Merge pull request #311 from Exabyte-io/feature/SOF-7527

feature/SOF-7527 Passivation Si(100) tutorial

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

@@ -0,0 +1,185 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Passivation of Silicon (100) Surface.
+
+## Introduction.
+
+This tutorial demonstrates how to passivate a reconstructed silicon (100) 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/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
+
+## 1. Obtain the Silicon (100) 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).
+
+![Si(100) Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp "Si(100) Structure")
+
+### 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`, select input material as the Si(100) structure, and set the supercell parameters in 1.1.:
+
+```python
+SUPERCELL_MATRIX = [
+    [1, 0, 0], 
+    [0, 1, 0], 
+    [0, 0, 1]
+] 
+
+# or use the scaling factor.
+SCALING_FACTOR = None # [3, 3, 1].
+```
+
+Also add to the "Get input materials" cell the following code to adjust the Si atom position:
+
+```python
+from utils.jupyterlite import get_materials
+materials = get_materials(globals())
+material = materials[0]
+
+# Find coordinates of the Si atoms, list in descending order, and change the 2nd one from the top
+si_atoms_coordinates = [coordinate for coordinate in slab.basis.coordinates.values]
+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 = slab.basis.coordinates.get_element_id_by_value(second_si_atom_coordinate)
+new_coordinates[index_to_adjust] = adjusted_coordinate
+slab.set_coordinates(new_coordinates)
+```
+
+![Supercell Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization")
+
+### 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/passivation/passivation_surface_silicon/3-wave-adjusted-material.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, set to be below the distance between top Si atoms pair.
+- `SURFACE`: Passivate only the top surface.
+- `DEPTH`: How deep to look for surface atoms, set to include only top Si atoms.
+
+![Passivation Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.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
+
+![Passivated Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp "H-Passivated Si(100) Structure")
+
+## 3. Analyze Results.
+
+After running both notebooks, examine the final structure:
+
+Check that:
+
+- The adjusted Si atom position is correct
+- Surface reconstruction is maintained
+- H atoms are properly placed above surface Si atoms
+
+![Final Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp "Final H-Passivated Si(100)")
+
+## 4. Save the Results.
+
+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/passivation_surface_silicon_surface.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`

mkdocs.yml

@@ -229,6 +229,7 @@ nav:
                 - Twisted Bilayer MoS2 commensurate lattices:                tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md
                 - 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
+                - H-Passivated Silicon (100) Surface:                           tutorials/materials/specific/passivation-surface-silicon-surface.md
                 - Gold Nanoclusters:                                             tutorials/materials/specific/nanocluster-gold.md
                 - SrTiO3 Slab:                                                  tutorials/materials/specific/slab-strontium-titanate.md
                 - Interface between Graphene and h-BN:                          tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md