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Merge pull request #306 from Exabyte-io/feature/SOF-7512
feature/SOF-7512 Step Pt tutorial
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lang/en/docs/tutorials/materials/specific/defect-surface-step-platinum.md
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| # YAML header | ||
| render_macros: true | ||
| --- | ||
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| # Terrace Steps on Platinum (111) Surface. | ||
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| ## Introduction. | ||
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| This tutorial demonstrates two different approaches to creating terrace steps on platinum surfaces, based on the work presented in the following manuscript: | ||
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| !!!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](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. | ||
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| We will focus on creating platinum surface with terrace steps, as shown in FIG. 1. B: | ||
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| We will demonstrate two methods: | ||
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| 1. Creating a Pt(211) surface which inherently contains steps | ||
| 2. Creating a terrace step on a Pt(111) surface using the TerraceSlabDefectBuilder | ||
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| ## 1. Method I: Create Pt(211) Surface. | ||
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| - Creates a surface with inherent steps | ||
| - Smaller unit cell | ||
| - Fixed step geometry | ||
| - Good for studying specific crystal faces | ||
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| ### 1.1. Import Base Material. | ||
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| First, we need to import the platinum material from Standata: | ||
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| 1. Navigate to [Materials Designer](../../../materials-designer/overview.md) | ||
| 2. Click on "Input/Output" menu | ||
| 3. Select "Import from Standata" | ||
| 4. Search for "Pt" and select the bulk platinum material | ||
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| ### 1.2. Launch JupyterLite Environment. | ||
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| Select "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" to open JupyterLite. | ||
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| ### 1.3. Configure Slab Parameters. | ||
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| Open a `create_slab.ipynb` notebook and set up the slab parameters in the "1.1. Set up notebook" cell: | ||
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| ```python | ||
| MATERIAL_NAME = "Pt" | ||
| MILLER_INDICES = (2, 1, 1) | ||
| THICKNESS = 6 # in atomic layers | ||
| VACUUM = 10.0 # in angstroms | ||
| XY_SUPERCELL_MATRIX = [[1, 0], [0, 1]] | ||
| USE_ORTHOGONAL_Z = True | ||
| USE_CONVENTIONAL_CELL = True | ||
| TERMINATION_INDEX = 0 | ||
| ``` | ||
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| These parameters will create a Pt(211) surface with: | ||
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| - 6 atomic layers thickness | ||
| - 10 Å vacuum region | ||
| - Orthogonal z-axis | ||
| - Using the conventional unit cell | ||
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| ### 1.4. Create the Slab. | ||
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| Run the notebook by clicking `Run` > `Run All` in the top menu. The notebook will generate the Pt(211) surface. | ||
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| ## 2. Method II: Create Terrace Step Defect on Pt(111). | ||
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| - More flexible control over step placement | ||
| - Larger surface area available | ||
| - Customizable terrace height | ||
| - Better for complex step arrangements | ||
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| ### 2.1. Open Terrace Defect Notebook. | ||
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| First, open `create_terrace_defect.ipynb`and select Pt as the input material. | ||
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| ### 2.2. Configure Terrace Parameters. | ||
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| `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) | ||
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| ```python | ||
| # Material selection | ||
| # Which material to use from input list | ||
| MATERIAL_INDEX = 0 | ||
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| # Terrace parameters: | ||
| # Normal vector describing a plane that cuts the terrace from added layers (Miller indices) | ||
| CUT_DIRECTION = [0,1,1] | ||
| # Point the cutting plane passes through, in crystal coordinates | ||
| PIVOT_COORDINATE = [0.5, 0.5, 0.5] | ||
| # Height of terrace in atomic layers | ||
| NUMBER_OF_ADDED_LAYERS = 1 | ||
| # Use cartesian instead of crystal coordinates | ||
| USE_CARTESIAN_COORDINATES = False | ||
| # Rotate to match periodic boundary conditions | ||
| ROTATE_TO_MATCH_PBC = True | ||
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| # 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_z": True, | ||
| "xy_supercell_matrix": [[2, 0], [0, 2]] | ||
| } | ||
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| # Visualization parameters | ||
| SHOW_INTERMEDIATE_STEPS = True | ||
| # Structure repeat in view | ||
| CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] | ||
| ``` | ||
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| ### 2.3. Create the Terrace. | ||
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| Run the notebook to create the Pt(111) surface with a terrace step. | ||
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| The same material with repetitions: | ||
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| The user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. | ||
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| ## Interactive JupyterLite Notebook. | ||
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| The following JupyterLite notebook demonstrates both approaches. Select "Run" > "Run All Cells" to execute the notebook. | ||
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| {% 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 %} | ||
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| ## References. | ||
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| 1. 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](https://doi.org/10.1016/s0039-6028(02)01908-8){:target='_blank'}. | ||
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| ## Tags. | ||
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| `surface`, `platinum`, `terrace`, `step`, `slab`, `Pt(211)`, `Pt(111)` |
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