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+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>1D shelf sea examples and test cases · PALEOocean Documentation</title><meta name="title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta property="og:title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta property="twitter:title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta name="description" content="Documentation for PALEOocean Documentation."/><meta property="og:description" content="Documentation for PALEOocean Documentation."/><meta property="twitter:description" content="Documentation for PALEOocean 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script data-outdated-warner src="../../../assets/warner.js"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="../../../">PALEOocean 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="../../../">PALEOocean.jl documentation</a></li><li><span class="tocitem">Examples and Tutorials</span><ul><li><input class="collapse-toggle" id="menuitem-2-1" type="checkbox"/><label class="tocitem" for="menuitem-2-1"><span class="docs-label">PTBClarkson2014</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../PTBClarkson2014/README/">PTB land-atmosphere-ocean model (Clarkson 2015)</a></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">mitgcm</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../mitgcm/README/">MITgcm transport matrix ocean-only 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">ocean3box</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../ocean3box/README/">3 Box Ocean Examples</a></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-4" type="checkbox" checked/><label class="tocitem" for="menuitem-2-4"><span class="docs-label">shelf1D</span><i class="docs-chevron"></i></label><ul class="collapsed"><li class="is-active"><a class="tocitem" href>1D shelf sea examples and test cases</a><ul class="internal"><li><a class="tocitem" href="#Installation-and-configuration"><span>Installation and configuration</span></a></li><li><a class="tocitem" href="#1D-shelf-examples"><span>1D shelf examples</span></a></li><li><a class="tocitem" href="#1D-shelf-sediment-examples"><span>1D shelf + sediment examples</span></a></li></ul></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-5" type="checkbox"/><label class="tocitem" for="menuitem-2-5"><span class="docs-label">skeleton_configuration</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../skeleton_configuration/README/">Skeleton ocean-atmosphere configuration</a></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-6" type="checkbox"/><label class="tocitem" for="menuitem-2-6"><span class="docs-label">transport_examples</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../transport_examples/README/">Transport examples</a></li></ul></li></ul></li><li><span class="tocitem">Design</span><ul><li><a class="tocitem" href="../../../PALEOocean_Domains/">PALEOocean Domains, fluxes, and standard Variables</a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="../../../PALEOocean_Reactions/">PALEOocean Reactions</a></li><li><a class="tocitem" href="../../../PALEOocean_functions/">PALEOocean functions</a></li></ul></li><li><a class="tocitem" href="../../../References/">References</a></li><li><a class="tocitem" href="../../../indexpage/">Index</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><a class="is-disabled">Examples and Tutorials</a></li><li><a class="is-disabled">shelf1D</a></li><li class="is-active"><a href>1D shelf sea examples and test cases</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>1D shelf sea examples and test cases</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOocean.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/PALEOocean.jl/blob/main/docs/src/collated_examples/shelf1D/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="1D-shelf-sea-examples-and-test-cases"><a class="docs-heading-anchor" href="#1D-shelf-sea-examples-and-test-cases">1D shelf sea examples and test cases</a><a id="1D-shelf-sea-examples-and-test-cases-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-sea-examples-and-test-cases" title="Permalink"></a></h1><h2 id="Installation-and-configuration"><a class="docs-heading-anchor" href="#Installation-and-configuration">Installation and configuration</a><a id="Installation-and-configuration-1"></a><a class="docs-heading-anchor-permalink" href="#Installation-and-configuration" title="Permalink"></a></h2><p>These examples require netcdf files defining an annual cycle of physical variables: </p><ul><li>water column eddy diffusivity Kz, temperature, density</li><li>surface windspeed</li></ul><p>The example configurations assume a zip file (available from <a href="https://github.com/PALEOtoolkit/PALEOocean.jl/releases">https://github.com/PALEOtoolkit/PALEOocean.jl/releases</a>) with an illustrative 80m deep seasonally-stratifying shelf (50N, Celtic sea) derived from the S2P3 model has been unpacked to subfolder <code>S2P3_transport_20240614</code></p><p>(this is collated output from the Windows &#39;Physics Biology Model&#39; (s2p3.exe), http://pcwww.liv.ac.uk/~jons/model.htm see &#39;Introduction to the Physical and Biological Oceanography of Shelf Seas&#39;, Simpson &amp; Sharples (2012), CUP)</p><h2 id="1D-shelf-examples"><a class="docs-heading-anchor" href="#1D-shelf-examples">1D shelf examples</a><a id="1D-shelf-examples-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-examples" title="Permalink"></a></h2><h3 id="O2-and-passive-tracer-test-case"><a class="docs-heading-anchor" href="#O2-and-passive-tracer-test-case">O2 and passive tracer test case</a><a id="O2-and-passive-tracer-test-case-1"></a><a class="docs-heading-anchor-permalink" href="#O2-and-passive-tracer-test-case" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia&gt; include(&quot;PALEO_examples_shelf1D_O2_only.jl&quot;)</code></pre><p>Test case demonstrating O2 air-sea exchange, and mixing of fast and slow sinking passive tracers.</p><h3 id="Minimal-phytoplankton-P,-O2"><a class="docs-heading-anchor" href="#Minimal-phytoplankton-P,-O2">Minimal phytoplankton P, O2</a><a id="Minimal-phytoplankton-P,-O2-1"></a><a class="docs-heading-anchor-permalink" href="#Minimal-phytoplankton-P,-O2" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia&gt; include(&quot;PALEO_examples_shelf1D_P_O2.jl&quot;)</code></pre><p>Minimal single-nutrient (parameterized as phosphorus) and light-limited phytoplankton population.</p><h3 id="Sulphur-and-carbonate-system"><a class="docs-heading-anchor" href="#Sulphur-and-carbonate-system">Sulphur and carbonate system</a><a id="Sulphur-and-carbonate-system-1"></a><a class="docs-heading-anchor-permalink" href="#Sulphur-and-carbonate-system" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia&gt; include(&quot;PALEO_examples_shelf1D_P_O2_S_CH4_carb.jl&quot;)</code></pre><p>Oxygenic and anoxygenic phytoplankton populations, with sulphur + methane and marine carbonate system.</p><h2 id="1D-shelf-sediment-examples"><a class="docs-heading-anchor" href="#1D-shelf-sediment-examples">1D shelf + sediment examples</a><a id="1D-shelf-sediment-examples-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-sediment-examples" title="Permalink"></a></h2><h3 id="Minimal-phytoplankton-water-column-sediment"><a class="docs-heading-anchor" href="#Minimal-phytoplankton-water-column-sediment">Minimal phytoplankton water-column sediment</a><a id="Minimal-phytoplankton-water-column-sediment-1"></a><a class="docs-heading-anchor-permalink" href="#Minimal-phytoplankton-water-column-sediment" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia&gt; include(&quot;PALEO_examples_shelf1Dsed.jl&quot;)</code></pre><p>Coupled water-column - sediment configuration, with single phytoplankton population, sulphur + methane.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../ocean3box/README/">« 3 Box Ocean Examples</a><a class="docs-footer-nextpage" href="../../skeleton_configuration/README/">Skeleton ocean-atmosphere configuration »</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 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		<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>1D shelf sea examples and test cases · PALEOocean Documentation</title><meta name="title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta property="og:title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta property="twitter:title" content="1D shelf sea examples and test cases · PALEOocean Documentation"/><meta name="description" content="Documentation for PALEOocean Documentation."/><meta property="og:description" content="Documentation for PALEOocean Documentation."/><meta property="twitter:description" content="Documentation for PALEOocean 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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class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../PTBClarkson2014/README/">PTB land-atmosphere-ocean model (Clarkson 2015)</a></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">mitgcm</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../mitgcm/README/">MITgcm transport matrix ocean-only 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">ocean3box</span><i class="docs-chevron"></i></label><ul class="collapsed"><li><a class="tocitem" href="../../ocean3box/README/">3 Box Ocean Examples</a></li></ul></li><li><input class="collapse-toggle" id="menuitem-2-4" type="checkbox" checked/><label class="tocitem" for="menuitem-2-4"><span class="docs-label">shelf1D</span><i 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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><a class="is-disabled">Examples and Tutorials</a></li><li><a class="is-disabled">shelf1D</a></li><li class="is-active"><a href>1D shelf sea examples and test cases</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>1D shelf sea examples and test cases</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOocean.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/PALEOocean.jl/blob/main/docs/src/collated_examples/shelf1D/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="1D-shelf-sea-examples-and-test-cases"><a class="docs-heading-anchor" href="#1D-shelf-sea-examples-and-test-cases">1D shelf sea examples and test cases</a><a id="1D-shelf-sea-examples-and-test-cases-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-sea-examples-and-test-cases" title="Permalink"></a></h1><h2 id="Installation-and-configuration"><a class="docs-heading-anchor" href="#Installation-and-configuration">Installation and configuration</a><a id="Installation-and-configuration-1"></a><a class="docs-heading-anchor-permalink" href="#Installation-and-configuration" title="Permalink"></a></h2><p>These examples require netcdf files defining an annual cycle of physical variables: </p><ul><li>water column eddy diffusivity Kz, temperature, density</li><li>surface windspeed</li></ul><p>The example configurations assume a zip file (available from <a href="https://github.com/PALEOtoolkit/PALEOocean.jl/releases">https://github.com/PALEOtoolkit/PALEOocean.jl/releases</a>) with an illustrative 80m deep seasonally-stratifying shelf (50N, Celtic sea) derived from the S2P3 model has been unpacked to subfolder <code>S2P3_transport_20240614</code></p><p>(this is collated output from the Windows 'Physics Biology Model' (s2p3.exe), http://pcwww.liv.ac.uk/~jons/model.htm see 'Introduction to the Physical and Biological Oceanography of Shelf Seas', Simpson & Sharples (2012), CUP)</p><h2 id="1D-shelf-examples"><a class="docs-heading-anchor" href="#1D-shelf-examples">1D shelf examples</a><a id="1D-shelf-examples-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-examples" title="Permalink"></a></h2><h3 id="O2-and-passive-tracer-test-case"><a class="docs-heading-anchor" href="#O2-and-passive-tracer-test-case">O2 and passive tracer test case</a><a id="O2-and-passive-tracer-test-case-1"></a><a class="docs-heading-anchor-permalink" href="#O2-and-passive-tracer-test-case" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia> include("PALEO_examples_shelf1D_O2_only.jl")</code></pre><p>Test case demonstrating O2 air-sea exchange, and mixing of fast and slow sinking passive tracers.</p><h3 id="Minimal-phytoplankton-P,-O2"><a class="docs-heading-anchor" href="#Minimal-phytoplankton-P,-O2">Minimal phytoplankton P, O2</a><a id="Minimal-phytoplankton-P,-O2-1"></a><a class="docs-heading-anchor-permalink" href="#Minimal-phytoplankton-P,-O2" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia> include("PALEO_examples_shelf1D_P_O2.jl")</code></pre><p>Minimal single-nutrient (parameterized as phosphorus) and light-limited phytoplankton population.</p><h3 id="Sulphur-and-carbonate-system"><a class="docs-heading-anchor" href="#Sulphur-and-carbonate-system">Sulphur and carbonate system</a><a id="Sulphur-and-carbonate-system-1"></a><a class="docs-heading-anchor-permalink" href="#Sulphur-and-carbonate-system" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia> include("PALEO_examples_shelf1D_P_O2_S_CH4_carb.jl")</code></pre><p>Oxygenic and anoxygenic phytoplankton populations, with sulphur + methane and marine carbonate system.</p><h2 id="1D-shelf-sediment-examples"><a class="docs-heading-anchor" href="#1D-shelf-sediment-examples">1D shelf + sediment examples</a><a id="1D-shelf-sediment-examples-1"></a><a class="docs-heading-anchor-permalink" href="#1D-shelf-sediment-examples" title="Permalink"></a></h2><h3 id="Minimal-phytoplankton-water-column-sediment"><a class="docs-heading-anchor" href="#Minimal-phytoplankton-water-column-sediment">Minimal phytoplankton water-column sediment</a><a id="Minimal-phytoplankton-water-column-sediment-1"></a><a class="docs-heading-anchor-permalink" href="#Minimal-phytoplankton-water-column-sediment" title="Permalink"></a></h3><pre><code class="nohighlight hljs">julia> include("PALEO_examples_shelf1Dsed.jl")</code></pre><p>Coupled water-column - sediment configuration, with single phytoplankton population, sulphur + methane.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../ocean3box/README/">« 3 Box Ocean Examples</a><a class="docs-footer-nextpage" href="../../skeleton_configuration/README/">Skeleton ocean-atmosphere configuration »</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 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