Merge pull request #298 from Exabyte-io/feature/SOF-7510

Feature/SOF-7510 feat: gold nanocluster tutorial

lang/en/docs/tutorials/materials/specific/nanocluster-gold.md

@@ -0,0 +1,171 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Gold Nanoclusters
+
+## Introduction
+
+This tutorial demonstrates the process of creating a gold nanoparticle structures based on the work presented in the following manuscript.
+
+!!!note "Manuscript"
+    > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**,
+    > "Electronic shell structure and chemisorption on gold nanoparticles",
+    > *Phys. Rev. B 84, 245429 (2011)*,
+    > [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}.
+
+We use the [Materials Designer](../../../materials-designer/overview.md) to create gold nanoparticle structures of cuboctahedral and icosahedral shapes as shown in the image below.
+
+
+![Gold Nanoparticles](/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles")
+
+## 1. Load and preview Gold structure
+
+First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Gold material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+![Standata Gold Import](/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp "Standata Gold Import")
+
+Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create gold nanoparticle structures.
+
+## 2. Create cuboctahedra
+
+### 2.1 Launch JupyterLite Session
+
+Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment.
+
+![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog")
+
+### 2.2. Open and modify the notebook
+
+Next, edit `create_cluster_ase.ipynb` notebook to modify the parameters by changing values:
+
+ - `shape = ASENanoparticleShapesEnum.OCTAHEDRON` - the shape of the nanocluster
+ - `parameters = {"length": 5, "cutoff": 2}` - the parameters of the nanocluster according to [ASE Cluster Octahedron](https://wiki.fysik.dtu.dk/ase/ase/cluster/cluster.html#ase.cluster.Octahedron) documentation.
+
+Cuboctahedron shape is achieved by setting parameters of the octahedron to be in relationship: `length = 2 * cutoff + 1`
+
+Copy the content below and adjust the "1.1. Set up slab parameters" cell in the notebook:
+
+```python
+shape = ASENanoparticleShapesEnum.OCTAHEDRON
+parameters = {
+    "length": 5,
+    "cutoff": 2
+}
+```
+
+![Setup for cuboctahedron cluster](/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp "Setup for cuboctahedron cluster")
+
+### 2.3. Run the notebook
+
+Run the notebook by selecting "Run > Run All Cells" from the menu.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+### 2.4. Analyze the Results
+
+After running the notebook, the octahedral gold nanoparticle structure will be created. 
+
+The user will be able to visualize the created structure and download the corresponding files.
+
+For better view of the solid symmetry rotation of image might be needed like `"rotation": "45y,45x"` for the cuboctahedron.
+
+![Cuboctahedron Gold Nanocluster](/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp "Cuboctahedron Gold Nanocluster")
+
+### 2.5. Pass the Material to the Materials Designer
+
+After reviewing the results, the user can pass the material to Materials Designer for further analysis.
+
+![Final Material](/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp "Final Material")
+
+Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format.
+
+## 3. Create clusters with other shapes and sizes
+
+### 3.1. Repeat the steps above
+
+Repeat the steps above to create gold nanoparticle structures with other shapes and sizes.
+
+To create the rest of the structures set the `shape` and other parameters accordingly:
+
+For Cuboctahedron with 147 atoms:
+
+```python
+shape = ASENanoparticleShapesEnum.OCTAHEDRON
+parameters = {
+    "length": 7,
+    "cutoff": 3
+}
+```
+
+![Cuboctahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp "Cuboctahedron 147")
+
+For Cuboctahedron with 309 atoms:
+
+```python
+shape = ASENanoparticleShapesEnum.OCTAHEDRON
+parameters = {
+    "length": 9,
+    "cutoff": 4
+}
+```
+
+![Cuboctahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp "Cuboctahedron 309")
+
+For Icosahedron with 55 atoms:
+
+```python
+shape = ASENanoparticleShapesEnum.ICOSAHEDRON
+parameters = {
+    "noshells": 3
+}
+```
+
+![Icosahedron 55](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp "Icosahedron 55")
+
+For Icosahedron with 147 atoms:
+
+```python
+shape = ASENanoparticleShapesEnum.ICOSAHEDRON
+parameters = {
+    "noshells": 4
+}
+```
+
+![Icosahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp "Icosahedron 147")
+
+For Icosahedron with 309 atoms:
+
+```python
+shape = ASENanoparticleShapesEnum.ICOSAHEDRON
+parameters = {
+    "noshells": 5
+}
+```
+
+![Icosahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp "Icosahedron 309")
+
+## Interactive JupiterLite Notebook
+
+The interactive JupyterLite notebook for creating Gold Nanoclusters can be accessed below. To run the notebook, click on the "Run All" button.
+
+{% with origin_url=config.extra.jupyterlite.origin_url %}
+{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
+{% with notebook_name='specific_examples/nanocluster_gold.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**,
+   "Electronic shell structure and chemisorption on gold nanoparticles",
+   *Phys. Rev. B 84, 245429 (2011)*,
+   [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}.
+
+
+## Tags
+
+`gold`, `cluster`, `nanoparticle`, `cuboctahedron`, `icosahedron`

mkdocs.yml

@@ -227,6 +227,7 @@ nav:
                 - Twisted Bilayer MoS2 commensurate lattices:                tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md
                 - Adatom Surface Defects on Graphene:                          tutorials/materials/specific/defect-surface-adatom-graphene.md
                 - H-Passivated Silicon Nanowire:                                      tutorials/materials/specific/passivation-edge-silicon-nanowire.md
+                - Gold Nanoclusters:                                             tutorials/materials/specific/nanocluster-gold.md
 
 # COMMON UI COMPONENTS
     - Interface Components: