From 41e06e727740710440344370ee38dddc22648d99 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Wed, 20 Nov 2024 12:55:44 -0800 Subject: [PATCH 1/3] chore: update JL urls plus cleanups --- .../specific/defect-point-substitution-graphene.md | 11 ++++++++++- .../specific/defect-surface-adatom-graphene.md | 6 ++---- .../defect-surface-island-titanium-nitride.md | 10 +++------- ...sted-commensurate-lattices-molybdenum-disulfide.md | 4 ++++ mkdocs.yml | 6 ++++-- 5 files changed, 23 insertions(+), 14 deletions(-) diff --git a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md index 006a99369..732bb6130 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-point-substitution-graphene.md @@ -126,9 +126,18 @@ 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="https://jupyterlite.mat3ra.com/retro/notebooks/?path=api-examples/other/materials_designer/specific_examples/defect_point_substitution_graphene.ipynb" %} +{% with origin_url=config.extra.jupyterlite.origin_url %} +{% with notebooks_path_root=config.extra.jupyterlite.notebooks_path_root %} +{% with notebook_name='specific_examples/defect_point_substitution_graphene.ipynb' %} {% include 'jupyterlite_embed.html' %} {% endwith %} +{% endwith %} +{% endwith %} + +## References + +1. 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'}. + ## Tags diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md index 9cfbdd628..1c63384d6 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-adatom-graphene.md @@ -221,10 +221,8 @@ The interactive JupyterLite notebook for creating Graphene structures with metal ## References -1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, - "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 - [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. +1. **Kevin T. Chan, J. B. Neaton, and Marvin L. Cohen**, "First-principles study of metal adatom adsorption on graphene" Phys. Rev. B 77, 235430, 2008 [DOI: 10.1103/PhysRevB.77.235430](https://doi.org/10.1103/PhysRevB.77.235430){:target='_blank'}. ## Tags -`adatom`, `graphene`, `metal`, `surface`, `defect` \ No newline at end of file +`adatom`, `graphene`, `metal`, `surface`, `defect` diff --git a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md index da2c256ed..5a1d62f11 100644 --- a/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md +++ b/lang/en/docs/tutorials/materials/specific/defect-surface-island-titanium-nitride.md @@ -172,13 +172,9 @@ The following JupyterLite notebook demonstrates the process of creating material {% endwith %} {% endwith %} - +## References + +1. 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'}. ## Tags diff --git a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md index 48d91dbac..97a287db8 100644 --- a/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md +++ b/lang/en/docs/tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md @@ -145,3 +145,7 @@ The interactive JupyterLite notebook for creating twisted bilayer MoS2 structure 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) + +## Tags + +`2d-materials`, `layers`, `bilayer`, `twisted`, `commensurate`, `molybdenum`, `disulfide` diff --git a/mkdocs.yml b/mkdocs.yml index 8593af428..0bee68c9a 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -47,8 +47,10 @@ extra: provider: google property: UA-69270713-5 jupyterlite: - origin_url: https://jupyterlite.mat3ra.com/lab - notebooks_path_root: api-examples/other/materials_designer + origin_url: https://jupyterlite.mat3ra.com/retro/notebook + # Ucomment to use lab instead of notebook + # origin_url: https://jupyterlite.mat3ra.com/lab + notebooks_path_root: made markdown_extensions: - admonition From b7a8f3507cb696a70595384e3783341fe90363fb Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Wed, 20 Nov 2024 13:02:39 -0800 Subject: [PATCH 2/3] fix: typo --- mkdocs.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index 0bee68c9a..8ade81c4c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -47,7 +47,7 @@ extra: provider: google property: UA-69270713-5 jupyterlite: - origin_url: https://jupyterlite.mat3ra.com/retro/notebook + origin_url: https://jupyterlite.mat3ra.com/retro/notebooks # Ucomment to use lab instead of notebook # origin_url: https://jupyterlite.mat3ra.com/lab notebooks_path_root: made From aca1d3644a0cafb1a8b477f47485b286cde6cb53 Mon Sep 17 00:00:00 2001 From: Timur Bazhirov Date: Wed, 20 Nov 2024 13:11:51 -0800 Subject: [PATCH 3/3] chore: fix JL embed url --- lang/en/docs/includes/jupyterlite_embed.html | 2 +- mkdocs.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lang/en/docs/includes/jupyterlite_embed.html b/lang/en/docs/includes/jupyterlite_embed.html index 9cc900384..d98b8fd59 100644 --- a/lang/en/docs/includes/jupyterlite_embed.html +++ b/lang/en/docs/includes/jupyterlite_embed.html @@ -1,7 +1,7 @@