Merge pull request #297 from Exabyte-io/feature/SOF-7508

feat: add tutorial on passivated nanowire

lang/en/docs/tutorials/materials/specific/passivation-edge-silicon-nanowire.md

@@ -0,0 +1,209 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Passivation of Silicon Nanowire
+
+## Introduction
+
+This tutorial demonstrates the process of creating passivated silicon nanowires based on the work presented in the following manuscript, where the chemical gap tuning in silicon nanowires is studied.
+
+
+!!!note "Manuscript"
+    B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim,
+    "Theoretical study of the chemical gap tuning in silicon nanowires"
+    Phys. Rev. B 76, 035305 (2007)
+    DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305)
+
+
+We will focus on creating silicon nanowires with hydrogen passivation from FIG. 1.
+
+Specifically, the material from FIG. 1. of the publication:
+
+![Passivated Silicon nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/0-figure-from-manuscript.webp "Passivated Silicon nanowire, FIG. 1.")
+
+
+## 1. Create Silicon Nanowire
+
+### 1.1. Load Silicon Material
+
+Since we're using Silicon, it can be already loaded as the default material and we can skip this step.
+
+Otherwise, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the silicon material from the [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.
+
+![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog")
+
+### 1.3. Open `create_nanowire_custom_shapeipynb` notebook
+
+Find `create_nanowire_custom_shape.ipynb` in the list of notebooks and click/double-click open it.
+
+### 1.4. Open and modify the notebook
+
+Next, we need to create a nanowire wit ha custom shape.
+
+We'll specify the orientation of the nanowire with Miller indices of `(1,1,0)` as described in the manuscript.
+
+Then we'll define a supercell matrix to add enough of material to cut the nanowire from: 
+
+`[[3, 0, 0], [0, 2, 0], [0, 0, 2]]`.
+
+Finally, we'll define a custom coordinate condition to create a rhombus-shaped nanowire with coordinates of the vertices corresponding to the corners of the rhombus.
+
+The vertices of the rhombus are defined as follows:
+
+Bottom:`[0.5, 0.2, 0]`, 
+
+Left:`[0, 0.5, 0]`,
+
+Top:`[0.5, 1, 0]`,
+
+Right:`[1, 0.5, 0]`
+
+
+For that, edit `create_nanowire_custom_shape.ipynb` notebook to modify the parameters by adding the following content to the "1.1. Set up nanowire parameters" cell:
+
+```python
+from typing import List
+import numpy as np
+from mat3ra.made.tools.utils.coordinate import CoordinateCondition
+# Flag to use Cartesian coordinates for the center and radii
+USE_CARTESIAN_COORDINATES = False 
+
+# Miller indices of the nanowire direction
+MILLER_INDICES= (1,1,0)  
+# Supercell matrix to cut the cylinder from
+SUPERCELL_MATRIX = [[3, 0, 0], [0, 2, 0], [0, 0, 2]] 
+# Vacuum thickness on the sides in Angstroms
+VACUUM = 10.0 
+ALIGN_ALONG_X = False
+
+# Custom Coordinate Condition for
+class CustomCoordinateCondition(CoordinateCondition):
+    vertices: List[List[float]]
+
+    def condition(self, coordinate: List[float]) -> bool:
+        coord = np.array(coordinate)
+        v0, v1, v2, v3 = np.array(self.vertices)
+        vec0 = v1 - v0
+        vec1 = v2 - v1
+        vec2 = v3 - v2
+        vec3 = v0 - v3
+
+        # Calculate cross products
+        cross0 = np.cross(vec0, coord[:2] - v0[:2])
+        cross1 = np.cross(vec1, coord[:2] - v1[:2])
+        cross2 = np.cross(vec2, coord[:2] - v2[:2])
+        cross3 = np.cross(vec3, coord[:2] - v3[:2])
+
+        # Check if point is inside the rhombus
+        return (np.all(cross0 >= 0) and np.all(cross1 >= 0) and \
+                np.all(cross2 >= 0) and np.all(cross3 >= 0)) or \
+               (np.all(cross0 <= 0) and np.all(cross1 <= 0) and \
+                np.all(cross2 <= 0) and np.all(cross3 <= 0))
+
+# Define the vertices of the rhombus
+vertices = [
+    [0.5, 0.2, 0],
+    [0, 0.5, 0],
+    [0.5, 1, 0],
+    [1, 0.5, 0]
+]
+
+condition = CustomCoordinateCondition(vertices=vertices).condition
+```
+
+## 1.5. Run the Notebook and use the Material
+
+Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and wait for the results to appear.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+After running the notebook and submitting the material, the user will be able to visualize the structure of Silicon Nanowire.
+
+![Silicon Nanowire](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/3-silicon-nanowire.webp "Silicon Nanowire")
+
+## 2. Passivate with Hydrogen
+
+### 2.1. Setup the Passivation
+
+Open JupyterLite Session again and select Silicon Nanowire material for Input Materials.
+
+Next, we need to passivate the silicon nanowire with hydrogen atoms.
+
+Open the `passivate_edge.ipynb` notebook and set:
+
+`BOND_LENGTH = 1.46` -- Si-H bond length in Angstroms,
+
+`COORDINATION_THRESHOLD = 3` -- Silicon that has less than 4 neighbors is undercoordinated in the silicon lattice, so all with 3 or less neighbors will be passivated,
+
+`COORDINATION_SEARCH_RADIUS = 2.5` -- Search radius for neighbors for every atom, in Angstroms,
+
+`MAX_BONDS_TO_PASSIVATE = 2`  -- Maximum number of bonds to saturate for undercoordinated atoms.
+
+
+Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows:
+
+```python
+# Enable interactive selection of coordination threshold
+IS_COORDINATION_SELECTION_INTERACTIVE = False
+
+MATERIAL_INDEX = 0
+
+BOND_LENGTH = 1.46 # in Angstroms
+PASSIVANT = "H" # Chemical symbol of the passivant
+COORDINATION_SEARCH_RADIUS = 2.5 # in Angstroms (sphere in which to search for neighbors)
+COORDINATION_THRESHOLD = 3 # Coordination number below which to passivate
+MAX_BONDS_TO_SATURATE = 2 # Maximum number of bonds to saturate
+
+SYMMETRY_TOLERANCE = 0.1 
+
+SHOW_INTERMEDIATE_STEPS = True
+CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1] 
+```
+
+Here's the visual of the updated content:
+
+![Notebook setup](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/5-jl-setup.webp "Notebook setup")
+
+### 2.2. Run the notebook and analyze the results
+
+After running the notebook, the user will be able to visualize the structure of Silicon Nanowire with substitution defects.
+
+![Review the Results](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/6-jl-result-preview.webp "Review the Results")
+
+## 3. Pass the Material to Materials Designer
+
+The user can pass the material with substitution defects in the current Materials Designer environment and save it.
+
+![Final Material](/images/tutorials/materials/passivation/passivation_edge_silicon_nanowire/7-wave-result.webp "H-Passivated Silicon Nanowire")
+
+Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format.
+
+
+## Interactive JupyterLite Notebook
+
+The following JupyterLite notebook demonstrates the process of creating materials with hydrogen passivation of silicon nanowire. 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/passivation_edge_silicon_nanowire.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. B. Aradi, L. E. Ramos, P. Deák, Th. Köhler, F. Bechstedt, R. Q. Zhang, and Th. Frauenheim,
+   Theoretical study of the chemical gap tuning in silicon nanowires
+   Phys. Rev. B 76, 035305 (2007)
+   DOI: [10.1103/PhysRevB.76.035305](https://doi.org/10.1103/PhysRevB.76.035305)
+
+## Tags
+
+ `silicon`, `hydrogen`, `passivation`, `nanowire`

mkdocs.yml

@@ -226,6 +226,7 @@ nav:
                 - 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
+                - H-Passivated Silicon Nanowire:                                      tutorials/materials/specific/passivation-edge-silicon-nanowire.md
 
 # COMMON UI COMPONENTS
     - Interface Components: