Add simulation gallery entries and computer links (#1160)

* Add 6 new simulations to docs gallery with computer links

New entries: burstwave lithotripsy, kidney stone stress waves,
pitching airfoil, Mach 10 triple jet, Mach 12 Starship, whale
bubble nets. Grouped cards by topic. Computer names now link
to their respective HPC center pages.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Add gallery cards, SEO improvements, and per-page dates

- Add 3 new simulation gallery cards (earplug, orifice, particle cloud)
- Add JSON-LD structured data to landing page for rich search results
- Add per-page meta description to Doxygen header template
- Switch sitemap from txt to xml format for better SEO
- Add inject-dates.py build step for per-page last-updated dates
- Use full git history in docs CI for accurate file dates

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Add YouTube icon and target_blank to gallery card links

Cards linking to YouTube show the YouTube brand icon instead of a
generic external-link icon. DOI links keep the original icon.
All card links now open in a new tab.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Fix JSON-LD schema type and walltime format consistency

- Change @type from SoftwareApplication to SoftwareSourceCode so
  programmingLanguage and codeRepository are conformant properties
- Normalize "30 min" to "30m" to match other gallery entries

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Link scaling plot to performance page, harden lychee CI config

- Make weak scaling card clickable (links to expectedPerformance.html)
- Fix lychee exclude_path: glob to regex syntax for CLI compatibility
- Add URL exclude for sitemap referenced in robots.txt
- Move publish step before lychee so deploys are not blocked by link errors
- Set lychee fail: true so broken links fail CI
- Add VERBATIM to inject-dates CMake custom command

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Remove invalid SoftwareSourceCode properties (applicationCategory, operatingSystem)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Exclude HPE Cray docs from lychee (broken SSL cert)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

.github/workflows/docs.yml

@@ -15,6 +15,8 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Full history for per-page last-updated dates
 
     # We build doxygen from source because of
     # https://github.com/doxygen/doxygen/issues/9016
@@ -51,20 +53,14 @@ jobs:
         base-url-path: https://mflowcode.github.io/
         path-to-root: build/install/docs/mfc
         include-pdf: false
-        sitemap-format: txt
+        sitemap-format: xml
 
     - name: Output stats
       run: |
         echo "sitemap-path = ${{ steps.sitemap.outputs.sitemap-path }}"
         echo "url-count = ${{ steps.sitemap.outputs.url-count }}"
         echo "excluded-count = ${{ steps.sitemap.outputs.excluded-count }}"
 
-    - name: Linkcheck - Lychee
-      uses: lycheeverse/lychee-action@v2
-      with:
-        args: -c .lychee.toml build/install/docs/mfc/
-        fail: false
-
     - name: Publish Documentation
       if:   github.repository == 'MFlowCode/MFC' && github.ref == 'refs/heads/master' &&  (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch' )
       run:  |
@@ -81,5 +77,11 @@ jobs:
         git -C ../www commit -m "Docs @ ${GITHUB_SHA::7}" || true
         git -C ../www push
 
+    - name: Linkcheck - Lychee
+      uses: lycheeverse/lychee-action@v2
+      with:
+        args: -c .lychee.toml build/install/docs/mfc/
+        fail: true
+
 # DOC_PUSH_URL should be of the format:
 # --> https://<username>:<token>@github.com/<username>/<repository>

.lychee.toml

@@ -16,5 +16,11 @@ accept = ["200", "429"]
 
 verbose = "error"
 
-# Exclude sitemap from link checking (it contains pre-publish production URLs)
-exclude_path = ["**/sitemap.txt"]
+# Exclude sitemap file from scanning (it contains pre-publish production URLs)
+exclude_path = ["sitemap\\.xml"]
+
+# Exclude URLs that fail due to external issues (broken SSL, pre-deploy only, etc.)
+exclude = [
+    "https://mflowcode\\.github\\.io/sitemap\\.xml",  # Only exists after deployment
+    "https://cpe\\.ext\\.hpe\\.com",                   # HPE Cray docs have broken SSL cert
+]

CMakeLists.txt

@@ -806,6 +806,25 @@ if (MFC_DOCUMENTATION)
     GEN_DOCS(post_process  "MFC: Post-Process")
     GEN_DOCS(documentation "MFC")
 
+    # Inject per-page last-updated dates into documentation markdown files.
+    # Runs after auto-generated .md files exist, before Doxygen processes them.
+    # Uses a stamp file so it only runs once per build.
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp"
+        DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/case_constraints.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/physics_constraints.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/cli-reference.md"
+                "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/parameters.md"
+        COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_SOURCE_DIR}/docs/inject-dates.py"
+                "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMAND "${CMAKE_COMMAND}" -E touch "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp"
+        COMMENT "Injecting page dates into documentation"
+        VERBATIM
+    )
+    add_custom_target(inject_page_dates DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/inject-dates.stamp")
+    add_dependencies(documentation_doxygen inject_page_dates)
+
     # > Copy Resources (main landing page & assets)
     install(DIRECTORY   "${CMAKE_CURRENT_SOURCE_DIR}/docs/res"
             DESTINATION "docs/mfc")

docs/header.html

@@ -18,7 +18,8 @@
 <meta name="viewport" content="width=device-width, initial-scale=1"/>
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
-<meta name=”keywords” content="exascale, fluid dynamics, cfd, computational fluid dynamics, compressible, hpc, bryngelson, colonius, subgrid, multiphase, frontier, summit, el capitan, aurora, amd gpu, gpu, nvidia"/>
+<meta name="description" content="$title — MFC documentation. Open-source exascale multiphase flow solver." />
+<meta name="keywords" content="exascale, fluid dynamics, cfd, computational fluid dynamics, compressible, hpc, bryngelson, colonius, subgrid, multiphase, frontier, summit, el capitan, aurora, amd gpu, gpu, nvidia"/>
 <link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath^jquery.js"></script>
 <script type="text/javascript" src="$relpath^dynsections.js"></script>

docs/index.html

@@ -23,20 +23,54 @@
     <meta property="og:url" content="https://mflowcode.github.io" />
     <meta property="og:type" content="website" />
     <meta name="twitter:card" content="summary_large_image" />
+    <script type="application/ld+json">
+    {
+      "@context": "https://schema.org",
+      "@type": "SoftwareSourceCode",
+      "name": "MFC",
+      "alternateName": "Multi-Component Flow Code",
+      "description": "Open-source exascale multiphase flow solver. 2025 Gordon Bell Prize Finalist. Scales to 200+ trillion grid points on 43,000+ GPUs.",
+      "url": "https://mflowcode.github.io",
+      "license": "https://opensource.org/licenses/MIT",
+      "programmingLanguage": ["Fortran", "Python"],
+      "codeRepository": "https://github.com/MFlowCode/MFC",
+      "author": {
+        "@type": "Organization",
+        "name": "MFlowCode",
+        "url": "https://github.com/MFlowCode"
+      },
+      "award": "2025 ACM Gordon Bell Prize Finalist"
+    }
+    </script>
     <script src="https://cdn.tailwindcss.com"></script>
     <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css">
     <link rel="icon" type="image/x-icon" href="res/icon.ico">
     <script>
         const sims = [
-            { name: "Viscous Taylor-Green vortex",       image: "res/simulations/h.png", computer: "Delta",   accelerators: "128 A100s", walltime: "17h",     source: "https://www.youtube.com/watch?v=7i2h08dlDQw" },
-            { name: "Shedding water droplet",            image: "res/simulations/a.png", computer: "Summit",  accelerators: "960 V100s", walltime: "4h",      source: "https://www.youtube.com/watch?v=Gjj-qZkXcrg" },
-            { name: "Flow over an airfoil (vorticity)",  image: "res/simulations/g.png", computer: "Delta",   accelerators: "128 A100s", walltime: "19h",     source: "https://www.youtube.com/watch?v=FvAgnBW59cY" },
-            { name: "Cavitation fragments kidney stone", image: "res/simulations/d.png", computer: "Summit",  accelerators: "576 V100s", walltime: "30 min",  source: "https://doi.org/10.48550/arXiv.2305.09163" },
-            { name: "Breakup of vibrated interface",     image: "res/simulations/f.png", computer: "Summit",  accelerators: "128 V100s", walltime: "4h",      source: "https://www.youtube.com/watch?v=XQ3g1oSg8mc" },
-            { name: "Mach 2 flow over a sphere",         image: "res/simulations/i.png", computer: "Phoenix", accelerators: "36 V100s",  walltime: "30m",     source: "https://www.youtube.com/watch?v=HQGSUvYEGqM" },
-            { name: "Mach 2 shear layer",                image: "res/simulations/j.png", computer: "Phoenix", accelerators: "32 V100s",  walltime: "15m",     source: "https://www.youtube.com/watch?v=GtcdCHLmJO8" },
-            { name: "Collapsing bubbles (pressure)",     image: "res/simulations/b.png", computer: "Summit",  accelerators: "216 V100s", walltime: "3h",      source: "https://doi.org/10.48550/arXiv.2305.09163" },
-            { name: "Collapsing bubbles (streamlines)",  image: "res/simulations/c.png", computer: "Summit",  accelerators: "216 V100s", walltime: "3h",      source: "https://doi.org/10.48550/arXiv.2305.09163" },
+            // Rockets & jets
+            { name: "Mach 12 Starship Super Heavy",      image: "res/simulations/o.png", computer: "Alps",     computerUrl: "https://www.cscs.ch/computers/alps/",                                          accelerators: "5K GH200s", walltime: "18h",     source: "https://www.youtube.com/watch?v=NSn3OVF8N4I" },
+            { name: "Mach 10 triple jet booster",        image: "res/simulations/n.png", computer: "Frontier", computerUrl: "https://www.olcf.ornl.gov/frontier/",                                          accelerators: "10K GCDs",  walltime: "12h",     source: "https://www.youtube.com/watch?v=pMUl55xqGgM" },
+            { name: "Mach 2 flow over a sphere",         image: "res/simulations/i.png", computer: "Phoenix",  computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "36 V100s",  walltime: "30m",     source: "https://www.youtube.com/watch?v=HQGSUvYEGqM" },
+            { name: "Mach 2 shear layer",                image: "res/simulations/j.png", computer: "Phoenix",  computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "32 V100s",  walltime: "15m",     source: "https://www.youtube.com/watch?v=GtcdCHLmJO8" },
+            // Aerodynamics
+            { name: "Flow over an airfoil (vorticity)",  image: "res/simulations/g.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "19h",     source: "https://www.youtube.com/watch?v=FvAgnBW59cY" },
+            { name: "Pitching airfoil (3D)",             image: "res/simulations/m.png", computer: "Phoenix",  computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "1 A100",    walltime: "5h",      source: "https://www.youtube.com/watch?v=2XH-9MumDHU" },
+            // Shock-droplet
+            { name: "Shedding water droplet",            image: "res/simulations/a.png", computer: "Summit",   computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "960 V100s", walltime: "4h",      source: "https://www.youtube.com/watch?v=Gjj-qZkXcrg" },
+            // Biomedical & acoustics
+            { name: "Burstwave lithotripsy",             image: "res/simulations/k.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "30m",     source: "https://www.youtube.com/watch?v=XWsUTaJXGF8" },
+            { name: "Cavitation fragments kidney stone", image: "res/simulations/d.png", computer: "Summit",   computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "576 V100s", walltime: "30m",  source: "https://doi.org/10.48550/arXiv.2305.09163" },
+            { name: "Kidney stone stress waves",         image: "res/simulations/l.png", computer: "Bridges2", computerUrl: "https://www.psc.edu/resources/bridges-2/",                                      accelerators: "8 V100s",   walltime: "20m",     source: "https://www.youtube.com/watch?v=Q2L0J68qnRw" },
+            { name: "Whale bubble net feeding",          image: "res/simulations/p.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "30m",     source: "https://www.youtube.com/watch?v=6EpP6tdCZSA" },
+            { name: "Earplug acoustics (kinetic energy)", image: "res/simulations/q.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "8 A100s",   walltime: "5h",      source: "https://www.youtube.com/watch?v=xSW5wZkdbrc" },
+            { name: "Circular orifice (1 kHz)",          image: "res/simulations/r.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "16 A100s",  walltime: "5h",      source: "https://www.youtube.com/watch?v=jOhJ_c7eco4" },
+            // Bubble dynamics
+            { name: "Collapsing bubbles (pressure)",     image: "res/simulations/b.png", computer: "Summit",   computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "216 V100s", walltime: "3h",      source: "https://doi.org/10.48550/arXiv.2305.09163" },
+            { name: "Collapsing bubbles (streamlines)",  image: "res/simulations/c.png", computer: "Summit",   computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "216 V100s", walltime: "3h",      source: "https://doi.org/10.48550/arXiv.2305.09163" },
+            { name: "Euler-Lagrange particle cloud",     image: "res/simulations/s.png", computer: "Phoenix",  computerUrl: "https://www.pace.gatech.edu/",                                                 accelerators: "8 A100s",   walltime: "<1h",     source: "https://www.youtube.com/watch?v=RoT-yC5Lxmg" },
+            // Fundamentals
+            { name: "Breakup of vibrated interface",     image: "res/simulations/f.png", computer: "Summit",   computerUrl: "https://www.olcf.ornl.gov/summit/",                                            accelerators: "128 V100s", walltime: "4h",      source: "https://www.youtube.com/watch?v=XQ3g1oSg8mc" },
+            { name: "Viscous Taylor-Green vortex",       image: "res/simulations/h.png", computer: "Delta",    computerUrl: "https://www.ncsa.illinois.edu/research/project-highlights/delta/",              accelerators: "128 A100s", walltime: "17h",     source: "https://www.youtube.com/watch?v=7i2h08dlDQw" },
         ];
 
         const scalings = [
@@ -54,14 +88,14 @@
                             <img class="h-10" src="res/logo.png" alt="">
                         </div>
                         <div class="flex-1 p-2 font-semibold text-center">${s.name}</div>
-                        <a class="w-10 text-center" href="${s.source}">
-                            <i class="fa-solid fa-arrow-up-right-from-square"></i>
+                        <a class="w-10 text-center text-xl" href="${s.source}" target="_blank">
+                            <i class="${s.source.includes('youtube.com') ? 'fa-brands fa-youtube' : 'fa-solid fa-arrow-up-right-from-square'}"></i>
                         </a>
                     </div>
                     <div class="grid grid-cols-3 gap-4 px-4 py-2">
                         <div class="flex flex-row items-center">
                             <div class="pr-2"><i class="fa-solid fa-server"></i></div>
-                            <div class="flex-1 text-center">${s.computer}</div>
+                            <div class="flex-1 text-center">${s.computerUrl ? `<a href="${s.computerUrl}" class="underline hover:text-amber-400" target="_blank">${s.computer}</a>` : s.computer}</div>
                         </div>
                         <div class="flex flex-row items-center">
                             <div class="pr-2"><i class="fa-solid fa-microchip"></i></div>
@@ -76,12 +110,12 @@
             `).join("");
 
             document.getElementById("ft-scaling").innerHTML = scalings.map(s => `
-                <div class="flex md:w-2/6 mx-auto flex-col text-white rounded bg-slate-900 rounded-b-lg">
+                <a href="documentation/expectedPerformance.html" class="flex md:w-2/6 mx-auto flex-col text-white rounded bg-slate-900 rounded-b-lg hover:ring-2 hover:ring-amber-400 transition-shadow no-underline">
                     <div class="flex-1 grid bg-white pb-2">
                         <img class="place-self-center" src="${s.image}" alt="${s.label}">
                     </div>
                     <div class="flex-1 p-2 font-semibold text-center">${s.label}</div>
-                </div>
+                </a>
             `).join("");
 
             fetch("https://api.github.com/repos/MFlowCode/MFC/releases/latest")

docs/inject-dates.py

@@ -0,0 +1,31 @@
+#!/usr/bin/env python3
+"""Inject last-updated dates into docs before Doxygen runs.
+
+Usage: python3 inject-dates.py [source_dir]
+  source_dir defaults to current directory.
+"""
+import subprocess
+import sys
+from pathlib import Path
+from datetime import date
+
+src_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(".")
+docs_dir = src_dir / "docs" / "documentation"
+
+for md_file in sorted(docs_dir.glob("*.md")):
+    if "Page last updated:" in md_file.read_text():
+        continue
+
+    result = subprocess.run(
+        ["git", "log", "-1", "--format=%as", "--", str(md_file)],
+        capture_output=True, text=True,
+        cwd=str(src_dir),
+    )
+    page_date = result.stdout.strip() or str(date.today())
+
+    with open(md_file, "a") as f:
+        f.write(
+            f"\n\n<div style='text-align:center; font-size:0.75rem; "
+            f"color:#888; padding:16px 0 0;'>"
+            f"Page last updated: {page_date}</div>\n"
+        )