feat: si (100) passivation tutorial (claude)

Author: VsevolodX

lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md

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+---
+# YAML header
+render_macros: true
+---
+
+# Passivation of Silicon (001) Surface
+
+## Introduction
+
+This tutorial demonstrates how to passivate a reconstructed silicon (001) surface with hydrogen atoms, following the methodology described in the literature.
+
+!!!note "Manuscript"
+    Hansen, U., & Vogl, P.
+    "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study."
+    Physical Review B, 57(20), 13295–13304. (1998)
+    [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}.
+
+We will recreate the passivated surface structure shown in Fig. 8:
+
+![Si(100) H-Passivated Surface](/images/tutorials/materials/surfaces/si_100_passivation/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
+
+## 1. Adjust Silicon Surface Structure
+
+### 1.1. Load Base Material
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the reconstructed Si(100) surface from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md) using the search term "Silicon.*100.*reconstructed".
+
+![Standata Si Import](/images/tutorials/materials/surfaces/si_100_passivation/standata-import.webp "Import Si(100) from Standata")
+
+### 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 Modified `create_supercell.ipynb` Notebook
+
+Open `create_supercell.ipynb` and replace the "Get input materials" cell with the following code to adjust the Si atom position:
+
+```python
+from utils.jupyterlite import get_materials
+materials = get_materials(globals())
+material = materials[0]
+
+# Find and adjust Si atom coordinates
+si_atoms_coordinates = [coordinate.value for coordinate in material.basis.coordinates.to_array_of_values_with_ids()]
+si_atoms_sorted = sorted(si_atoms_coordinates, key=lambda x: x[2], reverse=True)
+second_from_top_index = 1
+second_si_atom_coordinate = si_atoms_sorted[second_from_top_index]
+
+print(f"Coordinates of the second Si atom: {second_si_atom_coordinate}")
+adjusted_coordinate = [coord + delta for coord, delta in zip(second_si_atom_coordinate, [0.025, 0, 0.025])]
+print(f"Adjusted coordinate: {adjusted_coordinate}")
+
+new_coordinates = si_atoms_coordinates.copy()
+index_to_adjust = material.basis.coordinates.get_element_id_by_value(second_si_atom_coordinate)
+new_coordinates[index_to_adjust] = adjusted_coordinate
+material.set_coordinates(new_coordinates)
+```
+
+### 1.4. Run Structure Adjustment
+
+Run the notebook using "Run > Run All Cells". This will:
+1. Load the Si(100) structure
+2. Adjust the position of the specified Si atom
+3. Create a supercell if specified in the parameters
+4. Visualize the adjusted structure
+
+![Adjusted Structure](/images/tutorials/materials/surfaces/si_100_passivation/adjusted-structure.webp "Adjusted Si(100) Structure")
+
+## 2. Passivate the Surface
+
+### 2.1. Open `passivate_slab.ipynb` Notebook
+
+Find and open the `passivate_slab.ipynb` notebook to add hydrogen atoms to the surface.
+
+### 2.2. Set Passivation Parameters
+
+Configure the following parameters for hydrogen passivation:
+
+```python
+# Passivation parameters
+PASSIVANT = "H"  # Chemical symbol for hydrogen
+BOND_LENGTH = 1.46  # Si-H bond length in Angstroms
+SURFACE = "top"  # Passivate only the top surface
+
+# Surface detection parameters
+SHADOWING_RADIUS = 1.8  # In Angstroms
+DEPTH = 0.5  # In Angstroms
+
+# Visualization parameters
+CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]
+```
+
+Key parameters explained:
+- `BOND_LENGTH`: Si-H bond length from literature
+- `SHADOWING_RADIUS`: Controls which atoms are considered surface atoms
+- `DEPTH`: How deep to look for surface atoms
+
+![Passivation Parameters](/images/tutorials/materials/surfaces/si_100_passivation/passivation-params.webp "Passivation Parameters Visualization")
+
+### 2.3. Run Passivation
+
+Run all cells in the notebook. The passivation process will:
+1. Detect surface Si atoms
+2. Add H atoms at the specified bond length
+3. Generate the passivated structure
+
+## 3. Analyze Results
+
+After running both notebooks, examine the final structure:
+
+### 3.1. Surface Structure
+Check that:
+- The adjusted Si atom position is correct
+- Surface reconstruction is maintained
+- H atoms are properly placed above surface Si atoms
+
+### 3.2. Bond Geometry
+Verify:
+- Si-H bond length is ~1.46 Å
+- H atoms are approximately perpendicular to the surface
+- No H atoms are added to subsurface Si atoms
+
+![Final Structure](/images/tutorials/materials/surfaces/si_100_passivation/final-structure.webp "Final H-Passivated Si(100)")
+
+## 4. Save Passivated Structure
+
+The final 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/si_100_passivation.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## Parameter Fine-tuning
+
+To adjust the passivation:
+
+1. Surface Detection:
+   - Increase `SHADOWING_RADIUS` to be more selective about surface atoms
+   - Adjust `DEPTH` to control how deep to look for surface atoms
+
+2. Passivation:
+   - Modify `BOND_LENGTH` for different Si-H distances
+   - Change `SURFACE` to passivate different surfaces
+   - Change `PASSIVANT` to use different passivating species
+
+## References
+
+1. Hansen, U., & Vogl, P. (1998). Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study. Physical Review B, 57(20), 13295–13304.
+
+2. Northrup, J. E. (1991). Structure of Si(100)H: Dependence on the H chemical potential. Physical Review B, 44(3), 1419–1422.
+
+3. Boland, J. J. (1990). Structure of the H‐saturated Si(100) surface. Physical Review Letters, 65(26), 3325–3328.
+
+## Tags
+
+`silicon`, `surface`, `passivation`, `hydrogen`, `Si(100)`, `surface reconstruction`, `Si`, `H`