Merge pull request #313 from Exabyte-io/feature/SOF-7525

Feature/SOF-7525 Add O-interstitial in SnO Tutorial

lang/en/docs/tutorials/materials/specific/defect-point-interstitial-tin-oxide.md

@@ -0,0 +1,157 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Oxygen interstitial Defect(s) in SnO.
+
+## Introduction
+
+This tutorial demonstrates how to create an oxygen interstitial defect in tin monoxide (SnO), following the methodology described in the literature.
+
+!!!note "Manuscript"
+    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'}.
+
+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")
+
+## 1. Prepare Base Structure
+
+### 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
+
+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
+
+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
+
+Replace the default parameters in section 1.1 with:
+
+```python
+# Supercell parameters
+SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
+
+# Defect parameters
+DEFECT_CONFIGS = [
+    {
+        "defect_type": "vacancy",
+        # 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
+        "coordinate": [0.0, 0.25, 0.35], 
+        "chemical_element": "O",
+        "placement_method": "voronoi_site"
+    }
+]
+```
+![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:
+
+First defect:
+
+- `defect_type`: "vacancy" for removing an atom
+- `approximate_coordinate`: Position specified in crystal coordinates (Sn as in publication)
+
+Second defect:
+
+- `defect_type`: "interstitial" for adding an extra atom
+- `coordinate`: Position specified in crystal coordinates
+- `chemical_element`: "O" for oxygen interstitial
+- `placement_method`: "voronoi_site" to place atom at appropriate interstitial position
+
+## 2. Create the Defect
+
+### 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
+
+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
+
+- 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
+
+- Check distances to nearest Sn and O atoms
+- Verify no unrealistic atom overlaps
+- Confirm overall crystal structure is maintained
+
+## 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
+
+The following embedded 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/defect_point_interstitial_tin_oxide.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+
+## Parameter Fine-tuning
+
+To adjust the defect creation:
+
+1. Position Adjustment:
+
+   - Modify `coordinate` to place interstitial at different positions
+   - Try different `placement_method` options ("coordinate", "voronoi_site")
+   - Adjust position to match experimental observations
+
+2. Structure Size:
+
+   - Change `SUPERCELL_MATRIX` for larger/smaller systems
+   - Consider periodic boundary conditions effects
+
+## 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'}.
+
+
+## Tags
+
+`SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O`

mkdocs.yml

@@ -223,6 +223,7 @@ nav:
                 - 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