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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>PALEOaqchem.jl · PALEOaqchem Documentation</title><meta name="title" content="PALEOaqchem.jl · PALEOaqchem Documentation"/><meta property="og:title" content="PALEOaqchem.jl · PALEOaqchem Documentation"/><meta property="twitter:title" content="PALEOaqchem.jl · PALEOaqchem Documentation"/><meta name="description" content="Documentation for PALEOaqchem Documentation."/><meta property="og:description" content="Documentation for PALEOaqchem Documentation."/><meta property="twitter:description" content="Documentation for PALEOaqchem 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script data-outdated-warner src="assets/warner.js"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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href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><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>PALEOaqchem 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 class="is-active"><a class="tocitem" href>PALEOaqchem.jl</a><ul class="internal"><li><a class="tocitem" href="#Installation"><span>Installation</span></a></li><li><a class="tocitem" href="#Examples-of-usage"><span>Examples of usage</span></a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="Organic matter and remineralization/">Organic matter and remineralization</a></li><li><a class="tocitem" href="Generic Chemistry/">Generic Chemistry</a></li><li><a class="tocitem" href="Secondary Redox/">Secondary redox</a></li><li><a class="tocitem" href="Carbonate chemistry/">Carbonate chemistry</a></li><li><a class="tocitem" href="Molecular Diffusivity/">Molecular diffusivity</a></li><li><a class="tocitem" href="Isotopes/">Isotope systems</a></li><li><a class="tocitem" href="functions/">PALEOaqchem 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 class="is-active"><a href>PALEOaqchem.jl</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>PALEOaqchem.jl</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOaqchem.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/PALEOaqchem.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="PALEOaqchem.jl"><a class="docs-heading-anchor" href="#PALEOaqchem.jl">PALEOaqchem.jl</a><a id="PALEOaqchem.jl-1"></a><a class="docs-heading-anchor-permalink" href="#PALEOaqchem.jl" title="Permalink"></a></h1><p>Aquatic biogeochemistry components for the <a href="https://github.com/PALEOtoolkit">PALEOtoolkit</a> biogeochemical model framework.</p><p>The PALEOaqchem package implements biogeochemistry components that provide:</p><ul><li>representation of organic matter phases (as discrete reactivity fractions or as a reactive-continuum model) and remineralization by oxygen, nitrogen, manganese, iron, sulphur and disproportionation to methane.</li><li>generic equilibrium, kinetic, and precipitation-dissolution reactions, which can be configured into reaction networks using the PALEO YAML configuration file.</li><li>pre-packaged reactions to simplify implementation of marine carbonate chemistry and a subset of secondary redox reactions, including support for carbon and sulphur isotope systems.</li></ul><p>It can be used in two main ways:</p><ul><li>to construct arbitrary aqueous biogeochemical models, including equilibrium, kinetic and precipitation-dissolution reactions for a configurable set of solute and solid-phase species.</li><li>to construct more-or-less standard ocean or sediment biogeochemical models (with commonly used carbonate chemistry, primary and secondary redox reactions) out of predefined components.</li></ul><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>The PALEOaqchem Reactions are available to the <a href="https://github.com/PALEOtoolkit">PALEOtoolkit</a> framework when the registered PALEOaqchem package is installed and loaded:</p><pre><code class="nohighlight hljs">julia> Pkg.add("PALEOaqchem") # install PALEOaqchem in currently active Julia environment | ||
| julia> import PALEOaqchem</code></pre><h2 id="Examples-of-usage"><a class="docs-heading-anchor" href="#Examples-of-usage">Examples of usage</a><a id="Examples-of-usage-1"></a><a class="docs-heading-anchor-permalink" href="#Examples-of-usage" title="Permalink"></a></h2><p>The <a href="https://github.com/PALEOtoolkit/PALEOtutorials.jl">PALEOtutorials</a> repository includes a <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/stable/collated_examples/configurable_chemistry/README/">minimal model of the marine carbonate system </a> implementated using PALEOaqchem generic chemistry.</p><p>The <a href="https://github.com/PALEOtoolkit/PALEOocean.jl">PALEOocean</a> and <a href="https://github.com/PALEOtoolkit/PALEOsediment.jl">PALEOsediment</a> include examples of water column and sediment biogeochemistry.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="Organic matter and remineralization/">Organic matter and remineralization »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Tuesday 17 December 2024 09:55">Tuesday 17 December 2024</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> | ||
| julia> import PALEOaqchem</code></pre><h2 id="Examples-of-usage"><a class="docs-heading-anchor" href="#Examples-of-usage">Examples of usage</a><a id="Examples-of-usage-1"></a><a class="docs-heading-anchor-permalink" href="#Examples-of-usage" title="Permalink"></a></h2><p>The <a href="https://github.com/PALEOtoolkit/PALEOtutorials.jl">PALEOtutorials</a> repository includes a <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/stable/collated_examples/configurable_chemistry/README/">minimal model of the marine carbonate system </a> implementated using PALEOaqchem generic chemistry.</p><p>The <a href="https://github.com/PALEOtoolkit/PALEOocean.jl">PALEOocean</a> and <a href="https://github.com/PALEOtoolkit/PALEOsediment.jl">PALEOsediment</a> include examples of water column and sediment biogeochemistry.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="Organic matter and remineralization/">Organic matter and remineralization »</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><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Sunday 22 December 2024 18:31">Sunday 22 December 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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