Merge pull request #293 from Exabyte-io/chore/update-jupyterlite-urls-and-cleanups

chore: update JL urls plus cleanups

Author: timurbazhirov

lang/en/docs/includes/jupyterlite_embed.html

@@ -1,7 +1,7 @@
 <div id="jupyterlite-embed-container" class="jupyterlite-embed-container" style="position: relative; width:100%; height:600px;">
   <iframe
     id="jupyterlite-iframe"
-    src="{% if notebooks_path_root and notebook_name %}{{ origin_url }}/tree?path={{ notebooks_path_root }}/{{ notebook_name }}{% else %}{{ origin_url }}{% endif %}"
+    src="{% if notebooks_path_root and notebook_name %}{{ origin_url }}?path={{ notebooks_path_root }}/{{ notebook_name }}{% else %}{{ origin_url }}{% endif %}"
     width="100%"
     height="100%"
     style="border:none;"

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
 

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`
+`adatom`, `graphene`, `metal`, `surface`, `defect`

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 %}
 
-<!--
-{# TODO: Update the origin_url
-    {% 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 %}
-#}
--->
+## 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
 

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`

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/notebooks
+        # Ucomment to use lab instead of notebook
+        # origin_url: https://jupyterlite.mat3ra.com/lab/tree
+        notebooks_path_root: made
 
 markdown_extensions:
     - admonition