update: address pr comments

Author: VsevolodX

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

@@ -3,9 +3,9 @@
 render_macros: true
 ---
 
-# Passivation of Silicon (100) Surface
+# Passivation of Silicon (100) Surface.
 
-## Introduction
+## Introduction.
 
 This tutorial demonstrates how to passivate a reconstructed silicon (100) surface with hydrogen atoms, following the methodology described in the literature.
 
@@ -19,19 +19,19 @@ We will recreate the passivated surface structure shown in Fig. 8:
 
 ![Si(100) H-Passivated Surface](/images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
 
-## 1. Adjust Silicon Surface Structure
+## 1. Obtain the Silicon (100) Surface Structure.
 
-### 1.1. Load Base Material
+### 1.1. Load Base Material.
 
 Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the reconstructed Si(100) surface from [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
 
 ![Si(100) Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp "Si(100) Structure")
 
-### 1.2. Launch JupyterLite Session
+### 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 Modified `create_supercell.ipynb` Notebook
+### 1.3. Open Modified `create_supercell.ipynb` Notebook.
 
 Open `create_supercell.ipynb`, select input material as the Si(100) structure, and set the supercell parameters in 1.1.:
 
@@ -42,8 +42,8 @@ SUPERCELL_MATRIX = [
     [0, 0, 1]
 ] 
 
-# or use the scaling factor
-SCALING_FACTOR = None # [3, 3, 1]
+# or use the scaling factor.
+SCALING_FACTOR = None # [3, 3, 1].
 ```
 
 Also add to the "Get input materials" cell the following code to adjust the Si atom position:
@@ -53,25 +53,26 @@ from utils.jupyterlite import get_materials
 materials = get_materials(globals())
 material = materials[0]
 
-# Find and adjust Si atom coordinates
-si_atoms_coordinates = [coordinate.value for coordinate in material.basis.coordinates.to_array_of_values_with_ids()]
+# Find coordinates of the Si atoms, list in descending order, and change the 2nd one from the top
+si_atoms_coordinates = [coordinate for coordinate in slab.basis.coordinates.values]
 si_atoms_sorted = sorted(si_atoms_coordinates, key=lambda x: x[2], reverse=True)
 second_from_top_index = 1
 second_si_atom_coordinate = si_atoms_sorted[second_from_top_index]
 
 print(f"Coordinates of the second Si atom: {second_si_atom_coordinate}")
-adjusted_coordinate = [coord + delta for coord, delta in zip(second_si_atom_coordinate, [0.025, 0, 0.025])]
+adjusted_coordinate = [
+    coord + delta for coord, delta in zip(second_si_atom_coordinate, [0.025, 0, 0.025])
+]
 print(f"Adjusted coordinate: {adjusted_coordinate}")
-
 new_coordinates = si_atoms_coordinates.copy()
-index_to_adjust = material.basis.coordinates.get_element_id_by_value(second_si_atom_coordinate)
+index_to_adjust = slab.basis.coordinates.get_element_id_by_value(second_si_atom_coordinate)
 new_coordinates[index_to_adjust] = adjusted_coordinate
-material.set_coordinates(new_coordinates)
+slab.set_coordinates(new_coordinates)
 ```
 
 ![Supercell Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization")
 
-### 1.4. Run Structure Adjustment
+### 1.4. Run Structure Adjustment.
 
 Run the notebook using "Run > Run All Cells". This will:
 
@@ -82,27 +83,27 @@ Run the notebook using "Run > Run All Cells". This will:
 
 ![Adjusted Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp "Adjusted Si(100) Structure")
 
-## 2. Passivate the Surface
+## 2. Passivate the Surface.
 
-### 2.1. Open `passivate_slab.ipynb` Notebook
+### 2.1. Open `passivate_slab.ipynb` Notebook.
 
 Find and open the `passivate_slab.ipynb` notebook to add hydrogen atoms to the surface.
 
-### 2.2. Set Passivation Parameters
+### 2.2. Set Passivation Parameters.
 
 Configure the following parameters for hydrogen passivation:
 
 ```python
-# Passivation parameters
-PASSIVANT = "H"  # Chemical symbol for hydrogen
-BOND_LENGTH = 1.46  # Si-H bond length in Angstroms
-SURFACE = "top"  # Passivate only the top surface
+# Passivation parameters.
+PASSIVANT = "H"  # Chemical symbol for hydrogen.
+BOND_LENGTH = 1.46  # Si-H bond length in Angstroms.
+SURFACE = "top"  # Passivate only the top surface.
 
-# Surface detection parameters
-SHADOWING_RADIUS = 1.8  # In Angstroms
-DEPTH = 0.5  # In Angstroms
+# Surface detection parameters.
+SHADOWING_RADIUS = 1.8  # In Angstroms.
+DEPTH = 0.5  # In Angstroms.
 
-# Visualization parameters
+# Visualization parameters.
 CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]
 ```
 
@@ -115,7 +116,7 @@ Key parameters explained:
 
 ![Passivation Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp "Passivation Parameters Visualization")
 
-### 2.3. Run Passivation
+### 2.3. Run Passivation.
 
 Run all cells in the notebook. The passivation process will:
 
@@ -125,7 +126,7 @@ Run all cells in the notebook. The passivation process will:
 
 ![Passivated Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp "H-Passivated Si(100) Structure")
 
-## 3. Analyze Results
+## 3. Analyze Results.
 
 After running both notebooks, examine the final structure:
 
@@ -137,14 +138,14 @@ Check that:
 
 ![Final Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp "Final H-Passivated Si(100)")
 
-## 4. Save Passivated Structure
+## 4. Save the Results.
 
 The final structure will be automatically passed back to Materials Designer where you can:
 1. Save it in your workspace
 2. Export it in various formats
 3. Use it for further calculations
 
-## Interactive JupyterLite Notebook
+## Interactive JupyterLite Notebook.
 
 The following embedded notebook demonstrates the complete process. Select "Run" > "Run All Cells".
 
@@ -156,7 +157,7 @@ The following embedded notebook demonstrates the complete process. Select "Run"
 {% endwith %}
 {% endwith %}
 
-## Parameter Fine-tuning
+## Parameter Fine-tuning.
 
 To adjust the passivation:
 
@@ -171,14 +172,14 @@ To adjust the passivation:
    - Change `SURFACE` to passivate different surfaces
    - Change `PASSIVANT` to use different passivating species
 
-## References
+## References.
 
 1. Hansen, U., & Vogl, P. (1998). Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study. Physical Review B, 57(20), 13295–13304.
 
 2. Northrup, J. E. (1991). Structure of Si(100)H: Dependence on the H chemical potential. Physical Review B, 44(3), 1419–1422.
 
 3. Boland, J. J. (1990). Structure of the H‐saturated Si(100) surface. Physical Review Letters, 65(26), 3325–3328.
 
-## Tags
+## Tags.
 
 `silicon`, `surface`, `passivation`, `hydrogen`, `Si(100)`, `surface reconstruction`, `Si`, `H`