diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp new file mode 100644 index 00000000..02186099 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d78f1c9d092d63c84b3b2659a938600c2077b4dc24fb4e08fb2e54ff2e8b584 +size 65098 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp new file mode 100644 index 00000000..4528f45f --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c9882eaeb17e512c10fc7b9999e7212929849de69102aea6865043208c97c7e2 +size 13434 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp new file mode 100644 index 00000000..f44f029d --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2e7167af788f9fbc45118b26afad1ffe04bf86cd8ef27cab395a55ebbdf8e8f5 +size 56072 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp new file mode 100644 index 00000000..d7a8533d --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:0d6702ddce6ff301f7d92b031383cc1cb98cbd6402c423856e0befcaae50771c +size 57670 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp new file mode 100644 index 00000000..0eaba3c9 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:e62d8c77fa902d8cf9a8817e0e6eaf7cb0546da8aea451a6d65cb0cca192a592 +size 15412 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp new file mode 100644 index 00000000..e0bb1407 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d9f5d7cd0bb8b01388d6e6b1cb2c5bcf24f8e2e59e305fe9f5aa1f30c64ba1ee +size 61836 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp new file mode 100644 index 00000000..2fbb93d4 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8090689dc3934be29206bcac5d066b386dfac6600235e53efce31b932b5d986d +size 66176 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp new file mode 100644 index 00000000..d6a9b1d2 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:71ea83de67ecf0ba57d8c8ab27fd86b1f38ac5eb08f0762e071f9b274d2f6de3 +size 63784 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp new file mode 100644 index 00000000..9ed76f52 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:305b9c3067fb1c559406bc3f44589bb1575a14beda2ed5d11584293337055220 +size 68960 diff --git a/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp new file mode 100644 index 00000000..fc197264 --- /dev/null +++ b/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:94dca11a2af6bf17da202e8c89ce6f27021acde348623c2d1b944ed24aa01c8f +size 59956 diff --git a/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md new file mode 100644 index 00000000..bc5e4938 --- /dev/null +++ b/lang/en/docs/tutorials/materials/specific/nanocluster-gold.md @@ -0,0 +1,171 @@ +--- +# YAML header +render_macros: true +--- + +# Gold Nanoclusters + +## Introduction + +This tutorial demonstrates the process of creating a gold nanoparticle structures based on the work presented in the following manuscript. + +!!!note "Manuscript" + > **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, + > "Electronic shell structure and chemisorption on gold nanoparticles", + > *Phys. Rev. B 84, 245429 (2011)*, + > [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. + +We use the [Materials Designer](../../../materials-designer/overview.md) to create gold nanoparticle structures of cuboctahedral and icosahedral shapes as shown in the image below. + + +![Gold Nanoparticles](/images/tutorials/materials/0d_materials/nanocluster_gold/0-manuscript-image.webp "Fig. 2. Gold Nanoparticles") + +## 1. Load and preview Gold structure + +First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the Gold material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). + +![Standata Gold Import](/images/tutorials/materials/0d_materials/nanocluster_gold/1-standata-import-gold.webp "Standata Gold Import") + +Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create gold nanoparticle structures. + +## 2. Create cuboctahedra + +### 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_cluster_ase.ipynb` notebook to modify the parameters by changing values: + + - `shape = ASENanoparticleShapesEnum.OCTAHEDRON` - the shape of the nanocluster + - `parameters = {"length": 5, "cutoff": 2}` - the parameters of the nanocluster according to [ASE Cluster Octahedron](https://wiki.fysik.dtu.dk/ase/ase/cluster/cluster.html#ase.cluster.Octahedron) documentation. + +Cuboctahedron shape is achieved by setting parameters of the octahedron to be in relationship: `length = 2 * cutoff + 1` + +Copy the content below and adjust the "1.1. Set up slab parameters" cell in the notebook: + +```python +shape = ASENanoparticleShapesEnum.OCTAHEDRON +parameters = { + "length": 5, + "cutoff": 2 +} +``` + +![Setup for cuboctahedron cluster](/images/tutorials/materials/0d_materials/nanocluster_gold/2-jl-setup.webp "Setup for cuboctahedron cluster") + +### 2.3. Run the notebook + +Run the notebook by selecting "Run > Run All Cells" from the menu. + +![Run All](/images/jupyterlite/run-all.webp "Run All") + +### 2.4. Analyze the Results + +After running the notebook, the octahedral gold nanoparticle structure will be created. + +The user will be able to visualize the created structure and download the corresponding files. + +For better view of the solid symmetry rotation of image might be needed like `"rotation": "45y,45x"` for the cuboctahedron. + +![Cuboctahedron Gold Nanocluster](/images/tutorials/materials/0d_materials/nanocluster_gold/3-jl-result-preview.webp "Cuboctahedron Gold Nanocluster") + +### 2.5. Pass the Material to the Materials Designer + +After reviewing the results, the user can pass the material to Materials Designer for further analysis. + +![Final Material](/images/tutorials/materials/0d_materials/nanocluster_gold/4-wave-result.webp "Final Material") + +Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. + +## 3. Create clusters with other shapes and sizes + +### 3.1. Repeat the steps above + +Repeat the steps above to create gold nanoparticle structures with other shapes and sizes. + +To create the rest of the structures set the `shape` and other parameters accordingly: + +For Cuboctahedron with 147 atoms: + +```python +shape = ASENanoparticleShapesEnum.OCTAHEDRON +parameters = { + "length": 7, + "cutoff": 3 +} +``` + +![Cuboctahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-147.webp "Cuboctahedron 147") + +For Cuboctahedron with 309 atoms: + +```python +shape = ASENanoparticleShapesEnum.OCTAHEDRON +parameters = { + "length": 9, + "cutoff": 4 +} +``` + +![Cuboctahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-cuboctahedron-309.webp "Cuboctahedron 309") + +For Icosahedron with 55 atoms: + +```python +shape = ASENanoparticleShapesEnum.ICOSAHEDRON +parameters = { + "noshells": 3 +} +``` + +![Icosahedron 55](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-55.webp "Icosahedron 55") + +For Icosahedron with 147 atoms: + +```python +shape = ASENanoparticleShapesEnum.ICOSAHEDRON +parameters = { + "noshells": 4 +} +``` + +![Icosahedron 147](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-147.webp "Icosahedron 147") + +For Icosahedron with 309 atoms: + +```python +shape = ASENanoparticleShapesEnum.ICOSAHEDRON +parameters = { + "noshells": 5 +} +``` + +![Icosahedron 309](/images/tutorials/materials/0d_materials/nanocluster_gold/jl-result-preview-icosahedron-309.webp "Icosahedron 309") + +## Interactive JupiterLite Notebook + +The interactive JupyterLite notebook for creating Gold Nanoclusters 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/nanocluster_gold.ipynb' %} +{% include 'jupyterlite_embed.html' %} +{% endwith %} +{% endwith %} +{% endwith %} + +## References + +1. **A. H. Larsen, J. Kleis, K. S. Thygesen, J. K. Nørskov, and K. W. Jacobsen**, + "Electronic shell structure and chemisorption on gold nanoparticles", + *Phys. Rev. B 84, 245429 (2011)*, + [DOI: 10.1103/PhysRevB.84.245429](https://doi.org/10.1103/PhysRevB.84.245429){:target='_blank'}. + + +## Tags + +`gold`, `cluster`, `nanoparticle`, `cuboctahedron`, `icosahedron` \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 4c4abda6..605790f7 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -227,6 +227,7 @@ 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 + - Gold Nanoclusters: tutorials/materials/specific/nanocluster-gold.md # COMMON UI COMPONENTS - Interface Components: