Merge pull request #299 from Exabyte-io/feature/SOF-7521

feat: slab tutorial

lang/en/docs/tutorials/materials/specific/slab-strontium-titanate.md

@@ -0,0 +1,138 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Strontium Titanate Slabs
+
+## Introduction
+
+This tutorial demonstrates the process of creating strontium titanate (SrTiO<sub>3</sub>) slabs based on the work presented in the following manuscript, where the electronic properties of SrTiO<sub>3</sub> slabs are studied.
+
+
+!!!note "Manuscript"
+    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)
+
+
+We will focus on creating SrTiO<sub>3</sub> (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.")
+
+## 1. Create Strontium Titanate Slab
+
+### 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
+
+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
+
+Find `create_slab.ipynb` in the list of notebooks and click/double-click open it.
+
+### 1.4. Open and modify the notebook
+
+Next, we need to create a SrTiO<sub>3</sub> slab with the (011) orientation.
+
+We'll specify the orientation of the slab with Miller indices of `(0,1,1)` as described in the manuscript.
+
+The rest of the parameters can be left as default.
+
+The notebook detects possible terminations and allows for selection.
+
+Terminations can be selected interactively by setting the `IS_TERMINATIONS_SELECTION_INTERACTIVE` flag to `True` and after running the notebook waiting for the prompt to select the termination.
+
+
+Edit notebook in 1.1. to set parameters of slab:
+
+```python
+
+# Enable interactive selection of terminations via UI prompt
+IS_TERMINATIONS_SELECTION_INTERACTIVE = False 
+
+MILLER_INDICES = (0, 1, 1)
+THICKNESS = 3  # in atomic layers
+VACUUM = 10.0  # in angstroms
+XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]
+USE_ORTHOGONAL_Z = True
+USE_CONVENTIONAL_CELL = True
+
+# Index of the termination to be selected
+TERMINATION_INDEX = 0
+```
+
+![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:
+
+```python
+from utils.jupyterlite import get_materials
+from mat3ra.made.tools.modify import rotate
+
+materials = get_materials(globals())
+material = materials[0]
+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")
+
+### 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
+
+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
+
+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
+
+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")
+
+
+Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format.
+
+## Interactive JupyterLite Notebook
+
+The following JupyterLite notebook demonstrates the process of creating strontium titanate slabs. 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/slab_strontium_titanate.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## 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
+
+`slab`, `strontium titanate`, `SrTiO3`, `terminations`, `surface`

mkdocs.yml

@@ -228,6 +228,7 @@ nav:
                 - 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
                 - Gold Nanoclusters:                                             tutorials/materials/specific/nanocluster-gold.md
+                - SrTiO3 Slab:                                                  tutorials/materials/specific/slab-strontium-titanate.md
 
 # COMMON UI COMPONENTS
     - Interface Components: