Skip to content

Commit

Permalink
update: use images
Browse files Browse the repository at this point in the history
  • Loading branch information
VsevolodX committed Jan 1, 2025
1 parent c60cf91 commit cbcb502
Showing 1 changed file with 10 additions and 17 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -17,23 +17,25 @@ This tutorial demonstrates how to create an oxygen interstitial defect in tin mo

We will recreate the O-interstitial defect structure shown in Fig. 4b:

![SnO O-interstitial](/images/tutorials/materials/defects/sno_defect/fig4b-paper.webp "O-interstitial defect in SnO")
![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".

![Standata SnO Import](/images/tutorials/materials/defects/sno_defect/standata-import.webp "Import SnO from Standata")
![Original SnO](/images/tutorials/materials/defects/defect_point_interstitial_tin_oxide/2-wave-original-material.webp "SnO from Standata, 2x2 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. We'll modify its parameters to create the O-interstitial defect.
Find and open the `create_defect.ipynb` notebook. Select "SnO" input material.

We'll modify its parameters to create the O-interstitial defect.

### 1.4. Set Defect Parameters

Expand All @@ -51,6 +53,7 @@ DEFECT_CONFIGS = [{
"placement_method": "voronoi_site" # Use Voronoi analysis to find interstitial 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:

Expand All @@ -63,13 +66,7 @@ Key parameters explained:

### 2.1. Run Supercell Creation

Run the notebook cells through section 1.4 to create the supercell. Verify the structure looks correct:

![SnO Supercell](/images/tutorials/materials/defects/sno_defect/sno-supercell.webp "SnO supercell structure")

### 2.2. Create Defect Structure

Continue running the notebook through sections 2.1 and 2.2. The notebook will:
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
Expand All @@ -79,6 +76,8 @@ Continue running the notebook through sections 2.1 and 2.2. The notebook will:

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
Expand All @@ -91,8 +90,6 @@ After creating the defect, examine the structure to verify:
- Verify no unrealistic atom overlaps
- Confirm overall crystal structure is maintained

![Final Structure](/images/tutorials/materials/defects/sno_defect/final-structure.webp "SnO with O-interstitial defect")

## 4. Save Defect Structure

The defect structure will be automatically passed back to Materials Designer where you can:
Expand Down Expand Up @@ -136,10 +133,6 @@ To adjust the defect creation:

1. Togo, A., Oba, F., & Tanaka, I. (2006). First-principles calculations of native defects in tin monoxide. Physical Review B, 74(19), 195128.

2. Walsh, A., & Watson, G. W. (2004). Electronic structures of rocksalt, litharge, and herzenbergite SnO by density functional theory. Physical Review B, 70(23), 235114.

3. Ogo, Y., et al. (2008). p-channel thin-film transistor using p-type oxide semiconductor, SnO. Applied Physics Letters, 93(3), 032113.

## Tags

`SnO`, `defects`, `interstitial`, `oxygen`, `point defects`, `Sn`, `O`
`SnO`, `defects`, `interstitial`, `voronoi`, `oxygen`, `point defects`, `Sn`, `O`

0 comments on commit cbcb502

Please sign in to comment.