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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Sediment Boudreau (1996) test cases · PALEOsediment Documentation</title><meta name="title" content="Sediment Boudreau (1996) test cases · PALEOsediment Documentation"/><meta property="og:title" content="Sediment Boudreau (1996) test cases · PALEOsediment Documentation"/><meta property="twitter:title" content="Sediment Boudreau (1996) test cases · PALEOsediment Documentation"/><meta name="description" content="Documentation for PALEOsediment Documentation."/><meta property="og:description" content="Documentation for PALEOsediment Documentation."/><meta property="twitter:description" content="Documentation for PALEOsediment Documentation."/><script data-outdated-warner src="../../../assets/warner.js"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 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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="../../../">PALEOsediment Documentation</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><a class="tocitem" href="../../../">PALEOsediment.jl documentation</a></li><li><span class="tocitem">Examples and Tutorials</span><ul><li><input class="collapse-toggle" id="menuitem-2-1" type="checkbox" checked/><label class="tocitem" for="menuitem-2-1"><span class="docs-label">boudreau1996</span><i class="docs-chevron"></i></label><ul class="collapsed"><li class="is-active"><a class="tocitem" href>Sediment Boudreau (1996) test cases</a><ul class="internal"><li class="toplevel"><a class="tocitem" href="#Oceanfloor-[O2]-and-[SO4]-gradients"><span>Oceanfloor [O2] and [SO4] gradients</span></a></li><li class="toplevel"><a class="tocitem" href="#Sulphur-isotope-example"><span>Sulphur isotope example</span></a></li></ul></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-2" type="checkbox"/><label class="tocitem" for="menuitem-2-2"><span class="docs-label">ironsulphur</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../ironsulphur/README/">Sediment iron-sulphur chemistry examples</a></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-3" type="checkbox"/><label class="tocitem" for="menuitem-2-3"><span class="docs-label">transport_tests</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a 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is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Examples and Tutorials</a></li><li><a class="is-disabled">boudreau1996</a></li><li class="is-active"><a href>Sediment Boudreau (1996) test cases</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Sediment Boudreau (1996) test cases</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOsediment.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/PALEOtoolkit/PALEOsediment.jl/blob/main/docs/src/collated_examples/boudreau1996/README.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="Sediment-Boudreau-(1996)-test-cases"><a class="docs-heading-anchor" href="#Sediment-Boudreau-(1996)-test-cases">Sediment Boudreau (1996) test cases</a><a id="Sediment-Boudreau-(1996)-test-cases-1"></a><a class="docs-heading-anchor-permalink" href="#Sediment-Boudreau-(1996)-test-cases" title="Permalink"></a></h1><p>To run sediment test cases from (<a href="../../../References/#Boudreau1996">Boudreau, 1996</a>), assuming the Julia environment <code>PALEOsediment/examples</code> has already been activated:</p><pre><code class="nohighlight hljs">julia> cd("examples/boundreau1996") | ||
| julia> include("PALEO_examples_sediment.jl")</code></pre><p>This will run and plot output (NB: the first run will be slow as Julia JIT compiles the code).</p><p>The configuration includes three sediment columns, with:</p><ol><li>Shelf / slope case</li><li>Rise case</li><li>Rise, no bioturbation</li></ol><p>NB: this configuration doesn't include N, so results differ in detail from the paper.</p><h1 id="Oceanfloor-[O2]-and-[SO4]-gradients"><a class="docs-heading-anchor" href="#Oceanfloor-[O2]-and-[SO4]-gradients">Oceanfloor [O2] and [SO4] gradients</a><a id="Oceanfloor-[O2]-and-[SO4]-gradients-1"></a><a class="docs-heading-anchor-permalink" href="#Oceanfloor-[O2]-and-[SO4]-gradients" title="Permalink"></a></h1><pre><code class="nohighlight hljs">julia> include("PALEO_examples_sediment_x10.jl")</code></pre><p>The configuration includes ten sediment columns, with the physical environment for the (<a href="../../../References/#Boudreau1996">Boudreau, 1996</a>) shelf/slope case, no bioturbation, and Corg input with two reactivity fractions (a combination of the high-reactivity fraction from the shelf/slope case, and the low reactivity fraction from the rise case).</p><ol><li>Columns 1-5: oceanfloor [O2] gradient, constant [SO4] = 28mM</li><li>Columns 6-10: oceanfloor [SO4] gradient, at constant [O2] = 0</li></ol><p>Summary plots show oceanfloor solute fluxes and remineralization pathways:</p><p><img src="../figures/PALEO_examples_sediment_x10_summary.svg" alt="O2 and SO4 gradient summary figure"/></p><h6 id="Figure-1"><a class="docs-heading-anchor" href="#Figure-1">Figure 1</a><a id="Figure-1-1"></a><a class="docs-heading-anchor-permalink" href="#Figure-1" title="Permalink"></a></h6><p><em>Oceanfloor solute fluxes and remineralization pathways vs oceanfloor [O2] and [SO4] concentration</em></p><h1 id="Sulphur-isotope-example"><a class="docs-heading-anchor" href="#Sulphur-isotope-example">Sulphur isotope example</a><a id="Sulphur-isotope-example-1"></a><a class="docs-heading-anchor-permalink" href="#Sulphur-isotope-example" title="Permalink"></a></h1><pre><code class="nohighlight hljs">julia> include("PALEO_examples_sediment_Sisotopes.jl")</code></pre><p>three sediment column example as <code>PALEO_examples_sediment.jl</code>, with sulphur isotopes enabled and low (1 mM) oceanfloor [SO4] to illustrate Rayleigh fractionation within the sediment column as [SO4] becomes limiting.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../../">« PALEOsediment.jl documentation</a><a class="docs-footer-nextpage" href="../../ironsulphur/README/">Sediment iron-sulphur chemistry examples »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Thursday 29 February 2024 12:32">Thursday 29 February 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| julia> include("PALEO_examples_sediment.jl")</code></pre><p>This will run and plot output (NB: the first run will be slow as Julia JIT compiles the code).</p><p>The configuration includes three sediment columns, with:</p><ol><li>Shelf / slope case</li><li>Rise case</li><li>Rise, no bioturbation</li></ol><p>NB: this configuration doesn't include N, so results differ in detail from the paper.</p><h1 id="Oceanfloor-[O2]-and-[SO4]-gradients"><a class="docs-heading-anchor" href="#Oceanfloor-[O2]-and-[SO4]-gradients">Oceanfloor [O2] and [SO4] gradients</a><a id="Oceanfloor-[O2]-and-[SO4]-gradients-1"></a><a class="docs-heading-anchor-permalink" href="#Oceanfloor-[O2]-and-[SO4]-gradients" title="Permalink"></a></h1><pre><code class="nohighlight hljs">julia> include("PALEO_examples_sediment_x10.jl")</code></pre><p>The configuration includes ten sediment columns, with the physical environment for the (<a href="../../../References/#Boudreau1996">Boudreau, 1996</a>) shelf/slope case, no bioturbation, and Corg input with two reactivity fractions (a combination of the high-reactivity fraction from the shelf/slope case, and the low reactivity fraction from the rise case).</p><ol><li>Columns 1-5: oceanfloor [O2] gradient, constant [SO4] = 28mM</li><li>Columns 6-10: oceanfloor [SO4] gradient, at constant [O2] = 0</li></ol><p>Summary plots show oceanfloor solute fluxes and remineralization pathways:</p><p><img src="../figures/PALEO_examples_sediment_x10_summary.svg" alt="O2 and SO4 gradient summary figure"/></p><h6 id="Figure-1"><a class="docs-heading-anchor" href="#Figure-1">Figure 1</a><a id="Figure-1-1"></a><a class="docs-heading-anchor-permalink" href="#Figure-1" title="Permalink"></a></h6><p><em>Oceanfloor solute fluxes and remineralization pathways vs oceanfloor [O2] and [SO4] concentration</em></p><h1 id="Sulphur-isotope-example"><a class="docs-heading-anchor" href="#Sulphur-isotope-example">Sulphur isotope example</a><a id="Sulphur-isotope-example-1"></a><a class="docs-heading-anchor-permalink" href="#Sulphur-isotope-example" title="Permalink"></a></h1><pre><code class="nohighlight hljs">julia> include("PALEO_examples_sediment_Sisotopes.jl")</code></pre><p>three sediment column example as <code>PALEO_examples_sediment.jl</code>, with sulphur isotopes enabled and low (1 mM) oceanfloor [SO4] to illustrate Rayleigh fractionation within the sediment column as [SO4] becomes limiting.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../../">« PALEOsediment.jl documentation</a><a class="docs-footer-nextpage" href="../../ironsulphur/README/">Sediment iron-sulphur chemistry examples »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Thursday 29 February 2024 12:56">Thursday 29 February 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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