Feature/SOF-7456 feat: tutorials on twisted interfaces

lang/en/docs/tutorials/materials/specific/defect-creation-point-substitution-graphene.md → lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md

@@ -11,7 +11,7 @@ This tutorial demonstrates the process of creating materials with substitution d
 
 [//]: # (<embed src="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446" width="100%" height="300">)
 
-!!!note "Reference"
+!!!note "Manuscript"
     Yoshitaka Fujimoto and Susumu Saito, "Formation, stabilities, and electronic properties of nitrogen defects in graphene", Physical Review B, 2011. [DOI: 10.1103/PhysRevB.84.245446](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.84.245446){:target='_blank'}.
 
 We use the [Materials Designer](../../../materials-designer/overview.md) to create a supercell of graphene, identify the crystal site positions for defects, and introduce nitrogen atoms and vacancies accordingly.
@@ -20,7 +20,7 @@ We will focus on creating graphene-nitrogen structures from FIG. 1.
 Specifically, the material from FIG. 1. b) of the paper: 
 
 
-![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1. b)")
+![Point Defect, Substitution, 0](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/0-figure-from-manuscript.webp "Point Defect, Substitution, FIG. 1.")
 
 
 ## 1. Create Graphene Supercell
@@ -101,19 +101,19 @@ Here's the visual of the updated content:
 
 ![Notebook setup](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/5-jl-setup.webp "Notebook setup")
 
-## 5. Run the Notebook
+## 4. Run the Notebook
 
 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")
 
-## 6. Analyze the Results
+## 5. Analyze the Results
 
 After running the notebook, the user will be able to visualize the structure of Graphene with substitution defects.
 
 ![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results")
 
-## 7. Pass the Material to Materials Designer
+## 6. Pass the Material to Materials Designer
 
 The user can pass the material with substitution defects in the current Materials Designer environment and save it.
 
@@ -126,21 +126,9 @@ Or the user can [save or download](../../../materials-designer/header-menu/input
 
 The following JupyterLite notebook demonstrates the process of creating materials with substitution defects in graphene. 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/defect_creation_point_substitution_graphene.ipynb' %}
+{% with origin_url="https://jupyterlite.mat3ra.com/retro/notebooks/?path=api-examples/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb" %}
 {% include 'jupyterlite_embed.html' %}
 {% endwith %}
-{% endwith %}
-{% endwith %}
-
-<!--
-{# TODO: Update the origin_url
-    {% with origin_url="https://jupyterlite.mat3ra.com/retro/notebooks/?path=api-examples/other/materials_designer/specific_examples/defect_creation_point_substitution_graphene.ipynb" %}
-    {% include 'jupyterlite_embed.html' %}
-    {% endwith %}
-#}
--->
 
 ## Tags
 

lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md → lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md

@@ -11,7 +11,7 @@ This tutorial demonstrates the process of creating material with island on the s
 
 [//]: # (<embed src="https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406" width="100%" height="300">)
 
-!!!note "Reference"
+!!!note "Manuscript"
     **D. G. Sangiovanni, A. B. Mei, D. Edström, L. Hultman, V. Chirita, I. Petrov, and J. E. Greene**, 
     "Effects of surface vibrations on interlayer mass transport: Ab initio molecular dynamics investigation of Ti adatom descent pathways and rates from TiN/TiN(001) islands", Physical Review B, 2018. [DOI: 10.1103/PhysRevB.97.035406](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.97.035406){:target='_blank'}.
 
@@ -166,15 +166,15 @@ The following JupyterLite notebook demonstrates the process of creating material
 
 {% with origin_url=config.extra.jupyterlite.origin_url %}
 {% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %}
-{% with notebook_name='specific_examples/defect_creation_island.ipynb' %}
+{% with notebook_name='specific_examples/defect_surface_island_titanium_nitride.ipynb' %}
 {% include 'jupyterlite_embed.html' %}
 {% endwith %}
 {% endwith %}
 {% endwith %}
 
 <!--
 {# TODO: Update the origin_url
-    {% with origin_url="https://jupyterlite.mat3ra.com/retro/notebooks/?path=api-examples/other/materials_designer/specific_examples/defect_creation_island.ipynb" %}
+    {% with origin_url="https://jupyterlite.mat3ra.com/retro/notebooks/?path=api-examples/other/materials_designer/specific_examples/defect_surface_island_titanium_nitride.ipynb" %}
     {% include 'jupyterlite_embed.html' %}
     {% endwith %}
 #}

lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md

@@ -0,0 +1,147 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Twisted Bilayer Molybdenum Disulfide Structure Creation
+
+## Introduction
+
+This tutorial demonstrates the process of creating a twisted bilayer molybdenum disulfide (MoS2) structure based on the work presented in the following manuscript.
+
+!!!note "Manuscript"
+    **Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang**,
+    "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014)
+    [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966)
+
+
+We use the [Materials Designer](../../../materials-designer/overview.md) to create molybdenum disulfide bilayer structure configurations with multiple twist angles.
+
+The Figure 4 shows the twisted bilayer MoS2 configurations.
+
+![Twisted Bilayer Molybdenum Disulfide](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/MoS2-twisted-bilayers.png   "Twisted Bilayer Molybdenum Disulfide")
+
+## 1. Load and preview MoS2 structure
+
+First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the MoS2 material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+
+![Standata MoS2 Import](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/standata-import-mos2.png "Standata MoS2 Import")
+
+Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a twisted bilayer molybdenum disulfide structure.
+
+
+## 2. Create MoS2 bilayer with a twist angle of 22 degrees
+
+### 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_twisted_interface_with_commnesurate_lattices.ipynb` notebook to modify the parameters by adding: `TARGET_TWIST_ANGLE = 22` and `INTERFACE_DISTANCE = 6.5` -- found in the publication description.
+
+Adjust the "1.1. Set up slab parameters" cell in the notebook according to:
+
+```python
+# Material selection and basic parameters
+FILM_INDEX = 0 # Index in the list of materials, to access as materials[FILM_INDEX]
+SUBSTRATE_INDEX = None  # Can be None to use same material as film
+
+# Twisted interface parameters
+TARGET_TWIST_ANGLE = 22.0  # in degrees
+INTERFACE_DISTANCE = 6.5  # in Angstroms
+INTERFACE_VACUUM = 20.0  # in Angstroms
+
+# Search algorithm parameters
+MAX_REPETITION = 6  # Maximum supercell matrix element value
+ANGLE_TOLERANCE = 0.5  # in degrees
+RETURN_FIRST_MATCH = True  # If True, returns first solution within tolerance
+
+# Visualization parameters
+SHOW_INTERMEDIATE_STEPS = True
+VISUALIZE_REPETITIONS = [3, 3, 1]
+```
+
+![Notebook setup](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/jl-set-nb.png "Notebook setup")
+
+
+### 2.3. Run the Notebook
+
+After setting the parameters, run the notebook to create the twisted bilayer molybdenum disulfide structure.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+### 2.4. View Results and pass to Materials Designer
+
+The generation might take some time.
+After that, the user can pass the material to the Materials Designer for further analysis.
+
+The interface for 22 degrees twist is shown below.
+
+![Result Material, 22 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-22.png "MoS2 Twisted Bilayer, 22 degrees")
+
+## 3. Create bilayers with other twist angles
+
+### 3.1. Repeat the steps above
+To create a twisted bilayer MoS2 structure with a different twist angle, repeat the steps above, adjusting the `TARGET_TWIST_ANGLE` and `INTERFACE_DISTANCE` parameters accordingly.
+
+Values for angle and associated interlayer separation provided below come from the description of Figure 4 in the publication, below each example has an image of the resulting material.
+
+```python
+TARGET_TWIST_ANGLE = 0.0
+INTERFACE_DISTANCE = 6.8
+```
+
+![Result Material, 0 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-0.png "MoS2 Twisted Bilayer, 0 degrees")
+
+
+```python
+TARGET_TWIST_ANGLE =  13.0
+INTERFACE_DISTANCE =  6.5
+```
+
+![Result Material, 13 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-13.png "MoS2 Twisted Bilayer, 13 degrees")
+
+```python
+TARGET_TWIST_ANGLE = 38.0
+INTERFACE_DISTANCE = 6.5
+```
+
+![Result Material, 38 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-38.png "MoS2 Twisted Bilayer, 38 degrees")
+
+```python
+TARGET_TWIST_ANGLE = 47.0
+INTERFACE_DISTANCE = 6.5
+```
+
+![Result Material, 47 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-47.png "MoS2 Twisted Bilayer, 47 degrees")
+
+```python
+TARGET_TWIST_ANGLE = 60.0
+INTERFACE_DISTANCE = 6.2
+```
+
+![Result Material, 60 degrees](/images/tutorials/materials/interfaces/twisted-bilayer-molybdenum-disulfide/mos2-result-wavejs-60.png "MoS2 Twisted Bilayer, 60 degrees")
+
+
+## Interactive JupyterLite Notebook
+
+The interactive JupyterLite notebook for creating twisted bilayer MoS2 structures 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/interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. Kaihui Liu, Liming Zhang, Ting Cao, Chenhao Jin, Diana Qiu, Qin Zhou, Alex Zettl, Peidong Yang, Steve G. Louie & Feng Wang, "Evolution of interlayer coupling in twisted molybdenum disulfide bilayers" Nature Communications volume 5, Article number: 4966 (2014) [DOI: 10.1038/ncomms5966](https://doi.org/10.1038/ncomms5966)
+2. Cao, Y., Fatemi, V., Fang, S. et al. Unconventional superconductivity in magic-angle graphene superlattices. Nature 556, 43–50 (2018). [DOI: 10.1038/nature26160](https://doi.org/10.1038/nature26160)