passivation-surface-silicon.md

tags	hide	render_macros
silicon surface passivation hydrogen Si(100) surface reconstruction Si H	tags	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{:target='_blank'}. [@Hansen1998; @Northrup1991; @Boland1990]

We will recreate the passivated surface structure shown in Fig. 8:

1. Obtain the Silicon (100) Surface Structure.

1.1. Load Base Material.

Navigate to Materials Designer and import the reconstructed Si(100) surface from Standata.

1.2. Launch JupyterLite Session.

Select the "Advanced > JupyterLite Transformation" 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.:

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:

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)

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

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:

# Material selection
MATERIAL_INDEX = 0  # Which material to use from input list

# Passivation parameters
PASSIVANT = "H"  # Chemical symbol of passivating atom
BOND_LENGTH = 1.46  # Distance from surface to passivant, in Angstroms
SURFACE = "top"  # Which surface to passivate: "top", "bottom" or "both"

# Surface detection parameters
SHADOWING_RADIUS = 1.8  # Radius to exclude subsurface atoms, in Angstroms
DEPTH = 0.5  # How deep to look for surface atoms, in Angstroms

BYPASS_SLAB_CREATION = False  # If True, will use input material directly

# Slab parameters for creating a new slab if previous option is set to True
DEFAULT_SLAB_PARAMETERS = {
    "miller_indices": (0, 0, 1),
    "thickness": 3,
    "vacuum": 10.0,
    "USE_ORTHOGONAL_C": True,
    "xy_supercell_matrix": [[3, 0], [0, 3]]
}

# Visualization parameters
SHOW_INTERMEDIATE_STEPS = True
CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]  # Structure repeat in view

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.

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:

Check that:

• The adjusted Si atom position is correct
• Surface reconstruction is maintained
• H atoms are properly placed above surface Si atoms

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.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.