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Update/SOF-7544 cleanups #314

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40 changes: 20 additions & 20 deletions lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md
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Expand Up @@ -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.

Expand All @@ -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"
Expand All @@ -77,43 +77,43 @@ 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:

1. Initialize the defect configuration
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:

1. Save it in your workspace
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".

Expand All @@ -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:

Expand All @@ -141,7 +141,7 @@ 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. [DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}.

Expand All @@ -152,6 +152,6 @@ To adjust the defect creation:
[DOI: 10.1103/PhysRevB.73.125205](https://doi.org/10.1103/PhysRevB.73.125205){:target='_blank'}.


## Tags
## Tags.

`SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O`
28 changes: 14 additions & 14 deletions lang/en/docs/tutorials/materials/specific/defect-point-pair-gallium-nitride.md
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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.

Expand All @@ -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).

Expand All @@ -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.

Expand All @@ -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.

Expand Down Expand Up @@ -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.

Expand All @@ -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".

Expand All @@ -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.
Copy link
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We may use the in-built tags feature - https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/

In that case, we need to specify the tags on the top/frontmatter (also tags are shown on the top of the page):

---
tags:
  - defects
  - defect pair
---

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We don't seem to use them anywhere currently, do we?

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Ok, we need to place them before

# YAML header
render_macros: true

And also set to hide:

hide:
   - tags

For desired display

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Previously, we used tags to set YouTube hashtags. But they are set via JSON metadata (e.g., https://github.com/Exabyte-io/documentation/blob/master/lang/en/docs/metadata/general.json). We may think of modifying the tags plugin to include tags from JSON files and extend them.


`defects`, `defect pair`, `substitutional`, `vacancy`, `point defects`, `impurities`, `doped semiconductors`, `nitrogen`, `GaN`, `gallium nitride`
28 changes: 14 additions & 14 deletions lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md
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Expand Up @@ -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.

Expand All @@ -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).

Expand All @@ -33,29 +33,29 @@ 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.

![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.

## 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.

Expand Down Expand Up @@ -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.

Expand All @@ -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".

Expand All @@ -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`
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