Merge pull request #312 from Exabyte-io/feature/SOF-7528

Feature/SOF-7528 Pt adatoms island on MoS2 tutorial

lang/en/docs/tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md

@@ -0,0 +1,181 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Pt Nanoparticles on MoS2(001) Surface via Adatoms
+
+## Introduction
+
+This tutorial demonstrates how to create a platinum island on MoS2 by sequentially adding Pt adatoms, following the methodology described in the literature.
+
+!!!note "Manuscript"
+    Saidi, W. A.
+    "Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface"
+    Crystal Growth & Design, 15(2), 642–652. (2015)
+    [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}.
+
+We will recreate the Pt island structure shown in Figure 4b:
+
+![Pt Island on MoS2](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/0-figure-from-manuscript.webp "Pt island formation on MoS2")
+
+## 1. Create MoS2 Substrate
+
+### 1.1. Load Base Material
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 2D material from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+### 1.2. Launch JupyterLite Session
+
+Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment.
+
+### 1.3. Open `create_adatom_defect.ipynb` Notebook
+
+Find and open the `create_adatom_defect.ipynb` notebook. Select MoS2 as input material.
+
+## 2. Configure and Create Structure
+
+### 2.1. Set Parameters
+
+Set up the slab and defect parameters in the notebook:
+
+```python
+# Slab parameters
+MILLER_INDICES = (0, 0, 1)  # MoS2 basal plane
+SLAB_THICKNESS = 1  # Single layer
+VACUUM = 10.0  # in Angstrom
+SUPERCELL_MATRIX = [[3, 0, 0], [0, 3, 0], [0, 0, 1]]  # 3x3 supercell
+
+# Defect configurations for all Pt atoms
+DEFECT_CONFIGS = [
+    {
+        "defect_type": "adatom",
+        "placement_method": "coordinate",
+        "chemical_element": "Pt",
+        "position_on_surface": [5/9, 4/9],  # First Pt: atop central Mo
+        "distance_z": 1.2, # Distance from surface S atoms
+        "use_cartesian_coordinates": False
+    },
+    {
+        "defect_type": "adatom",
+        "placement_method": "coordinate",
+        "chemical_element": "Pt",
+        "position_on_surface": [2/9, 4/9],  # Second Pt: next clockwise atop Mo
+        "distance_z": 1.2, # Distance from surface S atoms
+        "use_cartesian_coordinates": False
+    },
+    {
+        "defect_type": "adatom",
+        "placement_method": "coordinate",
+        "chemical_element": "Pt",
+        "position_on_surface": [5/9, 7/9],  # Third Pt: next clockwise atop Mo
+        "distance_z": 1.2, # Distance from surface S atoms
+        "use_cartesian_coordinates": False
+    },
+    {
+        "defect_type": "adatom",
+        "placement_method": "coordinate",
+        "chemical_element": "Pt",
+        "position_on_surface": [4/9, 5/9],  # Fourth Pt: centered atop S
+        "distance_z": 1.6,  # Distance between Pt atom layers, in Angstrom
+        "use_cartesian_coordinates": False
+    }
+]
+```
+
+Key parameters explained:
+
+- Base layer Pt atoms (first three configs):
+
+  * Positioned atop Mo atoms in a triangular arrangement
+  * Height 1.2 Å from surface S atoms to achieve separation from Mo atoms of 2.8 A -- from publication
+- Top Pt atom (fourth config):
+
+  * Centered above the triangle, atop S atom
+  * Height 1.6 Å from base Pt atoms (as they become the new surface layer)
+
+- `distance_z` sets the distance along the z-axis from the adatom to the topmost atom directly below it
+
+![Adatoms Setup](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/1-jl-setup-nb.webp "Pt adatoms setup")
+
+### 2.2. Run the Notebook
+
+Execute the notebook to create the Pt island structure on MoS2 by selecting "Run" > "Run All Cells" from the JupyterLite menu.
+
+![Results Preview](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/2-jl-result-preview.webp "Pt island results preview")
+
+### 2.3. Pass the Result to Materials Designer
+
+The result can be passed to Materials Designer for visualization and viewed from the top:
+
+![Complete Island](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/4-wave-result-top.webp "Complete Pt island structure")
+
+And from the side:
+
+![Complete Island, side view](/images/tutorials/materials/defects/defect_point_adatom_island_mos2_pt/5-wave-result-side.webp "Complete Pt island structure, side view")
+
+## 3. Analyze the Structure
+
+After adding all Pt atoms, verify the following:
+
+### 3.1. Base Layer Geometry
+
+- Three Pt atoms should form a triangular base
+- Each base Pt should be positioned atop Mo atoms
+- Distance from surface S atoms should be ~1.2 Å
+- Relaxation is needed to achieve the exact geometry from the publication, can be performed elsewhere
+
+### 3.2. Top Atom Position
+
+- Fourth Pt should be centered above the triangle
+- Position should be approximately above a surface S atom
+- Height should be ~2.8 Å from surface (1.6 Å from base Pt atoms)
+
+## 4. Save the Structure
+
+The final structure will be automatically passed back to Materials Designer where user can:
+
+1. Save it on the platform
+2. Export it in various formats
+3. Use it for further transformations
+
+## 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/defect_point_adatom_island_mos2_pt.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## Parameter Fine-tuning
+
+To adjust the island structure:
+
+1. Base Layer:
+   - Adjust `APPROXIMATE_POSITION_ON_SURFACE` to shift Pt positions
+   - Modify `DISTANCE_Z` to change height from surface
+
+2. Top Atom:
+   - Adjust position to change island shape
+   - Modify height to change Pt-Pt spacing
+
+## References
+
+1. Saidi, W. A. (2015). Density Functional Theory Study of Nucleation and Growth of Pt Nanoparticles on MoS2(001) Surface. Crystal Growth & Design, 15(2), 642–652. [DOI: 10.1021/cg5013395](https://doi.org/10.1021/cg5013395){:target='_blank'}.
+
+2. Jiao, M., Song, W., Qian, H.-J., Wang, Y., Wu, Z., Irle, S., & Morokuma, K. (2016). QM/MD studies on graphene growth from small islands on the Ni(111) surface. Nanoscale, 8(5), 3067–3074. doi:10.1039/c5nr07680c  [DOI: 10.1039/c5nr07680c](https://doi.org/10.1039/c5nr07680c){:target='_blank'}.
+
+3. Kristen A. Fichthorn and Matthias Scheffler, "Island Nucleation in Thin-Film Epitaxy: A First-Principles Investigation", Phys. Rev. Lett. 84, 5371 (2000). [DOI: 10.1103/PhysRevLett.84.5371](https://doi.org/10.1103/PhysRevLett.84.5371){:target='_blank'}.
+
+4. Jörg Neugebauer and Matthias Scheffler, "Mechanisms of island formation of alkali-metal adsorbates on Al(111)", Phys. Rev. Lett. 71, 577 (1993). [DOI: 10.1103/PhysRevLett.71.577](https://doi.org/10.1103/PhysRevLett.71.577){:target='_blank'}.
+
+5. Mahbube Hortamani, Peter Kratzer, and Matthias Scheffler, "Density-functional study of Mn monosilicide on the Si(111) surface:
+Film formation versus island nucleation", Phys. Rev. B 76, 235426 (2007). [DOI: 10.1103/PhysRevB.76.235426](https://doi.org/10.1103/PhysRevB.76.235426){:target='_blank'}.
+
+## Tags
+
+`MoS2`, `platinum`, `adatoms`, `surface science`, `2D materials`, `nanoparticles`, `Mo`, `S`, `Pt`

mkdocs.yml

@@ -241,6 +241,7 @@ nav:
                 - Grain Boundary in FCC Metals (Copper):                                tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md
                 - Grain Boundary (2D) in h-BN:                                   tutorials/materials/specific/grain-boundary-2d-boron-nitride.md
                 - Gr/Ni(111) Interface Optimization:                                     tutorials/materials/specific/optimize-film-position-graphene-nickel-interface.md
+                - Pt Adatoms Island on MoS2:                                    tutorials/materials/specific/defect_point_adatom_island_mos2_pt.md
 
 # COMMON UI COMPONENTS
     - Interface Components: