Update/SOF-7544 cleanups

lang/en/docs/tutorials/materials/specific/grain-boundary-2d-boron-nitride.md → lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md

@@ -1,39 +1,49 @@
 ---
+tags:
+  - grain-boundary
+  - h-BN
+  - 2D-materials
+  - interface
+  - twist-angle
+  - atom-restoration
+
+hide:
+  - tags
 # YAML header
 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:
 
 !!!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:
 
-![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
+## 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).
 
 1. Click on "Input/Output" menu
 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
+### 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:
 
@@ -61,24 +71,24 @@ 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.
 
-## 2. Run the Notebook
+## 2. Run the Notebook.
 
 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
+## 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.
 
@@ -103,45 +113,39 @@ 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
+### 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
+## 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.
 
-## 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")
+![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
+## Interactive JupyterLite Notebook.
 
 The following JupyterLite notebook demonstrates the complete process. Select "Run" > "Run All Cells".
 
 {% with origin_url=config.extra.jupyterlite.origin_url %}
 {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
-{% with notebook_name='specific_examples/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 %}
 {% endwith %}
 
-## 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
-
-`grain-boundary`, `h-BN`, `2D-materials`, `interface`, `twist-angle`, `atom-restoration`
+## References.

lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md → lang/en/docs/tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md

@@ -1,41 +1,51 @@
 ---
+tags:
+  - grain boundary
+  - interface
+  - copper
+  - Cu
+  - FCC
+  - metal
+
+hide:
+  - tags
 # YAML header
 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.
 
 
 !!!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:
 
-![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
+## 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).
 
 1. Click on "Input/Output" menu
 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
+### 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")
+![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:
 
@@ -77,28 +87,28 @@ 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
+## 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")
+![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:
 
 - View from different angles using the rotation controls
 - 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
+### 3.2. Structure Details.
 
 The resulting structure should show:
 
@@ -108,36 +118,30 @@ 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.
 
-## 4. Save the Structure
+## 4. Save the Structure.
 
 The final structure can be:
 
 1. Passed back to Materials Designer
 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".
 
 {% 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 %}
 {% endwith %}
 
-## 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
-
-`grain boundary`, `interface`, `copper`, `Cu`,  `FCC`, `metal`
+## References.