chore: upgrade docusaurus to v3 and other related changes

pranabdas · Dec 1, 2023 · fef2af2 · fef2af2
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -1,9 +1,8 @@
 {
-  "image": "mcr.microsoft.com/vscode/devcontainers/base:ubuntu",
-  // https://github.com/microsoft/vscode-dev-containers/tree/main/containers
+  "image": "mcr.microsoft.com/devcontainers/base:ubuntu",
   "features": {
     "node": {
-      "version": "18"
+      "version": "20"
     }
   },
   "customizations": {

diff --git a/.github/workflows/deploy-gh-pages.yml b/.github/workflows/deploy-gh-pages.yml
@@ -16,21 +16,16 @@ jobs:
       group: ${{ github.workflow }}-${{ github.ref }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Prepare Node environment
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: '18'
+          node-version: '20'
 
       - name: Install NPM packages
         run: npm install
 
-      - name: Apply customizations
-        run: |
-          sed -i.bak 's/f6f8fa/f6f6f6/gI' node_modules/prism-react-renderer/themes/github/index.cjs.js
-#         sed -i.bak 's/box-shadow: var(--ifm-global-shadow-lw)/box-shadow: none/gI' node_modules/@docusaurus/theme-classic/src/theme/CodeBlock/styles.module.css
-
       - name: Build website
         run: npm run build
 

diff --git a/README.md b/README.md
@@ -6,4 +6,4 @@
 
 This repository contains the various input files and jupyter notebooks (for post
 processing and plotting) of the project. Please follow the tutorial at
-<https://pranabdas.github.io/espresso/>
+https://pranabdas.github.io/espresso/
diff --git a/docs/hands-on/bands.mdx b/docs/hands-on/bands.mdx
@@ -164,5 +164,5 @@ inorganic scintillator materials., ACS Combinatorial Science. (2011)
 
 ## Resources
 
-- <https://docs.materialsproject.org/methodology/materials-methodology/electronic-structure#accuracy-of-band-structures>
+- https://docs.materialsproject.org/methodology/materials-methodology/electronic-structure#accuracy-of-band-structures
 - [See K-pat online tool](https://www.materialscloud.org/work/tools/seekpath)
diff --git a/docs/hands-on/dft-u.mdx b/docs/hands-on/dft-u.mdx
@@ -7,7 +7,7 @@ Electronic structure for transition metals (with localized $$d$$ or $$f$$
 electrons) is not accurately described by standard DFT, and therefore the need
 for DFT+U formulation.
 
-```bash
+```fortran
 &SYSTEM
     ...
     lda_plus_u = .TRUE.
@@ -25,7 +25,7 @@ exchange interaction. Number of $$J$$ terms depends on the manifold of localized
 electrons. For $$p$$, we have 1; for $$d$$, we have 2; and for $$f$$, we have 3
 terms.
 
-```bash
+```fortran
     ...
     lda_plus_u = .TRUE.
     lda_plus_u_kind = 1

diff --git a/docs/hands-on/phonon.mdx b/docs/hands-on/phonon.mdx
@@ -147,4 +147,4 @@ plt.show()
 ## Resources
 
 - [School on Electron-Phonon Physics from First Principles (2018)](https://indico.ictp.it/event/8301/other-view?view=ictptimetable) ([Video lectures on YouTube](https://www.youtube.com/playlist?list=PLYc-eBoIpXTIboem6dKTYD1-1m0sMYnYz))
-- <https://github.com/nguyen-group/QE-SSP>
+- https://github.com/nguyen-group/QE-SSP
diff --git a/docs/hands-on/scf.mdx b/docs/hands-on/scf.mdx
@@ -157,5 +157,5 @@ In our calculation we have specified the number of bands = 8. Otherwise, there
 would be 4 bands for 8 electrons in case of non spin-polarized systems.
 
 ## Resources
-- <https://www.quantum-espresso.org/Doc/pw_user_guide/>
+- https://www.quantum-espresso.org/Doc/pw_user_guide/
 - [Quantum Espresso Input Generator](https://www.materialscloud.org/work/tools/qeinputgenerator) (can help crating QE input files)
diff --git a/docs/hands-on/soc.mdx b/docs/hands-on/soc.mdx
@@ -7,7 +7,7 @@ In order to consider spin orbit coupling effect in our electronic structure
 calculation in quantum espresso, we need to use a full relativistic pseudo
 potential. Following settings are needed in the `&SYSTEM` card:
 
-```bash
+```fortran
 &SYSTEM
     ...
     noncolin = .true.
@@ -31,7 +31,7 @@ coupling.
 
 We can constrain the magnetic moment:
 
-```bash
+```fortran
 &SYSTEM
   ...
   constrained_magnetization = 'atomic direction'
@@ -43,7 +43,7 @@ Starting magnetization can be specified by `angle1` (angle with $z$ axis) and
 `angle2` (angle of projection in $xy$-plane and with $x$-axis). Also check the
 penalty function ($\lambda$).
 
-```bash
+```fortran
 &SYSTEM
   ...
   angle1(i) = 0.0d0
@@ -63,7 +63,7 @@ Spin-orbit coupling calculations are often hard to converge. Use a smaller
 non-relativistic pseudopotential, and then start from the obtained charge
 density to perform non-colinear spin orbit calculation.
 
-```bash
+```fortran
 &ELECTRONS
   ...
   mixing_beta = 1.0000000000d-01
@@ -77,7 +77,7 @@ assumes previous density points in z direction, and rotates in the direction
 specified by `angle1` (initial magnetization angle with $z$-axis in degrees),
 and `angle2` (angle in degrees for projections in $xy$-plane and with $x$-axis).
 
-```bash
+```fortran
 &SYSTEM
 ...
   angle1(i) = 0.0

diff --git a/docs/hands-on/wannier.mdx b/docs/hands-on/wannier.mdx
@@ -61,4 +61,4 @@ mpirun -np 4 ${WANNIER_PATH}/wannier90.x silicon
 
 ## Resources
 
-- <https://sites.google.com/view/hubbard-koopmans/program>
+- https://sites.google.com/view/hubbard-koopmans/program
diff --git a/docs/setup/crystal-structure.md b/docs/setup/crystal-structure.md
@@ -41,7 +41,7 @@ problems may arrise.
 3,-3    | Body centered cubic
 4       | Hexagonal
 5       | Trigonal with c as 3-fold axis
--5      | Trigonal with <111> as 3-fold axis
+-5      | Trigonal with &lt;111&gt; as 3-fold axis
 6       | Simple tetragonal
 7       | Centered tetragonal
 8       | Simple orthorhombic
@@ -115,10 +115,10 @@ and set `export DISPLAY=:0` in your WSL instance.
 ### QE Input generator
 
 You can generate **PWscf** input files using tools in this website as well
-<https://www.materialscloud.org/work/tools/qeinputgenerator>
+https://www.materialscloud.org/work/tools/qeinputgenerator
 
 The same website also has a tool for k-path visualization and generation
-<https://www.materialscloud.org/work/tools/seekpath>
+https://www.materialscloud.org/work/tools/seekpath
 
 
 ## Resources

diff --git a/docs/setup/hpc.mdx b/docs/setup/hpc.mdx
@@ -145,7 +145,7 @@ Quantum Espresso project is primarily hosted on GitLab, and its mirror is
 maintained at [GitHub](https://github.com/QEF/q-e). You may check their
 repository at [GitLab](https://gitlab.com/QEF/q-e) for more up to date
 information. The releases via GitLab can be found under:
-<https://gitlab.com/QEF/q-e/-/releases>
+https://gitlab.com/QEF/q-e/-/releases
 
 :::
 
@@ -364,6 +364,6 @@ rm -rf build
 ```
 
 ## Resources
-- <https://nusit.nus.edu.sg/services/getting-started/introductory-guide-for-new-hpc-users/>
-- <https://help.nscc.sg/pbspro-quickstartguide/>
-- <https://www.youtube.com/watch?v=doudMLEaq3w>
+- https://nusit.nus.edu.sg/services/getting-started/introductory-guide-for-new-hpc-users/
+- https://help.nscc.sg/pbspro-quickstartguide/
+- https://www.youtube.com/watch?v=doudMLEaq3w
diff --git a/docs/setup/install.md b/docs/setup/install.md
@@ -15,7 +15,7 @@ HPC clusters.
 
 Perhaps the easiest way to install Quantum Espresso is from the package manager
 of respective Linux distribution. This should work fine for us and this is
-recommended option. Following commands are for Ubuntu / Debian. First make sure
+recommended option. Following commands are for Ubuntu/Debian. First make sure
 your system is up-to-date.
 
 ```bash
@@ -167,7 +167,7 @@ need to install following dependencies:
 sudo apt install tcl tcllib
 ```
 
-Download the file from - <http://pwtk.ijs.si/download/pwtk-2.0.tar.gz>
+Download the file from - http://pwtk.ijs.si/download/pwtk-2.0.tar.gz
 
 ```bash
 wget "http://pwtk.ijs.si/download/pwtk-2.0.tar.gz"

diff --git a/docs/setup/pseudo-potential.md b/docs/setup/pseudo-potential.md
@@ -16,12 +16,12 @@ we should choose a full relativistic pseudopotential. We need to be careful
 whether our chosen pseudopotential correctly reproduces physical properties.
 Various pseudopotential libraries:
 
-- <https://www.quantum-espresso.org/pseudopotentials>
-- <https://www.materialscloud.org/discover/sssp/table/efficiency>
-- <http://www.pseudo-dojo.org>
-- <https://www.physics.rutgers.edu/gbrv/>
-- <https://nninc.cnf.cornell.edu>
-- <http://www.quantum-simulation.org/potentials/>
+- https://www.quantum-espresso.org/pseudopotentials
+- https://www.materialscloud.org/discover/sssp/table/efficiency
+- http://www.pseudo-dojo.org
+- https://www.physics.rutgers.edu/gbrv/
+- https://nninc.cnf.cornell.edu
+- http://www.quantum-simulation.org/potentials/
 - [BLYP pseudopotentials](http://pseudopotentials.quantum-espresso.org/legacy_tables/hartwigesen-goedecker-hutter-pp)
 - [SCAN pseudopotentials](https://yaoyi92.github.io/scan-tm-pseudopotentials.html)
 

diff --git a/docs/theory/dft.md b/docs/theory/dft.md
@@ -158,10 +158,7 @@ consistency is achieved.
   <source type="image/webp" srcSet={require("/img/self-consistent-solution.webp").default} />
   <img src={require("/img/self-consistent-solution.png").default} alt="self-consistent-solution" />
 </picture>
-<p className="fig-caption">Self consistency loop in DFT calculation. The above
-screenshot was taken from lecture slide of Professor Ralph Gevauer from {" "}
-<a href="http://indico.ictp.it/event/9616/other-view?view=ictptimetable">
-ICTP MAX School 2021</a>.</p>
+<p className="fig-caption">Self consistency loop in DFT calculation. The above screenshot was taken from lecture slide of Professor Ralph Gevauer from <a href="http://indico.ictp.it/event/9616/other-view?view=ictptimetable"> ICTP MAX School 2021</a>.</p>
 
 The potential due to the ions is replaced by the pseudo potentials which removes
 the oscillations near the atomic core (reducing number of required plane wave

diff --git a/docs/theory/hartree-fock.md b/docs/theory/hartree-fock.md
@@ -55,4 +55,4 @@ The above antisymmetrized product can describe electrons that move independently
 of each other while they experience an average (mean-field) Coulomb force.
 
 ## Resources
-- <http://vergil.chemistry.gatech.edu/notes/hf-intro/hf-intro.html>
+- http://vergil.chemistry.gatech.edu/notes/hf-intro/hf-intro.html