build based on 53a826c

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-04-21T20:19:04","documenter_version":"1.4.0"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2024-04-21T20:32:55","documenter_version":"1.4.0"}}

dev/Subduction3D/index.html

@@ -35,4 +35,4 @@
 |-- Model setup options :  Type=files;
 |-- Output options      :  filename=Subduction_3D; pvd=1; avd=0; surf=0
 |-- Materials           :  3 phases;</code></pre><h2 id="4.-Run-the-model"><a class="docs-heading-anchor" href="#4.-Run-the-model">4. Run the model</a><a id="4.-Run-the-model-1"></a><a class="docs-heading-anchor-permalink" href="#4.-Run-the-model" title="Permalink"></a></h2><p>Add this stage, we are ready to run the simulation. On my machine it takes around 4 seconds per timestep on 8 cores:</p><pre><code class="language-julia hljs">run_lamem(model, 8)</code></pre><p>The results looks like this with paraview: <img src="../assets/Subduction_3D_pv.png" alt="3D subduction paraview"/> Note that this is a significantly higher resolution than the original paper, which was run on an HPC system (admittedly, this was 20 years ago).</p><p>The file <code>Subduction_3D.jl</code> in <code>/scripts</code> reproduces this example</p><h3 id="Markdown-page-generation"><a class="docs-heading-anchor" href="#Markdown-page-generation">Markdown page generation</a><a id="Markdown-page-generation-1"></a><a class="docs-heading-anchor-permalink" href="#Markdown-page-generation" title="Permalink"></a></h3><pre><code class="language-julia hljs">#This file was generated using Literate:
-#Literate.markdown(&quot;Subduction3D.jl&quot;,&quot;../docs/src/&quot;,keepcomments=true, execute=false, codefence = &quot;```julia&quot; =&gt; &quot;```&quot;)</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../juliasetup_TMSubduction/">« Example 3: 2D Subduction</a><a class="docs-footer-nextpage" href="../juliasetup_pluto/">Notebooks »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.0 on <span class="colophon-date" title="Sunday 21 April 2024 20:19">Sunday 21 April 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+#Literate.markdown(&quot;Subduction3D.jl&quot;,&quot;../docs/src/&quot;,keepcomments=true, execute=false, codefence = &quot;```julia&quot; =&gt; &quot;```&quot;)</code></pre><hr/><p><em>This page was generated using <a href="https://github.com/fredrikekre/Literate.jl">Literate.jl</a>.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../juliasetup_TMSubduction/">« Example 3: 2D Subduction</a><a class="docs-footer-nextpage" href="../juliasetup_pluto/">Notebooks »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.0 on <span class="colophon-date" title="Sunday 21 April 2024 20:32">Sunday 21 April 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -1,2 +1,2 @@
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-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · LaMEM.jl</title><meta name="title" content="Home · LaMEM.jl"/><meta property="og:title" content="Home · LaMEM.jl"/><meta property="twitter:title" content="Home · LaMEM.jl"/><meta name="description" content="Documentation for LaMEM.jl."/><meta property="og:description" content="Documentation for LaMEM.jl."/><meta property="twitter:description" content="Documentation for LaMEM.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>LaMEM.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><span class="tocitem">Installation</span><ul><li><a class="tocitem" href="installation/">General instructions</a></li><li><a class="tocitem" href="installation_HPC/">Installation on HPC systems</a></li></ul></li><li><span class="tocitem">Create &amp; run LaMEM models from julia</span><ul><li><a class="tocitem" href="juliasetups/">Overview</a></li><li><a class="tocitem" href="juliasetup_example_sphere/">Example 1: Sphere</a></li><li><a class="tocitem" href="juliasetup_LaPalma/">Example 2: Volcano</a></li><li><a class="tocitem" href="juliasetup_TMSubduction/">Example 3: 2D Subduction</a></li><li><a class="tocitem" href="Subduction3D/">Example 4: 3D Subduction</a></li><li><a class="tocitem" href="juliasetup_pluto/">Notebooks</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions/">Available functions</a></li></ul></li><li><a class="tocitem" href="runlamem/">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps/">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions/">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="LaMEM.jl"><a class="docs-heading-anchor" href="#LaMEM.jl">LaMEM.jl</a><a id="LaMEM.jl-1"></a><a class="docs-heading-anchor-permalink" href="#LaMEM.jl" title="Permalink"></a></h1><p>This is the julia interface to LaMEM, which does a number of handy things:</p><ul><li>It will automatically download a binary installation of LaMEM, along with the correct version of PETSc and mpiexec for your system. You can also use these binaries directly from your terminal, so you are not limited to julia. Gone are the days where you had to first spend hours or days to install PETSc on your system!</li><li>It provides the functionality to setup a model, run it and plot the results with a few lines of julia.</li><li>We provide many default options</li><li>You can do this with Jupyter or Pluto notebooks</li><li>We provide a simple function to run LaMEM from julia (also in parallel), using classical LaMEM <code>*.dat</code> files</li><li>We provide functions to read timesteps back into julia and compress out </li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="installation/">General instructions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.0 on <span class="colophon-date" title="Sunday 21 April 2024 20:19">Sunday 21 April 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · LaMEM.jl</title><meta name="title" content="Home · LaMEM.jl"/><meta property="og:title" content="Home · LaMEM.jl"/><meta property="twitter:title" content="Home · LaMEM.jl"/><meta name="description" content="Documentation for LaMEM.jl."/><meta property="og:description" content="Documentation for LaMEM.jl."/><meta property="twitter:description" content="Documentation for LaMEM.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href>LaMEM.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>Home</a></li><li><span class="tocitem">Installation</span><ul><li><a class="tocitem" href="installation/">General instructions</a></li><li><a class="tocitem" href="installation_HPC/">Installation on HPC systems</a></li></ul></li><li><span class="tocitem">Create &amp; run LaMEM models from julia</span><ul><li><a class="tocitem" href="juliasetups/">Overview</a></li><li><a class="tocitem" href="juliasetup_example_sphere/">Example 1: Sphere</a></li><li><a class="tocitem" href="juliasetup_LaPalma/">Example 2: Volcano</a></li><li><a class="tocitem" href="juliasetup_TMSubduction/">Example 3: 2D Subduction</a></li><li><a class="tocitem" href="Subduction3D/">Example 4: 3D Subduction</a></li><li><a class="tocitem" href="juliasetup_pluto/">Notebooks</a></li><li><a class="tocitem" href="LaMEM_ModelFunctions/">Available functions</a></li></ul></li><li><a class="tocitem" href="runlamem/">Run LaMEM</a></li><li><a class="tocitem" href="readtimesteps/">Reading timesteps</a></li><li><a class="tocitem" href="listfunctions/">List of functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Home</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/JuliaGeodynamics/LaMEM.jl/blob/main/docs/src/index.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="LaMEM.jl"><a class="docs-heading-anchor" href="#LaMEM.jl">LaMEM.jl</a><a id="LaMEM.jl-1"></a><a class="docs-heading-anchor-permalink" href="#LaMEM.jl" title="Permalink"></a></h1><p>This is the julia interface to LaMEM, which does a number of handy things:</p><ul><li>It will automatically download a binary installation of LaMEM, along with the correct version of PETSc and mpiexec for your system. You can also use these binaries directly from your terminal, so you are not limited to julia. Gone are the days where you had to first spend hours or days to install PETSc on your system!</li><li>It provides the functionality to setup a model, run it and plot the results with a few lines of julia.</li><li>We provide many default options</li><li>You can do this with Jupyter or Pluto notebooks</li><li>We provide a simple function to run LaMEM from julia (also in parallel), using classical LaMEM <code>*.dat</code> files</li><li>We provide functions to read timesteps back into julia and compress out </li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="installation/">General instructions »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.4.0 on <span class="colophon-date" title="Sunday 21 April 2024 20:32">Sunday 21 April 2024</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>