Merge pull request #264 from Exabyte-io/feature/SOF0-7166

feature/SOF-7166 Add tutorial for Python Transformation

Author: VsevolodX

images/tutorials/interface_with_python/after_run.png

@@ -0,0 +1,107 @@
+# Create an Interface with Python Transformation
+
+In this tutorial, we create an interface between two materials using the Python Transformation feature. Specifically, we will explore the creation of an interface between Graphene and Ni(111).
+
+## Step 0: Open Materials Designer
+
+We start with [opening](../../entities-general/actions/create.md) an instance of the [Materials Designer Interface](../../materials-designer/overview.md) for creating and designing new [Materials structures](../../materials/overview.md) on our platform.
+
+## Step 1: Import Materials
+
+In order to use Graphene and Ni, the user should first [import](../../materials-designer/header-menu/input-output/import.md) sample crystalline structures of the two respective materials into the current Materials Designer session, from the account-owned [collection](../../accounts/collections.md) of materials.
+
+In this example, we will import Graphene and Ni from Standata.
+
+- Open the 'Import from Standata' dialog by going to `Input/Output` > `Import from Standata`.
+<img src="/images/tutorials/interface_with_python/open_standata.png" alt="Open Import from Standata Dialog"/>
+- Select 'Graphene' and 'Ni' from the materials list.
+<img src="/images/tutorials/interface_with_python/import_from_standata.png" alt="Import Gr and Ni from Standata"/>
+- Click 'Submit' to import these materials into the Materials Designer session.
+- Default Material Silicon should be removed from the session.
+<img src="/images/tutorials/interface_with_python/remove_silicon.png" alt="Remove Silicon"/>
+- Graphene and Ni should now be available in the materials list.
+<img src="/images/tutorials/interface_with_python/graphene_and_ni_imported.png" alt="Gr and Ni available in materials list"/>
+
+## Step 2: Use Python Transformation Dialog
+
+Navigate to `Advanced` > `Python Transformation` from the main interface.
+<img src="/images/tutorials/interface_with_python/open_python_transformation.png" alt="Open Python Transformation Dialog"/>
+
+- Choose the transformation titled “Place a 2D materials Layer on a Surface”.
+<img src="/images/tutorials/interface_with_python/select_transformation.png" alt="Select Transformation"/>
+- Select Ni and Graphene from the materials list. The order of selection can be easily accounted for later, but the default expected order is substrate first and then the layer.
+<img src="/images/tutorials/interface_with_python/select_materials.png" alt="Select Materials"/>
+
+!!!warning "Key Considerations"
+    The user is responsible for calculating the appropriate superlattice matrices to ensure realistic interfaces.
+    Excessive straining during the scaling of the layer can result in unrealistic deformations, so use **`scale_layer_to_fit`** cautiously.
+
+In the Python code area:
+
+- Set the substrate index and layer index corresponding to the Selected Materials. In this example, the substrate (Ni) should be at index 0 and the layer (Graphene) at index 1.
+- Customize the **`SETTINGS`** for your specific use case, including:
+    - Miller indices for the substrate and layer, the default value is (1,1,1) for substrate and (0,0,1) for 2D layer.
+    - Vacuum space and number of layers, we can leave it at default values.
+    - The distance between the substrate and the layer in Angstroms.
+    - Superlattice matrices which should be precalculated for a good lattice match. For Graphene on Ni(111) matrix [[1,0], [0,1]] for both materials already provides a good match since lattices are of the same type (hexagonal) and have similar vectors.
+    - Flag **`scale_layer_to_fit`** scales 2D layer superlattice and basis to fit the superlattice of substrate. This is useful when the layer is not a perfect match to the substrate. In this example, we will leave it at default value of `False`. 
+
+<details>
+<summary>Click to view the Python code</summary>
+
+```python
+# Indices identify the substrate and layer from the list of input materials under `materials_in` in globals().
+SUBSTRATE_INDEX = 0
+LAYER_INDEX = 1
+
+SETTINGS = {
+    "substrate_surface": {
+        # Set Miller indices as a tuple for the resulting substrate surface.
+        "miller_indices": (1, 1, 1),
+        # The vacuum space (in Ångströms) added to the surface in the direction perpendicular to the surface.
+        "vacuum": 5,
+        # The number of atomic layers in the resulting substrate.
+        "number_of_layers": 3,
+        # The transformation matrix for the surface. Format is: [[v1x, v1y], [v2x, v2y]].
+        # fmt: off
+        "superlattice_matrix": [
+            [1, 0],
+            [0, 1]
+        ],
+        # fmt: on
+    },
+    "layer_surface": {
+        # Set Miller indices as a tuple for the resulting layer surface: (0,0,1) for 2D material
+        "miller_indices": (0, 0, 1),
+        # The vacuum space (in Ångströms) added to the surface in the direction perpendicular to the surface.
+        "vacuum": 5,
+        # The number of atomic layers in the resulting substrate: 1 for 2D material
+        "number_of_layers": 1,
+        # The transformation matrix for the surface. Format is: [[v1x, v1y], [v2x, v2y]].
+        # fmt: off
+        "superlattice_matrix": [
+            [1, 0],
+            [0, 1]
+        ],
+        # fmt: on
+    },
+    "interface": {
+        "distance": 3.0,
+    },
+    # If True the layer cell and basis vectors will be scaled to fit the substrate cell.
+    # Mind the strain that is introduced by this operation.
+    "scale_layer_to_fit": False,
+}
+```
+</details>
+
+- Click `Run All` to process the transformation.
+- The strain matrix will appear in the output, providing insight into the lattice deformation.
+- `Output Materials` will update with the newly created structure.
+<img src="/images/tutorials/interface_with_python/after_run.png" alt="Results of code execution: strain matrix and output materials"/>
+
+- Review the resulting strain matrix, if satisfied, submit the form to add the interface to your materials collection.
+- Verify the final structure using the Orthographic camera in the 3D Viewer to ensure proper alignment and centrality of the layer over the substrate.
+
+- Resulting Material with unit cell repeated 3 times in A and B directions:
+<img src="/images/tutorials/interface_with_python/resulting_material.png" alt="Graphene on Ni interface"/>