From a60a26816f8b3115f2fada392974534a07b779d3 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 31 Dec 2024 14:29:44 -0800
Subject: [PATCH 1/6] feat: si (100) passivation tutorial (claude)

---
 .../passivation-surface-silicon-surface.md    | 167 ++++++++++++++++++
 1 file changed, 167 insertions(+)
 create mode 100644 lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md

diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
new file mode 100644
index 00000000..30768059
--- /dev/null
+++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
@@ -0,0 +1,167 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Passivation of Silicon (001) Surface
+
+## Introduction
+
+This tutorial demonstrates how to passivate a reconstructed silicon (001) surface with hydrogen atoms, following the methodology described in the literature.
+
+!!!note "Manuscript"
+    Hansen, U., & Vogl, P.
+    "Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study."
+    Physical Review B, 57(20), 13295–13304. (1998)
+    [DOI: 10.1103/PhysRevB.57.13295](https://doi.org/10.1103/PhysRevB.57.13295){:target='_blank'}.
+
+We will recreate the passivated surface structure shown in Fig. 8:
+
+![Si(100) H-Passivated Surface](/images/tutorials/materials/surfaces/si_100_passivation/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
+
+## 1. Adjust Silicon Surface Structure
+
+### 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) using the search term "Silicon.*100.*reconstructed".
+
+![Standata Si Import](/images/tutorials/materials/surfaces/si_100_passivation/standata-import.webp "Import Si(100) from Standata")
+
+### 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
+
+Open `create_supercell.ipynb` and replace the "Get input materials" cell with the following code to adjust the Si atom position:
+
+```python
+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()]
+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])]
+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)
+new_coordinates[index_to_adjust] = adjusted_coordinate
+material.set_coordinates(new_coordinates)
+```
+
+### 1.4. Run Structure Adjustment
+
+Run the notebook using "Run > Run All Cells". This will:
+1. Load the Si(100) structure
+2. Adjust the position of the specified Si atom
+3. Create a supercell if specified in the parameters
+4. Visualize the adjusted structure
+
+![Adjusted Structure](/images/tutorials/materials/surfaces/si_100_passivation/adjusted-structure.webp "Adjusted Si(100) Structure")
+
+## 2. Passivate the Surface
+
+### 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
+
+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
+
+# Surface detection parameters
+SHADOWING_RADIUS = 1.8  # In Angstroms
+DEPTH = 0.5  # In Angstroms
+
+# Visualization parameters
+CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]
+```
+
+Key parameters explained:
+- `BOND_LENGTH`: Si-H bond length from literature
+- `SHADOWING_RADIUS`: Controls which atoms are considered surface atoms
+- `DEPTH`: How deep to look for surface atoms
+
+![Passivation Parameters](/images/tutorials/materials/surfaces/si_100_passivation/passivation-params.webp "Passivation Parameters Visualization")
+
+### 2.3. Run Passivation
+
+Run all cells in the notebook. The passivation process will:
+1. Detect surface Si atoms
+2. Add H atoms at the specified bond length
+3. Generate the passivated structure
+
+## 3. Analyze Results
+
+After running both notebooks, examine the final structure:
+
+### 3.1. Surface Structure
+Check that:
+- The adjusted Si atom position is correct
+- Surface reconstruction is maintained
+- H atoms are properly placed above surface Si atoms
+
+### 3.2. Bond Geometry
+Verify:
+- Si-H bond length is ~1.46 Å
+- H atoms are approximately perpendicular to the surface
+- No H atoms are added to subsurface Si atoms
+
+![Final Structure](/images/tutorials/materials/surfaces/si_100_passivation/final-structure.webp "Final H-Passivated Si(100)")
+
+## 4. Save Passivated Structure
+
+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
+
+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/si_100_passivation.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## Parameter Fine-tuning
+
+To adjust the passivation:
+
+1. Surface Detection:
+   - Increase `SHADOWING_RADIUS` to be more selective about surface atoms
+   - Adjust `DEPTH` to control how deep to look for surface atoms
+
+2. Passivation:
+   - Modify `BOND_LENGTH` for different Si-H distances
+   - Change `SURFACE` to passivate different surfaces
+   - Change `PASSIVANT` to use different passivating species
+
+## 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
+
+`silicon`, `surface`, `passivation`, `hydrogen`, `Si(100)`, `surface reconstruction`, `Si`, `H`
\ No newline at end of file

From 25e2f7e2b0aed9e364f7cafe84b668f106cde92e Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 31 Dec 2024 14:46:38 -0800
Subject: [PATCH 2/6] update: human touch

---
 .../passivation-surface-silicon-surface.md    | 55 ++++++++++++-------
 1 file changed, 36 insertions(+), 19 deletions(-)

diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
index 30768059..badc681d 100644
--- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
+++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
@@ -3,11 +3,11 @@
 render_macros: true
 ---
 
-# Passivation of Silicon (001) Surface
+# Passivation of Silicon (100) Surface
 
 ## Introduction
 
-This tutorial demonstrates how to passivate a reconstructed silicon (001) surface with hydrogen atoms, following the methodology described in the literature.
+This tutorial demonstrates how to passivate a reconstructed silicon (100) surface with hydrogen atoms, following the methodology described in the literature.
 
 !!!note "Manuscript"
     Hansen, U., & Vogl, P.
@@ -23,9 +23,9 @@ We will recreate the passivated surface structure shown in Fig. 8:
 
 ### 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) using the search term "Silicon.*100.*reconstructed".
+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).
 
-![Standata Si Import](/images/tutorials/materials/surfaces/si_100_passivation/standata-import.webp "Import Si(100) from Standata")
+![Si(100) Structure](/images/tutorials/materials/surfaces/si_100_passivation/1-wave-original-material.webp "Si(100) Structure")
 
 ### 1.2. Launch JupyterLite Session
 
@@ -33,7 +33,20 @@ Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/
 
 ### 1.3. Open Modified `create_supercell.ipynb` Notebook
 
-Open `create_supercell.ipynb` and replace the "Get input materials" cell with the following code to adjust the Si atom position:
+Open `create_supercell.ipynb`, select input material as the Si(100) structure, and set the supercell parameters in 1.1.:
+
+```python
+SUPERCELL_MATRIX = [
+    [1, 0, 0], 
+    [0, 1, 0], 
+    [0, 0, 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:
 
 ```python
 from utils.jupyterlite import get_materials
@@ -56,15 +69,18 @@ new_coordinates[index_to_adjust] = adjusted_coordinate
 material.set_coordinates(new_coordinates)
 ```
 
+![Supercell Parameters](/images/tutorials/materials/surfaces/si_100_passivation/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization")
+
 ### 1.4. Run Structure Adjustment
 
 Run the notebook using "Run > Run All Cells". This will:
+
 1. Load the Si(100) structure
 2. Adjust the position of the specified Si atom
 3. Create a supercell if specified in the parameters
 4. Visualize the adjusted structure
 
-![Adjusted Structure](/images/tutorials/materials/surfaces/si_100_passivation/adjusted-structure.webp "Adjusted Si(100) Structure")
+![Adjusted Structure](/images/tutorials/materials/surfaces/si_100_passivation/3-wave-adjusted-material.webp "Adjusted Si(100) Structure")
 
 ## 2. Passivate the Surface
 
@@ -91,36 +107,35 @@ CELL_REPETITIONS_FOR_VISUALIZATION = [1, 1, 1]
 ```
 
 Key parameters explained:
-- `BOND_LENGTH`: Si-H bond length from literature
-- `SHADOWING_RADIUS`: Controls which atoms are considered surface atoms
-- `DEPTH`: How deep to look for surface atoms
 
-![Passivation Parameters](/images/tutorials/materials/surfaces/si_100_passivation/passivation-params.webp "Passivation Parameters Visualization")
+- `BOND_LENGTH`: Si-H bond length from literature.
+- `SHADOWING_RADIUS`: Controls which atoms are considered surface atoms, set to be below the distance between top Si atoms pair.
+- `SURFACE`: Passivate only the top surface.
+- `DEPTH`: How deep to look for surface atoms, set to include only top Si atoms.
+
+![Passivation Parameters](/images/tutorials/materials/surfaces/si_100_passivation/4-jl-setup-nb-passivation.webp "Passivation Parameters Visualization")
 
 ### 2.3. Run Passivation
 
 Run all cells in the notebook. The passivation process will:
+
 1. Detect surface Si atoms
 2. Add H atoms at the specified bond length
 3. Generate the passivated structure
 
+![Passivated Structure](/images/tutorials/materials/surfaces/si_100_passivation/5-jl-result-preview.webp "H-Passivated Si(100) Structure")
+
 ## 3. Analyze Results
 
 After running both notebooks, examine the final structure:
 
-### 3.1. Surface Structure
 Check that:
+
 - The adjusted Si atom position is correct
 - Surface reconstruction is maintained
 - H atoms are properly placed above surface Si atoms
 
-### 3.2. Bond Geometry
-Verify:
-- Si-H bond length is ~1.46 Å
-- H atoms are approximately perpendicular to the surface
-- No H atoms are added to subsurface Si atoms
-
-![Final Structure](/images/tutorials/materials/surfaces/si_100_passivation/final-structure.webp "Final H-Passivated Si(100)")
+![Final Structure](/images/tutorials/materials/surfaces/si_100_passivation/6-wave-result.webp "Final H-Passivated Si(100)")
 
 ## 4. Save Passivated Structure
 
@@ -135,7 +150,7 @@ The following embedded notebook demonstrates the complete process. Select "Run"
 
 {% with origin_url=config.extra.jupyterlite.origin_url %}
 {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
-{% with notebook_name='specific_examples/si_100_passivation.ipynb' %}
+{% with notebook_name='specific_examples/passivation_surface_silicon_surface.ipynb' %}
 {% include 'jupyterlite_embed.html' %}
 {% endwith %}
 {% endwith %}
@@ -146,10 +161,12 @@ The following embedded notebook demonstrates the complete process. Select "Run"
 To adjust the passivation:
 
 1. Surface Detection:
+
    - Increase `SHADOWING_RADIUS` to be more selective about surface atoms
    - Adjust `DEPTH` to control how deep to look for surface atoms
 
 2. Passivation:
+
    - Modify `BOND_LENGTH` for different Si-H distances
    - Change `SURFACE` to passivate different surfaces
    - Change `PASSIVANT` to use different passivating species

From edf7af48af7ee0361b14f88616c8cfe8061ba991 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 31 Dec 2024 15:03:46 -0800
Subject: [PATCH 3/6] update: add images

---
 .../passivation_surface_silicon/0-figure-from-manuscript.webp  | 3 +++
 .../passivation_surface_silicon/1-wave-original-material.webp  | 3 +++
 .../passivation_surface_silicon/2-jl-setup-nb-adjust.webp      | 3 +++
 .../passivation_surface_silicon/3-wave-adjusted-material.webp  | 3 +++
 .../passivation_surface_silicon/4-jl-setup-nb-passivate.webp   | 3 +++
 .../passivation_surface_silicon/5-jl-result-preview.webp       | 3 +++
 .../passivation/passivation_surface_silicon/6-wave-result.webp | 3 +++
 7 files changed, 21 insertions(+)
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp
 create mode 100644 images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp

diff --git a/images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp b/images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp
new file mode 100644
index 00000000..452076ba
--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/0-figure-from-manuscript.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:a22284a32e55125f6ad52e9fbd2850895dd85a8b783143262b8d1817174bd753
+size 8986
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new file mode 100644
index 00000000..ea424ef6
--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:50255d6b9c505b4d8ca9dde55d842600ec5e17387b227d817dac44f669e7b53a
+size 8152
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new file mode 100644
index 00000000..5a8c492b
--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:0a23971af18b935232337c0734e5596052becd6d01b73895320130a345b0818c
+size 76190
diff --git a/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp b/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp
new file mode 100644
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--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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+size 7970
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new file mode 100644
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--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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new file mode 100644
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--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:c760d9659c4b100779ee891470575eafca37ffd62793691c9baa678d9d8fda79
+size 11382
diff --git a/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp b/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp
new file mode 100644
index 00000000..4a992c20
--- /dev/null
+++ b/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:115b21ca0913ff3242568d37fdb93a30b10c6a0506cfe332eca1884d9a08f698
+size 9830

From 590e2328ae0214e256a103c9085bd550a82a9739 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 31 Dec 2024 15:03:54 -0800
Subject: [PATCH 4/6] update: use images

---
 .../passivation-surface-silicon-surface.md         | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
index badc681d..14e6ca17 100644
--- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
+++ b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
@@ -17,7 +17,7 @@ This tutorial demonstrates how to passivate a reconstructed silicon (100) surfac
 
 We will recreate the passivated surface structure shown in Fig. 8:
 
-![Si(100) H-Passivated Surface](/images/tutorials/materials/surfaces/si_100_passivation/0-figure-from-manuscript.webp "H-Passivated Silicon (100)")
+![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
 
@@ -25,7 +25,7 @@ We will recreate the passivated surface structure shown in Fig. 8:
 
 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/surfaces/si_100_passivation/1-wave-original-material.webp "Si(100) Structure")
+![Si(100) Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/1-wave-original-material.webp "Si(100) Structure")
 
 ### 1.2. Launch JupyterLite Session
 
@@ -69,7 +69,7 @@ new_coordinates[index_to_adjust] = adjusted_coordinate
 material.set_coordinates(new_coordinates)
 ```
 
-![Supercell Parameters](/images/tutorials/materials/surfaces/si_100_passivation/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization")
+![Supercell Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/2-jl-setup-nb-adjust.webp "Supercell Parameters Visualization")
 
 ### 1.4. Run Structure Adjustment
 
@@ -80,7 +80,7 @@ Run the notebook using "Run > Run All Cells". This will:
 3. Create a supercell if specified in the parameters
 4. Visualize the adjusted structure
 
-![Adjusted Structure](/images/tutorials/materials/surfaces/si_100_passivation/3-wave-adjusted-material.webp "Adjusted Si(100) Structure")
+![Adjusted Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/3-wave-adjusted-material.webp "Adjusted Si(100) Structure")
 
 ## 2. Passivate the Surface
 
@@ -113,7 +113,7 @@ Key parameters explained:
 - `SURFACE`: Passivate only the top surface.
 - `DEPTH`: How deep to look for surface atoms, set to include only top Si atoms.
 
-![Passivation Parameters](/images/tutorials/materials/surfaces/si_100_passivation/4-jl-setup-nb-passivation.webp "Passivation Parameters Visualization")
+![Passivation Parameters](/images/tutorials/materials/passivation/passivation_surface_silicon/4-jl-setup-nb-passivate.webp "Passivation Parameters Visualization")
 
 ### 2.3. Run Passivation
 
@@ -123,7 +123,7 @@ Run all cells in the notebook. The passivation process will:
 2. Add H atoms at the specified bond length
 3. Generate the passivated structure
 
-![Passivated Structure](/images/tutorials/materials/surfaces/si_100_passivation/5-jl-result-preview.webp "H-Passivated Si(100) Structure")
+![Passivated Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/5-jl-result-preview.webp "H-Passivated Si(100) Structure")
 
 ## 3. Analyze Results
 
@@ -135,7 +135,7 @@ Check that:
 - Surface reconstruction is maintained
 - H atoms are properly placed above surface Si atoms
 
-![Final Structure](/images/tutorials/materials/surfaces/si_100_passivation/6-wave-result.webp "Final H-Passivated Si(100)")
+![Final Structure](/images/tutorials/materials/passivation/passivation_surface_silicon/6-wave-result.webp "Final H-Passivated Si(100)")
 
 ## 4. Save Passivated Structure
 

From 5960e50d5733e011e2f86086bb2e1f24e78b471f Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Tue, 31 Dec 2024 15:04:02 -0800
Subject: [PATCH 5/6] update: mkdocs

---
 mkdocs.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mkdocs.yml b/mkdocs.yml
index 4a31e3b0..555b1527 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -229,6 +229,7 @@ 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
+                - H-Passivated Silicon (100) Surface:                           tutorials/materials/specific/passivation-surface-silicon-surface.md
                 - Gold Nanoclusters:                                             tutorials/materials/specific/nanocluster-gold.md
                 - SrTiO3 Slab:                                                  tutorials/materials/specific/slab-strontium-titanate.md
                 - Interface between Graphene and h-BN:                          tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md

From 7f25d6c5f0669c4567918a84b8137d0827c3ee21 Mon Sep 17 00:00:00 2001
From: VsevolodX <79542055+VsevolodX@users.noreply.github.com>
Date: Wed, 1 Jan 2025 16:52:29 -0800
Subject: [PATCH 6/6] update: address pr comments

---
 .../passivation-surface-silicon-surface.md    | 67 ++++++++++---------
 1 file changed, 34 insertions(+), 33 deletions(-)

diff --git a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md b/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
index 14e6ca17..e7b8e70e 100644
--- a/lang/en/docs/tutorials/materials/specific/passivation-surface-silicon-surface.md
+++ b/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:
 
@@ -171,7 +172,7 @@ 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.
 
@@ -179,6 +180,6 @@ To adjust the passivation:
 
 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`
\ No newline at end of file