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{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-02-09T21:33:50","documenter_version":"1.2.1"}}
{"documenter":{"julia_version":"1.6.7","generation_timestamp":"2024-04-02T14:13:29","documenter_version":"1.3.0"}}
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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>PALEO COPSE Domains · PALEOcopse Documentation</title><meta name="title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta property="og:title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta property="twitter:title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta name="description" content="Documentation for PALEOcopse Documentation."/><meta property="og:description" content="Documentation for PALEOcopse Documentation."/><meta property="twitter:description" content="Documentation for PALEOcopse 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script data-outdated-warner src="../assets/warner.js"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 href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link 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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="../">PALEOcopse 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="../">PALEOcopse.jl documentation</a></li><li><span class="tocitem">Examples and Tutorials</span><ul><li><a class="tocitem" href="../ExampleCOPSEreloaded/">COPSE Reloaded</a></li></ul></li><li><span class="tocitem">Design</span><ul><li class="is-active"><a class="tocitem" href>PALEO COPSE Domains</a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="../PALEOcopse/">PALEOcopse Reactions</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">Design</a></li><li class="is-active"><a href>PALEO COPSE Domains</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>PALEO COPSE Domains</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOcopse.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/PALEOcopse.jl/blob/main/docs/src/COPSE_Domains.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="PALEO-COPSE-Domains"><a class="docs-heading-anchor" href="#PALEO-COPSE-Domains">PALEO COPSE Domains</a><a id="PALEO-COPSE-Domains-1"></a><a class="docs-heading-anchor-permalink" href="#PALEO-COPSE-Domains" title="Permalink"></a></h1><p>The PALEO version of the COPSE Reloaded model is componentized into land, atmosphere, ocean, oceanfloor and sedcrust Domains with explicit transfer of biogeochemical fluxes between them (<a href="#Figure-1">Figure 1</a>), allowing the PALEO Reactions for each Domain to be reused to create a hierarchy of coupled models eg including a spatially-resolved ocean component.</p><p>The implementation is mathematically equivalent to the <a href="https://github.com/sjdaines/COPSE">Matlab version</a> using for the paper ((<a href="../References/#Lenton2018">Lenton <em>et al.</em>, 2018</a>)) and is tested against archived model output.</p><p><img src="../images/COPSE_domains.png" alt/></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>PALEO COPSE reloaded model Domains (black), flux coupler Domains (green), and biogeochemical Reservoirs (blue). The &#39;atmocean&#39; Domain contains the COPSE A and O Reservoirs, which represent combined atmosphere + ocean inorganic carbon and oxygen respectively. The &#39;global&#39; Domain hosts Forcing Reactions, ReactionSum to check budgets, and a Reaction to calculate global mean temperature.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../ExampleCOPSEreloaded/">« COPSE Reloaded</a><a class="docs-footer-nextpage" href="../PALEOcopse/">PALEOcopse Reactions »</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="Friday 9 February 2024 21:33">Friday 9 February 2024</span>. Using Julia version 1.6.7.</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>PALEO COPSE Domains · PALEOcopse Documentation</title><meta name="title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta property="og:title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta property="twitter:title" content="PALEO COPSE Domains · PALEOcopse Documentation"/><meta name="description" content="Documentation for PALEOcopse Documentation."/><meta property="og:description" content="Documentation for PALEOcopse Documentation."/><meta property="twitter:description" content="Documentation for PALEOcopse 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 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="../">PALEOcopse 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="../">PALEOcopse.jl documentation</a></li><li><span class="tocitem">Examples and Tutorials</span><ul><li><a class="tocitem" href="../ExampleCOPSEreloaded/">COPSE Reloaded</a></li></ul></li><li><span class="tocitem">Design</span><ul><li class="is-active"><a class="tocitem" href>PALEO COPSE Domains</a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="../PALEOcopse/">PALEOcopse Reactions</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">Design</a></li><li class="is-active"><a href>PALEO COPSE Domains</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>PALEO COPSE Domains</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOcopse.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/PALEOcopse.jl/blob/main/docs/src/COPSE_Domains.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="PALEO-COPSE-Domains"><a class="docs-heading-anchor" href="#PALEO-COPSE-Domains">PALEO COPSE Domains</a><a id="PALEO-COPSE-Domains-1"></a><a class="docs-heading-anchor-permalink" href="#PALEO-COPSE-Domains" title="Permalink"></a></h1><p>The PALEO version of the COPSE Reloaded model is componentized into land, atmosphere, ocean, oceanfloor and sedcrust Domains with explicit transfer of biogeochemical fluxes between them (<a href="#Figure-1">Figure 1</a>), allowing the PALEO Reactions for each Domain to be reused to create a hierarchy of coupled models eg including a spatially-resolved ocean component.</p><p>The implementation is mathematically equivalent to the <a href="https://github.com/sjdaines/COPSE">Matlab version</a> using for the paper ((<a href="../References/#Lenton2018">Lenton <em>et al.</em>, 2018</a>)) and is tested against archived model output.</p><p><img src="../images/COPSE_domains.png" alt/></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>PALEO COPSE reloaded model Domains (black), flux coupler Domains (green), and biogeochemical Reservoirs (blue). The &#39;atmocean&#39; Domain contains the COPSE A and O Reservoirs, which represent combined atmosphere + ocean inorganic carbon and oxygen respectively. The &#39;global&#39; Domain hosts Forcing Reactions, ReactionSum to check budgets, and a Reaction to calculate global mean temperature.</em></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../ExampleCOPSEreloaded/">« COPSE Reloaded</a><a class="docs-footer-nextpage" href="../PALEOcopse/">PALEOcopse Reactions »</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 1.3.0 on <span class="colophon-date" title="Tuesday 2 April 2024 14:13">Tuesday 2 April 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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pCO2atm_6C = PALEOmodel.get_array(run.output, &quot;atm.pCO2atm&quot;) # get FieldArray
plot!(1e6*pCO2atm_6C, label=&quot;6C&quot;, ylabel=&quot;pCO2 (1e-6 atm)&quot;) # plot x1e6
plot!(xlim=(-600e6, 0), ylim=(0, 4000)) # rescale axes</code></pre><h2 id="Jupyter-notebook-version"><a class="docs-heading-anchor" href="#Jupyter-notebook-version">Jupyter notebook version</a><a id="Jupyter-notebook-version-1"></a><a class="docs-heading-anchor-permalink" href="#Jupyter-notebook-version" title="Permalink"></a></h2><p>The same content as above (with additional examples) is available as the Jupyter notebook <code>COPSE_reloaded_reloaded.ipynb</code>.</p><p>To start Jupyter from within the Julia REPL:</p><pre><code class="nohighlight hljs">julia&gt; using IJulia
julia&gt; notebook(dir=pwd(), detached=true)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« PALEOcopse.jl documentation</a><a class="docs-footer-nextpage" href="../COPSE_Domains/">PALEO COPSE Domains »</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="Friday 9 February 2024 21:33">Friday 9 February 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
julia&gt; notebook(dir=pwd(), detached=true)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« PALEOcopse.jl documentation</a><a class="docs-footer-nextpage" href="../COPSE_Domains/">PALEO COPSE Domains »</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 1.3.0 on <span class="colophon-date" title="Tuesday 2 April 2024 14:13">Tuesday 2 April 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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