From e93948297ca71fb1ca25e581cf6cfb20adbcea2a Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Mon, 21 Oct 2024 16:50:44 -0700 Subject: [PATCH 01/12] update: add island tutroial wip --- .../defect-creation-surface-island.md | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md new file mode 100644 index 000000000..371e41299 --- /dev/null +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -0,0 +1,125 @@ +--- +# YAML header +render_macros: true +--- + +# TiN/TiN(001) Islands + +## Introduction + +This tutorial demonstrates the process of creating material with island on the surface of TiN(001) based on the work presented in the following manuscript. + +[//]: # () + +!!!note "Reference" + 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'}. + +We use the [Materials Designer](../../../materials-designer/overview.md) to create a slab of TiN, identify the cartesian coordinates for an island on the surface, and build it. + +We will focus on creating graphene-nitrogen structures from FIG. 2. +Specifically, the material from FIG. 2. a) 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)") + + +## 1. Create TiN Slab + +First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). + +![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") + +We then use the [Advanced](../../../materials-designer/header-menu/advanced/supercell.md) menu to create a slab of TiN with Miller indices (001), a thickness of 3 unit cells, and a supercell size of 9x9. + +![Supercell Creation for Graphene](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/2-advanced-supercell.webp "Supercell Graphene") + +## 2. Identify Island vertices coordinates + +Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to identify the cartesian coordinates for the island vertices. + +![3D Editor](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/4-threejs-editor-coordinates.webp "3D Editor") + +Click on the atoms to get the coordinates on the surface. Then copy/paste these coordinates into a text file for later use. + +## 3. Create Island on the Surface + +For the defect creation, we will use the [JupyterLite](../../../jupyterlite/overview.md) environment with the corresponding notebook. + +### 3.1. 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") + +### 3.2. Open `create_point_defect.ipynb` notebook + +Find `create_island_defect.ipynb` in the list of notebooks and click/double-click open it. + +### 3.3. Open and modify the notebook + +Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. + +Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: + +```python +ISLAND_SHAPE = 'box' +AUTO_ADD_VACUUM = True +VACUUM_THICKNESS = 10.0 +NUMBER_OF_ADDED_LAYERS = 1 + +BOX_PARAMS = { + 'min_coordinate': [0.25, 0.3, 0], + 'max_coordinate': [0.75, 0.8, 0.7], + "use_cartesian_coordinates": False +} + +``` + +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 + +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 + +After running the notebook, the user will be able to visualize the created material with the island on the surface. + +![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 + +The user can pass the resulting material to the current Materials Designer environment and save it. + +![Final Material](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/7-wave-result.webp "N-doped Graphene") + +Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. + + +## Interactive JupyterLite Notebook + +The following JupyterLite notebook demonstrates the process of creating material with island. 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_island.ipynb' %} +{% include 'jupyterlite_embed.html' %} +{% endwith %} +{% endwith %} +{% endwith %} + + + +## Tags + +`defects`, `TiN`, `island`, `surface`, `surface-defects`, `nitrogen`, `titatium` From 14328305c0fab7da85b19897451c8a21f0eb2a25 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 13:37:43 -0700 Subject: [PATCH 02/12] udpate: add slab creation with nb to tutorial --- .../defect-creation-surface-island.md | 55 +++++++++++++++++-- 1 file changed, 50 insertions(+), 5 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index 371e41299..687cf0d83 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -29,9 +29,54 @@ First, we navigate to [Materials Designer](../../../materials-designer/overview. ![Standata Graphene Import](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/1-standata-graphene.webp "Standata Graphene Import") -We then use the [Advanced](../../../materials-designer/header-menu/advanced/supercell.md) menu to create a slab of TiN with Miller indices (001), a thickness of 3 unit cells, and a supercell size of 9x9. -![Supercell Creation for Graphene](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/2-advanced-supercell.webp "Supercell Graphene") +Then we will use the [JupyterLite](../../../jupyterlite/overview.md) environment to create a TiN slab. + +### 1.1. 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") + +### 1.2. Open `create_slab.ipynb` notebook + +Find `create_slab.ipynb` in the list of notebooks and click/double-click open it. + +### 1.3. Open and modify the notebook + +Next, edit `create_slab.ipynb` notebook to modify the parameters by adding the following content to the "1.1. Set up slab parameters" cell in the notebook: + +```python +# Enable interactive selection of terminations via UI prompt +IS_TERMINATIONS_SELECTION_INTERACTIVE = False + +MILLER_INDICES = (0, 0, 1) +THICKNESS = 3 # in atomic layers +VACUUM = 10.0 # in angstroms +XY_SUPERCELL_MATRIX = [[9, 0], [0, 9]] +USE_ORTHOGONAL_Z = True +USE_CONVENTIONAL_CELL = True + +# Index of the termination pair to be selected +TERMINATION_INDEX = 0 +``` + +### 1.4. 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") + +### 1.5. Analyze the Results + +After running the notebook, the user will be able to visualize the created TiN slab. + +![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results") + +### 1.6. Pass the Material to Materials Designer + +The user can pass the resulting material to the current Materials Designer environment for further analysis. + ## 2. Identify Island vertices coordinates @@ -65,11 +110,11 @@ Copy the below content and edit the "1.1. Set up defect parameters" cell in the ISLAND_SHAPE = 'box' AUTO_ADD_VACUUM = True VACUUM_THICKNESS = 10.0 -NUMBER_OF_ADDED_LAYERS = 1 +NUMBER_OF_ADDED_LAYERS = 0.5 BOX_PARAMS = { 'min_coordinate': [0.25, 0.3, 0], - 'max_coordinate': [0.75, 0.8, 0.7], + 'max_coordinate': [0.75, 0.8, 1], "use_cartesian_coordinates": False } @@ -122,4 +167,4 @@ The following JupyterLite notebook demonstrates the process of creating material ## Tags -`defects`, `TiN`, `island`, `surface`, `surface-defects`, `nitrogen`, `titatium` +`defects`, `island`, `surface`, `surface-defects`, `TiN`, `nitrogen`, `titanium` From 6cbc59e0022a6543adb6b286657aa5040106350d Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 17:20:43 -0700 Subject: [PATCH 03/12] update: add images --- .../defects/defect_creation_surface_island/0.png | 3 +++ .../defects/defect_creation_surface_island/1.png | 3 +++ .../specific/defect-creation-surface-island.md | 10 ++++------ mkdocs.yml | 1 + 4 files changed, 11 insertions(+), 6 deletions(-) create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/0.png create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/1.png diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/0.png b/images/tutorials/materials/defects/defect_creation_surface_island/0.png new file mode 100644 index 000000000..c1684aab2 --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/0.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:20e9a6b6bfbbf1fbcb39954c9481469f68a544391f6f3869ff310f5ea59d751e +size 285428 diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/1.png b/images/tutorials/materials/defects/defect_creation_surface_island/1.png new file mode 100644 index 000000000..fb445c94a --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/1.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:12f5c88a4d178da7aabfa7dffca043630276a7091850c23ef262315f9e166832 +size 185434 diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index 687cf0d83..a812dcfca 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -12,7 +12,7 @@ This tutorial demonstrates the process of creating material with island on the s [//]: # () !!!note "Reference" - 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'}. + **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'}. We use the [Materials Designer](../../../materials-designer/overview.md) to create a slab of TiN, identify the cartesian coordinates for an island on the surface, and build it. @@ -20,7 +20,7 @@ We will focus on creating graphene-nitrogen structures from FIG. 2. Specifically, the material from FIG. 2. a) 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)") +![Surface Defect](/images/tutorials/materials/defects/defect_creation_surface_island/0.png "Surface Defect, Island FIG. 2. a)") ## 1. Create TiN Slab @@ -67,13 +67,11 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 1.5. Analyze the Results +### 1.5. Pass the Slab to Materials Designer After running the notebook, the user will be able to visualize the created TiN slab. -![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results") - -### 1.6. Pass the Material to Materials Designer +![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/1.png "Review the Results") The user can pass the resulting material to the current Materials Designer environment for further analysis. diff --git a/mkdocs.yml b/mkdocs.yml index 9fa2773be..263e3d0e3 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -219,6 +219,7 @@ nav: - Specific: - Substitutional Point Defects in Graphene: tutorials/materials/specific/defect-creation-point-substitution-graphene.md + - Island Surface Defect Formation: tutorials/materials/specific/defect-creation-surface-island.md # COMMON UI COMPONENTS From cbd14e9d7c7dce9672a6d928dcb7c99538c65b57 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 19:10:32 -0700 Subject: [PATCH 04/12] update: explain fractional coordiantes of island --- .../specific/defect-creation-surface-island.md | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index a812dcfca..c439428f3 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -53,7 +53,7 @@ IS_TERMINATIONS_SELECTION_INTERACTIVE = False MILLER_INDICES = (0, 0, 1) THICKNESS = 3 # in atomic layers VACUUM = 10.0 # in angstroms -XY_SUPERCELL_MATRIX = [[9, 0], [0, 9]] +XY_SUPERCELL_MATRIX = [[10, 0], [0, 10]] USE_ORTHOGONAL_Z = True USE_CONVENTIONAL_CELL = True @@ -102,6 +102,16 @@ Find `create_island_defect.ipynb` in the list of notebooks and click/double-clic Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. +The expected island is 4.5x4.5 unit cells (9x9 atoms), for that on the supercell 10x10 (20x20 atoms) we need to choose coordinates to be 0.45 crystal units apart along lattice a and lattice b, and to make them in the center: [0.0, 0.0] and [0.45, 0.45]. +To adjust for the next layer to start from Ti atom on the edge, we'll shift the coordinates of left border by 0.05 (1/20 -- the fraction of every atom) and the top border by -0.05 (1/20). +The z component of the first vertex of the box is 0, and the z component of the second vertex is 1 in crystal coordinates -- to cover the whole supercell in the z direction. + +The resulting coordinates are: [0.05, 0.0, 0], [0.45, 0.4, 1]. + +To shift the island to the center of the supercell, we need to add 2 unit cells (2/10 of the supercell) to the coordinates of the island vertices. + +Resulting coordinates of centered island: [0.25, 0.2, 0], [0.65, 0.6, 1]. + Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: ```python @@ -111,8 +121,8 @@ VACUUM_THICKNESS = 10.0 NUMBER_OF_ADDED_LAYERS = 0.5 BOX_PARAMS = { - 'min_coordinate': [0.25, 0.3, 0], - 'max_coordinate': [0.75, 0.8, 1], + 'min_coordinate': [0.25, 0.2, 0], + 'max_coordinate': [0.65, 0.6, 1], "use_cartesian_coordinates": False } From 6baf70e1e956ea190e10953862a04312a0171a13 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 19:37:45 -0700 Subject: [PATCH 05/12] update: add other images --- .../defect_creation_surface_island/final-material.png | 3 +++ .../defects/defect_creation_surface_island/island-setup.png | 3 +++ .../defect_creation_surface_island/original-result.png | 3 +++ .../defects/defect_creation_surface_island/slab-setup.png | 3 +++ .../materials/specific/defect-creation-surface-island.md | 6 +++--- 5 files changed, 15 insertions(+), 3 deletions(-) create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/final-material.png create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/original-result.png create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png b/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png new file mode 100644 index 000000000..6a44c80c2 --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:8192b53159755eedb0f86f5f245079ec006443b0934ff1e3ec2c3cc8a714cb83 +size 304457 diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png b/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png new file mode 100644 index 000000000..1fa479d0d --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:116e9b5ac54d7b0c1ef4f4546c6930c0bd031a84c7e5dfd83c4d402bd5ef0967 +size 165813 diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png b/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png new file mode 100644 index 000000000..b82a80f53 --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:701ac67de69115f97ed19ffc35229b20d81a80fd6206aba91a84ed8ed079b0ac +size 628449 diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png b/images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png new file mode 100644 index 000000000..ce25880d7 --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:502d9a1a74110fb283c87dff21ae3ae06bc1f83fdae2e002eb58d640aa1120c4 +size 176397 diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index c439428f3..795a245f5 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -130,7 +130,7 @@ BOX_PARAMS = { 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") +![Notebook setup](/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png "Notebook setup") ## 5. Run the Notebook @@ -142,13 +142,13 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook, the user will be able to visualize the created material with the island on the surface. -![Review the Results](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/6-jl-result-preview.webp "Review the Results") +![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png "Review the Results") ## 7. Pass the Material to Materials Designer The user can pass the resulting material to the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/7-wave-result.webp "N-doped Graphene") +![Final Material](/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png "Island on the Surface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. From 0888d957d306cf5329f00a48ccbb15daa0571de6 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 19:55:08 -0700 Subject: [PATCH 06/12] update: rewrite with gpt-4 --- .../specific/defect-creation-surface-island.md | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index 795a245f5..f2e395807 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -102,15 +102,19 @@ Find `create_island_defect.ipynb` in the list of notebooks and click/double-clic Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. -The expected island is 4.5x4.5 unit cells (9x9 atoms), for that on the supercell 10x10 (20x20 atoms) we need to choose coordinates to be 0.45 crystal units apart along lattice a and lattice b, and to make them in the center: [0.0, 0.0] and [0.45, 0.45]. -To adjust for the next layer to start from Ti atom on the edge, we'll shift the coordinates of left border by 0.05 (1/20 -- the fraction of every atom) and the top border by -0.05 (1/20). -The z component of the first vertex of the box is 0, and the z component of the second vertex is 1 in crystal coordinates -- to cover the whole supercell in the z direction. +We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. The initial coordinates for this are `[0.0, 0.0]` and `[0.45, 0.45]`. -The resulting coordinates are: [0.05, 0.0, 0], [0.45, 0.4, 1]. +To ensure the island starts from the Ti atom on the edge in the next layer, we will slightly adjust the coordinates: -To shift the island to the center of the supercell, we need to add 2 unit cells (2/10 of the supercell) to the coordinates of the island vertices. +Shift the left border by `0.05` (1/20 of the distance between atoms), +Shift the top border by `-0.05` (also 1/20 of the atom spacing). +For the z-axis, the first vertex will have a z-component of `0` (starting at the base of the supercell), and the second vertex will have a z-component of `1` (reaching the top of the supercell), ensuring the island spans the entire z-direction. -Resulting coordinates of centered island: [0.25, 0.2, 0], [0.65, 0.6, 1]. +The coordinates after these adjustments are: `[0.05, 0.0, 0]` and `[0.45, 0.4, 1]`. + +Finally, to move the island to the center of the supercell, add 2 unit cells (2/10 of the supercell size) to both island vertex coordinates. + +The final centered coordinates of the island are: `[0.25, 0.2, 0]` and `[0.65, 0.6, 1]`. Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: From fe3d191ae5989696924528e8a06cb19e82c9d14d Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 20:36:35 -0700 Subject: [PATCH 07/12] update: merge two stages of tutotial --- .../defect-creation-surface-island.md | 64 +++++++++---------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index f2e395807..ec2ff1ada 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -23,7 +23,7 @@ Specifically, the material from FIG. 2. a) of the paper: ![Surface Defect](/images/tutorials/materials/defects/defect_creation_surface_island/0.png "Surface Defect, Island FIG. 2. a)") -## 1. Create TiN Slab +## 1. Create TiN Slab to preview the Surface First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -40,7 +40,7 @@ Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/ ### 1.2. Open `create_slab.ipynb` notebook -Find `create_slab.ipynb` in the list of notebooks and click/double-click open it. +Find `create_slab.ipynb` in the list of notebooks and double-click open it. ### 1.3. Open and modify the notebook @@ -67,54 +67,46 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and ![Run All](/images/jupyterlite/run-all.webp "Run All") -### 1.5. Pass the Slab to Materials Designer +### 1.5. Analyze the Results After running the notebook, the user will be able to visualize the created TiN slab. ![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/1.png "Review the Results") -The user can pass the resulting material to the current Materials Designer environment for further analysis. +## 2. Identifying the Island vertices coordinates -## 2. Identify Island vertices coordinates +We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. The initial coordinates for this are `[0.0, 0.0]` and `[0.45, 0.45]`. -Next, we open the [3D editor](../../../materials-designer/3d-editor.md) to identify the cartesian coordinates for the island vertices. +To ensure the island starts from the Ti atom on the edge in the next layer, we will slightly adjust the coordinates: -![3D Editor](/images/tutorials/materials/defects/defect_creation_point_substitution_graphene/4-threejs-editor-coordinates.webp "3D Editor") +Shift the left border by `0.05` (1/20 of the distance between atoms), +Shift the top border by `-0.05` (also 1/20 of the atom spacing). +For the z-axis, the first vertex will have a z-component of `0` (starting at the base of the supercell), and the second vertex will have a z-component of `1` (reaching the top of the supercell), ensuring the island spans the entire z-direction. -Click on the atoms to get the coordinates on the surface. Then copy/paste these coordinates into a text file for later use. +The coordinates after these adjustments are: `[0.05, 0.0, 0]` and `[0.45, 0.4, 1]`. -## 3. Create Island on the Surface +Finally, to move the island to the center of the supercell, add 2 unit cells (2/10 of the supercell size) to both island vertex coordinates. -For the defect creation, we will use the [JupyterLite](../../../jupyterlite/overview.md) environment with the corresponding notebook. +The final centered coordinates of the island are: `[0.25, 0.2, 0]` and `[0.65, 0.6, 1]`. -### 3.1. Launch JupyterLite Session +These coordinates will be used in the next step to create the island on the surface. -Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/header-menu/advanced/jupyterlite-dialog.md)" menu item to launch the JupyterLite environment. +## 3. Create Island on the Surface -![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") +### 3.1. Open `create_point_defect.ipynb` notebook -### 3.2. Open `create_point_defect.ipynb` notebook +Close the current notebook. `Introduction` notebook should be open by default. -Find `create_island_defect.ipynb` in the list of notebooks and click/double-click open it. +Find `create_island_defect.ipynb` in the list of notebooks and double-click open it. -### 3.3. Open and modify the notebook +### 3.2. Modify the notebook Next, edit `create_island_defect.ipynb` notebook to modify the parameters by adding a list of [defect configuration objects](https://github.com/Exabyte-io/made/blob/3d938b4d91a31323dca7a02acb12b646dbb26634/src/py/mat3ra/made/tools/build/defect/configuration.py#L191) containing the cartesian coordinates of the island vertices. -We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. The initial coordinates for this are `[0.0, 0.0]` and `[0.45, 0.45]`. - -To ensure the island starts from the Ti atom on the edge in the next layer, we will slightly adjust the coordinates: +With the same TiN material selected in the materials input and coordinates for the island vertices from the previous step, the user can create the island on the surface. -Shift the left border by `0.05` (1/20 of the distance between atoms), -Shift the top border by `-0.05` (also 1/20 of the atom spacing). -For the z-axis, the first vertex will have a z-component of `0` (starting at the base of the supercell), and the second vertex will have a z-component of `1` (reaching the top of the supercell), ensuring the island spans the entire z-direction. - -The coordinates after these adjustments are: `[0.05, 0.0, 0]` and `[0.45, 0.4, 1]`. - -Finally, to move the island to the center of the supercell, add 2 unit cells (2/10 of the supercell size) to both island vertex coordinates. - -The final centered coordinates of the island are: `[0.25, 0.2, 0]` and `[0.65, 0.6, 1]`. +Notice, that we did not create the slab yet, so it is necessary to provide slab parameters in this notebook. Copy the below content and edit the "1.1. Set up defect parameters" cell in the notebook as follows: @@ -124,31 +116,39 @@ AUTO_ADD_VACUUM = True VACUUM_THICKNESS = 10.0 NUMBER_OF_ADDED_LAYERS = 0.5 -BOX_PARAMS = { +BOX_PARAMETERS = { 'min_coordinate': [0.25, 0.2, 0], 'max_coordinate': [0.65, 0.6, 1], "use_cartesian_coordinates": False } +DEFAULT_SLAB_PARAMETERS = { + "miller_indices": (0,0,1), + "thickness": 3, + "vacuum": 0.0, + "use_orthogonal_z": True, + "xy_supercell_matrix": [[10, 0], [0, 10]] +} + ``` Here's the visual of the updated content: ![Notebook setup](/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png "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 created material with the island on the surface. ![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png "Review the Results") -## 7. Pass the Material to Materials Designer +## 6. Pass the Material to Materials Designer The user can pass the resulting material to the current Materials Designer environment and save it. From 0bd0dd79bf2f50d5c1a59f21bc15387f87f85f11 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Tue, 22 Oct 2024 20:40:25 -0700 Subject: [PATCH 08/12] update: merge two stages of tutotial --- .../materials/specific/defect-creation-surface-island.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index ec2ff1ada..e9b89ddfa 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -23,7 +23,7 @@ Specifically, the material from FIG. 2. a) of the paper: ![Surface Defect](/images/tutorials/materials/defects/defect_creation_surface_island/0.png "Surface Defect, Island FIG. 2. a)") -## 1. Create TiN Slab to preview the Surface +## 1. Create and preview TiN Slab First, we navigate to [Materials Designer](../../../materials-designer/overview.md) and import the graphene material from the [Standata](../../../materials-designer/header-menu/input-output/standata-import.md). @@ -73,6 +73,7 @@ After running the notebook, the user will be able to visualize the created TiN s ![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/1.png "Review the Results") +We don't need to save the material at this point, as we will recreate the slab with island on the surface in the next notebook. This step is needed to identify the coordinates of the island vertices. ## 2. Identifying the Island vertices coordinates From a5e286f193ed8a063c5f07e391ccc409ff6f3e4d Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 23 Oct 2024 10:54:21 -0700 Subject: [PATCH 09/12] update: add gif for final material --- .../defects/defect_creation_surface_island/final-material.gif | 3 +++ .../materials/specific/defect-creation-surface-island.md | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif b/images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif new file mode 100644 index 000000000..fb1eb708c --- /dev/null +++ b/images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4548f4451dc43e9223c9ee0501906c3c36f2aef36e2d30361a5c4d8aeb8bdaa3 +size 2687681 diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index e9b89ddfa..d1b8eda2c 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -153,7 +153,7 @@ After running the notebook, the user will be able to visualize the created mater The user can pass the resulting material to the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png "Island on the Surface") +![Final Material](/images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif "Island on the Surface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. From d0388ca2a799b20e7abb6805ab16eb8de8dd75e5 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 23 Oct 2024 11:01:47 -0700 Subject: [PATCH 10/12] chore: cleanups --- .../defect-creation-surface-island.md | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md index d1b8eda2c..4d14464c3 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md @@ -12,7 +12,8 @@ This tutorial demonstrates the process of creating material with island on the s [//]: # () !!!note "Reference" - **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'}. + **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'}. We use the [Materials Designer](../../../materials-designer/overview.md) to create a slab of TiN, identify the cartesian coordinates for an island on the surface, and build it. @@ -38,11 +39,8 @@ Select the "Advanced > [JupyterLite Transformation](../../../materials-designer/ ![JupyterLite Dialog](/images/jupyterlite/md-advanced-jl.webp "JupyterLite Dialog") -### 1.2. Open `create_slab.ipynb` notebook -Find `create_slab.ipynb` in the list of notebooks and double-click open it. - -### 1.3. Open and modify the notebook +### 1.2. Open and modify the notebook Next, edit `create_slab.ipynb` notebook to modify the parameters by adding the following content to the "1.1. Set up slab parameters" cell in the notebook: @@ -61,13 +59,13 @@ USE_CONVENTIONAL_CELL = True TERMINATION_INDEX = 0 ``` -### 1.4. Run the Notebook +### 1.3. 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") -### 1.5. Analyze the Results +### 1.4. Analyze the Results After running the notebook, the user will be able to visualize the created TiN slab. @@ -77,12 +75,16 @@ We don't need to save the material at this point, as we will recreate the slab w ## 2. Identifying the Island vertices coordinates -We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. The initial coordinates for this are `[0.0, 0.0]` and `[0.45, 0.45]`. +We are creating an island defect that covers an area of 4.5x4.5 unit cells (which corresponds to 9x9 atoms). This island will be placed inside a 10x10 supercell (20x20 atoms). +To position the island correctly, we need to select coordinates that are `0.45` crystal units apart along both lattice directions (a and b), ensuring the island is centered. + +The initial coordinates for this are `[0.0, 0.0]` and `[0.45, 0.45]`. To ensure the island starts from the Ti atom on the edge in the next layer, we will slightly adjust the coordinates: -Shift the left border by `0.05` (1/20 of the distance between atoms), -Shift the top border by `-0.05` (also 1/20 of the atom spacing). +- Shift the left border by `0.05` (1/20 of the distance between atoms), +- Shift the top border by `-0.05` (also 1/20 of the atom spacing). + For the z-axis, the first vertex will have a z-component of `0` (starting at the base of the supercell), and the second vertex will have a z-component of `1` (reaching the top of the supercell), ensuring the island spans the entire z-direction. The coordinates after these adjustments are: `[0.05, 0.0, 0]` and `[0.45, 0.4, 1]`. From 7f77fd1966fca3873ce27c6ad457dd5482397dfd Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 23 Oct 2024 20:00:12 -0700 Subject: [PATCH 11/12] chore: remove one image, rename nb --- .../0.png | 0 .../1.png | 0 .../final-material.gif | 0 .../island-setup.png | 0 .../original-result.png | 0 .../slab-setup.png | 0 .../defect_creation_surface_island/final-material.png | 3 --- ...defect-creation-surface-island-titanium-nitride.md} | 10 +++++----- mkdocs.yml | 2 +- 9 files changed, 6 insertions(+), 9 deletions(-) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/0.png (100%) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/1.png (100%) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/final-material.gif (100%) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/island-setup.png (100%) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/original-result.png (100%) rename images/tutorials/materials/defects/{defect_creation_surface_island => defect-creation-surface-island-titanium-nitride}/slab-setup.png (100%) delete mode 100644 images/tutorials/materials/defects/defect_creation_surface_island/final-material.png rename lang/en/docs/tutorials/materials/specific/{defect-creation-surface-island.md => defect-creation-surface-island-titanium-nitride.md} (92%) diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/0.png b/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png similarity index 100% rename from images/tutorials/materials/defects/defect_creation_surface_island/0.png rename to 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b/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png similarity index 100% rename from images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png rename to images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png b/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png similarity index 100% rename from images/tutorials/materials/defects/defect_creation_surface_island/original-result.png rename to images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png b/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/slab-setup.png similarity index 100% rename from images/tutorials/materials/defects/defect_creation_surface_island/slab-setup.png rename to images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/slab-setup.png diff --git a/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png b/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png deleted file mode 100644 index 6a44c80c2..000000000 --- a/images/tutorials/materials/defects/defect_creation_surface_island/final-material.png +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:8192b53159755eedb0f86f5f245079ec006443b0934ff1e3ec2c3cc8a714cb83 -size 304457 diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md similarity index 92% rename from lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md rename to lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md index 4d14464c3..ed215eaee 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md @@ -21,7 +21,7 @@ We will focus on creating graphene-nitrogen structures from FIG. 2. Specifically, the material from FIG. 2. a) of the paper: -![Surface Defect](/images/tutorials/materials/defects/defect_creation_surface_island/0.png "Surface Defect, Island FIG. 2. a)") +![Surface Defect](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/0.png "Surface Defect, Island FIG. 2. a)") ## 1. Create and preview TiN Slab @@ -69,7 +69,7 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook, the user will be able to visualize the created TiN slab. -![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/1.png "Review the Results") +![Review the Results](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/1.png "Review the Results") We don't need to save the material at this point, as we will recreate the slab with island on the surface in the next notebook. This step is needed to identify the coordinates of the island vertices. @@ -137,7 +137,7 @@ DEFAULT_SLAB_PARAMETERS = { Here's the visual of the updated content: -![Notebook setup](/images/tutorials/materials/defects/defect_creation_surface_island/island-setup.png "Notebook setup") +![Notebook setup](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/island-setup.png "Notebook setup") ## 4. Run the Notebook @@ -149,13 +149,13 @@ Run the notebook by clicking `Run` > `Run All` in the top menu to run cells and After running the notebook, the user will be able to visualize the created material with the island on the surface. -![Review the Results](/images/tutorials/materials/defects/defect_creation_surface_island/original-result.png "Review the Results") +![Review the Results](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/original-result.png "Review the Results") ## 6. Pass the Material to Materials Designer The user can pass the resulting material to the current Materials Designer environment and save it. -![Final Material](/images/tutorials/materials/defects/defect_creation_surface_island/final-material.gif "Island on the Surface") +![Final Material](/images/tutorials/materials/defects/defect-creation-surface-island-titanium-nitride/final-material.gif "Island on the Surface") Or the user can [save or download](../../../materials-designer/header-menu/input-output.md) the material in Material JSON format or POSCAR format. diff --git a/mkdocs.yml b/mkdocs.yml index 263e3d0e3..ed609a633 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -219,7 +219,7 @@ nav: - Specific: - Substitutional Point Defects in Graphene: tutorials/materials/specific/defect-creation-point-substitution-graphene.md - - Island Surface Defect Formation: tutorials/materials/specific/defect-creation-surface-island.md + - Island Surface Defect Formation in TiN: tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md # COMMON UI COMPONENTS From 729379369aa52ed69c3916f576272c2a3c5f0d89 Mon Sep 17 00:00:00 2001 From: VsevolodX <79542055+VsevolodX@users.noreply.github.com> Date: Wed, 23 Oct 2024 20:00:55 -0700 Subject: [PATCH 12/12] chore: change name in title --- .../specific/defect-creation-surface-island-titanium-nitride.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md index ed215eaee..05c002a88 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-creation-surface-island-titanium-nitride.md @@ -3,7 +3,7 @@ render_macros: true --- -# TiN/TiN(001) Islands +# Island Surface Defect Formation in TiN ## Introduction