to he values in the table 1 of the manuscript. Notice, that some of the adatoms have more favorable position on top or bridge sites. @@ -207,7 +207,7 @@ DISTANCE_Z = 2.69 ![Au Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-au.webp "Au Adatom on Graphene Surface") -## Interactive JupiterLite Notebook +## Interactive JupiterLite Notebook. The interactive JupyterLite notebook for creating Graphene structures with metal adatoms can be accessed below. To run the notebook, click on the "Run All" button. @@ -219,10 +219,10 @@ The interactive JupyterLite notebook for creating Graphene structures with metal {% endwith %} {% endwith %} -## References +## References. 1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. -## Tags +## Tags. `adatom`, `graphene`, `metal`, `surface`, `defect` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 5a1d62f1..d36338af 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -3,9 +3,9 @@ render_macros: true --- -# Island Surface Defect Formation in TiN +# Island Surface Defect Formation in TiN. -## Introduction +## Introduction. This tutorial demonstrates the process of creating material with island on the surface of TiN(001) based on the work presented in the following manuscript. @@ -24,7 +24,7 @@ Specifically, the material from FIG. 2. a) of the paper: ![Surface Defect](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a)") -## 1. Create and preview TiN Slab +## 1. Create and preview TiN Slab. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -33,14 +33,14 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a TiN slab. -### 1.1. Launch JupyterLite Session +### 1.1. 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") -### 1.2. Open and modify the notebook +### 1.2. Open and modify the notebook. Next, edit `create_slab.ipynb` notebook to modify the parameters by adding the following content to the "1.1. Set up slab parameters" cell in the notebook: @@ -59,13 +59,13 @@ USE_CONVENTIONAL_CELL = True TERMINATION_INDEX = 0 ``` -### 1.3. Run the Notebook +### 1.3. 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") -### 1.4. Analyze the Results +### 1.4. Analyze the Results. After running the notebook, the user will be able to visualize the created TiN slab. @@ -73,7 +73,7 @@ After running the notebook, the user will be able to visualize the created TiN s We don't need to save the material at this point, as we will recreate the slab with island on the surface in the next notebook. This step is needed to identify the coordinates of the island vertices. -## 2. Identifying the Island vertices coordinates +## 2. Identifying the Island vertices coordinates. We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. @@ -95,15 +95,15 @@ The final centered coordinates of the island are: `[0.25, 0.2, 0]` and `[0.65, 0 These coordinates will be used in the next step to create the island on the surface. -## 3. Create Island on the Surface +## 3. Create Island on the Surface. -### 3.1. Open `create_point_defect.ipynb` notebook +### 3.1. Open `create_point_defect.ipynb` notebook. Close the current notebook. `Introduction` notebook should be open by default. Find `create_island_defect.ipynb` in the list of notebooks and double-click open it. -### 3.2. Modify the notebook +### 3.2. Modify the notebook. Next, edit `create_island_defect.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#L191) containing the cartesian coordinates of the island vertices. @@ -139,19 +139,19 @@ Here's the visual of the updated content: ![Notebook setup](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png "Notebook setup") -## 4. Run the Notebook +## 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 +## 5. Analyze the Results. After running the notebook, the user will be able to visualize the created material with the island on the surface. ![Review the Results](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png "Review the Results") -## 6. Pass the Material to Materials Designer +## 6. Pass the Material to Materials Designer. The user can pass the resulting material to the current Materials Designer environment and save it. @@ -160,7 +160,7 @@ The user can pass the resulting material to the current Materials Designer envir 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 +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating material with island. Select "Run" > "Run All Cells". @@ -172,10 +172,10 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} {% endwith %} -## References +## References. 1. D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene, "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. -## Tags +## Tags. `defects`, `island`, `surface`, `surface-defects`, `TiN`, `nitrogen`, `titanium` diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md index 1bd80bb1..9eee444f 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md @@ -3,9 +3,9 @@ render_macros: true --- -# 2D Grain Boundaries in Hexagonal Boron Nitride +# 2D Grain Boundaries in Hexagonal Boron Nitride. -## Introduction +## Introduction. This tutorial demonstrates the process of creating 2D grain boundary structures in hexagonal boron nitride (h-BN), based on the work presented in the following manuscript: @@ -16,9 +16,9 @@ We will focus on creating h-BN grain boundary structures similar to Figure 2c fr ![h-BN Grain Boundary](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.") -## 1. Create Initial h-BN Structure +## 1. Create Initial h-BN Structure. -### 1.1. Load h-BN Material +### 1.1. Load h-BN Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the h-BN material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -29,11 +29,11 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im ![Standata h-BN Import](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata h-BN Import") -### 1.2. Launch JupyterLite Session +### 1.2. Launch JupyterLite Session. Select "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" to open JupyterLite. -### 1.3. Open and Configure Notebook +### 1.3. Open and Configure Notebook. Find and open `create_grain_boundary_film.ipynb`. Edit the grain boundary parameters in section 1.1: @@ -66,7 +66,7 @@ EDGE_INCLUSION_TOLERANCE = 0.0 # in Angstroms !!!note "Important Parameter" The `DISTANCE_TOLERANCE` parameter (1.43 Å) is larger than B-N distances at the one specific spot in the boundary. This will cause certain nitrogen atoms to be removed during structure generation, which we'll need to restore later. -## 2. Run the Notebook +## 2. Run the Notebook. Run the notebook by selecting "Run" > "Run All Cells". @@ -74,11 +74,11 @@ The notebook will generate the h-BN grain boundary structure based on the parame ![Initial h-BN Structure](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/4-wave-result-gb.webp "Initial h-BN Structure") -## 3. Restore Missing Nitrogen Atom +## 3. Restore Missing Nitrogen Atom. Due to the `DISTANCE_TOLERANCE` setting, one nitrogen atom at the boundary is removed. We need to restore it: -### 3.1. Add Missing Nitrogen +### 3.1. Add Missing Nitrogen. Open JupyterLite Session and find `create_point_defect.ipynb` notebook. @@ -105,13 +105,13 @@ DEFECT_CONFIGS = [ ![Notebook Setup](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/5-jl-setup-nb-final-gb.webp "Notebook Setup") -### 3.2. Run the Notebook +### 3.2. Run the Notebook. Run the notebook to add the missing nitrogen atom to the h-BN grain boundary structure. ![Final Structure Preview](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/6-jl-result-preview-final-gb.webp "Final Structure Preview") -## 4. Pass Final Material to Materials Designer +## 4. Pass Final Material to Materials Designer. The user can pass the material with substitution defects in the current Materials Designer environment and save it. @@ -119,14 +119,14 @@ The user can pass the material with substitution defects in the current Material Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. -## 5. Manual Adjustment +## 5. Manual Adjustment. To fill the gaps between two phases edge atoms can be adjusted manually in Materials Designer 3D editor. The resulting structure should be similar to the one shown in the manuscript. ![Adjusted Structure](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/8-wave-result-final-gb-relaxed.webp "Adjusted Structure") -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the complete process. Select "Run" > "Run All Cells". @@ -138,10 +138,10 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% endwith %} {% endwith %} -## References +## References. 1. Qiucheng Li, et al., "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)", ACS Nano 2015 9 (6), 6308-6315. [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852) -## Tags +## Tags. `grain-boundary`, `h-BN`, `2D-materials`, `interface`, `twist-angle`, `atom-restoration` diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md index a172b522..b7d22729 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md @@ -3,9 +3,9 @@ render_macros: true --- -# Grain Boundaries in FCC Metals (Copper) +# Grain Boundaries in FCC Metals (Copper). -## Introduction +## Introduction. This tutorial demonstrates the process of creating grain boundary structures in FCC metals, specifically copper, based on the work presented in the following manuscript, where structural phase transformations in metallic grain boundaries are studied. @@ -17,9 +17,9 @@ We will focus on creating copper grain boundary structures similar to Figure 1b ![Copper Grain Boundary](/images/tutorials/materials/defects/grain_boundary_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") -## 1. Create Initial Copper Structure +## 1. Create Initial Copper Structure. -### 1.1. Load Copper Material +### 1.1. Load Copper Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the copper material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -29,13 +29,13 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im ![Copper Material Import](/images/tutorials/materials/defects/grain_boundary_fcc_metal/1-standata-import-cu.webp "Copper Material Import") -### 1.2. Launch JupyterLite Session +### 1.2. Launch JupyterLite Session. Select "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" to open JupyterLite. ![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") -### 1.3. Open and Configure Notebook +### 1.3. Open and Configure Notebook. Find and open `create_grain_boundary.ipynb`. Edit the grain boundary parameters in section 1.1 of the notebook: @@ -79,16 +79,16 @@ These parameters will create: ![Grain Boundary Parameters](/images/tutorials/materials/defects/grain_boundary_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters") -## 2. Run the Notebook +## 2. Run the Notebook. After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. ![Run All](/images/jupyterlite/run-all.webp "Run All") -## 3. Analyze the Results +## 3. Analyze the Results. -### 3.1. Review the Structure +### 3.1. Review the Structure. After running the notebook, user can visualize the grain boundary structure: @@ -98,7 +98,7 @@ After running the notebook, user can visualize the grain boundary structure: ![Grain Boundary Preview](/images/tutorials/materials/defects/grain_boundary_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview") -### 3.2. Structure Details +### 3.2. Structure Details. The resulting structure should show: @@ -114,7 +114,7 @@ Grain boundary from the top (XY) and side (XZ) views: The structure has differences from the original figure in the manuscript, since grain boundary achieved by strain-matching two symmetrical surfaces with no changes to either surfaces. Discrepancies might be removed with further adjustments like shifting the phases, removing atom layers and reconstructing the interface. -## 4. Save the Structure +## 4. Save the Structure. The final structure can be: @@ -122,7 +122,7 @@ The final structure can be: 2. [Saved or downloaded](../../../materials-designer/header-menu/input-output.md) in Material JSON format 3. Exported as a POSCAR file -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the complete process. Select "Run" > "Run All Cells". @@ -134,10 +134,10 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% endwith %} {% endwith %} -## References +## References. 1. Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919) -## Tags +## Tags. `grain boundary`, `interface`, `copper`, `Cu`, `FCC`, `metal` diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index 5c3c1e23..5c477b0d 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -3,9 +3,9 @@ render_macros: true --- -# Creating High-k Metal Gate Stack: Si/SiO2/HfO2/TiN +# Creating High-k Metal Gate Stack: Si/SiO2/HfO2/TiN. -## Introduction +## Introduction. This tutorial demonstrates how to create a high-k metal gate stack heterostructure consisting of four materials: Si (substrate), SiO2 (gate oxide), HfO2 (high-k dielectric), and TiN (metal gate). The process involves: @@ -17,7 +17,7 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea ![High-k Metal Gate Stack](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack") -## 1. Set Up Materials +## 1. Set Up Materials. First, navigate to Materials Designer and import from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md) the following materials: @@ -28,11 +28,11 @@ First, navigate to Materials Designer and import from [Standata](../../../materi ![Standata Import](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/import-standata.webp "Standata Import") -## 2. Create HfO2 and TiN Slabs +## 2. Create HfO2 and TiN Slabs. Before building the stack, we need to create properly terminated slabs for HfO2 and TiN. -### 2.1. Create HfO2 Slab +### 2.1. Create HfO2 Slab. More detailed instructions on slab creation can be found in the [SrTiO3 Slab](slab-strontium-titanate.md) tutorial. @@ -55,7 +55,7 @@ Run the notebook to create the HfO2 slab and pass it to Materials Designer. ![HfO2 slab](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-hfo2-slab-wave.webp "HfO2 slab") -### 2.2. Create TiN Slab +### 2.2. Create TiN Slab. Open another instance of `create_slab_with_termination.ipynb` for TiN: @@ -75,9 +75,9 @@ Run the notebook to create and pass the TiN slab to Materials Designer. ![TiN slab](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-tin-slab.webp "TiN slab") -## 3. Create Si/SiO2 Interface +## 3. Create Si/SiO2 Interface. -### 3.1. Launch ZSL Interface Builder +### 3.1. Launch ZSL Interface Builder. Open `create_interface_with_min_strain_zsl.ipynb` and configure: @@ -110,13 +110,13 @@ We set a higher tolerances to achieve smaller cell with higher strain of the fil ![Interface Setup](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2.webp "Interface Setup") -### 3.2. Create Initial Interface +### 3.2. Create Initial Interface. Run the notebook to create the Si/SiO2 interface. This is the most critical interface, so we use strain matching to optimize it. -## 4. Add HfO2 Layer +## 4. Add HfO2 Layer. -### 4.1. Configure Simple Interface Builder +### 4.1. Configure Simple Interface Builder. Open JupyterLite Session again and select the Si/SiO2 interface and HfO2 slab as input materials. @@ -139,15 +139,15 @@ Film is the material that will be strained (scaled) to match the substrate. ![HfO2 Interface Setup](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2-hfo2.webp "HfO2 Interface Setup") -### 4.2. Add HfO2 +### 4.2. Add HfO2. Run the notebook to add the pre-created HfO2 slab to the Si/SiO2 structure. ![Si/SiO2/HfO2](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-si-sio2-hfo2.webp "Si/SiO2/HfO2") -## 5. Add TiN Layer +## 5. Add TiN Layer. -### 5.1. Configure Final Layer Addition +### 5.1. Configure Final Layer Addition. Similar to steps in Section 4, we add the TiN layer to the Si/SiO2/HfO2 stack. @@ -166,7 +166,7 @@ INTERFACE_DISTANCE = 2.5 # Angstroms INTERFACE_VACUUM = 10.0 # Final vacuum spacing ``` -### 5.2. Complete the Stack +### 5.2. Complete the Stack. Run the notebook to add the TiN layer and complete the stack. @@ -174,7 +174,7 @@ Run the notebook to add the TiN layer and complete the stack. The user then can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating target material. Select "Run" > "Run All Cells". @@ -186,7 +186,7 @@ The following JupyterLite notebook demonstrates the process of creating target m {% endwith %} {% endwith %} -## References +## References. 1. [QuantumATK tutorial](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) @@ -200,6 +200,6 @@ The following JupyterLite notebook demonstrates the process of creating target m Reports on Progress in Physics 69, 327 (2006) [DOI: 10.1088/0034-4885/69/2/R02](https://doi.org/10.1088/0034-4885/69/2/R02) -## Tags +## Tags. `slab-creation`, `interfaces`, `high-k`, `metal-gate`, `semiconductor`, `heterostructure`, `strain-matching`, `Si`, `SiO2`, `HfO2`, `TiN` diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md index 6d699f53..2204d60b 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md @@ -3,9 +3,9 @@ render_macros: true --- -# Interfaces between 2D Materials: h-BN and Graphene +# Interfaces between 2D Materials: h-BN and Graphene. -## Introduction +## Introduction. This tutorial demonstrates the process of creating interfaces with different stacking configurations between 2D materials, specifically hexagonal boron nitride (h-BN) and graphene, based on the work presented in the following manuscript, where the electronic properties of h-BN-graphene interfaces are studied. @@ -22,7 +22,7 @@ The Figure 7 shows the different stacking configurations of graphene on h-BN. ![Graphene on Hexagonal Boron Nitride](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/0-figure-from-manuscript.webp "Graphene on Hexagonal Boron Nitride, FIG. 7") -## 1. Load and preview materials +## 1. Load and preview materials. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Graphene and Hexagonal BN materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -32,16 +32,16 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create the target structures. -## 2. Create interface between h-BN and Graphene +## 2. Create interface between h-BN and Graphene. -### 2.1 Launch JupyterLite Session +### 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 +### 2.2. Open and modify the notebook. Select the input materials with first one being the substrate (h-BN) and the second one being the film (Graphene). @@ -87,13 +87,13 @@ INTERFACE_VACUUM = 20.0 # in Angstrom ![Notebook setup](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/2-jl-setup-notebook.webp "Notebook setup") -### 2.3. Run the Notebook +### 2.3. Run the Notebook. After setting the parameters, run the notebook to create the interface between h-BN and Graphene. ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 2.4. View Results and shift the layers +### 2.4. View Results and shift the layers. The generation might take some time. After that, the user can pass the material to the Materials Designer for further analysis. @@ -127,7 +127,7 @@ Preview of interfaces with different stacking configurations is shown below. ![Shifted Interfaces](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/5-jl-result-preview.webp "Shifted Interfaces") -## 3. Pass the Material to Materials Designer +## 3. Pass the Material to Materials Designer. The user can pass the material with the interface in the current Materials Designer environment and save it. @@ -136,7 +136,7 @@ The user can pass the material with the interface in the current Materials Desig 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 +## Interactive JupyterLite Notebook. The interactive JupyterLite notebook for creating Gr/h-BN interface can be accessed below. To run the notebook, click on the "Run All" button. @@ -149,7 +149,7 @@ The interactive JupyterLite notebook for creating Gr/h-BN interface can be acces {% endwith %} {% endwith %} -## References +## References. 1. **Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam** @@ -169,6 +169,6 @@ The interactive JupyterLite notebook for creating Gr/h-BN interface can be acces RSC Adv., 2024, 4, 1-10 [DOI: 10.1039/D3RA06559F](https://doi.org/10.1039/D3RA06559F) -## Tags +## Tags. `2D`, `Graphene`, `Hexagonal Boron Nitride`, `interface`, `stacking` From b45946e649d06ae7f045289e558032fa84311a40 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Thu, 2 Jan 2025 18:36:40 -0800 Subject: [PATCH 02/20] chore: add periods 2 --- .../defect_point_adatom_island_mos2_pt.md | 36 +++++++++---------- ...mensurate-lattices-molybdenum-disulfide.md | 26 +++++++------- ...layer-twisted-nanoribbons-boron-nitride.md | 30 ++++++++-------- .../materials/specific/nanocluster-gold.md | 28 +++++++-------- ...film-position-graphene-nickel-interface.md | 36 +++++++++---------- .../passivation-edge-silicon-nanowire.md | 30 ++++++++-------- .../specific/perturbation-ripples-graphene.md | 32 ++++++++--------- .../specific/slab-strontium-titanate.md | 28 +++++++-------- 8 files changed, 123 insertions(+), 123 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md index 59333e9c..fbf1afab 100644 --- a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md +++ b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md @@ -3,9 +3,9 @@ render_macros: true --- -# Pt Nanoparticles on MoS2(001) Surface via Adatoms +# Pt Nanoparticles on MoS2(001) Surface via Adatoms. -## Introduction +## Introduction. This tutorial demonstrates how to create a platinum island on MoS2 by sequentially adding Pt adatoms, following the methodology described in the literature. @@ -19,23 +19,23 @@ We will recreate the Pt island structure shown in Figure 4b: ![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/0-figure-from-manuscript.webp "Pt island formation on MoS2") -## 1. Create MoS2 Substrate +## 1. Create MoS2 Substrate. -### 1.1. Load Base Material +### 1.1. Load Base Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 2D material from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -### 1.2. Launch JupyterLite Session +### 1.2. Launch JupyterLite Session. Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment. -### 1.3. Open `create_adatom_defect.ipynb` Notebook +### 1.3. Open `create_adatom_defect.ipynb` Notebook. Find and open the `create_adatom_defect.ipynb` notebook. Select MoS2 as input material. -## 2. Configure and Create Structure +## 2. Configure and Create Structure. -### 2.1. Set Parameters +### 2.1. Set Parameters. Set up the slab and defect parameters in the notebook: @@ -98,13 +98,13 @@ Key parameters explained: ![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/1-jl-setup-nb.webp "Pt adatoms setup") -### 2.2. Run the Notebook +### 2.2. Run the Notebook. Execute the notebook to create the Pt island structure on MoS2 by selecting "Run" > "Run All Cells" from the JupyterLite menu. ![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/2-jl-result-preview.webp "Pt island results preview") -### 2.3. Pass the Result to Materials Designer +### 2.3. Pass the Result to Materials Designer. The result can be passed to Materials Designer for visualization and viewed from the top: @@ -114,24 +114,24 @@ And from the side: ![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/5-wave-result-side.webp "Complete Pt island structure, side view") -## 3. Analyze the Structure +## 3. Analyze the Structure. After adding all Pt atoms, verify the following: -### 3.1. Base Layer Geometry +### 3.1. Base Layer Geometry. - Three Pt atoms should form a triangular base - Each base Pt should be positioned atop Mo atoms - Distance from surface S atoms should be ~1.2 Å - Relaxation is needed to achieve the exact geometry from the publication, can be performed elsewhere -### 3.2. Top Atom Position +### 3.2. Top Atom Position. - Fourth Pt should be centered above the triangle - Position should be approximately above a surface S atom - Height should be ~2.8 Å from surface (1.6 Å from base Pt atoms) -## 4. Save the Structure +## 4. Save the Structure. The final structure will be automatically passed back to Materials Designer where user can: @@ -139,7 +139,7 @@ The final structure will be automatically passed back to Materials Designer wher 2. Export it in various formats 3. Use it for further transformations -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells". @@ -151,7 +151,7 @@ The following embedded notebook demonstrates the complete process. Select "Run" {% endwith %} {% endwith %} -## Parameter Fine-tuning +## Parameter Fine-tuning. To adjust the island structure: @@ -163,7 +163,7 @@ To adjust the island structure: - Adjust position to change island shape - Modify height to change Pt-Pt spacing -## References +## References. 1. Saidi, W. A. (2015). Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface. Crystal Growth & Design, 15(2), 642–652. [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. @@ -176,6 +176,6 @@ To adjust the island structure: 5. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler, "Density-functional study of Mn monosilicide on the Si(111) surface: Film formation versus island nucleation", Phys. Rev. B 76, 235426 (2007). [DOI: 10.1103/PhysRevB.76.235426](https://doi.org/10.1103/PhysRevB.76.235426){:target='_blank'}. -## Tags +## Tags. `MoS2`, `platinum`, `adatoms`, `surface science`, `2D materials`, `nanoparticles`, `Mo`, `S`, `Pt` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index 97a287db..5160f9ee 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -3,9 +3,9 @@ render_macros: true --- -# Twisted Bilayer Molybdenum Disulfide Structure Creation +# Twisted Bilayer Molybdenum Disulfide Structure Creation. -## Introduction +## Introduction. This tutorial demonstrates the process of creating a twisted bilayer molybdenum disulfide (MoS2) structure based on the work presented in the following manuscript. @@ -21,7 +21,7 @@ The Figure 4 shows the twisted bilayer MoS2 configurations. ![Twisted Bilayer Molybdenum Disulfide](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide") -## 1. Load and preview MoS2 structure +## 1. Load and preview MoS2 structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -31,16 +31,16 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a twisted bilayer molybdenum disulfide structure. -## 2. Create MoS2 bilayer with a twist angle of 22 degrees +## 2. Create MoS2 bilayer with a twist angle of 22 degrees. -### 2.1 Launch JupyterLite Session +### 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 +### 2.2. Open and modify the notebook. Next, edit `create_twisted_interface_with_commnesurate_lattices.ipynb` notebook to modify the parameters by adding: `TARGET_TWIST_ANGLE = 22` and `INTERFACE_DISTANCE = 6.5` -- found in the publication description. @@ -69,13 +69,13 @@ VISUALIZE_REPETITIONS = [3, 3, 1] ![Notebook setup](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/jl-set-nb.png "Notebook setup") -### 2.3. Run the Notebook +### 2.3. Run the Notebook. After setting the parameters, run the notebook to create the twisted bilayer molybdenum disulfide structure. ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 2.4. View Results and pass to Materials Designer +### 2.4. View Results and pass to Materials Designer. The generation might take some time. After that, the user can pass the material to the Materials Designer for further analysis. @@ -84,9 +84,9 @@ The interface for 22 degrees twist is shown below. ![Result Material, 22 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-22.png "MoS2 Twisted Bilayer, 22 degrees") -## 3. Create bilayers with other twist angles +## 3. Create bilayers with other twist angles. -### 3.1. Repeat the steps above +### 3.1. Repeat the steps above. To create a twisted bilayer MoS2 structure with a different twist angle, repeat the steps above, adjusting the `TARGET_TWIST_ANGLE` and `INTERFACE_DISTANCE` parameters accordingly. Values for angle and associated interlayer separation provided below come from the description of Figure 4 in the publication, below each example has an image of the resulting material. @@ -128,7 +128,7 @@ INTERFACE_DISTANCE = 6.2 ![Result Material, 60 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-60.png "MoS2 Twisted Bilayer, 60 degrees") -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The interactive JupyterLite notebook for creating twisted bilayer MoS2 structures can be accessed below. To run the notebook, click on the "Run All" button. @@ -141,11 +141,11 @@ The interactive JupyterLite notebook for creating twisted bilayer MoS2 structure {% endwith %} {% endwith %} -## References +## References. 1. Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang, "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014) [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) 2. Cao, Y., Fatemi, V., Fang, S. et al. Unconventional superconductivity in magic-angle graphene superlattices. Nature 556, 43–50 (2018). [DOI: 10.1038/nature26160](https://doi.org/10.1038/nature26160) -## Tags +## Tags. `2d-materials`, `layers`, `bilayer`, `twisted`, `commensurate`, `molybdenum`, `disulfide` diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md index 62010b9d..db1016fc 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md @@ -3,9 +3,9 @@ render_macros: true --- -# Twisted Bilayer Boron Nitride (TBBN) Structure Creation +# Twisted Bilayer Boron Nitride (TBBN) Structure Creation. -## Introduction +## Introduction. This tutorial demonstrates the process of creating a twisted bilayer boron nitride (TBBN) structure based on the work presented in the following manuscript. @@ -21,7 +21,7 @@ The image shows the twisted bilayer h-BN structure with a twist angle of 2.64° ![Twisted Bilayer Boron Nitride](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride") -## 1. Load and preview BN structure +## 1. Load and preview BN structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the BN material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -29,15 +29,15 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a twisted bilayer boron nitride structure. -## 2. Create bilayer with a twist angle of 2.64° +## 2. Create bilayer with a twist angle of 2.64°. -### 2.1 Launch JupyterLite Session +### 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 +### 2.2. Open and modify the notebook. Next, edit `create_twisted_interface_with_nanoribbons.ipynb` notebook to modify the parameters by adding: `RIBBON_WIDTH = 50` and `RIBBON_LENGTH = 50`, `TWIST_ANGLE = 2.64`. Adjust the "1.1. Set up slab parameters" cell in the notebook according to: @@ -64,34 +64,34 @@ VISUALIZE_REPETITIONS = [1, 1, 1] ![Notebook setup](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/jl-set-nb.png "Notebook setup") -### 2.3. Run the Notebook +### 2.3. Run the Notebook. After setting the parameters, run the notebook with "Run" > "Run All" option to create the twisted bilayer boron nitride structure. ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 2.4. Analyze the Results +### 2.4. Analyze the Results. After running the notebook, the user will be able to visualize the created twisted bilayer boron nitride structure. ![Review the Results](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-jl.png "Review the Results") -### 2.5. Pass Results to the Materials Designer +### 2.5. Pass Results to the Materials Designer. After reviewing the results, the user can pass the material to the Materials Designer for further analysis. ![Result Material](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-wavejs.png "Result Material") -## 3. Create a TBBN structure with a twist angle of 62.64° +## 3. Create a TBBN structure with a twist angle of 62.64°. -### 3.1. Repeat the steps above +### 3.1. Repeat the steps above. To create a twisted bilayer boron nitride structure with a twist angle of 62.64°, repeat the above steps 2.1 -- 2.5 with the following modifications. Set `TWIST_ANGLE = 62.64` in the "1.1. Set up slab parameters" cell in the notebook. -### 3.2. View Results and pass to the Materials Designer +### 3.2. View Results and pass to the Materials Designer. After running the notebook, the user will be able to visualize the created twisted bilayer boron nitride structure with a twist angle of 62.64°. @@ -99,7 +99,7 @@ After reviewing the results, the user can pass the material to the Materials Des ![Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-62_64.png "Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle") -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The interactive JupyterLite notebook for creating the twisted bilayer boron nitride structure can be accessed below. Select "Run" > "Run All Cells" to create two materials. @@ -111,12 +111,12 @@ The interactive JupyterLite notebook for creating the twisted bilayer boron nitr {% endwith %} {% endwith %} -## References +## References. 1. **Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**, "Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402 – Published 20 August 2020 DOI: 10.1021/acs.nanolett.9b00986 -## Tags +## Tags. `twisted-bilayer`,`nanoribbons`, `boron-nitride`, `BN`, `boron`, `nitrogen` diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md index bc5e4938..9a829660 100644 --- a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -3,9 +3,9 @@ render_macros: true --- -# Gold Nanoclusters +# Gold Nanoclusters. -## Introduction +## Introduction. This tutorial demonstrates the process of creating a gold nanoparticle structures based on the work presented in the following manuscript. @@ -20,7 +20,7 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea ![Gold Nanoparticles](/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") -## 1. Load and preview Gold structure +## 1. Load and preview Gold structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Gold material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -28,15 +28,15 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create gold nanoparticle structures. -## 2. Create cuboctahedra +## 2. Create cuboctahedra. -### 2.1 Launch JupyterLite Session +### 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 +### 2.2. Open and modify the notebook. Next, edit `create_cluster_ase.ipynb` notebook to modify the parameters by changing values: @@ -57,13 +57,13 @@ parameters = { ![Setup for cuboctahedron cluster](/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp "Setup for cuboctahedron cluster") -### 2.3. Run the notebook +### 2.3. Run the notebook. Run the notebook by selecting "Run > Run All Cells" from the menu. ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 2.4. Analyze the Results +### 2.4. Analyze the Results. After running the notebook, the octahedral gold nanoparticle structure will be created. @@ -73,7 +73,7 @@ For better view of the solid symmetry rotation of image might be needed like `"r ![Cuboctahedron Gold Nanocluster](/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp "Cuboctahedron Gold Nanocluster") -### 2.5. Pass the Material to the Materials Designer +### 2.5. Pass the Material to the Materials Designer. After reviewing the results, the user can pass the material to Materials Designer for further analysis. @@ -81,9 +81,9 @@ After reviewing the results, the user can pass the material to Materials Designe Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. -## 3. Create clusters with other shapes and sizes +## 3. Create clusters with other shapes and sizes. -### 3.1. Repeat the steps above +### 3.1. Repeat the steps above. Repeat the steps above to create gold nanoparticle structures with other shapes and sizes. @@ -146,7 +146,7 @@ parameters = { ![Icosahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp "Icosahedron 309") -## Interactive JupiterLite Notebook +## Interactive JupiterLite Notebook. The interactive JupyterLite notebook for creating Gold Nanoclusters can be accessed below. To run the notebook, click on the "Run All" button. @@ -158,7 +158,7 @@ The interactive JupyterLite notebook for creating Gold Nanoclusters can be acces {% endwith %} {% endwith %} -## References +## References. 1. **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, "Electronic shell structure and chemisorption on gold nanoparticles", @@ -166,6 +166,6 @@ The interactive JupyterLite notebook for creating Gold Nanoclusters can be acces [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. -## Tags +## Tags. `gold`, `cluster`, `nanoparticle`, `cuboctahedron`, `icosahedron` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md index 7b7e4666..7567f060 100644 --- a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md +++ b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md @@ -3,9 +3,9 @@ render_macros: true --- -# Graphene/Ni(111) Interface Optimization +# Graphene/Ni(111) Interface Optimization. -## Introduction +## Introduction. This tutorial demonstrates how to create and optimize a Graphene/Ni(111) interface structure following the experimental observations presented in the literature. We will focus on finding the most energetically favorable position of graphene on the Ni(111) surface. @@ -19,23 +19,23 @@ We will recreate the interface structure and optimize the film position to match ![Gr/Ni Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)") -## 1. Create Interface Structure +## 1. Create Interface Structure. -### 1.1. Load Base Materials +### 1.1. Load Base Materials. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import both graphene and nickel materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). ![Import Graphene and Ni](/images/materials-designer/import/import_from_standata.webp "Import Gr and Ni from Standata") -### 1.2. Launch JupyterLite Session +### 1.2. Launch JupyterLite Session. Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment. -### 1.3. Open `create_interface_with_min_strain_zsl.ipynb` notebook +### 1.3. Open `create_interface_with_min_strain_zsl.ipynb` notebook. Find and open the `create_interface_with_min_strain_zsl.ipynb` notebook. This notebook will help us create the initial interface structure. -### 1.4. Set up interface parameters +### 1.4. Set up interface parameters. Edit the notebook parameters to create the Gr/Ni(111) interface: @@ -57,7 +57,7 @@ INTERFACE_VACUUM = 20.0 # in Angstrom ![Interface Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)") -### 1.5. Run interface creation +### 1.5. Run interface creation. Run the notebook using "Run > Run All Cells". This will: @@ -65,13 +65,13 @@ Run the notebook using "Run > Run All Cells". This will: 2. Find the optimal lattice matching using the ZSL algorithm 3. Generate the initial interface structure -## 2. Optimize Film Position +## 2. Optimize Film Position. -### 2.1. Open `optimize_film_position.ipynb` notebook +### 2.1. Open `optimize_film_position.ipynb` notebook. Find and open the `optimize_film_position.ipynb` notebook which will help us find the optimal position of the graphene layer. -### 2.2. Set optimization parameters +### 2.2. Set optimization parameters. Configure the optimization parameters: @@ -93,7 +93,7 @@ Key parameters explained: ![Optimization Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)") -### 2.3. Run optimization +### 2.3. Run optimization. Run all cells in the notebook. The optimization will: @@ -105,7 +105,7 @@ Run all cells in the notebook. The optimization will: ![Energy Heatmap](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/5-energy-heatmap.webp "Energy heatmap of film positions") -## 3. Analyze Results +## 3. Analyze Results. Compare the original and optimized interface structures to see the difference in the graphene position. @@ -114,14 +114,14 @@ Compare the original and optimized interface structures to see the difference in ![Final Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/7-wave-result-final.webp "Optimized Gr/Ni Interface") -## 4. Save Optimized Structure +## 4. Save Optimized Structure. The optimized interface structure will be automatically passed back to Materials Designer where you can: 1. Save it in the workspace 2. Export it in various formats (JSON, POSCAR, etc.) 3. Use it for further calculations -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the complete process. Select "Run" > "Run All Cells". @@ -133,7 +133,7 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% endwith %} {% endwith %} -## Parameter Fine-tuning +## Parameter Fine-tuning. To adjust the interface optimization: @@ -147,7 +147,7 @@ To adjust the interface optimization: - Adjust `GRID_RANGE` to search different areas - Enable 3D visualization with `SHOW_3D_LANDSCAPE = True` -## References +## References. 1. Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. Nanoscale, 6(5), 2548-2562. [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f) @@ -155,6 +155,6 @@ To adjust the interface optimization: 3. Bertoni, G., Calmels, L., Altibelli, A., & Serin, V. (2004). First-principles calculation of the electronic structure and EELS spectra at the graphene/Ni(111) interface. Physical Review B, 71(7). [DOI: 10.1103/PhysRevB.71.075402](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402) -## Tags +## Tags. `graphene`, `nickel`, `interface`, `optimization`, `2D materials`, `surface science`, `Gr/Ni(111)`, `C`, `Ni` diff --git a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md index 8be86554..f1b59854 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md @@ -3,9 +3,9 @@ render_macros: true --- -# Passivation of Silicon Nanowire +# Passivation of Silicon Nanowire. -## Introduction +## Introduction. This tutorial demonstrates the process of creating passivated silicon nanowires based on the work presented in the following manuscript, where the chemical gap tuning in silicon nanowires is studied. @@ -24,25 +24,25 @@ Specifically, the material from FIG. 1. of the publication: ![Passivated Silicon nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") -## 1. Create Silicon Nanowire +## 1. Create Silicon Nanowire. -### 1.1. Load Silicon Material +### 1.1. Load Silicon Material. Since we're using Silicon, it can be already loaded as the default material and we can skip this step. Otherwise, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the silicon material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -### 1.2. Launch JupyterLite Session +### 1.2. 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") -### 1.3. Open `create_nanowire_custom_shapeipynb` notebook +### 1.3. Open `create_nanowire_custom_shapeipynb` notebook. Find `create_nanowire_custom_shape.ipynb` in the list of notebooks and click/double-click open it. -### 1.4. Open and modify the notebook +### 1.4. Open and modify the notebook. Next, we need to create a nanowire wit ha custom shape. @@ -117,7 +117,7 @@ vertices = [ condition = CustomCoordinateCondition(vertices=vertices).condition ``` -## 1.5. Run the Notebook and use the Material +## 1.5. Run the Notebook and use the Material. Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and wait for the results to appear. @@ -127,9 +127,9 @@ After running the notebook and submitting the material, the user will be able to ![Silicon Nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp "Silicon Nanowire") -## 2. Passivate with Hydrogen +## 2. Passivate with Hydrogen. -### 2.1. Setup the Passivation +### 2.1. Setup the Passivation. Open JupyterLite Session again and select Silicon Nanowire material for Input Materials. @@ -170,13 +170,13 @@ Here's the visual of the updated content: ![Notebook setup](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp "Notebook setup") -### 2.2. Run the notebook and analyze the results +### 2.2. Run the notebook and analyze the results. After running the notebook, the user will be able to visualize the structure of Silicon Nanowire with substitution defects. ![Review the Results](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp "Review the Results") -## 3. Pass the Material to Materials Designer +## 3. Pass the Material to Materials Designer. The user can pass the material with substitution defects in the current Materials Designer environment and save it. @@ -185,7 +185,7 @@ The user can pass the material with substitution defects in the current Material 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 +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating materials with hydrogen passivation of silicon nanowire. Select "Run" > "Run All Cells". @@ -197,13 +197,13 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} {% endwith %} -## References +## References. 1. B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim, Theoretical study of the chemical gap tuning in silicon nanowires Phys. Rev. B 76, 035305 (2007) DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305) -## Tags +## Tags. `silicon`, `hydrogen`, `passivation`, `nanowire` diff --git a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md index 23651af0..691af053 100644 --- a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md @@ -5,7 +5,7 @@ render_macros: true # Ripple perturbation of a Graphene sheet. -## Introduction +## Introduction. This tutorial demonstrates the process of creating edge induced ripples in graphene nanosheet based on the work presented in the following manuscript, where the mechanical properties of graphene edges were studied. @@ -19,25 +19,25 @@ We will focus on creating graphene with edge-induced ripples that match the patt ![Rippled Graphene](/images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.") -## 1. Create Graphene Nanoribbon +## 1. Create Graphene Nanoribbon. -### 1.1. Load Graphene Material +### 1.1. Load Graphene Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). ![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") -### 1.2. Launch JupyterLite Session +### 1.2. 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") -### 1.3. Open `create_nanoribbon.ipynb` notebook +### 1.3. Open `create_nanoribbon.ipynb` notebook. Find `create_nanoribbon.ipynb` in the list of notebooks and click/double-click to open it. -### 1.4. Set up nanoribbon parameters +### 1.4. Set up nanoribbon parameters. Edit notebook to set the nanoribbon parameters: @@ -52,19 +52,19 @@ EDGE_TYPE = "zigzag" # "zigzag" or "armchair" ![Setup Nanoribbon Parameters](/images/tutorials/materials/defects/perturbation_ripple_graphene/2-jl-setup-nb-nanoribbon.webp "Setup Nanoribbon Parameters") -### 1.5. Run the notebook +### 1.5. Run the notebook. After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. This will create a graphene nanoribbon with the specified dimensions. ![Nanoribbon Result](/images/tutorials/materials/defects/perturbation_ripple_graphene/3-wave-result-nanoribbon.webp "Graphene Nanoribbon") -## 2. Create Ripples in the Nanoribbon +## 2. Create Ripples in the Nanoribbon. -### 2.1. Open `create_perturbation_custom.ipynb` notebook +### 2.1. Open `create_perturbation_custom.ipynb` notebook. Find `create_perturbation_custom.ipynb` in the list of notebooks and click/double-click to open it. -### 2.2. Set up perturbation parameters +### 2.2. Set up perturbation parameters. Next, we need to set up the parameters for creating rippled graphene. @@ -125,13 +125,13 @@ Key parameters explained: - `EDGE_WIDTH` Controls how far the ripples extend from the edges (0.25 in crystal coordinates) - `PHASE_X`/`PHASE_Y` Controls the phase shift of the ripple pattern -### 2.3. Run the notebook +### 2.3. Run the notebook. After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. ![Run All](/images/jupyterlite/run-all.webp "Run All") -## 3. Pass the Material to Materials Designer +## 3. Pass the Material to Materials Designer. The rippled graphene structure will be automatically passed back to the current Materials Designer environment where user can save it. @@ -145,7 +145,7 @@ Graphene with edge-induced ripples with amplitude of 0.27 crystal units. Or user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. -## Interactive JupyterLite Notebook +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating rippled graphene. Select "Run" > "Run All Cells". @@ -157,7 +157,7 @@ The following JupyterLite notebook demonstrates the process of creating rippled {% endwith %} {% endwith %} -## Parameters Fine-tuning +## Parameters Fine-tuning. If user need to adjust the ripple pattern, user can modify these key parameters: @@ -173,7 +173,7 @@ If user need to adjust the ripple pattern, user can modify these key parameters: 4. To change the ripple pattern: - Adjust PHASE_X and PHASE_Y to modify the wave interference pattern -## References +## References. 1. Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. (2009). Rippling of graphene. EPL (Europhysics Letters), 85(4), 46002. [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002) @@ -181,6 +181,6 @@ If user need to adjust the ripple pattern, user can modify these key parameters: 3. L. A. Openov & A. I. Podlivaev, "Interaction of the Stone-Wales defects in graphene", Physics of the Solid State, 52, 1, 2010. [DOI: 10.1134/S1063783415070240](https://doi.org/10.1134/S1063783415070240) -## Tags +## Tags. `graphene`, `ripples`, `perturbation`, `2D materials`, `edge effects`, `C` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md index 546b4d45..ea0f511a 100644 --- a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md +++ b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md @@ -3,9 +3,9 @@ render_macros: true --- -# Strontium Titanate Slabs +# Strontium Titanate Slabs. -## Introduction +## Introduction. This tutorial demonstrates the process of creating strontium titanate (SrTiO3) slabs based on the work presented in the following manuscript, where the electronic properties of SrTiO3 slabs are studied. @@ -21,25 +21,25 @@ We will focus on creating SrTiO3 (011) slabs with different terminati ![Strontium Titanate Slabs](/images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.") -## 1. Create Strontium Titanate Slab +## 1. Create Strontium Titanate Slab. -### 1.1. Load Strontium Titanate Material +### 1.1. Load Strontium Titanate Material. Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the strontium titanate material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). ![Strontium Titanate Material](/images/tutorials/materials/2d_materials/slab_strontium_titanate/original-material.webp "Strontium Titanate Material") -### 1.2. Launch JupyterLite Session +### 1.2. 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") -### 1.3. Open `create_slab.ipynb` notebook +### 1.3. Open `create_slab.ipynb` notebook. Find `create_slab.ipynb` in the list of notebooks and click/double-click open it. -### 1.4. Open and modify the notebook +### 1.4. Open and modify the notebook. Next, we need to create a SrTiO3 slab with the (011) orientation. @@ -88,24 +88,24 @@ This will allow for symmetry breaking and correct detection for all possible ter ![Rotate Material](/images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-setup-rotation.webp "Rotate Material") -### 1.5. Run the notebook +### 1.5. Run the notebook. After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. ![Run All](/images/jupyterlite/run-all.webp "Run All") -## 2. Analyze the Results +## 2. Analyze the Results. After running the notebook, the slabs for different possible terminations should apper in the preview. ![Strontium Titanate Slab](/images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-result-preview.webp "Strontium Titanate Slab") -### 2.1. Select the desired termination +### 2.1. Select the desired termination. If the interactive selection of terminations is enabled, select the desired termination from the list or change the `TERMINATION_INDEX` parameter in the notebook and rerun it. -## 3. Pass the Material to Materials Designer +## 3. Pass the Material to Materials Designer. The user can pass the material with the selected termination in the current Materials Designer environment and save it. @@ -114,7 +114,7 @@ The user can pass the material with the selected termination in the current Mate 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 +## Interactive JupyterLite Notebook. The following JupyterLite notebook demonstrates the process of creating strontium titanate slabs. Select "Run" > "Run All Cells". @@ -127,12 +127,12 @@ The following JupyterLite notebook demonstrates the process of creating strontiu {% endwith %} {% endwith %} -## References +## References. 1. R. I. Eglitis and David Vanderbilt, "First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces", Phys. Rev. B 77, 195408 (2008) [DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408) 2. Atashi B. Mukhopadhyay, Javier F. Sanz, and Charles B. Musgrave "First-principles calculations of structural and electronic properties of monoclinic hafnia surfaces", Phys. Rev. B 73, 115330 (2006) DOI: [10.1103/PhysRevB.73.115330](https://doi.org/10.1103/PhysRevB.73.115330) -## Tags +## Tags. `slab`, `strontium titanate`, `SrTiO3`, `terminations`, `surface` From f08ed5f7766d2fce78f5b37b6bef7cb22027941c Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 13:58:25 -0800 Subject: [PATCH 03/20] update: place tags to yaml ath the top, remove from bottom --- .../defect-point-interstitial-tin-oxide.md | 15 ++++++++++++--- .../defect-point-pair-gallium-nitride.md | 17 ++++++++++++++--- .../defect-point-substitution-graphene.md | 12 +++++++++--- .../defect-point-vacancy-boron-nitride.md | 13 ++++++++++--- .../specific/defect-surface-adatom-graphene.md | 12 +++++++++--- .../defect-surface-island-titanium-nitride.md | 14 +++++++++++--- .../specific/defect-surface-step-platinum.md | 14 +++++++++++--- .../defect_point_adatom_island_mos2_pt.md | 16 +++++++++++++--- .../grain-boundary-2d-boron-nitride.md | 13 ++++++++++--- .../grain-boundary-3d-fcc-metals-copper.md | 13 ++++++++++--- ...dioxide-hafnium-dioxide-titanium-nitride.md | 18 +++++++++++++++--- .../interface-2d-2d-graphene-boron-nitride.md | 12 +++++++++--- ...interface-2d-3d-graphene-silicon-dioxide.md | 14 +++++++++++--- .../interface-3d-3d-copper-silicon-dioxide.md | 14 +++++++++++--- ...mmensurate-lattices-molybdenum-disulfide.md | 14 +++++++++++--- ...ilayer-twisted-nanoribbons-boron-nitride.md | 14 ++++++++++---- .../materials/specific/nanocluster-gold.md | 12 +++++++++--- ...-film-position-graphene-nickel-interface.md | 16 +++++++++++++--- .../passivation-surface-silicon-surface.md | 15 ++++++++++++--- .../specific/perturbation-ripples-graphene.md | 13 ++++++++++--- .../specific/slab-strontium-titanate.md | 12 +++++++++--- 21 files changed, 229 insertions(+), 64 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index 3a4f0d51..8577ec96 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -1,4 +1,16 @@ --- +tags: + - SnO + - defects + - interstitial + - voronoi + - oxygen + - point defects + - Sn + - O + +hide: + - tags # YAML header render_macros: true --- @@ -152,6 +164,3 @@ To adjust the defect creation: [DOI: 10.1103/PhysRevB.73.125205](https://doi.org/10.1103/PhysRevB.73.125205){:target='_blank'}. -## Tags. - -`SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O` 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 b93f0c32..d417e658 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 @@ -1,4 +1,18 @@ --- +tags: + - defects + - defect pair + - substitutional + - vacancy + - point defects + - impurities + - doped semiconductors + - nitrogen + - GaN + - gallium nitride + +hide: + - tags # YAML header render_macros: true --- @@ -125,6 +139,3 @@ The following JupyterLite notebook demonstrates the process of creating material "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/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 15b6a97e..85a01ba5 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -1,4 +1,13 @@ --- +tags: + - defects + - graphene + - substitutional + - point-defects + - nitrogen + +hide: + - tags # YAML header render_macros: true --- @@ -139,6 +148,3 @@ The following JupyterLite notebook demonstrates the process of creating material 1. Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}. -## Tags. - -`defects`, `graphene`, `substitutional`, `point-defects`, `nitrogen` diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md index bbb0d6f2..d3430285 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md @@ -1,4 +1,14 @@ --- +tags: + - defects + - vacancy + - point-defects + - h-BN + - boron-nitride + - 2D-materials + +hide: + - tags # YAML header render_macros: true --- @@ -133,6 +143,3 @@ The following JupyterLite notebooks demonstrate the complete process. Select "Ru 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` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 88a89f63..731af573 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -1,4 +1,13 @@ --- +tags: + - adatom + - graphene + - metal + - surface + - defect + +hide: + - tags # YAML header render_macros: true --- @@ -223,6 +232,3 @@ The interactive JupyterLite notebook for creating Graphene structures with metal 1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. -## Tags. - -`adatom`, `graphene`, `metal`, `surface`, `defect` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index d36338af..6a85173f 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -1,4 +1,15 @@ --- +tags: + - defects + - island + - surface + - surface-defects + - TiN + - nitrogen + - titanium + +hide: + - tags # YAML header render_macros: true --- @@ -176,6 +187,3 @@ The following JupyterLite notebook demonstrates the process of creating material 1. D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene, "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. -## Tags. - -`defects`, `island`, `surface`, `surface-defects`, `TiN`, `nitrogen`, `titanium` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md index 3c018b27..bc53250d 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md @@ -1,4 +1,15 @@ --- +tags: + - surface + - platinum + - terrace + - step + - slab + - Pt(211) + - Pt(111) + +hide: + - tags # YAML header render_macros: true --- @@ -153,6 +164,3 @@ The following JupyterLite notebook demonstrates both approaches. Select "Run" > 1. Šljivančanin, Ž., & Hammer, B., "Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory." Surface Science, 515(1), 235–244. [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. -## Tags. - -`surface`, `platinum`, `terrace`, `step`, `slab`, `Pt(211)`, `Pt(111)` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md index fbf1afab..08aa82f8 100644 --- a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md +++ b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md @@ -1,4 +1,17 @@ --- +tags: + - MoS2 + - platinum + - adatoms + - surface science + - 2D materials + - nanoparticles + - Mo + - S + - Pt + +hide: + - tags # YAML header render_macros: true --- @@ -176,6 +189,3 @@ To adjust the island structure: 5. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler, "Density-functional study of Mn monosilicide on the Si(111) surface: Film formation versus island nucleation", Phys. Rev. B 76, 235426 (2007). [DOI: 10.1103/PhysRevB.76.235426](https://doi.org/10.1103/PhysRevB.76.235426){:target='_blank'}. -## Tags. - -`MoS2`, `platinum`, `adatoms`, `surface science`, `2D materials`, `nanoparticles`, `Mo`, `S`, `Pt` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md index 9eee444f..a233fed4 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md @@ -1,4 +1,14 @@ --- +tags: + - grain-boundary + - h-BN + - 2D-materials + - interface + - twist-angle + - atom-restoration + +hide: + - tags # YAML header render_macros: true --- @@ -142,6 +152,3 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru 1. Qiucheng Li, et al., "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)", ACS Nano 2015 9 (6), 6308-6315. [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852) -## Tags. - -`grain-boundary`, `h-BN`, `2D-materials`, `interface`, `twist-angle`, `atom-restoration` diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md index b7d22729..5e9fb929 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md @@ -1,4 +1,14 @@ --- +tags: + - grain boundary + - interface + - copper + - Cu + - FCC + - metal + +hide: + - tags # YAML header render_macros: true --- @@ -138,6 +148,3 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru 1. Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919) -## Tags. - -`grain boundary`, `interface`, `copper`, `Cu`, `FCC`, `metal` diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index 5c477b0d..3673e695 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -1,4 +1,19 @@ --- +tags: + - slab-creation + - interfaces + - high-k + - metal-gate + - semiconductor + - heterostructure + - strain-matching + - Si + - SiO2 + - HfO2 + - TiN + +hide: + - tags # YAML header render_macros: true --- @@ -200,6 +215,3 @@ The following JupyterLite notebook demonstrates the process of creating target m Reports on Progress in Physics 69, 327 (2006) [DOI: 10.1088/0034-4885/69/2/R02](https://doi.org/10.1088/0034-4885/69/2/R02) -## Tags. - -`slab-creation`, `interfaces`, `high-k`, `metal-gate`, `semiconductor`, `heterostructure`, `strain-matching`, `Si`, `SiO2`, `HfO2`, `TiN` diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md index 2204d60b..d2df14c0 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md @@ -1,4 +1,13 @@ --- +tags: + - 2D + - Graphene + - Hexagonal Boron Nitride + - interface + - stacking + +hide: + - tags # YAML header render_macros: true --- @@ -169,6 +178,3 @@ The interactive JupyterLite notebook for creating Gr/h-BN interface can be acces RSC Adv., 2024, 4, 1-10 [DOI: 10.1039/D3RA06559F](https://doi.org/10.1039/D3RA06559F) -## Tags. - -`2D`, `Graphene`, `Hexagonal Boron Nitride`, `interface`, `stacking` diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md index f36440c3..ba42d61c 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md @@ -1,4 +1,15 @@ --- +tags: + - graphene + - silicon dioxide + - interface + - 2D + - 3D + - oxygen + - termination + +hide: + - tags # YAML header render_macros: true --- @@ -129,6 +140,3 @@ The interactive JupyterLite notebook for creating interfaces between graphene an Nanoscale 6, 2548-2562 (2014) [DOI: 10.1039/C3NR05279F](https://doi.org/10.1039/C3NR05279F) -## Tags. - -`graphene`, `silicon dioxide`, `interface`, `2D`,`3D`, `oxygen`, `termination` diff --git a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md index 891ecd7b..a0355190 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md @@ -1,4 +1,15 @@ --- +tags: + - 3D + - copper + - cristobalite + - interface + - termination + - SiO2 + - Cu + +hide: + - tags # YAML header render_macros: true --- @@ -136,6 +147,3 @@ The interactive JupyterLite notebook for creating interfaces between Copper and Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential. Physical Review B, 83(11). [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) -## Tags. - -`3D`, `copper`, `cristobalite`, `interface`, `termination`, `SiO2`, `Cu` diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index 5160f9ee..22833520 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -1,4 +1,15 @@ --- +tags: + - 2d-materials + - layers + - bilayer + - twisted + - commensurate + - molybdenum + - disulfide + +hide: + - tags # YAML header render_macros: true --- @@ -146,6 +157,3 @@ The interactive JupyterLite notebook for creating twisted bilayer MoS2 structure 1. Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang, "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014) [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) 2. Cao, Y., Fatemi, V., Fang, S. et al. Unconventional superconductivity in magic-angle graphene superlattices. Nature 556, 43–50 (2018). [DOI: 10.1038/nature26160](https://doi.org/10.1038/nature26160) -## Tags. - -`2d-materials`, `layers`, `bilayer`, `twisted`, `commensurate`, `molybdenum`, `disulfide` diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md index db1016fc..4fbc2335 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md @@ -1,4 +1,14 @@ --- +tags: + - twisted-bilayer + - nanoribbons + - boron-nitride + - BN + - boron + - nitrogen + +hide: + - tags # YAML header render_macros: true --- @@ -116,7 +126,3 @@ The interactive JupyterLite notebook for creating the twisted bilayer boron nitr 1. **Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**, "Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402 – Published 20 August 2020 DOI: 10.1021/acs.nanolett.9b00986 -## Tags. - -`twisted-bilayer`,`nanoribbons`, `boron-nitride`, `BN`, `boron`, `nitrogen` - diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md index 9a829660..de41190c 100644 --- a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -1,4 +1,13 @@ --- +tags: + - gold + - cluster + - nanoparticle + - cuboctahedron + - icosahedron + +hide: + - tags # YAML header render_macros: true --- @@ -166,6 +175,3 @@ The interactive JupyterLite notebook for creating Gold Nanoclusters can be acces [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. -## Tags. - -`gold`, `cluster`, `nanoparticle`, `cuboctahedron`, `icosahedron` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md index 7567f060..a99137a2 100644 --- a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md +++ b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md @@ -1,4 +1,17 @@ --- +tags: + - graphene + - nickel + - interface + - optimization + - 2D materials + - surface science + - Gr/Ni(111) + - C + - Ni + +hide: + - tags # YAML header render_macros: true --- @@ -155,6 +168,3 @@ To adjust the interface optimization: 3. Bertoni, G., Calmels, L., Altibelli, A., & Serin, V. (2004). First-principles calculation of the electronic structure and EELS spectra at the graphene/Ni(111) interface. Physical Review B, 71(7). [DOI: 10.1103/PhysRevB.71.075402](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402) -## Tags. - -`graphene`, `nickel`, `interface`, `optimization`, `2D materials`, `surface science`, `Gr/Ni(111)`, `C`, `Ni` diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md index e7b8e70e..a0af1aae 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md @@ -1,4 +1,16 @@ --- +tags: + - silicon + - surface + - passivation + - hydrogen + - Si(100) + - surface reconstruction + - Si + - H + +hide: + - tags # YAML header render_macros: true --- @@ -180,6 +192,3 @@ To adjust the passivation: 3. Boland, J. J. (1990). Structure of the H‐saturated Si(100) surface. Physical Review Letters, 65(26), 3325–3328. -## Tags. - -`silicon`, `surface`, `passivation`, `hydrogen`, `Si(100)`, `surface reconstruction`, `Si`, `H` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md index 691af053..67f08893 100644 --- a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md @@ -1,4 +1,14 @@ --- +tags: + - graphene + - ripples + - perturbation + - 2D materials + - edge effects + - C + +hide: + - tags # YAML header render_macros: true --- @@ -181,6 +191,3 @@ If user need to adjust the ripple pattern, user can modify these key parameters: 3. L. A. Openov & A. I. Podlivaev, "Interaction of the Stone-Wales defects in graphene", Physics of the Solid State, 52, 1, 2010. [DOI: 10.1134/S1063783415070240](https://doi.org/10.1134/S1063783415070240) -## Tags. - -`graphene`, `ripples`, `perturbation`, `2D materials`, `edge effects`, `C` \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md index ea0f511a..f76d4d9a 100644 --- a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md +++ b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md @@ -1,4 +1,13 @@ --- +tags: + - slab + - strontium titanate + - SrTiO3 + - terminations + - surface + +hide: + - tags # YAML header render_macros: true --- @@ -133,6 +142,3 @@ The following JupyterLite notebook demonstrates the process of creating strontiu 2. Atashi B. Mukhopadhyay, Javier F. Sanz, and Charles B. Musgrave "First-principles calculations of structural and electronic properties of monoclinic hafnia surfaces", Phys. Rev. B 73, 115330 (2006) DOI: [10.1103/PhysRevB.73.115330](https://doi.org/10.1103/PhysRevB.73.115330) -## Tags. - -`slab`, `strontium titanate`, `SrTiO3`, `terminations`, `surface` From 748916ad02343c93e3e6d8b5de92b77c209e5bda Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 16:43:06 -0800 Subject: [PATCH 04/20] update: add bibtex plugin --- mkdocs.yml | 4 ++++ requirements.txt | 1 + 2 files changed, 5 insertions(+) diff --git a/mkdocs.yml b/mkdocs.yml index 05a44be1..c516086e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -114,6 +114,10 @@ plugins: include_dir: "lang/en/docs/includes/" render_by_default: false # add header from https://mkdocs-macros-plugin.readthedocs.io/en/stable/rendering/#opt-in-through-the-config-file to enable in the specific markdown + - bibtex: + bib_file: "lang/en/docs/includes/references.bib" + citation_template: "{{author}} ({{year}})" + bibliography_template: "{{author}} ({{year}}). {{title}}. {{journal}}. {{volume}}. {{pages}}." nav: - Home: index.md diff --git a/requirements.txt b/requirements.txt index c985e928..3361a2ee 100644 --- a/requirements.txt +++ b/requirements.txt @@ -25,6 +25,7 @@ importlib_metadata==8.5.0 Jinja2==3.1.4 livereload==2.6.3 mkdocs-macros-plugin==1.2.0 +mkdocs-bibtex==2.16.2 Markdown==3.7 MarkupSafe==2.1.5 mergedeep==1.3.4 From 110ad6a05215848182576874f776d038c3529219 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 16:43:22 -0800 Subject: [PATCH 05/20] feat: add bibtex file --- lang/en/docs/includes/references.bib | 33 ++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 lang/en/docs/includes/references.bib diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib new file mode 100644 index 00000000..1f923de5 --- /dev/null +++ b/lang/en/docs/includes/references.bib @@ -0,0 +1,33 @@ +@article{Togo2006, + title={First-principles calculations of native defects in tin monoxide}, + author={Togo, A. and Oba, F. and Tanaka, I.}, + journal={Physical Review B}, + volume={74}, + number={19}, + pages={195128}, + year={2006}, + doi={10.1103/PhysRevB.74.195128}, + url={https://doi.org/10.1103/PhysRevB.74.195128} +} + +@article{Wang2014, + title={Carbon related defects in irradiated silicon revisited}, + author={Wang, H. and Chroneos, A. and Londos, C. A. and Sgourou, E. N. and Schwingenschlögl, U.}, + journal={Scientific Reports}, + volume={4}, + pages={4909}, + year={2014}, + doi={10.1038/srep04909}, + url={https://doi.org/10.1038/srep04909} +} + +@article{Na-Phattalung2006, + title={First-principles study of native defects in anatase TiO2}, + author={Na-Phattalung, Sutassana and Smith, M. F. and Kim, Kwiseon and Du, Mao-Hua and Wei, Su-Huai and Zhang, S. B. and Limpijumnong, Sukit}, + journal={Physical Review B}, + volume={73}, + pages={125205}, + year={2006}, + doi={10.1103/PhysRevB.73.125205}, + url={https://doi.org/10.1103/PhysRevB.73.125205} +} \ No newline at end of file From c99c551a89ec849041e55e4b9faeccc5362be212 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 16:43:42 -0800 Subject: [PATCH 06/20] update: add bibtex references 1 --- .../specific/defect-point-interstitial-tin-oxide.md | 10 +--------- 1 file changed, 1 insertion(+), 9 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index 8577ec96..fe617ec6 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -155,12 +155,4 @@ To adjust the defect creation: ## References. -1. Togo, A., Oba, F., & Tanaka, I. (2006). First-principles calculations of native defects in tin monoxide. Physical Review B, 74(19), 195128. [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. - -2. H. Wang, A. Chroneos, C. A. Londos, E. N. Sgourou & U. Schwingenschlögl, "Carbon related defects in irradiated silicon revisited" Scientific Reports 4, 4909 (2014). - [DOI: 10.1038/srep04909](https://doi.org/10.1038/srep04909){:target='_blank'}. - -3. Sutassana Na-Phattalung, M. F. Smith, Kwiseon Kim, Mao-Hua Du, Su-Huai Wei, S. B. Zhang, and Sukit Limpijumnong, "First-principles study of native defects in anatase Ti⁢O2", Phys. Rev. B 73, 125205 (2006). - [DOI: 10.1103/PhysRevB.73.125205](https://doi.org/10.1103/PhysRevB.73.125205){:target='_blank'}. - - +Cite the following works: [@Togo2006], [@Wang2014], and [@Na-Phattalung2006]. From 31605feb06185c65b38e6f306ba051f2120e14aa Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 18:02:06 -0800 Subject: [PATCH 07/20] update: add bibtex references 2 --- lang/en/docs/includes/references.bib | 172 ++++++++++++++++++ .../defect-point-pair-gallium-nitride.md | 5 +- .../defect-point-substitution-graphene.md | 4 +- .../defect-point-vacancy-boron-nitride.md | 4 +- .../defect-surface-adatom-graphene.md | 3 +- .../defect-surface-island-titanium-nitride.md | 3 +- .../specific/defect-surface-step-platinum.md | 3 +- .../defect_point_adatom_island_mos2_pt.md | 11 +- .../grain-boundary-2d-boron-nitride.md | 3 +- .../grain-boundary-3d-fcc-metals-copper.md | 3 +- ...nterface-2d-3d-graphene-silicon-dioxide.md | 12 +- 11 files changed, 182 insertions(+), 41 deletions(-) diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index 1f923de5..dd1881fb 100644 --- a/lang/en/docs/includes/references.bib +++ b/lang/en/docs/includes/references.bib @@ -30,4 +30,176 @@ @article{Na-Phattalung2006 year={2006}, doi={10.1103/PhysRevB.73.125205}, url={https://doi.org/10.1103/PhysRevB.73.125205} +} + +@article{Kang2008, + title = {Electronic structure of graphene and doping effect on SiO2}, + author = {Kang, Yong-Ju and Kang, Joongoo and Chang, K. J.}, + journal = {Physical Review B}, + volume = {78}, + pages = {115404}, + year = {2008}, + doi = {10.1103/PhysRevB.78.115404}, +} + +@article{Dahal2014, + title = {Graphene–nickel interfaces: a review}, + author = {Dahal, Arjun and Batzill, Matthias}, + journal = {Nanoscale}, + volume = {6}, + pages = {2548-2562}, + year = {2014}, + doi = {10.1039/C3NR05279F}, +} + +@article{Miceli2016, + title = {Self-compensation due to point defects in Mg-doped GaN}, + author = {Miceli, Giacomo and Pasquarello, Alfredo}, + journal = {Physical Review B}, + volume = {93}, + pages = {165207}, + year = {2016}, + doi = {10.1103/PhysRevB.93.165207}, +} + +@article{Yoshitaka2011, + title = {Formation, stabilities, and electronic properties of nitrogen defects in graphene}, + author = {Fujimoto, Yoshitaka and Saito, Susumu}, + journal = {Phys. Rev. B}, + volume = {84}, + issue = {24}, + pages = {245446}, + numpages = {9}, + year = {2011}, + month = {Dec}, + publisher = {American Physical Society}, + doi = {10.1103/PhysRevB.84.245446}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.84.245446} +} + +@article{Bertoldo2022, + title = {Quantum point defects in 2D materials - the QPOD database}, + author = {Bertoldo, Fabian and Ali, Sajid and Manti, Simone and Thygesen, Kristian S.}, + journal = {Nature}, + year = {2022}, + doi = {10.1038/s41524-022-00730-w} +} + +@article{Kohan2000, + title = {First-principles study of native point defects in h-BN}, + author = {Kohan, A. F. and Ceder, G. and Morgan, D. and Van de Walle, C. G.}, + journal = {Physical Review B}, + volume = {61}, + number = {23}, + pages = {15019-15027}, + year = {2000}, + doi = {10.1103/PhysRevB.61.15019} +} + +@article{Chan2008, + title = {First-principles study of metal adatom adsorption on graphene}, + author = {Chan, Kevin T. and Neaton, J. B. and Cohen, Marvin L.}, + journal = {Phys. Rev. B}, + volume = {77}, + pages = {235430}, + year = {2008}, + doi = {10.1103/PhysRevB.77.235430}, +} + +@article{Sangiovanni2018, + title={Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands}, + author={Sangiovanni, D. G. and Mei, A. B. and Edström, D. and Hultman, L. and Chirita, V. and Petrov, I. and Greene, J. E.}, + journal={Physical Review B}, + volume={97}, + pages={035406}, + year={2018}, + publisher={APS} +} + +@article{Sljivancanin2002, + doi = {10.1016/s0039-6028(02)01908-8}, + url = {https://doi.org/10.1016/s0039-6028(02)01908-8}, + year = {2002}, + publisher = {Elsevier {BV}}, + volume = {515}, + number = {1}, + pages = {235--244}, + author = {Z. Šljivančanin and B. Hammer}, + title = {Oxygen dissociation at close-packed {Pt} terraces, {Pt} steps, and {Ag}-covered {Pt} steps studied with density functional theory}, + journal = {Surface Science} +} + +@article{Saidi2015, + title = {Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface}, + author = {Saidi, W. A.}, + journal = {Crystal Growth & Design}, + volume = {15}, + number = {2}, + pages = {642–652}, + year = {2015}, + doi = {10.1021/cg5013395} +} + +@article{Jiao2016, + title = {QM/MD studies on graphene growth from small islands on the Ni(111) surface}, + author = {Jiao, M. and Song, W. and Qian, H.-J. and Wang, Y. and Wu, Z. and Irle, S. and Morokuma, K.}, + journal = {Nanoscale}, + volume = {8}, + number = {5}, + pages = {3067–3074}, + year = {2016}, + doi = {10.1039/c5nr07680c} +} + +@article{Fichthorn2000, + title = {Island Nucleation in Thin-Film Epitaxy: A First-Principles Investigation}, + author = {Kristen A. Fichthorn and Matthias Scheffler}, + journal = {Phys. Rev. Lett.}, + volume = {84}, + pages = {5371}, + year = {2000}, + doi = {10.1103/PhysRevLett.84.5371} +} + +@article{Neugebauer1993, + title = {Mechanisms of island formation of alkali-metal adsorbates on Al(111)}, + author = {Jörg Neugebauer and Matthias Scheffler}, + journal = {Phys. Rev. Lett.}, + volume = {71}, + pages = {577}, + year = {1993}, + doi = {10.1103/PhysRevLett.71.577} +} + +@article{Hortamani2007, + title = {Density-functional study of Mn monosilicide on the Si(111) surface: Film formation versus island nucleation}, + author = {Mahbube Hortamani and Peter Kratzer and Matthias Scheffler}, + journal = {Phys. Rev. B}, + volume = {76}, + pages = {235426}, + year = {2007}, + doi = {10.1103/PhysRevB.76.235426} +} + +@article{Li2015, + doi = {10.1021/acs.nanolett.5b01852}, + url = {https://doi.org/10.1021/acs.nanolett.5b01852}, + year = {2015}, + publisher = {American Chemical Society ({ACS})}, + volume = {9}, + number = {6}, + pages = {6308--6315}, + author = {Qiucheng Li and Xiaolong Zou and Mengxi Liu and Jingyu Sun and Yabo Gao and Yue Qi and Xiebo Zhou and Boris I. Yakobson and Yanfeng Zhang and Zhongfan Liu}, + title = {Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)}, + journal = {{ACS} Nano} +} + +@article{Frolov2013, + title={Structural phase transformations in metallic grain boundaries}, + author={Frolov, Timofey and Olmsted, David L and Asta, Mark and Mishin, Yuri}, + journal={Nature Communications}, + volume={4}, + pages={1899}, + year={2013}, + publisher={Nature Publishing Group} } \ No newline at end of file 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 d417e658..5e58e9ff 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 @@ -135,7 +135,4 @@ The following JupyterLite notebook demonstrates the process of creating material ## 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'}. - +Cite the following works: [@Miceli2016] diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 85a01ba5..76e562ef 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -145,6 +145,4 @@ The following JupyterLite notebook demonstrates the process of creating material ## References. -1. Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}. - - +Cite the following works: [@Yoshitaka2011] diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md index d3430285..4cdb2ea3 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md @@ -139,7 +139,5 @@ The following JupyterLite notebooks demonstrate the complete process. Select "Ru ## 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'}. +Cite the following works: [@Bertoldo2022; @Kohan2000] diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 731af573..1ab9e8ed 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -230,5 +230,4 @@ The interactive JupyterLite notebook for creating Graphene structures with metal ## References. -1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. - +Cite the following works: [@Chan2008] diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 6a85173f..1d0ed7e1 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -185,5 +185,4 @@ The following JupyterLite notebook demonstrates the process of creating material ## References. -1. D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene, "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. - +Cite the following work: [@Sangiovanni2018] diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md index bc53250d..06756824 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md @@ -162,5 +162,4 @@ The following JupyterLite notebook demonstrates both approaches. Select "Run" > ## References. -1. Šljivančanin, Ž., & Hammer, B., "Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory." Surface Science, 515(1), 235–244. [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. - +Cite the following work: [@Sljivancanin2002] diff --git a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md index 08aa82f8..52849214 100644 --- a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md +++ b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md @@ -178,14 +178,5 @@ To adjust the island structure: ## References. -1. Saidi, W. A. (2015). Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface. Crystal Growth & Design, 15(2), 642–652. [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. - -2. Jiao, M., Song, W., Qian, H.-J., Wang, Y., Wu, Z., Irle, S., & Morokuma, K. (2016). QM/MD studies on graphene growth from small islands on the Ni(111) surface. Nanoscale, 8(5), 3067–3074. doi:10.1039/c5nr07680c  [DOI: 10.1039/c5nr07680c](https://doi.org/10.1039/c5nr07680c){:target='_blank'}. - -3. Kristen A. Fichthorn and Matthias Scheffler, "Island Nucleation in Thin-Film Epitaxy: A First-Principles Investigation", Phys. Rev. Lett. 84, 5371 (2000). [DOI: 10.1103/PhysRevLett.84.5371](https://doi.org/10.1103/PhysRevLett.84.5371){:target='_blank'}. - -4. Jörg Neugebauer and Matthias Scheffler, "Mechanisms of island formation of alkali-metal adsorbates on Al(111)", Phys. Rev. Lett. 71, 577 (1993). [DOI: 10.1103/PhysRevLett.71.577](https://doi.org/10.1103/PhysRevLett.71.577){:target='_blank'}. - -5. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler, "Density-functional study of Mn monosilicide on the Si(111) surface: -Film formation versus island nucleation", Phys. Rev. B 76, 235426 (2007). [DOI: 10.1103/PhysRevB.76.235426](https://doi.org/10.1103/PhysRevB.76.235426){:target='_blank'}. +Cite the following works: [@Saidi2015], [@Jiao2016], [@Fichthorn2000], [@Neugebauer1993], [@Hortamani2007] diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md index a233fed4..4e73a622 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md @@ -150,5 +150,4 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru ## References. -1. Qiucheng Li, et al., "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)", ACS Nano 2015 9 (6), 6308-6315. [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852) - +Cite the following work: [@Li2015] diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md index 5e9fb929..9b3ffae6 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md @@ -146,5 +146,4 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru ## References. -1. Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919) - +Cite the following work: [@Frolov2013] diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md index ba42d61c..7bfea5a6 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md @@ -129,14 +129,4 @@ The interactive JupyterLite notebook for creating interfaces between graphene an ## 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) - +Cite the following works: [@Kang2008; @Dahal2014] From b72b4c97c36d2860c4c7a1967a3cdd7ac6157f55 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 18:11:05 -0800 Subject: [PATCH 08/20] update: add links --- lang/en/docs/includes/references.bib | 53 ++++++++++++++++++++++++---- 1 file changed, 46 insertions(+), 7 deletions(-) diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index dd1881fb..12a9722f 100644 --- a/lang/en/docs/includes/references.bib +++ b/lang/en/docs/includes/references.bib @@ -40,6 +40,7 @@ @article{Kang2008 pages = {115404}, year = {2008}, doi = {10.1103/PhysRevB.78.115404}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.78.115404} } @article{Dahal2014, @@ -50,6 +51,7 @@ @article{Dahal2014 pages = {2548-2562}, year = {2014}, doi = {10.1039/C3NR05279F}, + url = {https://doi.org/10.1039/C3NR05279F} } @article{Miceli2016, @@ -60,6 +62,7 @@ @article{Miceli2016 pages = {165207}, year = {2016}, doi = {10.1103/PhysRevB.93.165207}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.93.165207} } @article{Yoshitaka2011, @@ -83,6 +86,7 @@ @article{Bertoldo2022 journal = {Nature}, year = {2022}, doi = {10.1038/s41524-022-00730-w} + url = {https://doi.org/10.1038/s41524-022-00730-w} } @article{Kohan2000, @@ -94,6 +98,7 @@ @article{Kohan2000 pages = {15019-15027}, year = {2000}, doi = {10.1103/PhysRevB.61.15019} + url = {https://link.aps.org/doi/10.1103/PhysRevB.61.15019} } @article{Chan2008, @@ -104,6 +109,7 @@ @article{Chan2008 pages = {235430}, year = {2008}, doi = {10.1103/PhysRevB.77.235430}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.77.235430} } @article{Sangiovanni2018, @@ -113,7 +119,9 @@ @article{Sangiovanni2018 volume={97}, pages={035406}, year={2018}, - publisher={APS} + publisher={APS}, + doi={10.1103/PhysRevB.97.035406}, + url={https://link.aps.org/doi/10.1103/PhysRevB.97.035406} } @article{Sljivancanin2002, @@ -137,7 +145,8 @@ @article{Saidi2015 number = {2}, pages = {642–652}, year = {2015}, - doi = {10.1021/cg5013395} + doi = {10.1021/cg5013395}, + url = {https://doi.org/10.1021/cg5013395} } @article{Jiao2016, @@ -148,7 +157,8 @@ @article{Jiao2016 number = {5}, pages = {3067–3074}, year = {2016}, - doi = {10.1039/c5nr07680c} + doi = {10.1039/c5nr07680c}, + url = {https://doi.org/10.1039/c5nr07680c} } @article{Fichthorn2000, @@ -158,7 +168,8 @@ @article{Fichthorn2000 volume = {84}, pages = {5371}, year = {2000}, - doi = {10.1103/PhysRevLett.84.5371} + doi = {10.1103/PhysRevLett.84.5371}, + url = {https://link.aps.org/doi/10.1103/PhysRevLett.84.5371} } @article{Neugebauer1993, @@ -168,7 +179,8 @@ @article{Neugebauer1993 volume = {71}, pages = {577}, year = {1993}, - doi = {10.1103/PhysRevLett.71.577} + doi = {10.1103/PhysRevLett.71.577}, + url = {https://link.aps.org/doi/10.1103/PhysRevLett.71.577} } @article{Hortamani2007, @@ -178,7 +190,8 @@ @article{Hortamani2007 volume = {76}, pages = {235426}, year = {2007}, - doi = {10.1103/PhysRevB.76.235426} + doi = {10.1103/PhysRevB.76.235426}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.76.235426} } @article{Li2015, @@ -201,5 +214,31 @@ @article{Frolov2013 volume={4}, pages={1899}, year={2013}, - publisher={Nature Publishing Group} + publisher={Nature Publishing Group}, + doi={10.1038/ncomms2924}, + url={https://doi.org/10.1038/ncomms2924} +} + +@article{Muller1999, + title={The electronic structure at the atomic scale of ultrathin gate oxides}, + author={Muller, D A and Nakagawa, N and Ohtomo, A and Grazul, J L and Hwang, H Y}, + journal={Nature}, + volume={399}, + pages={758--761}, + year={1999}, + publisher={Nature Publishing Group}, + doi={10.1038/21667}, + url={https://doi.org/10.1038/21667} +} + +@article{Robertson2006, + title={High dielectric constant gate oxides for metal oxide Si transistors}, + author={Robertson, J}, + journal={Reports on Progress in Physics}, + volume={69}, + pages={327}, + year={2006}, + publisher={IOP Publishing}, + doi={10.1088/0034-4885/69/2/R02}, + url={https://doi.org/10.1088/0034-4885/69/2/R02} } \ No newline at end of file From 2d64f21c9da13e9fb09c32e0ba9fdc560281fcc8 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 20:17:40 -0800 Subject: [PATCH 09/20] update: use new references style --- ...ioxide-hafnium-dioxide-titanium-nitride.md | 12 +---------- .../interface-2d-2d-graphene-boron-nitride.md | 20 +------------------ .../interface-3d-3d-copper-silicon-dioxide.md | 8 +------- 3 files changed, 3 insertions(+), 37 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index 3673e695..22a52e66 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -203,15 +203,5 @@ The following JupyterLite notebook demonstrates the process of creating target m ## References. -1. [QuantumATK tutorial](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) - -2. **D. A. Muller et al.** - "The electronic structure at the atomic scale of ultrathin gate oxides" - Nature 399, 758–761 (1999) - [DOI: 10.1038/21602](https://doi.org/10.1038/21602) - -3. **J. Robertson** - "High dielectric constant gate oxides for metal oxide Si transistors" - Reports on Progress in Physics 69, 327 (2006) - [DOI: 10.1088/0034-4885/69/2/R02](https://doi.org/10.1088/0034-4885/69/2/R02) +Cite the following works: [@Muller1999; @Robertson2006], [QuantumATK tutorial](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md index d2df14c0..cc0ebeee 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md @@ -22,7 +22,7 @@ This tutorial demonstrates the process of creating interfaces with different sta **Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam** **Origin of the band gap in graphene on hexagonal boron nitride** Nature Communications volume 6, Article number: 6308 (2015) - [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) + [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) [@Jung2015; @Novoselov2016; @Gupta2024] We use the [Materials Designer](../../../materials-designer/overview.md) to create interfaces and shift the layers along the y-axis to achieve different stacking configurations. @@ -160,21 +160,3 @@ The interactive JupyterLite notebook for creating Gr/h-BN interface can be acces ## References. -1. **Jeil Jung, Ashley M. DaSilva, Allan H. MacDonald & Shaffique Adam** - - "Origin of the band gap in graphene on hexagonal boron nitride" - Nature Communications volume 6, Article number: 6308 (2015) - [DOI: 10.1038/ncomms7308](https://doi.org/10.1038/ncomms7308) - -2. **K. S. Novoselov, A. Mishchenko, A. Carvalho, A. H. Castro Neto** - - "2D materials and van der Waals heterostructures" - Science 353, 6298 (2016) - [DOI: 10.1126/science.aac9439](https://doi.org/10.1126/science.aac9439) - -3. **Neelam Gupta, Saurav Sachin, Puja Kumari, Shivani Rania and Soumya Jyoti Ray** - - "Twistronics in two-dimensional transition metal dichalcogenide (TMD)-based van der Waals interface" - RSC Adv., 2024, 4, 1-10 - [DOI: 10.1039/D3RA06559F](https://doi.org/10.1039/D3RA06559F) - diff --git a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md index a0355190..764914d0 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md @@ -24,8 +24,7 @@ This tutorial demonstrates the process of creating interfaces between 3D materia **Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B.** "Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential." Physical Review B, 83(11). - [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) - + [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) [@Shan2011]. We use the [Materials Designer](../../../materials-designer/overview.md) to create interfaces between Cu and Cristobalite with different termination pairs. @@ -142,8 +141,3 @@ The interactive JupyterLite notebook for creating interfaces between Copper and {% endwith %} ## References. - -1. Shan, T.-R., Devine, B. D., Phillpot, S. R., & Sinnott, S. B. (2011). - Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential. Physical Review B, 83(11). - [DOI: 10.1103/PhysRevB.83.115327](https://doi.org/10.1103/PhysRevB.83.115327) - From 32c6247c8b106850bcb728f049e023567818c103 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Fri, 3 Jan 2025 20:19:11 -0800 Subject: [PATCH 10/20] update: bibtex refs --- lang/en/docs/includes/references.bib | 411 +++++++++++++++------------ 1 file changed, 229 insertions(+), 182 deletions(-) diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index 12a9722f..039d6f2f 100644 --- a/lang/en/docs/includes/references.bib +++ b/lang/en/docs/includes/references.bib @@ -1,244 +1,291 @@ @article{Togo2006, - title={First-principles calculations of native defects in tin monoxide}, - author={Togo, A. and Oba, F. and Tanaka, I.}, - journal={Physical Review B}, - volume={74}, - number={19}, - pages={195128}, - year={2006}, - doi={10.1103/PhysRevB.74.195128}, - url={https://doi.org/10.1103/PhysRevB.74.195128} + title = {First-principles calculations of native defects in tin monoxide}, + author = {Togo, A. and Oba, F. and Tanaka, I.}, + journal = {Physical Review B}, + volume = {74}, + number = {19}, + pages = {195128}, + year = {2006}, + @doi = {10.1103/PhysRevB.74.195128}, + url = {https://doi.org/10.1103/PhysRevB.74.195128} } @article{Wang2014, - title={Carbon related defects in irradiated silicon revisited}, - author={Wang, H. and Chroneos, A. and Londos, C. 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Castro Neto}, + journal = {Science}, + volume = {353}, + number = {6298}, + pages = {aac9439}, + year = {2016}, + @doi = {10.1126/science.aac9439}, + url = {https://doi.org/10.1126/science.aac9439} +} + +@article{Gupta2024, + title = {Twistronics in two-dimensional transition metal dichalcogenide (TMD)-based van der Waals interface}, + author = {Neelam Gupta and Saurav Sachin and Puja Kumari and Shivani Rania and Soumya Jyoti Ray}, + journal = {RSC Adv.}, + volume = {2024}, + number = {4}, + pages = {1-10}, + year = {2024}, + @doi = {10.1039/D3RA06559F}, + url = {https://doi.org/10.1039/D3RA06559F} +} + + +@article{Shan2011, + title = {Molecular dynamics study of the adhesion of Cu/SiO2interfaces using a variable-charge interatomic potential}, + author = {Shan, T.-R. and Devine, B. D. and Phillpot, S. R. and Sinnott, S. B.}, + journal = {Physical Review B}, + volume = {83}, + number = {11}, + year = {2011}, + @doi = {10.1103/PhysRevB.83.115327}, + url = {https://doi.org/10.1103/PhysRevB.83.115327} } \ No newline at end of file From 318e258fde627eb7371408ba00cabe93ab7782b4 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 11:15:52 -0800 Subject: [PATCH 11/20] update: more bibtex refs --- lang/en/docs/includes/references.bib | 70 +++++++++++++++++++ ...mensurate-lattices-molybdenum-disulfide.md | 6 +- ...layer-twisted-nanoribbons-boron-nitride.md | 7 +- .../materials/specific/nanocluster-gold.md | 9 +-- ...film-position-graphene-nickel-interface.md | 9 +-- 5 files changed, 75 insertions(+), 26 deletions(-) diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index 039d6f2f..a1766cd5 100644 --- a/lang/en/docs/includes/references.bib +++ b/lang/en/docs/includes/references.bib @@ -288,4 +288,74 @@ @article{Shan2011 year = {2011}, @doi = {10.1103/PhysRevB.83.115327}, url = {https://doi.org/10.1103/PhysRevB.83.115327} +} + +@article{Liu2014, + title = {Evolution of interlayer coupling in twisted molybdenum disulfide bilayers}, + author = {Kaihui Liu and Liming Zhang and Ting Cao and Chenhao Jin and Diana Qiu and Qin Zhou and Alex Zettl and Peidong Yang and Steve G. Louie and Feng Wang}, + journal = {Nature Communications}, + volume = {5}, + pages = {4966}, + year = {2014}, + doi = {10.1038/ncomms5966}, + url = {https://doi.org/10.1038/ncomms5966} +} + +@article{Cao2018, + title = {Unconventional superconductivity in magic-angle graphene superlattices}, + author = {Cao, Y. and Fatemi, V. and Fang, S. and et al.}, + journal = {Nature}, + volume = {556}, + pages = {43–50}, + year = {2018}, + @doi = {10.1038/nature26160}, + url = {https://doi.org/10.1038/nature26160} +} +} + +@article{Xian2020, + title = {Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor}, + author = {Lede Xian and Dante M. Kennes and Nicolas Tancogne-Dejean and Massimo Altarelli and Angel Rubio}, + journal = {Phys. Rev. Lett.}, + volume = {125}, + pages = {086402}, + year = {2020}, + @doi = {10.1021/acs.nanolett.9b00986}, + url = {https://doi.org/10.1021/acs.nanolett.9b00986} +} + + +@article{Larsen2011, + author = {Larsen, Ask Hjorth and Kleis, Jesper and Thygesen, Kristian Sommer and N{\o}rskov, Jens K. and Jacobsen, Karsten Wedel}, + journal = {Phys. Rev. B}, + number = {24}, + pages = {245429}, + title = {Electronic shell structure and chemisorption on gold nanoparticles}, + volume = {84}, + year = {2011}, + @doi = {10.1103/PhysRevB.84.245429}, + url = {https://doi.org/10.1103/PhysRevB.84.245429} +} + +@article{Gamo1997, + title = {Atomic structure of monolayer graphite formed on Ni(111)}, + author = {Gamo, Y. and Nagashima, A. and Wakabayashi, M. and Terai, M. and Oshima, C.}, + journal = {Surface Science}, + volume = {374}, + number = {1-3}, + pages = {61-64}, + year = {1997}, + @doi = {10.1016/S0039-6028(96)01307-3}, + url = {https://www.sciencedirect.com/science/article/abs/pii/S0039602896007856} +} + +@article{Bertoni2004, + title = {First-principles calculation of the electronic structure and EELS spectra at the graphene/Ni(111) interface}, + author = {Bertoni, G. and Calmels, L. and Altibelli, A. and Serin, V.}, + journal = {Physical Review B}, + volume = {71}, + number = {7}, + year = {2004}, + @doi = {10.1103/PhysRevB.71.075402}, + url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402} } \ No newline at end of file diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index 22833520..ee0812f9 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -23,7 +23,7 @@ This tutorial demonstrates the process of creating a twisted bilayer molybdenum !!!note "Manuscript" **Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang**, "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014) - [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) + [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) [@Liu2014; @Zhang2016; @Cao2018] We use the [Materials Designer](../../../materials-designer/overview.md) to create molybdenum disulfide bilayer structure configurations with multiple twist angles. @@ -153,7 +153,3 @@ The interactive JupyterLite notebook for creating twisted bilayer MoS2 structure {% endwith %} ## References. - -1. Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang, "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014) [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966) -2. Cao, Y., Fatemi, V., Fang, S. et al. Unconventional superconductivity in magic-angle graphene superlattices. Nature 556, 43–50 (2018). [DOI: 10.1038/nature26160](https://doi.org/10.1038/nature26160) - diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md index 4fbc2335..f1ccc5bf 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md @@ -22,7 +22,7 @@ This tutorial demonstrates the process of creating a twisted bilayer boron nitri !!!note "Manuscript" **Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**, "Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402, 20 August 2020 - [DOI: 10.1021/acs.nanolett.9b00986](https://doi.org/10.1021/acs.nanolett.9b00986) + [DOI: 10.1021/acs.nanolett.9b00986](https://doi.org/10.1021/acs.nanolett.9b00986) [@Xian2020] We use the [Materials Designer](../../../materials-designer/overview.md) to create Hexagonal boron nitride bilayer structure configurations with 2 specific twist angles. @@ -121,8 +121,5 @@ The interactive JupyterLite notebook for creating the twisted bilayer boron nitr {% endwith %} {% endwith %} -## References. - -1. **Lede Xian, Dante M. Kennes, Nicolas Tancogne-Dejean, Massimo Altarelli, and Angel Rubio**, - "Multiflat Bands and Strong Correlations in Twisted Bilayer Boron Nitride: Doping-Induced Correlated Insulator and Superconductor" Phys. Rev. Lett. 125, 086402 – Published 20 August 2020 DOI: 10.1021/acs.nanolett.9b00986 +## References. diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md index de41190c..540a2b30 100644 --- a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -22,7 +22,7 @@ This tutorial demonstrates the process of creating a gold nanoparticle structure > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, > "Electronic shell structure and chemisorption on gold nanoparticles", > *Phys. Rev. B 84, 245429 (2011)*, - > [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. + > [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. [@Larsen2011] We use the [Materials Designer](../../../materials-designer/overview.md) to create gold nanoparticle structures of cuboctahedral and icosahedral shapes as shown in the image below. @@ -168,10 +168,3 @@ The interactive JupyterLite notebook for creating Gold Nanoclusters can be acces {% endwith %} ## References. - -1. **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, - "Electronic shell structure and chemisorption on gold nanoparticles", - *Phys. Rev. B 84, 245429 (2011)*, - [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. - - diff --git a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md index a99137a2..677f11a1 100644 --- a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md +++ b/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md @@ -26,7 +26,7 @@ This tutorial demonstrates how to create and optimize a Graphene/Ni(111) interfa Arjun Dahal, Matthias Batzill "Graphene–nickel interfaces: a review" Nanoscale, 6(5), 2548. (2014) - [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. + [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f){:target='_blank'}. [@Dahal2014; @Gamo1997; @Bertoni2004] We will recreate the interface structure and optimize the film position to match the experimental findings shown in the figure below: @@ -161,10 +161,3 @@ To adjust the interface optimization: - Enable 3D visualization with `SHOW_3D_LANDSCAPE = True` ## References. - -1. Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. Nanoscale, 6(5), 2548-2562. [DOI: 10.1039/c3nr05279f](https://doi.org/10.1039/c3nr05279f) - -2. Gamo, Y., Nagashima, A., Wakabayashi, M., Terai, M., & Oshima, C. (1997). Atomic structure of monolayer graphite formed on Ni(111). Surface Science, 374(1-3), 61-64. [DOI: 10.1016/S0039-6028(96)01307-3](https://www.sciencedirect.com/science/article/abs/pii/S0039602896007856) - -3. Bertoni, G., Calmels, L., Altibelli, A., & Serin, V. (2004). First-principles calculation of the electronic structure and EELS spectra at the graphene/Ni(111) interface. Physical Review B, 71(7). [DOI: 10.1103/PhysRevB.71.075402](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402) - From 091800322f3949b8141d783f5f41fe3f0a986f1f Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 11:32:07 -0800 Subject: [PATCH 12/20] update: more bibtex refs 2 --- lang/en/docs/includes/references.bib | 116 +++++++++++++++++- .../passivation-edge-silicon-nanowire.md | 19 +-- .../passivation-surface-silicon-surface.md | 9 +- .../specific/perturbation-ripples-graphene.md | 9 +- .../specific/slab-strontium-titanate.md | 6 +- 5 files changed, 128 insertions(+), 31 deletions(-) diff --git a/lang/en/docs/includes/references.bib b/lang/en/docs/includes/references.bib index a1766cd5..7b4f3fea 100644 --- a/lang/en/docs/includes/references.bib +++ b/lang/en/docs/includes/references.bib @@ -358,4 +358,118 @@ @article{Bertoni2004 year = {2004}, @doi = {10.1103/PhysRevB.71.075402}, url = {https://journals.aps.org/prb/abstract/10.1103/PhysRevB.71.075402} -} \ No newline at end of file +} + +@article{Aradi2007, + author = {Aradi, B. and Ramos, L. E. and Deák, P. and Köhler, Th. and Bechstedt, F. and Zhang, R. Q. and Frauenheim, Th.}, + journal = {Phys. Rev. B}, + number = {3}, + pages = {035305}, + title = {Theoretical study of the chemical gap tuning in silicon nanowires}, + volume = {76}, + year = {2007}, + @doi = {10.1103/PhysRevB.76.035305}, +url = {https://doi.org/10.1103/PhysRevB.76.035305} +} + + +@article{Hansen1998, +title = {Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study}, +author = {Hansen, U. and Vogl, P.}, +journal = {Physical Review B}, +number = {20}, +pages = {13295--13304}, +volume = {57}, +year = {1998}, + @doi = {10.1103/physrevb.57.13295}, + url = {https://doi.org/10.1103/physrevb.57.13295}, +} + +@article{Northrup1991, +title = {Structure of Si(100)H: Dependence on the H chemical potential}, +author = {Northrup, J. E.}, +journal = {Physical Review B}, +number = {3}, +pages = {1419--1422}, +volume = {44}, +year = {1991}, +@doi = {10.1103/physrevb.44.1419}, +url = {https://doi.org/10.1103/physrevb.44.1419}, +} + +@article{Boland1990, +title = {Structure of the H‐saturated Si(100) surface}, +author = {Boland, J. J.}, +journal = {Physical Review Letters}, +number = {26}, +pages = {3325--3328}, +volume = {65}, +year = {1990}, +@doi = {10.1103/physrevlett.65.3325}, +url = {https://doi.org/10.1103/physrevlett.65.3325}, +} + +@article{ThompsonFlagg2009, + title = {Rippling of graphene}, + author = {Thompson-Flagg, R. C. and Moura, M. J. B. and Marder, M.}, + journal = {EPL (Europhysics Letters)}, + volume = {85}, + number = {4}, + pages = {46002}, + year = {2009}, + @doi = {10.1209/0295-5075/85/46002}, +url={https://doi.org/10.1209/0295-5075/85/46002} +} + +@article{Fasolino2007, + title = {Intrinsic ripples in graphene}, + author = {Fasolino, A. and Los, J. H. and Katsnelson, M. I.}, + journal = {Nature Materials}, + volume = {6}, + pages = {858-861}, + year = {2007}, + @doi = {10.1038/nmat2011}, +url={https://doi.org/10.1038/nmat2011} +} + +@article{Openov2010, + title = {Interaction of the Stone-Wales defects in graphene}, + author = {Openov, L. A. and Podlivaev, A. I.}, + journal = {Physics of the Solid State}, + volume = {52}, + number = {1}, + pages = {2010}, + year = {2010}, + @doi = {10.1134/S1063783415070240}, +url={https://doi.org/10.1134/S1063783415070240} +} + +@article{Eglitis2008, + title = {First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces}, + author = {Eglitis, R. I. and Vanderbilt, David}, + journal = {Phys. Rev. B}, + volume = {77}, + issue = {19}, + pages = {195408}, + numpages = {10}, + year = {2008}, + month = {May}, + publisher = {American Physical Society}, + @doi = {10.1103/PhysRevB.77.195408}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.77.195408} +} + +@article{Mukhopadhyay2006, + title = {First-principles calculations of structural and electronic properties of monoclinic hafnia surfaces}, + author = {Mukhopadhyay, Atashi B. and Sanz, Javier F. and Musgrave, Charles B.}, + journal = {Phys. Rev. B}, + volume = {73}, + issue = {11}, + pages = {115330}, + numpages = {9}, + year = {2006}, + month = {Mar}, + publisher = {American Physical Society}, + @doi = {10.1103/PhysRevB.73.115330}, + url = {https://link.aps.org/doi/10.1103/PhysRevB.73.115330} +} diff --git a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md index f1b59854..07b696d4 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md @@ -1,4 +1,13 @@ --- +tags: + - silicon + - hydrogen + - passivation + - nanowire + - Si + - H +hide: + - tags # YAML header render_macros: true --- @@ -14,7 +23,7 @@ This tutorial demonstrates the process of creating passivated silicon nanowires B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim, "Theoretical study of the chemical gap tuning in silicon nanowires" Phys. Rev. B 76, 035305 (2007) - DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305) + DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305) [@Aradi2007] We will focus on creating silicon nanowires with hydrogen passivation from FIG. 1. @@ -199,11 +208,3 @@ The following JupyterLite notebook demonstrates the process of creating material ## References. -1. B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim, - Theoretical study of the chemical gap tuning in silicon nanowires - Phys. Rev. B 76, 035305 (2007) - DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305) - -## Tags. - - `silicon`, `hydrogen`, `passivation`, `nanowire` diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md index a0af1aae..457e7f56 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md @@ -25,7 +25,7 @@ This tutorial demonstrates how to passivate a reconstructed silicon (100) surfac Hansen, U., & Vogl, P. "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study." Physical Review B, 57(20), 13295–13304. (1998) - [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. + [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990] We will recreate the passivated surface structure shown in Fig. 8: @@ -185,10 +185,3 @@ To adjust the passivation: - Change `PASSIVANT` to use different passivating species ## References. - -1. Hansen, U., & Vogl, P. (1998). Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study. Physical Review B, 57(20), 13295–13304. - -2. Northrup, J. E. (1991). Structure of Si(100)H: Dependence on the H chemical potential. Physical Review B, 44(3), 1419–1422. - -3. Boland, J. J. (1990). Structure of the H‐saturated Si(100) surface. Physical Review Letters, 65(26), 3325–3328. - diff --git a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md index 67f08893..b13ed2c2 100644 --- a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md @@ -23,7 +23,7 @@ This tutorial demonstrates the process of creating edge induced ripples in graph Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. "Rippling of graphene" EPL (Europhysics Letters), 85(4), 46002 (2009) - [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. + [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002){:target='_blank'}. [@ThompsonFlagg2009; @Fasolino2007; @Openov2010] We will focus on creating graphene with edge-induced ripples that match the patterns observed in experimental studies, as shown in FIG. 1. @@ -184,10 +184,3 @@ If user need to adjust the ripple pattern, user can modify these key parameters: - Adjust PHASE_X and PHASE_Y to modify the wave interference pattern ## References. - -1. Thompson-Flagg, R. C., Moura, M. J. B., & Marder, M. (2009). Rippling of graphene. EPL (Europhysics Letters), 85(4), 46002. [DOI: 10.1209/0295-5075/85/46002](https://doi.org/10.1209/0295-5075/85/46002) - -2. A. Fasolino, J. H. Los and M. I. Katsnelson, "Intrinsic ripples in graphene," Nature Materials, 6, 858-861 (2007). [DOI: 10.1038/nmat2011](https://doi.org/10.1038/nmat2011) - -3. L. A. Openov & A. I. Podlivaev, "Interaction of the Stone-Wales defects in graphene", Physics of the Solid State, 52, 1, 2010. [DOI: 10.1134/S1063783415070240](https://doi.org/10.1134/S1063783415070240) - diff --git a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md index f76d4d9a..064a0e07 100644 --- a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md +++ b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md @@ -23,7 +23,7 @@ This tutorial demonstrates the process of creating strontium titanate (SrTiO3 (011) slabs with different terminations from FIG. 2. @@ -138,7 +138,3 @@ The following JupyterLite notebook demonstrates the process of creating strontiu ## References. -1. R. I. Eglitis and David Vanderbilt, "First-principles calculations of atomic and electronic structure of SrTiO3 (001) and (011) surfaces", Phys. Rev. B 77, 195408 (2008) [DOI: 10.1103/PhysRevB.77.195408](https://doi.org/10.1103/PhysRevB.77.195408) - -2. Atashi B. Mukhopadhyay, Javier F. Sanz, and Charles B. Musgrave "First-principles calculations of structural and electronic properties of monoclinic hafnia surfaces", Phys. Rev. B 73, 115330 (2006) DOI: [10.1103/PhysRevB.73.115330](https://doi.org/10.1103/PhysRevB.73.115330) - From e6831f22a261aed695d68095cba2d4ebb4e28388 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 11:49:51 -0800 Subject: [PATCH 13/20] update: use new references style --- .../specific/defect-point-interstitial-tin-oxide.md | 4 +--- .../materials/specific/defect-point-pair-gallium-nitride.md | 4 +--- .../specific/defect-point-substitution-graphene.md | 4 +--- .../specific/defect-point-vacancy-boron-nitride.md | 4 +--- .../materials/specific/defect-surface-adatom-graphene.md | 4 +--- .../specific/defect-surface-island-titanium-nitride.md | 4 +--- .../materials/specific/defect-surface-step-platinum.md | 4 +--- .../specific/defect_point_adatom_island_mos2_pt.md | 4 +--- .../materials/specific/grain-boundary-2d-boron-nitride.md | 4 +--- .../specific/grain-boundary-3d-fcc-metals-copper.md | 4 +--- ...icon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md | 6 ++++-- .../specific/interface-2d-3d-graphene-silicon-dioxide.md | 4 +--- 12 files changed, 15 insertions(+), 35 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index fe617ec6..7d9c4400 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -25,7 +25,7 @@ This tutorial demonstrates how to create an oxygen interstitial defect in tin mo A. Togo, F. Oba, and I. Tanaka "First-principles calculations of native defects in tin monoxide" Physical Review B 74, 195128 (2006) - [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. + [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}. [@Togo2006; @Wang2014; @Na-Phattalung2006] We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [Voronoi](https://github.com/Exabyte-io/made/blob/9e13b350eaaa5d49c81a3b30f76c165480825d72/src/py/mat3ra/made/tools/build/defect/builders.py#L125) placement method. @@ -154,5 +154,3 @@ To adjust the defect creation: - Consider periodic boundary conditions effects ## References. - -Cite the following works: [@Togo2006], [@Wang2014], and [@Na-Phattalung2006]. 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 5e58e9ff..01f5e292 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 @@ -27,7 +27,7 @@ This tutorial demonstrates the process of creating material with nitrogen vacanc !!!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'}. + [DOI: 10.1103/PhysRevB.93.165207](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.165207){:target='_blank'}. [@Miceli2016] 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. @@ -134,5 +134,3 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} ## References. - -Cite the following works: [@Miceli2016] diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 76e562ef..9f0bceab 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -21,7 +21,7 @@ This tutorial demonstrates the process of creating materials with substitution d [//]: # () !!!note "Manuscript" - Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}. + Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}. [@Yoshitaka2011] We use the [Materials Designer](../../../materials-designer/overview.md) to create a supercell of graphene, identify the crystal site positions for defects, and introduce nitrogen atoms and vacancies accordingly. @@ -144,5 +144,3 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} ## References. - -Cite the following works: [@Yoshitaka2011] diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md index 4cdb2ea3..a9dd167f 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md @@ -20,7 +20,7 @@ render_macros: true 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'}. + 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'}. [@Bertoldo2022; @Kohan2000] 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. @@ -139,5 +139,3 @@ The following JupyterLite notebooks demonstrate the complete process. Select "Ru ## References. -Cite the following works: [@Bertoldo2022; @Kohan2000] - diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 1ab9e8ed..a5d35056 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -21,7 +21,7 @@ This tutorial demonstrates the process of creating a graphene structure with an !!!note "Manuscript" **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 - [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. + [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. [@Chan2008] We use the [Materials Designer](../../../materials-designer/overview.md) to create a graphene structure with a metal adatom on the surface. @@ -229,5 +229,3 @@ The interactive JupyterLite notebook for creating Graphene structures with metal {% endwith %} ## References. - -Cite the following works: [@Chan2008] diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 1d0ed7e1..417275d1 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -24,7 +24,7 @@ This tutorial demonstrates the process of creating material with island on the s !!!note "Manuscript" **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, - "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. + "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}. [@Sangiovanni2018] We use the [Materials Designer](../../../materials-designer/overview.md) to create a slab of TiN, identify the cartesian coordinates for an island on the surface, and build it. @@ -184,5 +184,3 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} ## References. - -Cite the following work: [@Sangiovanni2018] diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md index 06756824..60238624 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md @@ -21,7 +21,7 @@ render_macros: true This tutorial demonstrates two different approaches to creating terrace steps on platinum surfaces, based on the work presented in the following manuscript: !!!note "Manuscript" - Šljivančanin, Ž., & Hammer, B., "Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory." Surface Science, 515(1), 235–244. [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. + Šljivančanin, Ž., & Hammer, B., "Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory." Surface Science, 515(1), 235–244. [DOI: 10.1016/s0039-6028(02)01908-8](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. [@Sljivancanin2002] We will focus on creating platinum surface with terrace steps, as shown in FIG. 1. B: @@ -161,5 +161,3 @@ The following JupyterLite notebook demonstrates both approaches. Select "Run" > {% endwith %} ## References. - -Cite the following work: [@Sljivancanin2002] diff --git a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md index 52849214..b731f052 100644 --- a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md +++ b/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md @@ -26,7 +26,7 @@ This tutorial demonstrates how to create a platinum island on MoS2 by sequential Saidi, W. A. "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface" Crystal Growth & Design, 15(2), 642–652. (2015) - [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. + [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}. [@Saidi2015; @Jiao2016; @Fichthorn2000; @Neugebauer1993; @Hortamani2007] We will recreate the Pt island structure shown in Figure 4b: @@ -178,5 +178,3 @@ To adjust the island structure: ## References. -Cite the following works: [@Saidi2015], [@Jiao2016], [@Fichthorn2000], [@Neugebauer1993], [@Hortamani2007] - diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md index 4e73a622..fde46572 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md @@ -20,7 +20,7 @@ render_macros: true This tutorial demonstrates the process of creating 2D grain boundary structures in hexagonal boron nitride (h-BN), based on the work presented in the following manuscript: !!!note "Manuscript" - Qiucheng Li, Xiaolong Zou, Mengxi Liu, Jingyu Sun, Yabo Gao, Yue Qi, Xiebo Zhou, Boris I. Yakobson, Yanfeng Zhang, and Zhongfan Liu, "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)", ACS Nano 2015 9 (6), 6308-6315. [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852){:target='_blank'}. + Qiucheng Li, Xiaolong Zou, Mengxi Liu, Jingyu Sun, Yabo Gao, Yue Qi, Xiebo Zhou, Boris I. Yakobson, Yanfeng Zhang, and Zhongfan Liu, "Grain Boundary Structures and Electronic Properties of Hexagonal Boron Nitride on Cu(111)", ACS Nano 2015 9 (6), 6308-6315. [DOI: 10.1021/acs.nanolett.5b01852](https://doi.org/10.1021/acs.nanolett.5b01852){:target='_blank'}. [@Li2015] We will focus on creating h-BN grain boundary structures similar to Figure 2c from the manuscript: @@ -149,5 +149,3 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% endwith %} ## References. - -Cite the following work: [@Li2015] diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md index 9b3ffae6..3abf646a 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md @@ -21,7 +21,7 @@ This tutorial demonstrates the process of creating grain boundary structures in !!!note "Manuscript" - Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. + Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}. [@Frolov2013] We will focus on creating copper grain boundary structures similar to Figure 1b from the manuscript: @@ -145,5 +145,3 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% endwith %} ## References. - -Cite the following work: [@Frolov2013] diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index 22a52e66..6fd2fda8 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -28,6 +28,10 @@ This tutorial demonstrates how to create a high-k metal gate stack heterostructu 2. Building the Si/SiO2 interface using strain matching 3. Adding the pre-created slabs sequentially using simple interface builder +!!!note "Reference" + QuantumATK tutorial: [High-k Metal Gate Stack Builder](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) [@Muller1999; @Robertson2006] + + We use the [Materials Designer](../../../materials-designer/overview.md) to create the high-k metal gate stack as shown in the figure below. ![High-k Metal Gate Stack](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack") @@ -203,5 +207,3 @@ The following JupyterLite notebook demonstrates the process of creating target m ## References. -Cite the following works: [@Muller1999; @Robertson2006], [QuantumATK tutorial](https://docs.quantumatk.com/tutorials/hkmg_builder/hkmg_builder.html) - diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md index 7bfea5a6..dd41af1c 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md @@ -25,7 +25,7 @@ This tutorial demonstrates the process of creating interfaces between 2D and 3D **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) + [DOI: 10.1103/PhysRevB.78.115404](https://doi.org/10.1103/PhysRevB.78.115404) [@Kang2008; @Dahal2014] 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. @@ -128,5 +128,3 @@ The interactive JupyterLite notebook for creating interfaces between graphene an {% endwith %} ## References. - -Cite the following works: [@Kang2008; @Dahal2014] From 4df49e91daf24f07fb8ca8a52807ec012fe28095 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 14:17:19 -0800 Subject: [PATCH 14/20] update: rename to reflect categories --- ...planar-grain-boundary-2d-boron-nitride.md} | 2 +- ...ar-grain-boundary-3d-fcc-metals-copper.md} | 2 +- ...m-island-molybdenum-disulfide-platinum.md} | 2 +- ...ioxide-hafnium-dioxide-titanium-nitride.md | 2 +- ...rface-film-xy-position-graphene-nickel.md} | 2 +- mkdocs.yml | 38 +++++++++---------- 6 files changed, 24 insertions(+), 24 deletions(-) rename lang/en/docs/tutorials/materials/specific/{grain-boundary-2d-boron-nitride.md => defect-planar-grain-boundary-2d-boron-nitride.md} (98%) rename lang/en/docs/tutorials/materials/specific/{grain-boundary-3d-fcc-metals-copper.md => defect-planar-grain-boundary-3d-fcc-metals-copper.md} (98%) rename lang/en/docs/tutorials/materials/specific/{defect_point_adatom_island_mos2_pt.md => defect-point-adatom-island-molybdenum-disulfide-platinum.md} (99%) rename lang/en/docs/tutorials/materials/specific/{optimize-film-position-graphene-nickel-interface.md => optimization-interface-film-xy-position-graphene-nickel.md} (98%) diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md similarity index 98% rename from lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md rename to lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md index fde46572..94f4b6fd 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md @@ -142,7 +142,7 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/grain_boundary_2d_boron_nitride.ipynb' %} +{% with notebook_name='specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md similarity index 98% rename from lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md rename to lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md index 3abf646a..9a770385 100644 --- a/lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md @@ -138,7 +138,7 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/grain_boundary_3d_fcc_metals_copper.ipynb' %} +{% with notebook_name='specific_examples/defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md similarity index 99% rename from lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md rename to lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md index b731f052..a7422bad 100644 --- a/lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md @@ -158,7 +158,7 @@ The following embedded notebook demonstrates the complete process. Select "Run" {% 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_adatom_island_mos2_pt.ipynb' %} +{% with notebook_name='specific_examples/defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index 6fd2fda8..de60dec2 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -199,7 +199,7 @@ The following JupyterLite notebook demonstrates the process of creating target m {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/heterostructure_high_k_metal_gate_stack.ipynb' %} +{% with notebook_name='specific_examples/heterostructure_silicon_silicon_dioxide_hafnium_dioxide_titanium_nitride.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md similarity index 98% rename from lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md rename to lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md index 677f11a1..91d837a5 100644 --- a/lang/en/docs/tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md +++ b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md @@ -140,7 +140,7 @@ The following JupyterLite notebook demonstrates the complete process. Select "Ru {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/optimize_film_position_graphene_nickel_interface.ipynb' %} +{% with notebook_name='specific_examples/optimization_interface_film_xy_position_graphene_nickel.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/mkdocs.yml b/mkdocs.yml index c516086e..5abd913d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -224,28 +224,28 @@ nav: - Import materials from files in various formats: tutorials/materials/import-from-files.md - 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 - - Interstitial Point Defect in SnO: tutorials/materials/specific/defect-point-interstitial-tin-oxide.md - - Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-surface-island-titanium-nitride.md - - Step Surface Defect on Pt(111): tutorials/materials/specific/defect-surface-step-platinum.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 - - Adatom Surface Defects on Graphene: tutorials/materials/specific/defect-surface-adatom-graphene.md - - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-silicon-nanowire.md + - 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 + - Interstitial Point Defect in SnO: tutorials/materials/specific/defect-point-interstitial-tin-oxide.md + - Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-surface-island-titanium-nitride.md + - Step Surface Defect on Pt(111): tutorials/materials/specific/defect-surface-step-platinum.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 + - Adatom Surface Defects on Graphene: tutorials/materials/specific/defect-surface-adatom-graphene.md + - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-silicon-nanowire.md - H-Passivated Silicon (100) Surface: tutorials/materials/specific/passivation-surface-silicon-surface.md - - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md + - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md - SrTiO3 Slab: tutorials/materials/specific/slab-strontium-titanate.md - Interface between Graphene and h-BN: 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 - - High-k Metal Gate Stack (Si/SiO2/HfO2/TiN): tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md - - Ripple perturbation of a Graphene sheet: tutorials/materials/specific/perturbation-ripples-graphene.md - - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md - - Grain Boundary (2D) in h-BN: tutorials/materials/specific/grain-boundary-2d-boron-nitride.md - - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md - - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect_point_adatom_island_mos2_pt.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 + - High-k Metal Gate Stack (Si/SiO2/HfO2/TiN): tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md + - Ripple perturbation of a Graphene sheet: tutorials/materials/specific/perturbation-ripples-graphene.md + - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md + - Grain Boundary (2D) in h-BN: tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md + - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-interface.md + - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md # COMMON UI COMPONENTS - Interface Components: From 21fc7f2d73f89ca05eb47ec0e711daafc13625f0 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 18:44:25 -0800 Subject: [PATCH 15/20] update: images path --- .../0-figure-from-manuscript.webp | 0 .../2-jl-setup-nb-gb.webp | 0 .../3-jl-result-preview-gb.webp | 0 .../4-wave-result-gb.webp | 0 .../5-jl-setup-nb-final-gb.webp | 0 .../6-jl-result-preview-final-gb.webp | 0 .../7-wave-result-final-gb.webp | 0 .../8-wave-result-final-gb-relaxed.webp | 0 .../0-figure-from-manuscript.webp | 0 .../1-standata-import-cu.webp | 0 .../2-jl-setup-nb.webp | 0 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b/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/7-wave-result-final.webp similarity index 100% rename from images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/7-wave-result-final.webp rename to images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/7-wave-result-final.webp diff --git a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md index 94f4b6fd..47829ee0 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md @@ -24,7 +24,7 @@ This tutorial demonstrates the process of creating 2D grain boundary structures We will focus on creating h-BN grain boundary structures similar to Figure 2c from the manuscript: -![h-BN Grain Boundary](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.") +![h-BN Grain Boundary](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.") ## 1. Create Initial h-BN Structure. @@ -71,7 +71,7 @@ DISTANCE_TOLERANCE = 1.43 # in Angstroms EDGE_INCLUSION_TOLERANCE = 0.0 # in Angstroms ``` -![Notebook Setup](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/2-jl-setup-nb-gb.webp "Notebook Setup") +![Notebook Setup](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/2-jl-setup-nb-gb.webp "Notebook Setup") !!!note "Important Parameter" The `DISTANCE_TOLERANCE` parameter (1.43 Å) is larger than B-N distances at the one specific spot in the boundary. This will cause certain nitrogen atoms to be removed during structure generation, which we'll need to restore later. @@ -82,7 +82,7 @@ Run the notebook by selecting "Run" > "Run All Cells". The notebook will generate the h-BN grain boundary structure based on the parameters provided. -![Initial h-BN Structure](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/4-wave-result-gb.webp "Initial h-BN Structure") +![Initial h-BN Structure](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/4-wave-result-gb.webp "Initial h-BN Structure") ## 3. Restore Missing Nitrogen Atom. @@ -113,19 +113,19 @@ DEFECT_CONFIGS = [ ] ``` -![Notebook Setup](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/5-jl-setup-nb-final-gb.webp "Notebook Setup") +![Notebook Setup](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/5-jl-setup-nb-final-gb.webp "Notebook Setup") ### 3.2. Run the Notebook. Run the notebook to add the missing nitrogen atom to the h-BN grain boundary structure. -![Final Structure Preview](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/6-jl-result-preview-final-gb.webp "Final Structure Preview") +![Final Structure Preview](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/6-jl-result-preview-final-gb.webp "Final Structure Preview") ## 4. Pass Final 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/grain_boundary_2d_boron_nitride/7-wave-result-final-gb.webp "Final Material") +![Final Material](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/7-wave-result-final-gb.webp "Final Material") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. @@ -134,7 +134,7 @@ Or the user can [save or download](../../../materials-designer/header-menu/input To fill the gaps between two phases edge atoms can be adjusted manually in Materials Designer 3D editor. The resulting structure should be similar to the one shown in the manuscript. -![Adjusted Structure](/images/tutorials/materials/defects/grain_boundary_2d_boron_nitride/8-wave-result-final-gb-relaxed.webp "Adjusted Structure") +![Adjusted Structure](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/8-wave-result-final-gb-relaxed.webp "Adjusted Structure") ## Interactive JupyterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md index 9a770385..c5b096f5 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md @@ -25,7 +25,7 @@ This tutorial demonstrates the process of creating grain boundary structures in We will focus on creating copper grain boundary structures similar to Figure 1b from the manuscript: -![Copper Grain Boundary](/images/tutorials/materials/defects/grain_boundary_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") +![Copper Grain Boundary](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") ## 1. Create Initial Copper Structure. @@ -37,7 +37,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im 2. Select "Import from Standata" 3. Search for "Cu" and select the bulk copper material -![Copper Material Import](/images/tutorials/materials/defects/grain_boundary_fcc_metal/1-standata-import-cu.webp "Copper Material Import") +![Copper Material Import](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/1-standata-import-cu.webp "Copper Material Import") ### 1.2. Launch JupyterLite Session. @@ -87,7 +87,7 @@ These parameters will create: - 2 Å gap between phases - Maximum area of 100 Ų for strain matching -![Grain Boundary Parameters](/images/tutorials/materials/defects/grain_boundary_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters") +![Grain Boundary Parameters](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters") ## 2. Run the Notebook. @@ -106,7 +106,7 @@ After running the notebook, user can visualize the grain boundary structure: - Check the atomic arrangement at the interface - Verify the orientation relationship between the two phases -![Grain Boundary Preview](/images/tutorials/materials/defects/grain_boundary_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview") +![Grain Boundary Preview](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview") ### 3.2. Structure Details. @@ -118,9 +118,9 @@ The resulting structure should show: Grain boundary from the top (XY) and side (XZ) views: -![Final Material (XY)](/images/tutorials/materials/defects/grain_boundary_fcc_metal/4-wave-result.webp "Final Copper Grain Boundary, XY view") +![Final Material (XY)](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/4-wave-result.webp "Final Copper Grain Boundary, XY view") -![Final Material (XZ)](/images/tutorials/materials/defects/grain_boundary_fcc_metal/5-wave-result-xz.webp "Final Copper Grain Boundary, XZ view") +![Final Material (XZ)](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/5-wave-result-xz.webp "Final Copper Grain Boundary, XZ view") The structure has differences from the original figure in the manuscript, since grain boundary achieved by strain-matching two symmetrical surfaces with no changes to either surfaces. Discrepancies might be removed with further adjustments like shifting the phases, removing atom layers and reconstructing the interface. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md index a7422bad..ea563b62 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md @@ -30,7 +30,7 @@ This tutorial demonstrates how to create a platinum island on MoS2 by sequential We will recreate the Pt island structure shown in Figure 4b: -![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/0-figure-from-manuscript.webp "Pt island formation on MoS2") +![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/0-figure-from-manuscript.webp "Pt island formation on MoS2") ## 1. Create MoS2 Substrate. @@ -109,23 +109,23 @@ Key parameters explained: - `distance_z` sets the distance along the z-axis from the adatom to the topmost atom directly below it -![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/1-jl-setup-nb.webp "Pt adatoms setup") +![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/1-jl-setup-nb.webp "Pt adatoms setup") ### 2.2. Run the Notebook. Execute the notebook to create the Pt island structure on MoS2 by selecting "Run" > "Run All Cells" from the JupyterLite menu. -![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/2-jl-result-preview.webp "Pt island results preview") +![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/2-jl-result-preview.webp "Pt island results preview") ### 2.3. Pass the Result to Materials Designer. The result can be passed to Materials Designer for visualization and viewed from the top: -![Complete Island](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/4-wave-result-top.webp "Complete Pt island structure") +![Complete Island](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/4-wave-result-top.webp "Complete Pt island structure") And from the side: -![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/5-wave-result-side.webp "Complete Pt island structure, side view") +![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/5-wave-result-side.webp "Complete Pt island structure, side view") ## 3. Analyze the Structure. diff --git a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md index 91d837a5..e6f8867a 100644 --- a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md +++ b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md @@ -30,7 +30,7 @@ This tutorial demonstrates how to create and optimize a Graphene/Ni(111) interfa We will recreate the interface structure and optimize the film position to match the experimental findings shown in the figure below: -![Gr/Ni Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)") +![Gr/Ni Interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)") ## 1. Create Interface Structure. @@ -68,7 +68,7 @@ INTERFACE_DISTANCE = 2.58 # in Angstrom from literature INTERFACE_VACUUM = 20.0 # in Angstrom ``` -![Interface Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)") +![Interface Parameters](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)") ### 1.5. Run interface creation. @@ -104,7 +104,7 @@ Key parameters explained: - `GRID_RANGE`: Search range in crystal coordinates - `USE_CARTESIAN`: Set to False for hexagonal systems -![Optimization Parameters](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)") +![Optimization Parameters](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)") ### 2.3. Run optimization. @@ -114,17 +114,17 @@ Run all cells in the notebook. The optimization will: 2. Find the global minimum energy position 3. Generate visualizations of the results -![Energy Landscape](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/4-energy-landscape.webp "Energy landscape of film positions") +![Energy Landscape](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/4-energy-landscape.webp "Energy landscape of film positions") -![Energy Heatmap](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/5-energy-heatmap.webp "Energy heatmap of film positions") +![Energy Heatmap](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/5-energy-heatmap.webp "Energy heatmap of film positions") ## 3. Analyze Results. Compare the original and optimized interface structures to see the difference in the graphene position. -![Initial and optimized interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/6-jl-result-preview-compare.webp "Initial and optimized interface structures") +![Initial and optimized interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/6-jl-result-preview-compare.webp "Initial and optimized interface structures") -![Final Interface](/images/tutorials/materials/optimization/optimize_film_position_graphene_nickel_interface/7-wave-result-final.webp "Optimized Gr/Ni Interface") +![Final Interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/7-wave-result-final.webp "Optimized Gr/Ni Interface") ## 4. Save Optimized Structure. From 2ee9daa0ffbe0170372e07325fdcacf55b0f4ce9 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 18:56:11 -0800 Subject: [PATCH 16/20] update: images path to relative --- ...-planar-grain-boundary-2d-boron-nitride.md | 16 +++++----- ...nar-grain-boundary-3d-fcc-metals-copper.md | 12 ++++---- ...om-island-molybdenum-disulfide-platinum.md | 10 +++---- .../defect-point-interstitial-tin-oxide.md | 8 ++--- .../defect-point-pair-gallium-nitride.md | 14 ++++----- .../defect-point-substitution-graphene.md | 14 ++++----- .../defect-point-vacancy-boron-nitride.md | 14 ++++----- .../defect-surface-adatom-graphene.md | 30 +++++++++---------- .../defect-surface-island-titanium-nitride.md | 10 +++---- .../specific/defect-surface-step-platinum.md | 14 ++++----- ...ioxide-hafnium-dioxide-titanium-nitride.md | 16 +++++----- .../interface-2d-2d-graphene-boron-nitride.md | 14 ++++----- ...nterface-2d-3d-graphene-silicon-dioxide.md | 8 ++--- .../interface-3d-3d-copper-silicon-dioxide.md | 8 ++--- ...mensurate-lattices-molybdenum-disulfide.md | 18 +++++------ ...layer-twisted-nanoribbons-boron-nitride.md | 12 ++++---- .../materials/specific/nanocluster-gold.md | 20 ++++++------- ...erface-film-xy-position-graphene-nickel.md | 14 ++++----- .../passivation-edge-silicon-nanowire.md | 10 +++---- .../passivation-surface-silicon-surface.md | 14 ++++----- .../specific/perturbation-ripples-graphene.md | 14 ++++----- .../specific/slab-strontium-titanate.md | 12 ++++---- 22 files changed, 151 insertions(+), 151 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md index 47829ee0..80eca168 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md @@ -24,7 +24,7 @@ This tutorial demonstrates the process of creating 2D grain boundary structures We will focus on creating h-BN grain boundary structures similar to Figure 2c from the manuscript: -![h-BN Grain Boundary](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.") +![h-BN Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/0-figure-from-manuscript.webp "h-BN Grain Boundary, FIG. 2c.") ## 1. Create Initial h-BN Structure. @@ -36,7 +36,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im 2. Select "Import from Standata" 3. Search for "Boron_Nitride" and select the 2D h-BN material -![Standata h-BN Import](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata h-BN Import") +![Standata h-BN Import](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata h-BN Import") ### 1.2. Launch JupyterLite Session. @@ -71,7 +71,7 @@ DISTANCE_TOLERANCE = 1.43 # in Angstroms EDGE_INCLUSION_TOLERANCE = 0.0 # in Angstroms ``` -![Notebook Setup](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/2-jl-setup-nb-gb.webp "Notebook Setup") +![Notebook Setup](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/2-jl-setup-nb-gb.webp "Notebook Setup") !!!note "Important Parameter" The `DISTANCE_TOLERANCE` parameter (1.43 Å) is larger than B-N distances at the one specific spot in the boundary. This will cause certain nitrogen atoms to be removed during structure generation, which we'll need to restore later. @@ -82,7 +82,7 @@ Run the notebook by selecting "Run" > "Run All Cells". The notebook will generate the h-BN grain boundary structure based on the parameters provided. -![Initial h-BN Structure](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/4-wave-result-gb.webp "Initial h-BN Structure") +![Initial h-BN Structure](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/4-wave-result-gb.webp "Initial h-BN Structure") ## 3. Restore Missing Nitrogen Atom. @@ -113,19 +113,19 @@ DEFECT_CONFIGS = [ ] ``` -![Notebook Setup](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/5-jl-setup-nb-final-gb.webp "Notebook Setup") +![Notebook Setup](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/5-jl-setup-nb-final-gb.webp "Notebook Setup") ### 3.2. Run the Notebook. Run the notebook to add the missing nitrogen atom to the h-BN grain boundary structure. -![Final Structure Preview](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/6-jl-result-preview-final-gb.webp "Final Structure Preview") +![Final Structure Preview](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/6-jl-result-preview-final-gb.webp "Final Structure Preview") ## 4. Pass Final 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_planar_grain_boundary_2d_boron_nitride/7-wave-result-final-gb.webp "Final Material") +![Final Material](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/7-wave-result-final-gb.webp "Final Material") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. @@ -134,7 +134,7 @@ Or the user can [save or download](../../../materials-designer/header-menu/input To fill the gaps between two phases edge atoms can be adjusted manually in Materials Designer 3D editor. The resulting structure should be similar to the one shown in the manuscript. -![Adjusted Structure](/images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/8-wave-result-final-gb-relaxed.webp "Adjusted Structure") +![Adjusted Structure](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_2d_boron_nitride/8-wave-result-final-gb-relaxed.webp "Adjusted Structure") ## Interactive JupyterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md index c5b096f5..cfbd03c3 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md @@ -25,7 +25,7 @@ This tutorial demonstrates the process of creating grain boundary structures in We will focus on creating copper grain boundary structures similar to Figure 1b from the manuscript: -![Copper Grain Boundary](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") +![Copper Grain Boundary](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1") ## 1. Create Initial Copper Structure. @@ -37,7 +37,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im 2. Select "Import from Standata" 3. Search for "Cu" and select the bulk copper material -![Copper Material Import](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/1-standata-import-cu.webp "Copper Material Import") +![Copper Material Import](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/1-standata-import-cu.webp "Copper Material Import") ### 1.2. Launch JupyterLite Session. @@ -87,7 +87,7 @@ These parameters will create: - 2 Å gap between phases - Maximum area of 100 Ų for strain matching -![Grain Boundary Parameters](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters") +![Grain Boundary Parameters](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters") ## 2. Run the Notebook. @@ -106,7 +106,7 @@ After running the notebook, user can visualize the grain boundary structure: - Check the atomic arrangement at the interface - Verify the orientation relationship between the two phases -![Grain Boundary Preview](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview") +![Grain Boundary Preview](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview") ### 3.2. Structure Details. @@ -118,9 +118,9 @@ The resulting structure should show: Grain boundary from the top (XY) and side (XZ) views: -![Final Material (XY)](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/4-wave-result.webp "Final Copper Grain Boundary, XY view") +![Final Material (XY)](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/4-wave-result.webp "Final Copper Grain Boundary, XY view") -![Final Material (XZ)](/images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/5-wave-result-xz.webp "Final Copper Grain Boundary, XZ view") +![Final Material (XZ)](../../../images/tutorials/materials/defects/defect_planar_grain_boundary_3d_fcc_metal/5-wave-result-xz.webp "Final Copper Grain Boundary, XZ view") The structure has differences from the original figure in the manuscript, since grain boundary achieved by strain-matching two symmetrical surfaces with no changes to either surfaces. Discrepancies might be removed with further adjustments like shifting the phases, removing atom layers and reconstructing the interface. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md index ea563b62..0d005056 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md @@ -30,7 +30,7 @@ This tutorial demonstrates how to create a platinum island on MoS2 by sequential We will recreate the Pt island structure shown in Figure 4b: -![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/0-figure-from-manuscript.webp "Pt island formation on MoS2") +![Pt Island on MoS2](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/0-figure-from-manuscript.webp "Pt island formation on MoS2") ## 1. Create MoS2 Substrate. @@ -109,23 +109,23 @@ Key parameters explained: - `distance_z` sets the distance along the z-axis from the adatom to the topmost atom directly below it -![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/1-jl-setup-nb.webp "Pt adatoms setup") +![Adatoms Setup](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/1-jl-setup-nb.webp "Pt adatoms setup") ### 2.2. Run the Notebook. Execute the notebook to create the Pt island structure on MoS2 by selecting "Run" > "Run All Cells" from the JupyterLite menu. -![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/2-jl-result-preview.webp "Pt island results preview") +![Results Preview](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/2-jl-result-preview.webp "Pt island results preview") ### 2.3. Pass the Result to Materials Designer. The result can be passed to Materials Designer for visualization and viewed from the top: -![Complete Island](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/4-wave-result-top.webp "Complete Pt island structure") +![Complete Island](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/4-wave-result-top.webp "Complete Pt island structure") And from the side: -![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/5-wave-result-side.webp "Complete Pt island structure, side view") +![Complete Island, side view](../../../images/tutorials/materials/defects/defect_point_adatom_island_molybdenum_disulfide_platinum/5-wave-result-side.webp "Complete Pt island structure, side view") ## 3. Analyze the Structure. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md index 7d9c4400..28aad98f 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md @@ -29,7 +29,7 @@ This tutorial demonstrates how to create an oxygen interstitial defect in tin mo We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [Voronoi](https://github.com/Exabyte-io/made/blob/9e13b350eaaa5d49c81a3b30f76c165480825d72/src/py/mat3ra/made/tools/build/defect/builders.py#L125) placement method. -![SnO O-interstitial](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") +![SnO O-interstitial](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO") ## 1. Prepare Base Structure. @@ -37,7 +37,7 @@ We will recreate the O-interstitial defect structure shown in Fig. 4 a) using [V Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the SnO material from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md) using the search term "SnO". -![Original SnO](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp "SnO from Standata, 2x2x2 repetitions") +![Original SnO](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp "SnO from Standata, 2x2x2 repetitions") ### 1.2. Launch JupyterLite Session. @@ -73,7 +73,7 @@ DEFECT_CONFIGS = [ } ] ``` -![Defect Parameters](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/3-jl-setup-nb.webp "Defect parameters for O-interstitial in SnO") +![Defect Parameters](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/3-jl-setup-nb.webp "Defect parameters for O-interstitial in SnO") Key parameters explained: @@ -103,7 +103,7 @@ Run the notebook by selecting "Run" > "Run All Cells". This will: After creating the defect, examine the structure to verify: -![SnO with O-interstitial defect](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/4-wave-result-material.webp "SnO with O-interstitial defect") +![SnO with O-interstitial defect](../../../images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/4-wave-result-material.webp "SnO with O-interstitial defect") ### 3.1. Defect Position. 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 01f5e292..c793950c 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 @@ -35,24 +35,24 @@ 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.") +![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") +![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") +![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") +![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. @@ -98,7 +98,7 @@ 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.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/defects/defect_point_pair_gallium_nitride/5-jl-setup.webp "Notebook setup") ## 4. Run the Notebook. @@ -110,13 +110,13 @@ 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 and vacancy 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.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") +![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. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 9f0bceab..999609d7 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -29,24 +29,24 @@ We will focus on creating graphene-nitrogen structures from FIG. 1. Specifically, the material from FIG. 1. b) of the paper: -![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") +![Point Defect, Substitution, 0](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.") ## 1. Create Graphene Supercell. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") +![Standata Graphene Import](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") We then use the [Advanced](../../../materials-designer/header-menu/advanced/supercell.md) menu to create a supercell of graphene with a size of 4x4x1. -![Supercell Creation for Graphene](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/2-advanced-supercell.webp "Supercell Graphene") +![Supercell Creation for Graphene](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/2-advanced-supercell.webp "Supercell Graphene") ## 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_creation_point_substitution_graphene/4-threejs-editor-coordinates.webp "3D Editor") +![3D Editor](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/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. @@ -108,7 +108,7 @@ DEFECT_CONFIGS = [ Here's the visual of the updated content: -![Notebook setup](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/5-jl-setup.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/5-jl-setup.webp "Notebook setup") ## 4. Run the Notebook. @@ -120,13 +120,13 @@ 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 Graphene with substitution defects. -![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results") +![Review the Results](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/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_creation_point_substitution_graphene/7-wave-result.webp "N-doped Graphene") +![Final Material](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/7-wave-result.webp "N-doped Graphene") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md index a9dd167f..2f3a2843 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md @@ -26,7 +26,7 @@ We use the [Materials Designer](../../../materials-designer/overview.md) and Jup 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") +![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. @@ -42,7 +42,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and cl 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") +![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. @@ -66,7 +66,7 @@ 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") +![Nanoribbon Parameters](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/2-jl-nb-setup-nanoribbon.webp "Nanoribbon Parameters") ### 2.3. Run the Notebook. @@ -80,7 +80,7 @@ After the notebook completes: 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") +![Nanoribbon Preview](../../../images/tutorials/materials/defects/defect_point_vacancy_boron_nitride/3-wave-preview-nanoribbon.webp "Nanoribbon Preview") ## 3. Create the Vacancy Defect. @@ -108,19 +108,19 @@ The configuration specifies: - `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") +![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") +![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") +![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 diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index a5d35056..80cc0c81 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -27,13 +27,13 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea The image shows the adatom on the graphene surface. -![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface") +![Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface") ## 1. Load and preview Graphene structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") +![Standata Graphene Import](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a graphene structure with an adatom on the surface. @@ -90,13 +90,13 @@ After running the notebook, the Graphene structure with a Li adatom on the surfa The user will be able to visualize the created structure and download the corresponding files. -![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-li.webp "Li Adatom on Graphene Surface") +![Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-li.webp "Li Adatom on Graphene Surface") ### 2.5. Pass the Material to the Materials Designer. After reviewing the results, the user can pass the material to Materials Designer for further analysis. -![Final Material](/images/tutorials/materials/defects/defect-surface-adatom-graphene/wave-result-li.webp "Li Adatom on Graphene Surface") +![Final Material](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/wave-result-li.webp "Li Adatom on Graphene Surface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. @@ -115,7 +115,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.28 ``` -![Na Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-na.webp "Na Adatom on Graphene Surface") +![Na Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-na.webp "Na Adatom on Graphene Surface") For K adatom on hollow site: ```python @@ -124,7 +124,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.60 ``` -![K Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-k.webp "K Adatom on Graphene Surface") +![K Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-k.webp "K Adatom on Graphene Surface") For Ca adatom on hollow site: @@ -134,7 +134,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.29 ``` -![Ca Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ca.webp "Ca Adatom on Graphene Surface") +![Ca Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ca.webp "Ca Adatom on Graphene Surface") For Al adatom on hollow site: @@ -144,7 +144,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.13 ``` -![Al Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-al.webp "Al Adatom on Graphene Surface") +![Al Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-al.webp "Al Adatom on Graphene Surface") For Ga adatom on hollow site: @@ -154,7 +154,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.20 ``` -![Ga Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ga.webp "Ga Adatom on Graphene Surface") +![Ga Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ga.webp "Ga Adatom on Graphene Surface") For In adatom on hollow site: @@ -164,7 +164,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 2.45 ``` -![In Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-in.webp "In Adatom on Graphene Surface") +![In Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-in.webp "In Adatom on Graphene Surface") For Sn adatom on top site: @@ -174,7 +174,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [7/12, 5/12] DISTANCE_Z = 2.82 ``` -![Sn Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-sn.webp "Sn Adatom on Graphene Surface") +![Sn Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-sn.webp "Sn Adatom on Graphene Surface") For Ti adatom on hollow site: @@ -184,7 +184,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 1.80 ``` -![Ti Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ti.webp "Ti Adatom on Graphene Surface") +![Ti Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ti.webp "Ti Adatom on Graphene Surface") For Fe adatom on hollow site: ```python @@ -193,7 +193,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5] DISTANCE_Z = 1.53 ``` -![Fe Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-fe.webp "Fe Adatom on Graphene Surface") +![Fe Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-fe.webp "Fe Adatom on Graphene Surface") For Pd adatom on bridge site: @@ -204,7 +204,7 @@ DISTANCE_Z = 2.21 ``` -![Pd Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-pd.webp "Pd Adatom on Graphene Surface") +![Pd Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-pd.webp "Pd Adatom on Graphene Surface") For Au adatom on top site: @@ -214,7 +214,7 @@ APPROXIMATE_POSITION_ON_SURFACE = [7/12, 5/12] DISTANCE_Z = 2.69 ``` -![Au Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-au.webp "Au Adatom on Graphene Surface") +![Au Adatom on Graphene Surface](../../../images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-au.webp "Au Adatom on Graphene Surface") ## Interactive JupiterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 417275d1..59bb49c1 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -32,14 +32,14 @@ We will focus on creating graphene-nitrogen structures from FIG. 2. Specifically, the material from FIG. 2. a) of the paper: -![Surface Defect](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a)") +![Surface Defect](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a)") ## 1. Create and preview TiN Slab. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") +![Standata Graphene Import](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a TiN slab. @@ -80,7 +80,7 @@ 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 created TiN slab. -![Review the Results](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/1.png "Review the Results") +![Review the Results](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/1.png "Review the Results") We don't need to save the material at this point, as we will recreate the slab with island on the surface in the next notebook. This step is needed to identify the coordinates of the island vertices. @@ -148,7 +148,7 @@ DEFAULT_SLAB_PARAMETERS = { Here's the visual of the updated content: -![Notebook setup](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png "Notebook setup") ## 4. Run the Notebook. @@ -160,7 +160,7 @@ 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 created material with the island on the surface. -![Review the Results](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png "Review the Results") +![Review the Results](../../../images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png "Review the Results") ## 6. Pass the Material to Materials Designer. diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md index 60238624..cc205878 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md @@ -25,7 +25,7 @@ This tutorial demonstrates two different approaches to creating terrace steps on We will focus on creating platinum surface with terrace steps, as shown in FIG. 1. B: -![Fig. 1.](/images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.") +![Fig. 1.](../../../images/tutorials/materials/defects/defect_surface_step_platinum/0-figure-from-manuscript.webp "Fig. 1.") We will demonstrate two methods: @@ -48,7 +48,7 @@ First, we need to import the platinum material from Standata: 3. Select "Import from Standata" 4. Search for "Pt" and select the bulk platinum material -![Standata Import](/images/tutorials/materials/defects/defect_surface_step_platinum/1-standata-import-platinum.webp "Standata Import") +![Standata Import](../../../images/tutorials/materials/defects/defect_surface_step_platinum/1-standata-import-platinum.webp "Standata Import") ### 1.2. Launch JupyterLite Environment. @@ -76,13 +76,13 @@ These parameters will create a Pt(211) surface with: - Orthogonal z-axis - Using the conventional unit cell -![Pt(211) Surface Setup](/images/tutorials/materials/defects/defect_surface_step_platinum/2-jl-setup-nb-surface.webp "Pt(211) Surface Setup") +![Pt(211) Surface Setup](../../../images/tutorials/materials/defects/defect_surface_step_platinum/2-jl-setup-nb-surface.webp "Pt(211) Surface Setup") ### 1.4. Create the Slab. Run the notebook by clicking `Run` > `Run All` in the top menu. The notebook will generate the Pt(211) surface. -![Pt(211) Surface](/images/tutorials/materials/defects/defect_surface_step_platinum/3-wave-result-pt-211-surface.webp "Pt(211) Surface") +![Pt(211) Surface](../../../images/tutorials/materials/defects/defect_surface_step_platinum/3-wave-result-pt-211-surface.webp "Pt(211) Surface") ## 2. Method II: Create Terrace Step Defect on Pt(111). @@ -134,17 +134,17 @@ SHOW_INTERMEDIATE_STEPS = True CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] ``` -![Terrace Parameters](/images/tutorials/materials/defects/defect_surface_step_platinum/4-jl-setup-nb-terrace.webp "Terrace Parameters") +![Terrace Parameters](../../../images/tutorials/materials/defects/defect_surface_step_platinum/4-jl-setup-nb-terrace.webp "Terrace Parameters") ### 2.3. Create the Terrace. Run the notebook to create the Pt(111) surface with a terrace step. -![Pt(111) Surface with Terrace Step](/images/tutorials/materials/defects/defect_surface_step_platinum/5-wave-result-pt-terrace.webp "Pt(111) Surface with Terrace Step") +![Pt(111) Surface with Terrace Step](../../../images/tutorials/materials/defects/defect_surface_step_platinum/5-wave-result-pt-terrace.webp "Pt(111) Surface with Terrace Step") The same material with repetitions: -![Pt(111) Surface with Terrace Step with repetitions](/images/tutorials/materials/defects/defect_surface_step_platinum/6-wave-result-pt-terrace-repetitions.webp "Pt(111) Surface with Terrace Step with repetitions") +![Pt(111) Surface with Terrace Step with repetitions](../../../images/tutorials/materials/defects/defect_surface_step_platinum/6-wave-result-pt-terrace-repetitions.webp "Pt(111) Surface with Terrace Step with repetitions") The user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md index de60dec2..0c5012ed 100644 --- a/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md @@ -34,7 +34,7 @@ This tutorial demonstrates how to create a high-k metal gate stack heterostructu We use the [Materials Designer](../../../materials-designer/overview.md) to create the high-k metal gate stack as shown in the figure below. -![High-k Metal Gate Stack](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack") +![High-k Metal Gate Stack](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/original-figure.webp "High-k Metal Gate Stack") ## 1. Set Up Materials. @@ -45,7 +45,7 @@ First, navigate to Materials Designer and import from [Standata](../../../materi - Hafnium dioxide (HfO2) - Titanium nitride (TiN) -![Standata Import](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/import-standata.webp "Standata Import") +![Standata Import](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/import-standata.webp "Standata Import") ## 2. Create HfO2 and TiN Slabs. @@ -72,7 +72,7 @@ TERMINATION_INDEX = 0 Run the notebook to create the HfO2 slab and pass it to Materials Designer. -![HfO2 slab](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-hfo2-slab-wave.webp "HfO2 slab") +![HfO2 slab](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-hfo2-slab-wave.webp "HfO2 slab") ### 2.2. Create TiN Slab. @@ -92,7 +92,7 @@ TERMINATION_INDEX = 0 Run the notebook to create and pass the TiN slab to Materials Designer. -![TiN slab](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-tin-slab.webp "TiN slab") +![TiN slab](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-tin-slab.webp "TiN slab") ## 3. Create Si/SiO2 Interface. @@ -127,7 +127,7 @@ TERMINATION_PAIR_INDEX = 0 We set a higher tolerances to achieve smaller cell with higher strain of the film (SiO2). -![Interface Setup](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2.webp "Interface Setup") +![Interface Setup](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2.webp "Interface Setup") ### 3.2. Create Initial Interface. @@ -156,13 +156,13 @@ INTERFACE_VACUUM = 0.5 # Angstroms Film is the material that will be strained (scaled) to match the substrate. -![HfO2 Interface Setup](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2-hfo2.webp "HfO2 Interface Setup") +![HfO2 Interface Setup](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/jl-setup-notebook-si-sio2-hfo2.webp "HfO2 Interface Setup") ### 4.2. Add HfO2. Run the notebook to add the pre-created HfO2 slab to the Si/SiO2 structure. -![Si/SiO2/HfO2](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-si-sio2-hfo2.webp "Si/SiO2/HfO2") +![Si/SiO2/HfO2](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-si-sio2-hfo2.webp "Si/SiO2/HfO2") ## 5. Add TiN Layer. @@ -189,7 +189,7 @@ INTERFACE_VACUUM = 10.0 # Final vacuum spacing Run the notebook to add the TiN layer and complete the stack. -![Final Stack](/images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-si-sio2-hfo2-tin.webp "Final Stack") +![Final Stack](../../../images/tutorials/materials/heterostructures/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride/wave-result-si-sio2-hfo2-tin.webp "Final Stack") The user then can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md index cc0ebeee..fe5caeac 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md @@ -29,14 +29,14 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea The Figure 7 shows the different stacking configurations of graphene on h-BN. -![Graphene on Hexagonal Boron Nitride](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/0-figure-from-manuscript.webp "Graphene on Hexagonal Boron Nitride, FIG. 7") +![Graphene on Hexagonal Boron Nitride](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/0-figure-from-manuscript.webp "Graphene on Hexagonal Boron Nitride, FIG. 7") ## 1. Load and preview materials. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Graphene and Hexagonal BN materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Graphene and h-BN Import](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/1-standata-import-gr-hbn.webp "Standata Graphene and h-BN Import") +![Standata Graphene and h-BN Import](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/1-standata-import-gr-hbn.webp "Standata Graphene and h-BN Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create the target structures. @@ -93,7 +93,7 @@ INTERFACE_DISTANCE = 3.4 # in Angstrom INTERFACE_VACUUM = 20.0 # in Angstrom ``` -![Notebook setup](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/2-jl-setup-notebook.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/2-jl-setup-notebook.webp "Notebook setup") ### 2.3. Run the Notebook. @@ -109,7 +109,7 @@ After that, the user can pass the material to the Materials Designer for further Interface between h-BN and Graphene with the specified parameters is shown below. -![Gr/h-BN Interface ](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/3-jl-result-preview.webp "Gr/h-BN Interface") +![Gr/h-BN Interface ](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/3-jl-result-preview.webp "Gr/h-BN Interface") To shift graphene layer along the y-axis, the user can modify the last cell in the notebook to achieve different stacking configurations. @@ -130,17 +130,17 @@ shifted_interface = interface_displace_part( ``` -![Shift Interface](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/4-jl-setup-shift.webp "Shift Interface") +![Shift Interface](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/4-jl-setup-shift.webp "Shift Interface") Preview of interfaces with different stacking configurations is shown below. -![Shifted Interfaces](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/5-jl-result-preview.webp "Shifted Interfaces") +![Shifted Interfaces](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/5-jl-result-preview.webp "Shifted Interfaces") ## 3. Pass the Material to Materials Designer. The user can pass the material with the interface in the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/6-wave-result.webp "Graphene on Hexagonal Boron Nitride Interface") +![Final Material](../../../images/tutorials/materials/interfaces/interface_2d_2d_graphene_boron_nitride/6-wave-result.webp "Graphene on Hexagonal Boron Nitride Interface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md index dd41af1c..bad84b7a 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md @@ -31,7 +31,7 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea We will focus on replicating the material from FIG. 1. (b) -- with Graphene on O-terminated SiO2. 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)") +![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. @@ -90,7 +90,7 @@ 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") +![Notebook Setup](../../../images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/2-jl-setup-notebook.webp "Notebook Setup") ### 2.3 Run the Notebook @@ -103,7 +103,7 @@ Run the notebook to generate the interface structure between graphene and silico 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") +![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. @@ -111,7 +111,7 @@ After generating the interface structure, pass the material to the Materials Des 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") +![Gr/SiO2 Interface](../../../images/tutorials/materials/interfaces/interface_2d_3d_graphene_silicon_dioxide/4-wave-result-material.webp "Gr/SiO2 Interface") ## Interactive JupyterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md index 764914d0..fed1291e 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md @@ -30,7 +30,7 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea The FIG. 1. shows the interfaces with different terminations between Cu and Cristobalite. -![Copper on Cristobalite](/images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1") +![Copper on Cristobalite](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/0-figure-from-manuscript.webp "Copper on Cristobalite, FIG. 1") ## 1. Load and Preview Materials. @@ -93,7 +93,7 @@ INTERFACE_DISTANCE = 2.4 # in Angstrom INTERFACE_VACUUM = 18.0 # in Angstrom ``` -![Notebook setup](/images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/1-jl-setup-notebook.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/1-jl-setup-notebook.webp "Notebook setup") ### 2.3. Run the Notebook. @@ -109,14 +109,14 @@ After that, the user can pass the material to the Materials Designer for further Interface between Copper and Cristobalite with the specified parameters is shown below. -![Cu/SiO2 Interface](/images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/2-jl-result-preview.webp "Cu/SiO2 Interface") +![Cu/SiO2 Interface](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/2-jl-result-preview.webp "Cu/SiO2 Interface") ## 3. Pass the Material to Materials Designer. The user can pass the material with the interface in the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/3-wave-result.webp "Cu/SiO2 Interface") +![Final Material](../../../images/tutorials/materials/interfaces/interface_3d_3d_copper_cristobalite/3-wave-result.webp "Cu/SiO2 Interface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index ee0812f9..4e61ee0e 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -30,14 +30,14 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to crea The Figure 4 shows the twisted bilayer MoS2 configurations. -![Twisted Bilayer Molybdenum Disulfide](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide") +![Twisted Bilayer Molybdenum Disulfide](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png "Twisted Bilayer Molybdenum Disulfide") ## 1. Load and preview MoS2 structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata MoS2 Import](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/standata-import-mos2.png "Standata MoS2 Import") +![Standata MoS2 Import](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/standata-import-mos2.png "Standata MoS2 Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a twisted bilayer molybdenum disulfide structure. @@ -77,7 +77,7 @@ SHOW_INTERMEDIATE_STEPS = True VISUALIZE_REPETITIONS = [3, 3, 1] ``` -![Notebook setup](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/jl-set-nb.png "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/jl-set-nb.png "Notebook setup") ### 2.3. Run the Notebook. @@ -93,7 +93,7 @@ After that, the user can pass the material to the Materials Designer for further The interface for 22 degrees twist is shown below. -![Result Material, 22 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-22.png "MoS2 Twisted Bilayer, 22 degrees") +![Result Material, 22 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-22.png "MoS2 Twisted Bilayer, 22 degrees") ## 3. Create bilayers with other twist angles. @@ -107,7 +107,7 @@ TARGET_TWIST_ANGLE = 0.0 INTERFACE_DISTANCE = 6.8 ``` -![Result Material, 0 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-0.png "MoS2 Twisted Bilayer, 0 degrees") +![Result Material, 0 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-0.png "MoS2 Twisted Bilayer, 0 degrees") ```python @@ -115,28 +115,28 @@ TARGET_TWIST_ANGLE = 13.0 INTERFACE_DISTANCE = 6.5 ``` -![Result Material, 13 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-13.png "MoS2 Twisted Bilayer, 13 degrees") +![Result Material, 13 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-13.png "MoS2 Twisted Bilayer, 13 degrees") ```python TARGET_TWIST_ANGLE = 38.0 INTERFACE_DISTANCE = 6.5 ``` -![Result Material, 38 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-38.png "MoS2 Twisted Bilayer, 38 degrees") +![Result Material, 38 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-38.png "MoS2 Twisted Bilayer, 38 degrees") ```python TARGET_TWIST_ANGLE = 47.0 INTERFACE_DISTANCE = 6.5 ``` -![Result Material, 47 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-47.png "MoS2 Twisted Bilayer, 47 degrees") +![Result Material, 47 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-47.png "MoS2 Twisted Bilayer, 47 degrees") ```python TARGET_TWIST_ANGLE = 60.0 INTERFACE_DISTANCE = 6.2 ``` -![Result Material, 60 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-60.png "MoS2 Twisted Bilayer, 60 degrees") +![Result Material, 60 degrees](../../../images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-60.png "MoS2 Twisted Bilayer, 60 degrees") ## Interactive JupyterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md index f1ccc5bf..bce7b13f 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md @@ -29,13 +29,13 @@ We use the [Materials Designer](../../../materials-designer/overview.md) to cre The image shows the twisted bilayer h-BN structure with a twist angle of 2.64° (a) and 62.64° (b). -![Twisted Bilayer Boron Nitride](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride") +![Twisted Bilayer Boron Nitride](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-paper-image.png "Twisted Bilayer Boron Nitride") ## 1. Load and preview BN structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the BN material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata BN Import](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata BN Import") +![Standata BN Import](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/standata-import-bn.png "Standata BN Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a twisted bilayer boron nitride structure. @@ -72,7 +72,7 @@ SHOW_INTERMEDIATE_STEPS = True VISUALIZE_REPETITIONS = [1, 1, 1] ``` -![Notebook setup](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/jl-set-nb.png "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/jl-set-nb.png "Notebook setup") ### 2.3. Run the Notebook. @@ -84,14 +84,14 @@ After setting the parameters, run the notebook with "Run" > "Run All" option to After running the notebook, the user will be able to visualize the created twisted bilayer boron nitride structure. -![Review the Results](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-jl.png "Review the Results") +![Review the Results](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-jl.png "Review the Results") ### 2.5. Pass Results to the Materials Designer. After reviewing the results, the user can pass the material to the Materials Designer for further analysis. -![Result Material](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-wavejs.png "Result Material") +![Result Material](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-result-wavejs.png "Result Material") ## 3. Create a TBBN structure with a twist angle of 62.64°. @@ -107,7 +107,7 @@ After running the notebook, the user will be able to visualize the created twist After reviewing the results, the user can pass the material to the Materials Designer for further analysis. -![Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle](/images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-62_64.png "Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle") +![Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle](../../../images/tutorials/materials/interfaces/twisted-bilayer-boron-nitride/tbbn-62_64.png "Twisted Bilayer Boron Nitride Structure with 62.64° Twist Angle") ## Interactive JupyterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md index 540a2b30..1b026cb4 100644 --- a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -27,13 +27,13 @@ This tutorial demonstrates the process of creating a gold nanoparticle structure We use the [Materials Designer](../../../materials-designer/overview.md) to create gold nanoparticle structures of cuboctahedral and icosahedral shapes as shown in the image below. -![Gold Nanoparticles](/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") +![Gold Nanoparticles](../../../images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") ## 1. Load and preview Gold structure. First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Gold material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Gold Import](/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp "Standata Gold Import") +![Standata Gold Import](../../../images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp "Standata Gold Import") Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create gold nanoparticle structures. @@ -64,7 +64,7 @@ parameters = { } ``` -![Setup for cuboctahedron cluster](/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp "Setup for cuboctahedron cluster") +![Setup for cuboctahedron cluster](../../../images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp "Setup for cuboctahedron cluster") ### 2.3. Run the notebook. @@ -80,13 +80,13 @@ The user will be able to visualize the created structure and download the corres For better view of the solid symmetry rotation of image might be needed like `"rotation": "45y,45x"` for the cuboctahedron. -![Cuboctahedron Gold Nanocluster](/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp "Cuboctahedron Gold Nanocluster") +![Cuboctahedron Gold Nanocluster](../../../images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp "Cuboctahedron Gold Nanocluster") ### 2.5. Pass the Material to the Materials Designer. After reviewing the results, the user can pass the material to Materials Designer for further analysis. -![Final Material](/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp "Final Material") +![Final Material](../../../images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp "Final Material") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. @@ -108,7 +108,7 @@ parameters = { } ``` -![Cuboctahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp "Cuboctahedron 147") +![Cuboctahedron 147](../../../images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp "Cuboctahedron 147") For Cuboctahedron with 309 atoms: @@ -120,7 +120,7 @@ parameters = { } ``` -![Cuboctahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp "Cuboctahedron 309") +![Cuboctahedron 309](../../../images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp "Cuboctahedron 309") For Icosahedron with 55 atoms: @@ -131,7 +131,7 @@ parameters = { } ``` -![Icosahedron 55](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp "Icosahedron 55") +![Icosahedron 55](../../../images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp "Icosahedron 55") For Icosahedron with 147 atoms: @@ -142,7 +142,7 @@ parameters = { } ``` -![Icosahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp "Icosahedron 147") +![Icosahedron 147](../../../images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp "Icosahedron 147") For Icosahedron with 309 atoms: @@ -153,7 +153,7 @@ parameters = { } ``` -![Icosahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp "Icosahedron 309") +![Icosahedron 309](../../../images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp "Icosahedron 309") ## Interactive JupiterLite Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md index e6f8867a..afce3f00 100644 --- a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md +++ b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md @@ -30,7 +30,7 @@ This tutorial demonstrates how to create and optimize a Graphene/Ni(111) interfa We will recreate the interface structure and optimize the film position to match the experimental findings shown in the figure below: -![Gr/Ni Interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)") +![Gr/Ni Interface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/0-figure-from-manuscript.webp "Optimal position of graphene on Ni(111)") ## 1. Create Interface Structure. @@ -68,7 +68,7 @@ INTERFACE_DISTANCE = 2.58 # in Angstrom from literature INTERFACE_VACUUM = 20.0 # in Angstrom ``` -![Interface Parameters](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)") +![Interface Parameters](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/2-jl-setup-nb-interface.webp "Interface parameters for Gr/Ni(111)") ### 1.5. Run interface creation. @@ -104,7 +104,7 @@ Key parameters explained: - `GRID_RANGE`: Search range in crystal coordinates - `USE_CARTESIAN`: Set to False for hexagonal systems -![Optimization Parameters](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)") +![Optimization Parameters](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/3-jl-setup-nb-final.webp "Optimization parameters for Gr/Ni(111)") ### 2.3. Run optimization. @@ -114,17 +114,17 @@ Run all cells in the notebook. The optimization will: 2. Find the global minimum energy position 3. Generate visualizations of the results -![Energy Landscape](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/4-energy-landscape.webp "Energy landscape of film positions") +![Energy Landscape](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/4-energy-landscape.webp "Energy landscape of film positions") -![Energy Heatmap](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/5-energy-heatmap.webp "Energy heatmap of film positions") +![Energy Heatmap](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/5-energy-heatmap.webp "Energy heatmap of film positions") ## 3. Analyze Results. Compare the original and optimized interface structures to see the difference in the graphene position. -![Initial and optimized interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/6-jl-result-preview-compare.webp "Initial and optimized interface structures") +![Initial and optimized interface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/6-jl-result-preview-compare.webp "Initial and optimized interface structures") -![Final Interface](/images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/7-wave-result-final.webp "Optimized Gr/Ni Interface") +![Final Interface](../../../images/tutorials/materials/optimization/optimization_interface_film_xy_position_graphene_nickel/7-wave-result-final.webp "Optimized Gr/Ni Interface") ## 4. Save Optimized Structure. diff --git a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md index 07b696d4..aad91672 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md @@ -30,7 +30,7 @@ We will focus on creating silicon nanowires with hydrogen passivation from FIG. Specifically, the material from FIG. 1. of the publication: -![Passivated Silicon nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") +![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") ## 1. Create Silicon Nanowire. @@ -134,7 +134,7 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook and submitting the material, the user will be able to visualize the structure of Silicon Nanowire. -![Silicon Nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp "Silicon Nanowire") +![Silicon Nanowire](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp "Silicon Nanowire") ## 2. Passivate with Hydrogen. @@ -177,19 +177,19 @@ CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] Here's the visual of the updated content: -![Notebook setup](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp "Notebook setup") ### 2.2. Run the notebook and analyze the results. After running the notebook, the user will be able to visualize the structure of Silicon Nanowire with substitution defects. -![Review the Results](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp "Review the Results") +![Review the Results](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp "Review the Results") ## 3. 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/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp "H-Passivated Silicon Nanowire") +![Final Material](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp "H-Passivated Silicon Nanowire") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md index 457e7f56..d005bd80 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md @@ -29,7 +29,7 @@ This tutorial demonstrates how to passivate a reconstructed silicon (100) surfac We will recreate the passivated surface structure shown in Fig. 8: -![Si(100) H-Passivated Surface](/images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)") +![Si(100) H-Passivated Surface](../../../images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)") ## 1. Obtain the Silicon (100) Surface Structure. @@ -37,7 +37,7 @@ We will recreate the passivated surface structure shown in Fig. 8: Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the reconstructed Si(100) surface from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Si(100) Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp "Si(100) Structure") +![Si(100) Structure](../../../images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp "Si(100) Structure") ### 1.2. Launch JupyterLite Session. @@ -82,7 +82,7 @@ new_coordinates[index_to_adjust] = adjusted_coordinate slab.set_coordinates(new_coordinates) ``` -![Supercell Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization") +![Supercell Parameters](../../../images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization") ### 1.4. Run Structure Adjustment. @@ -93,7 +93,7 @@ Run the notebook using "Run > Run All Cells". This will: 3. Create a supercell if specified in the parameters 4. Visualize the adjusted structure -![Adjusted Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp "Adjusted Si(100) Structure") +![Adjusted Structure](../../../images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp "Adjusted Si(100) Structure") ## 2. Passivate the Surface. @@ -126,7 +126,7 @@ Key parameters explained: - `SURFACE`: Passivate only the top surface. - `DEPTH`: How deep to look for surface atoms, set to include only top Si atoms. -![Passivation Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp "Passivation Parameters Visualization") +![Passivation Parameters](../../../images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp "Passivation Parameters Visualization") ### 2.3. Run Passivation. @@ -136,7 +136,7 @@ Run all cells in the notebook. The passivation process will: 2. Add H atoms at the specified bond length 3. Generate the passivated structure -![Passivated Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp "H-Passivated Si(100) Structure") +![Passivated Structure](../../../images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp "H-Passivated Si(100) Structure") ## 3. Analyze Results. @@ -148,7 +148,7 @@ Check that: - Surface reconstruction is maintained - H atoms are properly placed above surface Si atoms -![Final Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp "Final H-Passivated Si(100)") +![Final Structure](../../../images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp "Final H-Passivated Si(100)") ## 4. Save the Results. diff --git a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md index b13ed2c2..506ccb4b 100644 --- a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md @@ -27,7 +27,7 @@ This tutorial demonstrates the process of creating edge induced ripples in graph We will focus on creating graphene with edge-induced ripples that match the patterns observed in experimental studies, as shown in FIG. 1. -![Rippled Graphene](/images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.") +![Rippled Graphene](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/0-figure-from-manuscript.webp "Rippled Graphene, FIG. 1.") ## 1. Create Graphene Nanoribbon. @@ -35,7 +35,7 @@ We will focus on creating graphene with edge-induced ripples that match the patt Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") +![Standata Graphene Import](../../../images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") ### 1.2. Launch JupyterLite Session. @@ -60,13 +60,13 @@ VACUUM_LENGTH = 10 EDGE_TYPE = "zigzag" # "zigzag" or "armchair" ``` -![Setup Nanoribbon Parameters](/images/tutorials/materials/defects/perturbation_ripple_graphene/2-jl-setup-nb-nanoribbon.webp "Setup Nanoribbon Parameters") +![Setup Nanoribbon Parameters](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/2-jl-setup-nb-nanoribbon.webp "Setup Nanoribbon Parameters") ### 1.5. Run the notebook. After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. This will create a graphene nanoribbon with the specified dimensions. -![Nanoribbon Result](/images/tutorials/materials/defects/perturbation_ripple_graphene/3-wave-result-nanoribbon.webp "Graphene Nanoribbon") +![Nanoribbon Result](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/3-wave-result-nanoribbon.webp "Graphene Nanoribbon") ## 2. Create Ripples in the Nanoribbon. @@ -126,7 +126,7 @@ wave_pattern = ( custom_sympy_function = AMPLITUDE * wave_pattern * edge_mask ``` -![Setup Perturbation Function](/images/tutorials/materials/defects/perturbation_ripple_graphene/4-jl-setup-nb-final.webp "Setup Perturbation Function") +![Setup Perturbation Function](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/4-jl-setup-nb-final.webp "Setup Perturbation Function") Key parameters explained: @@ -147,11 +147,11 @@ The rippled graphene structure will be automatically passed back to the current Graphene with edge-induced ripples with amplitude of 0.09 crystal units. -![Final Material](/images/tutorials/materials/defects/perturbation_ripple_graphene/5-wave-result-final.webp "Final Rippled Graphene, amplitude 0.09 crystal units") +![Final Material](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/5-wave-result-final.webp "Final Rippled Graphene, amplitude 0.09 crystal units") Graphene with edge-induced ripples with amplitude of 0.27 crystal units. -![Final Material](/images/tutorials/materials/defects/perturbation_ripple_graphene/6-wave-result-final-2.webp "Final Rippled Graphene, amplitude 0.27 crystal units") +![Final Material](../../../images/tutorials/materials/defects/perturbation_ripple_graphene/6-wave-result-final-2.webp "Final Rippled Graphene, amplitude 0.27 crystal units") Or user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md index 064a0e07..09d60c08 100644 --- a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md +++ b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md @@ -28,7 +28,7 @@ This tutorial demonstrates the process of creating strontium titanate (SrTiO3 (011) slabs with different terminations from FIG. 2. -![Strontium Titanate Slabs](/images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.") +![Strontium Titanate Slabs](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/0-figure-from-manuscript.webp "Strontium Titanate Slabs, FIG. 2.") ## 1. Create Strontium Titanate Slab. @@ -36,7 +36,7 @@ We will focus on creating SrTiO3 (011) slabs with different terminati Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the strontium titanate material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Strontium Titanate Material](/images/tutorials/materials/2d_materials/slab_strontium_titanate/original-material.webp "Strontium Titanate Material") +![Strontium Titanate Material](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/original-material.webp "Strontium Titanate Material") ### 1.2. Launch JupyterLite Session. @@ -79,7 +79,7 @@ USE_CONVENTIONAL_CELL = True TERMINATION_INDEX = 0 ``` -![Setup Slab Parameters](/images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-setup.webp "Setup Slab Parameters") +![Setup Slab Parameters](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-setup.webp "Setup Slab Parameters") In the case of some terminations not being detected, we'll need to rotate input material before creating the configuration by adding `rotate(material, axis=[1,0,0], angle=10)` (angle set in degrees) to the cell 1.3. Get input materials: @@ -95,7 +95,7 @@ material = rotate(material, axis=[1,0,0], angle=10) This will allow for symmetry breaking and correct detection for all possible terminations. -![Rotate Material](/images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-setup-rotation.webp "Rotate Material") +![Rotate Material](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-setup-rotation.webp "Rotate Material") ### 1.5. Run the notebook. @@ -108,7 +108,7 @@ After setting the parameters, run the notebook by selecting "Run > Run All Cells After running the notebook, the slabs for different possible terminations should apper in the preview. -![Strontium Titanate Slab](/images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-result-preview.webp "Strontium Titanate Slab") +![Strontium Titanate Slab](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/jl-result-preview.webp "Strontium Titanate Slab") ### 2.1. Select the desired termination. @@ -118,7 +118,7 @@ If the interactive selection of terminations is enabled, select the desired term The user can pass the material with the selected termination in the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/2d_materials/slab_strontium_titanate/wave-result.webp "Strontium Titanate Slab") +![Final Material](../../../images/tutorials/materials/2d_materials/slab_strontium_titanate/wave-result.webp "Strontium Titanate Slab") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. From 3ad0a49792f1f1e0b5fc81afd9fd45c9b81191a4 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 19:08:41 -0800 Subject: [PATCH 17/20] update: images path to relative 2 --- .../defect-planar-grain-boundary-3d-fcc-metals-copper.md | 4 ++-- .../materials/specific/defect-point-pair-gallium-nitride.md | 4 ++-- .../specific/defect-point-substitution-graphene.md | 4 ++-- .../specific/defect-point-vacancy-boron-nitride.md | 2 +- .../materials/specific/defect-surface-adatom-graphene.md | 4 ++-- .../specific/defect-surface-island-titanium-nitride.md | 6 +++--- .../specific/interface-2d-2d-graphene-boron-nitride.md | 4 ++-- .../specific/interface-2d-3d-graphene-silicon-dioxide.md | 4 ++-- .../specific/interface-3d-3d-copper-silicon-dioxide.md | 4 ++-- ...er-twisted-commensurate-lattices-molybdenum-disulfide.md | 4 ++-- .../interface-bilayer-twisted-nanoribbons-boron-nitride.md | 4 ++-- .../docs/tutorials/materials/specific/nanocluster-gold.md | 4 ++-- ...timization-interface-film-xy-position-graphene-nickel.md | 2 +- .../materials/specific/passivation-edge-silicon-nanowire.md | 4 ++-- .../materials/specific/perturbation-ripples-graphene.md | 4 ++-- .../tutorials/materials/specific/slab-strontium-titanate.md | 4 ++-- 16 files changed, 31 insertions(+), 31 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md index cfbd03c3..4e22d533 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md +++ b/lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md @@ -43,7 +43,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im Select "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" to open JupyterLite. -![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") +![JupyterLite Dialog](../../../images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") ### 1.3. Open and Configure Notebook. @@ -93,7 +93,7 @@ These parameters will create: After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 3. Analyze the Results. 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 c793950c..41818a69 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 @@ -66,7 +66,7 @@ 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.webp "JupyterLite Dialog") ### 3.2. Open `create_point_defect_pair.ipynb` notebook. @@ -104,7 +104,7 @@ Here's the visual of the updated content: 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 5. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 999609d7..c5cd3408 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -58,7 +58,7 @@ 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.webp "JupyterLite Dialog") ### 3.2. Open `create_point_defect.ipynb` notebook. @@ -114,7 +114,7 @@ Here's the visual of the updated content: 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 5. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md index 2f3a2843..fac37694 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-vacancy-boron-nitride.md @@ -52,7 +52,7 @@ Next, we'll create a nanoribbon structure using the JupyterLite environment. 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.webp "JupyterLite Dialog") ### 2.2. Open and Configure Nanoribbon Notebook. diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 80cc0c81..263a55da 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -43,7 +43,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 2.2. Open and modify the notebook. @@ -82,7 +82,7 @@ SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]] Run the notebook by selecting "Run > Run All Cells" from the menu. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index 59bb49c1..1119fa8e 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -48,7 +48,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 1.2. Open and modify the notebook. @@ -74,7 +74,7 @@ TERMINATION_INDEX = 0 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 1.4. Analyze the Results. @@ -154,7 +154,7 @@ Here's the visual of the updated content: 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 5. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md index fe5caeac..6aed6233 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md @@ -48,7 +48,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 2.2. Open and modify the notebook. @@ -100,7 +100,7 @@ INTERFACE_VACUUM = 20.0 # in Angstrom After setting the parameters, run the notebook to create the interface between h-BN and Graphene. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. View Results and shift the layers. diff --git a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md index bad84b7a..8c88720f 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md @@ -45,7 +45,7 @@ Then use the [JupyterLite](../../../jupyterlite/overview.md) environment to crea 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.webp "JupyterLite Dialog") ### 2.2 Open and Modify the Notebook. @@ -96,7 +96,7 @@ INTERFACE_VACUUM = 20.0 # in Angstrom -- from manuscript 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. View Results. diff --git a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md index fed1291e..75723837 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md @@ -46,7 +46,7 @@ Then use the [JupyterLite](../../../jupyterlite/overview.md) environment to crea 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.webp "JupyterLite Dialog") ### 2.2 Open and Modify the Notebook. @@ -100,7 +100,7 @@ INTERFACE_VACUUM = 18.0 # in Angstrom After setting the parameters, run the notebook to create the interface between Cu and SiO₂. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. View Results. diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index 4e61ee0e..6836d668 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -49,7 +49,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 2.2. Open and modify the notebook. @@ -84,7 +84,7 @@ VISUALIZE_REPETITIONS = [3, 3, 1] After setting the parameters, run the notebook to create the twisted bilayer molybdenum disulfide structure. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. View Results and pass to Materials Designer. diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md index bce7b13f..1e6d94e5 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md @@ -45,7 +45,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 2.2. Open and modify the notebook. @@ -78,7 +78,7 @@ VISUALIZE_REPETITIONS = [1, 1, 1] After setting the parameters, run the notebook with "Run" > "Run All" option to create the twisted bilayer boron nitride structure. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md index 1b026cb4..bcc6f78c 100644 --- a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -43,7 +43,7 @@ Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment 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.webp "JupyterLite Dialog") ### 2.2. Open and modify the notebook. @@ -70,7 +70,7 @@ parameters = { Run the notebook by selecting "Run > Run All Cells" from the menu. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ### 2.4. Analyze the Results. diff --git a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md index afce3f00..cd8e24c5 100644 --- a/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md +++ b/lang/en/docs/tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md @@ -38,7 +38,7 @@ We will recreate the interface structure and optimize the film position to match Navigate to [Materials Designer](../../../materials-designer/overview.md) and import both graphene and nickel materials from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). -![Import Graphene and Ni](/images/materials-designer/import/import_from_standata.webp "Import Gr and Ni from Standata") +![Import Graphene and Ni](../../../images/materials-designer/import/import_from_standata.webp "Import Gr and Ni from Standata") ### 1.2. Launch JupyterLite Session. diff --git a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md index aad91672..725d4a38 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md @@ -45,7 +45,7 @@ Otherwise, we navigate to [Materials Designer](../../../materials-designer/overv 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.webp "JupyterLite Dialog") ### 1.3. Open `create_nanowire_custom_shapeipynb` notebook. @@ -130,7 +130,7 @@ condition = CustomCoordinateCondition(vertices=vertices).condition 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") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") After running the notebook and submitting the material, the user will be able to visualize the structure of Silicon Nanowire. diff --git a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md index 506ccb4b..d5822bb0 100644 --- a/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/perturbation-ripples-graphene.md @@ -41,7 +41,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im 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.webp "JupyterLite Dialog") ### 1.3. Open `create_nanoribbon.ipynb` notebook. @@ -139,7 +139,7 @@ Key parameters explained: After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 3. Pass the Material to Materials Designer. diff --git a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md index 09d60c08..6834cee1 100644 --- a/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md +++ b/lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md @@ -42,7 +42,7 @@ Navigate to [Materials Designer](../../../materials-designer/overview.md) and im 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.webp "JupyterLite Dialog") ### 1.3. Open `create_slab.ipynb` notebook. @@ -101,7 +101,7 @@ This will allow for symmetry breaking and correct detection for all possible ter After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu. -![Run All](/images/jupyterlite/run-all.webp "Run All") +![Run All](../../../images/jupyterlite/run-all.webp "Run All") ## 2. Analyze the Results. From a46a6999bb1462253a40943e4838c2aabf5c3f61 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 19:10:41 -0800 Subject: [PATCH 18/20] update: update mkdocs --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 5abd913d..fc654da4 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -244,7 +244,7 @@ nav: - Ripple perturbation of a Graphene sheet: tutorials/materials/specific/perturbation-ripples-graphene.md - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md - Grain Boundary (2D) in h-BN: tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md - - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel-interface.md + - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md # COMMON UI COMPONENTS From 4ee8602a2ccc9fd29620a5bd60985337608ae5df Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 6 Jan 2025 19:40:51 -0800 Subject: [PATCH 19/20] update: rename to reflect categories 2 --- .../0-figure-from-manuscript.webp | 0 .../3-silicon-nanowire.webp | 0 .../5-jl-setup.webp | 0 .../6-jl-result-preview.webp | 0 .../7-wave-result.webp | 0 ...owire.md => passivation-edge-nanowire-silicon.md} | 12 ++++++------ ...con-surface.md => passivation-surface-silicon.md} | 2 +- mkdocs.yml | 4 ++-- 8 files changed, 9 insertions(+), 9 deletions(-) rename images/tutorials/materials/passivation/{passivation_edge_silicon_nanowire => passivation_edge_nanowire_silicon}/0-figure-from-manuscript.webp (100%) rename images/tutorials/materials/passivation/{passivation_edge_silicon_nanowire => passivation_edge_nanowire_silicon}/3-silicon-nanowire.webp (100%) rename images/tutorials/materials/passivation/{passivation_edge_silicon_nanowire => passivation_edge_nanowire_silicon}/5-jl-setup.webp (100%) rename images/tutorials/materials/passivation/{passivation_edge_silicon_nanowire => passivation_edge_nanowire_silicon}/6-jl-result-preview.webp (100%) rename images/tutorials/materials/passivation/{passivation_edge_silicon_nanowire => passivation_edge_nanowire_silicon}/7-wave-result.webp (100%) rename lang/en/docs/tutorials/materials/specific/{passivation-edge-silicon-nanowire.md => passivation-edge-nanowire-silicon.md} (94%) rename lang/en/docs/tutorials/materials/specific/{passivation-surface-silicon-surface.md => passivation-surface-silicon.md} (99%) diff --git a/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp b/images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp similarity index 100% rename from images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp rename to images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp diff --git a/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp b/images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/3-silicon-nanowire.webp similarity index 100% rename from images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp rename to images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/3-silicon-nanowire.webp diff --git a/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp b/images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/5-jl-setup.webp similarity index 100% rename from images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp rename to images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/5-jl-setup.webp diff --git a/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp b/images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/6-jl-result-preview.webp similarity index 100% rename from images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp rename to images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/6-jl-result-preview.webp diff --git a/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp b/images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/7-wave-result.webp similarity index 100% rename from images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp rename to images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/7-wave-result.webp diff --git a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md b/lang/en/docs/tutorials/materials/specific/passivation-edge-nanowire-silicon.md similarity index 94% rename from lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md rename to lang/en/docs/tutorials/materials/specific/passivation-edge-nanowire-silicon.md index 725d4a38..743558b9 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-edge-nanowire-silicon.md @@ -30,7 +30,7 @@ We will focus on creating silicon nanowires with hydrogen passivation from FIG. Specifically, the material from FIG. 1. of the publication: -![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") +![Passivated Silicon nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.") ## 1. Create Silicon Nanowire. @@ -134,7 +134,7 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook and submitting the material, the user will be able to visualize the structure of Silicon Nanowire. -![Silicon Nanowire](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp "Silicon Nanowire") +![Silicon Nanowire](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/3-silicon-nanowire.webp "Silicon Nanowire") ## 2. Passivate with Hydrogen. @@ -177,19 +177,19 @@ CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] Here's the visual of the updated content: -![Notebook setup](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp "Notebook setup") +![Notebook setup](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/5-jl-setup.webp "Notebook setup") ### 2.2. Run the notebook and analyze the results. After running the notebook, the user will be able to visualize the structure of Silicon Nanowire with substitution defects. -![Review the Results](../../../images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp "Review the Results") +![Review the Results](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/6-jl-result-preview.webp "Review the Results") ## 3. 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/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp "H-Passivated Silicon Nanowire") +![Final Material](../../../images/tutorials/materials/passivation/passivation_edge_nanowire_silicon/7-wave-result.webp "H-Passivated Silicon Nanowire") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. @@ -200,7 +200,7 @@ The following JupyterLite notebook demonstrates the process of creating material {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/passivation_edge_silicon_nanowire.ipynb' %} +{% with notebook_name='specific_examples/passivation_edge_nanowire_silicon.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon.md similarity index 99% rename from lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md rename to lang/en/docs/tutorials/materials/specific/passivation-surface-silicon.md index d005bd80..7e94c262 100644 --- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md +++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon.md @@ -163,7 +163,7 @@ The following embedded notebook demonstrates the complete process. Select "Run" {% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} -{% with notebook_name='specific_examples/passivation_surface_silicon_surface.ipynb' %} +{% with notebook_name='specific_examples/passivation_surface_silicon.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} diff --git a/mkdocs.yml b/mkdocs.yml index fc654da4..67fada42 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -233,8 +233,8 @@ nav: - 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 - Adatom Surface Defects on Graphene: tutorials/materials/specific/defect-surface-adatom-graphene.md - - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-silicon-nanowire.md - - H-Passivated Silicon (100) Surface: tutorials/materials/specific/passivation-surface-silicon-surface.md + - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-nanowire-silicon.md + - H-Passivated Silicon (100) Surface: tutorials/materials/specific/passivation-surface-silicon.md - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md - SrTiO3 Slab: tutorials/materials/specific/slab-strontium-titanate.md - Interface between Graphene and h-BN: tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md From 0f70ad90208c6065b7ede136eca275456e163e03 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 7 Jan 2025 18:25:37 -0800 Subject: [PATCH 20/20] update: bring tutorials one layer up --- mkdocs.yml | 46 +++++++++++++++++++++++----------------------- 1 file changed, 23 insertions(+), 23 deletions(-) diff --git a/mkdocs.yml b/mkdocs.yml index 67fada42..a74f5db0 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -223,29 +223,29 @@ nav: - Interface, minimal strain (JupyterLite Session): tutorials/materials/jupyterlite-zsl.md - Import materials from files in various formats: tutorials/materials/import-from-files.md - - 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 - - Interstitial Point Defect in SnO: tutorials/materials/specific/defect-point-interstitial-tin-oxide.md - - Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-surface-island-titanium-nitride.md - - Step Surface Defect on Pt(111): tutorials/materials/specific/defect-surface-step-platinum.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 - - Adatom Surface Defects on Graphene: tutorials/materials/specific/defect-surface-adatom-graphene.md - - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-nanowire-silicon.md - - H-Passivated Silicon (100) Surface: tutorials/materials/specific/passivation-surface-silicon.md - - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md - - SrTiO3 Slab: tutorials/materials/specific/slab-strontium-titanate.md - - Interface between Graphene and h-BN: 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 - - High-k Metal Gate Stack (Si/SiO2/HfO2/TiN): tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md - - Ripple perturbation of a Graphene sheet: tutorials/materials/specific/perturbation-ripples-graphene.md - - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md - - Grain Boundary (2D) in h-BN: tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md - - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md - - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md + - Publication Reproductions: + - 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 + - Interstitial Point Defect in SnO: tutorials/materials/specific/defect-point-interstitial-tin-oxide.md + - Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-surface-island-titanium-nitride.md + - Step Surface Defect on Pt(111): tutorials/materials/specific/defect-surface-step-platinum.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 + - Adatom Surface Defects on Graphene: tutorials/materials/specific/defect-surface-adatom-graphene.md + - H-Passivated Silicon Nanowire: tutorials/materials/specific/passivation-edge-nanowire-silicon.md + - H-Passivated Silicon (100) Surface: tutorials/materials/specific/passivation-surface-silicon.md + - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md + - SrTiO3 Slab: tutorials/materials/specific/slab-strontium-titanate.md + - Interface between Graphene and h-BN: 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 + - High-k Metal Gate Stack (Si/SiO2/HfO2/TiN): tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md + - Ripple perturbation of a Graphene sheet: tutorials/materials/specific/perturbation-ripples-graphene.md + - Grain Boundary in FCC Metals (Copper): tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md + - Grain Boundary (2D) in h-BN: tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md + - Gr/Ni(111) Interface Optimization: tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md + - Pt Adatoms Island on MoS2: tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md # COMMON UI COMPONENTS - Interface Components: