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Merge pull request #313 from Exabyte-io/feature/SOF-7525
Feature/SOF-7525 Add O-interstitial in SnO Tutorial
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‎images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp

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‎images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp

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‎images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/3-jl-setup-nb.webp

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‎images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/4-wave-result-material.webp

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

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---
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# YAML header
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render_macros: true
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---
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# Oxygen interstitial Defect(s) in SnO.
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## Introduction
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This tutorial demonstrates how to create an oxygen interstitial defect in tin monoxide (SnO), following the methodology described in the literature.
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!!!note "Manuscript"
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A. Togo, F. Oba, and I. Tanaka
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"First-principles calculations of native defects in tin monoxide"
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Physical Review B 74, 195128 (2006)
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[DOI: 10.1103/PhysRevB.74.195128](https://doi.org/10.1103/PhysRevB.74.195128){:target='_blank'}.
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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.
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![SnO O-interstitial](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/0-figure-from-manuscript.webp "O-interstitial defect in SnO")
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## 1. Prepare Base Structure
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### 1.1. Load Base Material
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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".
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![Original SnO](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp "SnO from Standata, 2x2x2 repetitions")
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### 1.2. Launch JupyterLite Session
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Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment.
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### 1.3. Open `create_defect.ipynb` Notebook
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Find and open the `create_defect.ipynb` notebook. Select "SnO" input material.
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We'll modify its parameters to create the Sn-vacancy O-interstitial defects according to the image above.
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### 1.4. Set Defect Parameters
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Replace the default parameters in section 1.1 with:
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```python
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# Supercell parameters
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SUPERCELL_MATRIX = [[2, 0, 0], [0, 2, 0], [0, 0, 2]]
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# Defect parameters
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DEFECT_CONFIGS = [
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{
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"defect_type": "vacancy",
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# Coordiante will be resolved to nearest atom
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"approximate_coordinate": [0.0, 0.25, 0.525],
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},
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{
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"defect_type": "interstitial",
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# Coordiante will be resolved to nearest Voronoi site
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"coordinate": [0.0, 0.25, 0.35],
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"chemical_element": "O",
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"placement_method": "voronoi_site"
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}
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]
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```
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![Defect Parameters](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/3-jl-setup-nb.webp "Defect parameters for O-interstitial in SnO")
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Key parameters explained:
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First defect:
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- `defect_type`: "vacancy" for removing an atom
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- `approximate_coordinate`: Position specified in crystal coordinates (Sn as in publication)
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Second defect:
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- `defect_type`: "interstitial" for adding an extra atom
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- `coordinate`: Position specified in crystal coordinates
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- `chemical_element`: "O" for oxygen interstitial
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- `placement_method`: "voronoi_site" to place atom at appropriate interstitial position
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## 2. Create the Defect
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### 2.1. Run Supercell Creation
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Run the notebook by selecting "Run" > "Run All Cells". This will:
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1. Initialize the defect configuration
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2. Create the O-interstitial at the specified position
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3. Generate the final defect structure
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## 3. Analyze Results
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After creating the defect, examine the structure to verify:
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![SnO with O-interstitial defect](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/4-wave-result-material.webp "SnO with O-interstitial defect")
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### 3.1. Defect Position
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- O interstitial should be at (0.0, 0.5, 0.5) in crystal coordinates
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- Position should be in a void space between Sn-O layers
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- Verify symmetry of surrounding atoms
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### 3.2. Local Structure
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- Check distances to nearest Sn and O atoms
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- Verify no unrealistic atom overlaps
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- Confirm overall crystal structure is maintained
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## 4. Save Defect Structure
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The defect structure will be automatically passed back to Materials Designer where you can:
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1. Save it in your workspace
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2. Export it in various formats
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3. Use it for further calculations
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## Interactive JupyterLite Notebook
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The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells".
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{% with origin_url=config.extra.jupyterlite.origin_url %}
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{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
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{% with notebook_name='specific_examples/defect_point_interstitial_tin_oxide.ipynb' %}
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{% include 'jupyterlite_embed.html' %}
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{% endwith %}
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{% endwith %}
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{% endwith %}
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## Parameter Fine-tuning
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To adjust the defect creation:
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1. Position Adjustment:
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- Modify `coordinate` to place interstitial at different positions
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- Try different `placement_method` options ("coordinate", "voronoi_site")
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- Adjust position to match experimental observations
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2. Structure Size:
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- Change `SUPERCELL_MATRIX` for larger/smaller systems
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- Consider periodic boundary conditions effects
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## References
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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'}.
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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).
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[DOI: 10.1038/srep04909](https://doi.org/10.1038/srep04909){:target='_blank'}.
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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).
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[DOI: 10.1103/PhysRevB.73.125205](https://doi.org/10.1103/PhysRevB.73.125205){:target='_blank'}.
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## Tags
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`SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O`

‎mkdocs.yml

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- Substitutional Point Defects in Graphene: tutorials/materials/specific/defect-point-substitution-graphene.md
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- Vacancy-Substitution Pair Defects in GaN: tutorials/materials/specific/defect-point-pair-gallium-nitride.md
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- Vacancy Point Defect in h-BN: tutorials/materials/specific/defect-point-vacancy-boron-nitride.md
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- Interstitial Point Defect in SnO: tutorials/materials/specific/defect-point-interstitial-tin-oxide.md
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- Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-surface-island-titanium-nitride.md
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- Step Surface Defect on Pt(111): tutorials/materials/specific/defect-surface-step-platinum.md
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- Twisted Bilayer h-BN nanoribbons: tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md

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