Merge pull request #307 from Exabyte-io/feature/SOF-7522

feature/SOF-7522 GB 3D Cu tutorial

lang/en/docs/tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md

@@ -0,0 +1,143 @@
+---
+# YAML header
+render_macros: true
+---
+
+# Grain Boundaries in FCC Metals (Copper)
+
+## Introduction
+
+This tutorial demonstrates the process of creating grain boundary structures in FCC metals, specifically copper, based on the work presented in the following manuscript, where structural phase transformations in metallic grain boundaries are studied.
+
+
+!!!note "Manuscript"
+    Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919){:target='_blank'}.
+
+We will focus on creating copper grain boundary structures similar to Figure 1b from the manuscript:
+
+![Copper Grain Boundary](/images/tutorials/materials/defects/grain_boundary_fcc_metal/0-figure-from-manuscript.webp "Copper Grain Boundary, FIG. 1")
+
+## 1. Create Initial Copper Structure
+
+### 1.1. Load Copper Material
+
+Navigate to [Materials Designer](../../../materials-designer/overview.md) and import the copper material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md).
+
+1. Click on "Input/Output" menu
+2. Select "Import from Standata"
+3. Search for "Cu" and select the bulk copper material
+
+![Copper Material Import](/images/tutorials/materials/defects/grain_boundary_fcc_metal/1-standata-import-cu.webp "Copper Material Import")
+
+### 1.2. Launch JupyterLite Session
+
+Select "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" to open JupyterLite.
+
+![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog")
+
+### 1.3. Open and Configure Notebook
+
+Find and open `create_grain_boundary.ipynb`. Edit the grain boundary parameters in section 1.1 of the notebook:
+
+`PHASE_1_MILLER_INDICES = (3, 1, 0)` -- As described in the manuscript.
+`PHASE_2_MILLER_INDICES = (-3, -1, 0)` -- Opposite orientation to phase 1 to achieve symmetrical grain boundary.
+
+```python
+# Enable interactive selection of terminations via UI prompt
+IS_TERMINATIONS_SELECTION_INTERACTIVE = False
+
+# Parameters for Phase 1
+PHASE_1_MILLER_INDICES = (3, 1, 0)
+PHASE_1_THICKNESS = 4  # in atomic layers
+PHASE_1_USE_ORTHOGONAL_Z = True
+
+# Parameters for Phase 2
+PHASE_2_MILLER_INDICES = (-3, -1, 0)
+PHASE_2_THICKNESS = 4  # in atomic layers
+PHASE_2_USE_ORTHOGONAL_Z = True
+
+INTERPHASE_GAP = 2.0  # in Angstrom
+
+# Maximum area for the superlattice search algorithm
+MAX_AREA = 100  # in Angstrom^2
+
+# Parameters for the final material
+SLAB_MILLER_INDICES = (0, 0, 1)
+SLAB_THICKNESS = 4  # in atomic layers
+SLAB_VACUUM = 20.0  # in Angstrom
+
+# Set the termination pair index
+TERMINATION_PAIR_INDEX = 0
+```
+
+These parameters will create:
+
+- Two copper slabs with (310) and (-3-10) orientations
+- 4 atomic layers thickness for each phase
+- 2 Å gap between phases
+- Maximum area of 100 Ų for strain matching
+
+![Grain Boundary Parameters](/images/tutorials/materials/defects/grain_boundary_fcc_metal/2-jl-setup-nb.webp "Grain Boundary Parameters")
+
+## 2. Run the Notebook
+
+After setting the parameters, run the notebook by selecting "Run > Run All Cells" from the menu.
+
+![Run All](/images/jupyterlite/run-all.webp "Run All")
+
+
+## 3. Analyze the Results
+
+### 3.1. Review the Structure
+
+After running the notebook, user can visualize the grain boundary structure:
+
+- View from different angles using the rotation controls
+- Check the atomic arrangement at the interface
+- Verify the orientation relationship between the two phases
+
+![Grain Boundary Preview](/images/tutorials/materials/defects/grain_boundary_fcc_metal/3-jl-result-preview.webp "Grain Boundary Preview")
+
+### 3.2. Structure Details
+
+The resulting structure should show:
+
+- A clear interface between the two orientations
+- A proper atomic arrangement at the boundary
+- Minimal strain in the interface region
+
+Grain boundary from the top (XY) and side (XZ) views:
+
+![Final Material (XY)](/images/tutorials/materials/defects/grain_boundary_fcc_metal/4-wave-result.webp "Final Copper Grain Boundary, XY view")
+
+![Final Material (XZ)](/images/tutorials/materials/defects/grain_boundary_fcc_metal/5-wave-result-xz.webp "Final Copper Grain Boundary, XZ view")
+
+The structure has differences from the original figure in the manuscript, since grain boundary achieved by strain-matching two symmetrical surfaces with no changes to either surfaces. Discrepancies might be removed with further adjustments like shifting the phases, removing atom layers and reconstructing the interface.
+
+## 4. Save the Structure
+
+The final structure can be:
+
+1. Passed back to Materials Designer
+2. [Saved or downloaded](../../../materials-designer/header-menu/input-output.md) in Material JSON format
+3. Exported as a POSCAR file
+
+## Interactive JupyterLite Notebook
+
+The following JupyterLite 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/grain_boundary_3d_fcc_metals_copper.ipynb' %}
+{% include 'jupyterlite_embed.html' %}
+{% endwith %}
+{% endwith %}
+{% endwith %}
+
+## References
+
+1. Timofey Frolov, David L. Olmsted, Mark Asta & Yuri Mishin, "Structural phase transformations in metallic grain boundaries", Nature Communications, volume 4, Article number: 1899 (2013). [DOI: 10.1038/ncomms2919](https://www.nature.com/articles/ncomms2919)
+
+## Tags
+
+`grain boundary`, `interface`, `copper`, `Cu`,  `FCC`, `metal`

mkdocs.yml

@@ -236,6 +236,7 @@ nav:
                 - Interface between Graphene and SiO2 (alpha-quartz):                tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md
                 - High-k Metal Gate Stack (Si/SiO2/HfO2/TiN):                        tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md
                 - Ripple perturbation of a Graphene sheet:                               tutorials/materials/specific/perturbation-ripples-graphene.md
+                - Grain Boundary in FCC Metals (Copper):                                tutorials/materials/specific/grain-boundary-3d-fcc-metals-copper.md
 
 # COMMON UI COMPONENTS
     - Interface Components: