Merge pull request #6 from simongravelle/migrate-to-hugo-v0.140

start migrating to v0.140

.github/workflows/gh-pages.yml

@@ -22,7 +22,7 @@ jobs:
       - name: Setup Hugo
         uses: peaceiris/actions-hugo@v2
         with:
-          hugo-version: 0.121.0
+          hugo-version: 0.140.2
           extended: true
 
       - name: Build

.gitmodules

@@ -0,0 +1,3 @@
+[submodule ".submodule/scholar-collector"]
+	path = .submodule/scholar-collector
+	url = git@github.com:simongravelle/scholar-collector.git

README.md

@@ -7,6 +7,11 @@ A simple academic template that is easy to deploy on GitHub page, and relatively
 easy to customize using css. You can find the [live](https://simongravelle.github.io/)
 version, and my resume [here](https://simongravelle.github.io/files/resume/resume-simon-gravelle.pdf).
 
+## Automatic update of the publication list
+
+The list of publications is updated automatically from Google Scholar using
+the [scholar-collector](https://github.com/simongravelle/scholar-collector).
+
 ## Overview
 
 [![image](https://user-images.githubusercontent.com/43388542/216845033-cc7b0a28-60ff-4e86-a5ce-2c93930e08e2.png)](https://simongravelle.github.io/)
@@ -17,10 +22,10 @@ version, and my resume [here](https://simongravelle.github.io/files/resume/resum
 
 ## Credit
 
-This template was originally taken from [wowchemy](https://wowchemy.com/), with some custom CSS
-adapted from [nickballousite](https://github.com/nballou) webpage.
+This template was originally taken from [wowchemy](https://wowchemy.com/), with
+some custom CSS adapted from [nickballousite](https://github.com/nballou) webpage.
 
-## Build locally
+## How to build locally
 
 To build locally on your computer, type:
 

config/_default/config.yaml

@@ -29,10 +29,10 @@ module:
 ############################
 ## ADVANCED
 ############################
-
 enableGitInfo: false
 summaryLength: 30
-paginate: 10
+pagination:
+  pagerSize: 10
 enableEmoji: true
 enableRobotsTXT: true
 footnotereturnlinkcontents: <sup>^</sup>

content/news/2023-cnrs-start/index.md

@@ -19,5 +19,7 @@ links:
     icon: scroll
     name: CNRS
     url: 'https://www.cnrs.fr/fr'
+type: "news"
+layout: "single"
 ---
 In the continuity of my MSCA fellowship, I've been hired by the French CNRS (Section 11) as a tenured full time researcher at [LIPhy](https://liphy.univ-grenoble-alpes.fr/) (UGA).

content/news/2023-lammpstutorial-v2.0/index.md

@@ -19,6 +19,8 @@ links:
     icon: github
     name: Source
     url: 'https://github.com/lammpstutorials/lammpstutorials.github.io'
+type: "news"
+layout: "single"
 ---
 The [version 2.0](https://lammpstutorials.github.io/) of LAMMPS tutorial has just been published, and offers:
 * a new structure with a sphinx template

content/news/2023-liphy-arrival/index.md

@@ -19,5 +19,7 @@ links:
     icon: scroll
     name: MSCA
     url: 'https://marie-sklodowska-curie-actions.ec.europa.eu/'
+type: "news"
+layout: "single"
 ---
 After 2 great years at the ICP in Stuttgart, I am starting my own MSCA project (NanoSep) at [LIPhy](https://liphy.univ-grenoble-alpes.fr/) (UGA) in [Benoit Coasne group](https://benoitcoasne.github.io/).

content/news/2023-maicos-v0.7/index.md

@@ -10,7 +10,6 @@ summary: Use it to analyze your molecular simulations of confined fluids.
 tags:
 - Outreach
 title: The version 0.7 of MAICoS has been released
-#url_code: "https://gitlab.com/maicos-devel/maicos/-/tree/release-0-7"
 links:
   - icon_pack: fab
     icon: gitlab
@@ -20,8 +19,7 @@ links:
     icon: scroll
     name: Documentation
     url: 'http://maicos-analysis.org'
+type: "news"
+layout: "single"
 ---
-The version 0.7 of MAICoS has been released. It comes with:
-* an improved documentation with theory and tutorials
-* a 'Jitter' option to produce smooth density profiles
-* new modules for cylindrical and spherical geometries
+The version 0.7 of MAICoS has been released. It comes with (1) an improved documentation with theory and tutorials, (2) a 'Jitter' option to produce smooth density profiles, and (3) new modules for cylindrical and spherical geometries.

content/news/2023-phd-offer/index.md

@@ -15,6 +15,8 @@ links:
     icon: scroll
     name: LIPhy
     url: 'https://liphy.univ-grenoble-alpes.fr/'
+type: "news"
+layout: "single"
 ---
 **Update.** The offer has now expired, and the selection process has moved to the next step.
 

content/news/2024-MDCourse/index.md

@@ -23,6 +23,8 @@ links:
     icon: github
     name: Source
     url: 'https://github.com/mdcourse/python-codes'
+type: "news"
+layout: "single"
 ---
 
 [Learn Molecular Simulations with Python](https://mdcourse.github.io/)

content/news/2024-postdoc-offer/index.md

@@ -15,6 +15,8 @@ links:
     icon: scroll
     name: LIPhy
     url: 'https://liphy.univ-grenoble-alpes.fr/'
+type: "news"
+layout: "single"
 ---
 **Scope.**
 

content/publication/2024_2_4_Carral_APL_Machine_Learning/index.md

@@ -0,0 +1,15 @@
+---
+title: "In silico design and prediction of metastable quaternary phases in Cu–Ni–Si–Cr alloys"
+date: 2024-01-01
+publishDate: 2024-01-01
+authors: ["Ángel Díaz Carral", "**Simon Gravelle**", "Maria Fyta"]
+publication_types: ["2"]
+abstract: "Quaternary phases formed in copper alloys are investigated through a combination of quantum-mechanical and classical computer simulations and active machine learning. Focus is given to nickel, silicon, and chromium impurities in a copper matrix. The analysis of the formation enthalpies of candidate quaternary structures leads to the prediction of two novel quaternary phases and the assessment of their stability. For the predicted two phases, machine learned atomistic potentials are developed using active learning with quantum-mechanical accuracy. The use of these potentials in atomistic simulations further elucidates the structure, temperature-dependent dynamics, and elastic behavior of the predicted quaternary phases in copper alloys. The combined in silico approach is thus proven highly efficient in both designing materials and elucidating their properties and potential combining different spatiotemporal …"
+featured: true
+publication: "APL Machine Learning 2024 2 (4)"
+links:
+  - icon_pack: fas
+    icon: scroll
+    name: Link
+    url: 'https://pubs.aip.org/aip/aml/article/2/4/046109/3321488'
+---

content/publication/2024_Gravelle_arXiv/index.md

@@ -0,0 +1,15 @@
+---
+title: "Effect of thermal fluctuations on the average shape of a graphene nanosheet suspended in a shear flow"
+date: 2024-01-01
+publishDate: 2024-01-01
+authors: ["**Simon Gravelle**", "Catherine Kamal", "Lorenzo Botto"]
+publication_types: ["3"]
+abstract: "Graphene nanosheets display large hydrodynamic slip lengths in most solvents, and because of this, adopt a stable orientation in a shear flow instead of rotating when thermal fluctuations are negligible [Kamal et al., Nature Comm., 11.1,2020]. In this paper, we combine molecular dynamics simulations and boundary integral simulations to demonstrate that the time-averaged 'S' shape adopted by a flexible graphene nanosheet subject to moderate thermal fluctuation is comparable to the shape predicted when neglecting thermal fluctuations. The stable 'S' shape adopted by the particle results primarily from the normal hydrodynamic traction, which is sensitive to the orientation of the particle with respect to the flow direction. Our results imply that thermally-induced shape fluctuations have a relatively minor effect on the time-averaged rheology of dilute suspensions of graphene nanosheets for relatively large but finite P\'eclet numbers."
+featured: true
+publication: "arXiv 2024 "
+links:
+  - icon_pack: fas
+    icon: scroll
+    name: Link
+    url: 'https://arxiv.org/abs/2412.09139'
+---

hugo.toml

@@ -1,4 +1,12 @@
+# The base URL for your website. 
+# This is typically the domain where your site will be hosted. 
+# Use "/" if hosting locally or configuring later for deployment.
 baseurl = "/"
+
+# Enable relative URLs to avoid absolute paths in links. 
+# This is useful for testing locally or deploying to non-root domains.
 relativeURLs = true
+
+# Use "ugly" URLs for pages (e.g., "/about.html" instead of "/about/").
+# This can be useful for certain server setups or preferences.
 uglyURLs = true
-# googleAnalytics = 'UA-36911186-4'

themes/github.com/wowchemy/wowchemy-hugo-themes/modules/wowchemy/v5/layouts/_default/baseof.html

@@ -6,7 +6,16 @@
 
 {{ $show_navbar := ((site.Params.header.navbar.enable | default true) | and (ne .Params.header.navbar.enable false)) | or .Params.header.navbar.enable }}
 {{- $highlight_active_link := site.Params.header.navbar.highlight_active_link | default true -}}
-<body id="top" data-spy="scroll" {{ if $show_navbar }}data-offset="70"{{end}} data-target="{{ if or .IsHome (eq .Type "widget_page") | and $highlight_active_link }}#navbar-main{{else}}#TableOfContents{{end}}" class="page-wrapper {{with .Params.design.css_class}}{{.}}{{end}} {{ if not (.Scratch.Get "light") }}dark{{end}} {{ if not $show_navbar }}no-navbar{{end}}" {{with .File}}data-wc-page-id="{{.File.UniqueID}}"{{end}} {{with .Params.design.css_style}}style="{{. | safeCSS}}"{{end}}>
+
+<body id="top" data-spy="scroll" 
+  {{ if $show_navbar }}data-offset="70"{{end}} 
+  data-target="{{ if or .IsHome (eq .Type "widget_page") | and $highlight_active_link }}#navbar-main{{else}}#TableOfContents{{end}}" 
+  class="page-wrapper 
+    {{ with .Params.design.css_class }}{{ . }}{{ end }} 
+    {{ if not (.Scratch.Get "light") }}dark{{ end }} 
+    {{ if not $show_navbar }}no-navbar{{ end }}"
+  {{ with .File }}data-wc-page-id="{{ .UniqueID }}"{{ else }}data-wc-page-id="default"{{ end }}
+  {{ with .Params.design.css_style }}style="{{ . | safeCSS }}"{{ end }}>
 
   {{/* Initialise Wowchemy. */}}
   {{ $js_license := printf "/*! Wowchemy v%s | https://wowchemy.com/ */\n" site.Data.wowchemy.version }}

themes/github.com/wowchemy/wowchemy-hugo-themes/modules/wowchemy/v5/layouts/partials/marketing/google_analytics.html

@@ -1,42 +1,4 @@
-{{ $ga := site.Params.marketing.analytics.google_analytics | default site.GoogleAnalytics | default "" }}
-
-{{ if hugo.IsProduction | and $ga }}
-
-{{ $gtag_config := cond site.Params.features.privacy_pack.enable "{ 'anonymize_ip': true }" "{}" }}
-<script async src="https://www.googletagmanager.com/gtag/js?id={{$ga}}"></script>
+<!-- Google Analytics has been disabled -->
 <script>
-  window.dataLayer = window.dataLayer || [];
-
-  function gtag() {
-      dataLayer.push(arguments);
-  }
-
-  function trackOutboundLink(url, target) {
-    gtag('event', 'click', {
-         'event_category': 'outbound',
-         'event_label': url,
-         'transport_type': 'beacon',
-         'event_callback': function () {
-           if (target !== '_blank') {
-             document.location = url;
-           }
-         }
-    });
-    console.debug("Outbound link clicked: " + url);
-  }
-
-  function onClickCallback(event) {
-    if ((event.target.tagName !== 'A') || (event.target.host === window.location.host)) {
-      return;
-    }
-    trackOutboundLink(event.target, event.target.getAttribute('target'));  // Send GA event.
-  }
-
-  gtag('js', new Date());
-  gtag('config', '{{$ga}}', {{$gtag_config|safeJS}});
-  gtag('set', {'cookie_flags': 'SameSite=None;Secure'});
-
-  // Outbound link tracking.
-  document.addEventListener('click', onClickCallback, false);
+  console.info("Google Analytics is disabled.");
 </script>
-{{ end }}

themes/github.com/wowchemy/wowchemy-hugo-themes/modules/wowchemy/v5/layouts/partials/site_head.html

@@ -36,9 +36,10 @@
     {{ end }}
   {{ end }}
 
+  <!---
   {{ if site.Params.marketing.analytics.google_optimize | and hugo.IsProduction }}
     <script src="https://www.googleoptimize.com/optimize.js?id={{ site.Params.marketing.analytics.google_optimize }}"></script>
-  {{- end -}}
+  {{- end -}} -->
 
   {{/* Attempt to load superuser. */}}
   {{ $superuser_name := "" }}

update-publications.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+set -e
+
+echo "Ensuring submodules are initialized and updated..."
+git submodule update --init
+git submodule update --remote
+
+# Navigate to the submodule directory
+SUBMODULE_DIR=".submodule/scholar-collector"
+if [ -d "$SUBMODULE_DIR" ]; then
+    echo "Navigating to submodule directory: $SUBMODULE_DIR"
+    cd "$SUBMODULE_DIR"
+else
+    echo "Error: Submodule directory '$SUBMODULE_DIR' does not exist."
+    exit 1
+fi
+
+# Run the Python script with the specified path
+SCRIPT="collect_publications.py"
+TARGET_PATH="../../content/publication/"
+
+if [ -f "$SCRIPT" ]; then
+    echo "Executing $SCRIPT with path $TARGET_PATH"
+    python3 "$SCRIPT" "$TARGET_PATH"
+else
+    echo "Error: Script '$SCRIPT' not found in the submodule directory."
+    exit 1
+fi