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Passivation of Silicon (100) Surface.

1. Introduction

This tutorial demonstrates how to passivate a reconstructed silicon (100) surface with hydrogen atoms, following the methodology described in the literature.

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. 123

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

Si(100) H-Passivated Surface

2. Obtain the Silicon (100) Surface Structure

2.1. Load Base Material

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

Si(100) Structure

2.2. Launch JupyterLite Session

Select the "Advanced > JupyterLite Transformation" menu item to launch the JupyterLite environment.

2.3. 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.:

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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:

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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

2.4. 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

3. Passivate the Surface

3.1. Open passivate_slab.ipynb Notebook

Find and open the passivate_slab.ipynb notebook to add hydrogen atoms to the surface.

3.2. Set Passivation Parameters

Configure the following parameters for hydrogen passivation:

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# 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.

Passivation Parameters

3.3. 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

4. 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

5. 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

6. Interactive JupyterLite Notebook

The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells".

7. Parameter Fine-tuning

To adjust the passivation:

  1. Surface Detection:

  2. Increase SHADOWING_RADIUS to be more selective about surface atoms

  3. Adjust DEPTH to control how deep to look for surface atoms

  4. Passivation:

  5. Modify BOND_LENGTH for different Si-H distances

  6. Change SURFACE to passivate different surfaces
  7. Change PASSIVANT to use different passivating species

8. References

  1. U. Hansen and P. Vogl. Hydrogen passivation of silicon surfaces: a classical molecular-dynamics study. Physical Review B, 57(20):13295–13304, 1998. URL: https://doi.org/10.1103/physrevb.57.13295. ↩

  2. J. E. Northrup. Structure of si(100)h: dependence on the h chemical potential. Physical Review B, 44(3):1419–1422, 1991. URL: https://doi.org/10.1103/physrevb.44.1419. ↩

  3. J. J. Boland. Structure of the h‐saturated si(100) surface. Physical Review Letters, 65(26):3325–3328, 1990. URL: https://doi.org/10.1103/physrevlett.65.3325. ↩