Merge pull request #292 from Exabyte-io/feature/SOF-7414

Feature/SOF-7414 Adatom on graphene tutorial

lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md

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+---
+# YAML header
+render_macros: true
+---
+
+# Adatom on Graphene Surface
+
+## Introduction
+
+This tutorial demonstrates the process of creating a graphene structure with an adatom on the surface based on the work presented in the following manuscript.
+
+!!!note "Manuscript"
+    **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, 
+    "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008
+    [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}.
+
+We use the [Materials Designer](../../../materials-designer/overview.md) to create a graphene structure with a metal adatom on the surface.
+
+The image shows the adatom on the graphene surface.
+
+![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/me_adatom_on_hollow_graphene.webp "Fig. 1. Adatom on Graphene Surface")
+
+## 1. Load and preview Graphene structure
+
+First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import")
+
+Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a graphene structure with an adatom on the surface.
+
+## 2. Add Li adatom
+
+### 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_adatom_defect.ipynb` notebook to modify the parameters by changing values:
+
+ - `CHEMICAL_ELEMENT = "Li"` - the element of the adatom
+
+ - `APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]` - position that corresponds to the hollow site in the center of the cell
+
+ - `DISTANCE_Z = 1.71` - the distance between the adatom and the graphene surface (from the Table 1 in the manuscript)
+
+ - `MILLER_INDICES = (0,0,1)` - the Miller indices of the plane of Graphene
+
+ - `SLAB_THICKNESS = 1` - the thickness of the Graphene monolayer slab
+
+ - `SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]]` - the supercell matrix
+
+Copy the content below and adjust the "1.1. Set up slab parameters" cell in the notebook:
+
+```python
+DEFECT_TYPE = "adatom"  
+PLACEMENT_METHOD = "equidistant"
+CHEMICAL_ELEMENT = "Li"  
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]  
+USE_CARTESIAN_COORDINATES = False 
+DISTANCE_Z = 1.71
+
+# Slab parameters
+MILLER_INDICES = (0, 0, 1)  
+SLAB_THICKNESS = 1  
+VACUUM = 6 
+SUPERCELL_MATRIX = [[4, 0, 0], [0, 4, 0], [0, 0, 1]] 
+```
+
+### 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 Graphene structure with a Li adatom on the surface will be created.
+
+The user will be able to visualize the created structure and download the corresponding files.
+
+![Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-li.webp "Li Adatom on Graphene Surface")
+
+### 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/defects/defect-surface-adatom-graphene/wave-result-li.webp "Li Adatom on Graphene Surface")
+
+Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format.
+
+## 3. Add other metal adatoms
+
+### 3.1. Repeat the steps above
+
+To create a Graphene structure with other metal adatoms, repeat the steps above by changing the `CHEMICAL_ELEMENT`, `APPORXIMATE_POSITION_ON_SURFACE`, and `DISTANCE_Z` parameters according to he values in the table 1 of the manuscript.
+Notice, that some of the adatoms have more favorable position on top or bridge sites.
+
+For example, to create a Graphene structure with a Na adatom, adjust the parameters as follows:
+
+```python
+CHEMICAL_ELEMENT = "Na"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.28
+```
+
+![Na Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-na.webp "Na Adatom on Graphene Surface")
+
+For K adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "K"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.60
+```
+
+![K Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-k.webp "K Adatom on Graphene Surface")
+
+
+For Ca adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "Ca"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.29
+```
+
+![Ca Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ca.webp "Ca Adatom on Graphene Surface")
+
+
+For Al adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "Al"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.13
+```
+
+![Al Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-al.webp "Al Adatom on Graphene Surface")
+
+
+For Ga adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "Ga"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.20
+```
+
+![Ga Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ga.webp "Ga Adatom on Graphene Surface")
+
+
+For In adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "In"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 2.45
+```
+
+![In Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-in.webp "In Adatom on Graphene Surface")
+
+
+For Sn adatom on top site:
+```python
+CHEMICAL_ELEMENT = "Sn"
+APPROXIMATE_POSITION_ON_SURFACE = [7/12, 5/12]
+DISTANCE_Z = 2.82
+```
+
+![Sn Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-sn.webp "Sn Adatom on Graphene Surface")
+
+
+For Ti adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "Ti"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 1.80
+```
+
+![Ti Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-ti.webp "Ti Adatom on Graphene Surface")
+
+For Fe adatom on hollow site:
+```python
+CHEMICAL_ELEMENT = "Fe"
+APPROXIMATE_POSITION_ON_SURFACE = [0.5, 0.5]
+DISTANCE_Z = 1.53
+```
+
+![Fe Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-fe.webp "Fe Adatom on Graphene Surface")
+
+
+For Pd adatom on bridge site:
+```python
+CHEMICAL_ELEMENT = "Pd"
+APPROXIMATE_POSITION_ON_SURFACE = [3/8, 1/2]
+DISTANCE_Z = 2.21
+```
+
+
+![Pd Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-pd.webp "Pd Adatom on Graphene Surface")
+
+
+For Au adatom on top site:
+```python
+CHEMICAL_ELEMENT = "Au"
+APPROXIMATE_POSITION_ON_SURFACE = [7/12, 5/12]
+DISTANCE_Z = 2.69
+```
+
+![Au Adatom on Graphene Surface](/images/tutorials/materials/defects/defect-surface-adatom-graphene/jl-result-preview-au.webp "Au Adatom on Graphene Surface")
+
+## Interactive JupiterLite Notebook
+
+The interactive JupyterLite notebook for creating Graphene structures with metal adatoms 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/defect_surface_adatom_graphene.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, 
+    "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008
+    [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}.
+
+## Tags
+
+`adatom`, `graphene`, `metal`, `surface`, `defect`

mkdocs.yml

@@ -222,6 +222,7 @@ nav:
                 - Island Surface Defect Formation in TiN:                     tutorials/materials/specific/defect-surface-island-titanium-nitride.md
                 - Twisted Bilayer h-BN nanoribbons:                       tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md
                 - 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
 
 # COMMON UI COMPONENTS
     - Interface Components: