defect-surface-step-platinum.md

tags	hide	render_macros
surface platinum terrace step slab Pt(211) Pt(111)	tags	true

Terrace Steps on Platinum (111) Surface.

Introduction.

This tutorial demonstrates two different approaches to creating terrace steps on platinum surfaces, based on the work presented in the following manuscript:

!!!note "Manuscript" Šljivančanin, Ž., & Hammer, B., "Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory." Surface Science, 515(1), 235–244. DOI: 10.1016/s0039-6028(02)01908-8{:target='_blank'}. [@Sljivancanin2002]

We will focus on creating platinum surface with terrace steps, as shown in FIG. 1. B:

We will demonstrate two methods:

1. Creating a Pt(211) surface which inherently contains steps
2. Creating a terrace step on a Pt(111) surface using the TerraceSlabDefectBuilder

1. Method I: Create Pt(211) Surface.

• Creates a surface with inherent steps
• Smaller unit cell
• Fixed step geometry
• Good for studying specific crystal faces

1.1. Import Base Material.

First, we need to import the platinum material from Standata:

1. Navigate to Materials Designer
2. Click on "Input/Output" menu
3. Select "Import from Standata"
4. Search for "Pt" and select the bulk platinum material

1.2. Launch JupyterLite Environment.

Select "Advanced > JupyterLite Transformation" to open JupyterLite.

1.3. Configure Slab Parameters.

Open a create_slab.ipynb notebook and set up the slab parameters in the "1.1. Set up notebook" cell:

# Enable interactive selection of terminations via UI prompt
IS_TERMINATIONS_SELECTION_INTERACTIVE = False 

MILLER_INDICES = (2, 1, 1)
THICKNESS = 6  # in atomic layers
VACUUM = 10.0  # in angstroms
XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]]
USE_ORTHOGONAL_C = True
USE_CONVENTIONAL_CELL = True

# Stoichiometric formula of the slab termination to be used.
SLAB_TERMINATION_FORMULA = None
# if None, the index of all possible terminations will be used
TERMINATION_INDEX = 0

These parameters will create a Pt(211) surface with:

• 6 atomic layers thickness
• 10 Å vacuum region
• Orthogonal z-axis
• Using the conventional unit cell

1.4. Create the Slab.

Run the notebook by clicking Run > Run All in the top menu. The notebook will generate the Pt(211) surface.

2. Method II: Create Terrace Step Defect on Pt(111).

• More flexible control over step placement
• Larger surface area available
• Customizable terrace height
• Better for complex step arrangements

2.1. Open Terrace Defect Notebook.

First, open create_terrace_defect.ipynband select Pt as the input material.

2.2. Configure Terrace Parameters.

CUT_DIRECTION = [0, 1, 1] -- Normal vector for cutting plane, which will give a perfect periodic match along x and a match along y after rotation. DEFAULT_SLAB_PARAMETERS["miller_indices"] = (1, 1, 1) -- Miller indices for Pt(111) surface DEFAULT_SLAB_PARAMETERS["xy_supercell_matrix"] = [[2, 0], [0, 2]] -- Supercell matrix for final structure (which will effectively control the size of the terrace)

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

# Terrace parameters
CUT_DIRECTION = [0, 1, 1]  # Normal vector describing a plane that cuts the terrace from added layers (Miller indices)
PIVOT_COORDINATE = [0.5, 0.5, 0.5]  # Point the cutting plane passes through, in crystal coordinates
NUMBER_OF_ADDED_LAYERS = 1  # Height of terrace in atomic layers
USE_CARTESIAN_COORDINATES = False  # Use cartesian instead of crystal coordinates
ROTATE_TO_MATCH_PBC = True  # Rotate to match periodic boundary conditions

# Slab parameters for creating a new slab if provided material is not a slab
DEFAULT_SLAB_PARAMETERS = {
    "miller_indices": (1, 1, 1),
    "thickness": 6,
    "vacuum": 10.0,
    "USE_ORTHOGONAL_C": True,
    "xy_supercell_matrix": [[2, 0], [0, 2]]
}

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

2.3. Create the Terrace.

Run the notebook to create the Pt(111) surface with a terrace step.

The same material with repetitions:

The user can save or download the material in Material JSON format or POSCAR format.

Interactive JupyterLite Notebook.

The following JupyterLite notebook demonstrates both approaches. Select "Run" > "Run All Cells" to execute the notebook.

{% with origin_url=config.extra.jupyterlite.origin_url %} {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} {% with notebook_name='specific_examples/defect_surface_step_platinum.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} {% endwith %} {% endwith %}

References.