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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Displaying model configuration and output from the Julia REPL · PALEOmodel Documentation</title><meta name="title" content="Displaying model configuration and output from the Julia REPL · PALEOmodel Documentation"/><meta property="og:title" content="Displaying model configuration and output from the Julia REPL · PALEOmodel Documentation"/><meta property="twitter:title" content="Displaying model configuration and output from the Julia REPL · PALEOmodel Documentation"/><meta name="description" content="Documentation for PALEOmodel Documentation."/><meta property="og:description" content="Documentation for PALEOmodel Documentation."/><meta property="twitter:description" content="Documentation for PALEOmodel Documentation."/><script data-outdated-warner src="../assets/warner.js"></script><link 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src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" 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="../">PALEOmodel 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="../">PALEOmodel.jl</a></li><li><span class="tocitem">Design</span><ul><li><a class="tocitem" href="../MathematicalFormulation/">Mathematical formulation of the reaction-transport problem</a></li></ul></li><li><span class="tocitem">HOWTOs</span><ul><li class="is-active"><a class="tocitem" href>Displaying model configuration and output from the Julia REPL</a></li><li><a class="tocitem" href="../HOWTOsmallnegativevalues/">Managing small and negative values</a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="../PALEOmodelSolvers/">PALEOmodel solvers</a></li><li><a class="tocitem" href="../PALEOmodelOutput/">PALEOmodel output</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">HOWTOs</a></li><li class="is-active"><a href>Displaying model configuration and output from the Julia REPL</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Displaying model configuration and output from the Julia REPL</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOmodel.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/PALEOmodel.jl/blob/main/docs/src/HOWTOshowmodelandoutput.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="Displaying-model-configuration-and-output-from-the-Julia-REPL"><a class="docs-heading-anchor" href="#Displaying-model-configuration-and-output-from-the-Julia-REPL">Displaying model configuration and output from the Julia REPL</a><a id="Displaying-model-configuration-and-output-from-the-Julia-REPL-1"></a><a class="docs-heading-anchor-permalink" href="#Displaying-model-configuration-and-output-from-the-Julia-REPL" title="Permalink"></a></h1><p>Page moved to <a href="https://paleotoolkit.github.io/PALEOtutorials.jl/dev/ExampleInstallConfig/HOWTOshowmodelandoutput">PALEOtutorials</a></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../MathematicalFormulation/">« Mathematical formulation of the reaction-transport problem</a><a class="docs-footer-nextpage" href="../HOWTOsmallnegativevalues/">Managing small and negative values »</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 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Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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| <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Managing small and negative values · PALEOmodel Documentation</title><meta name="title" content="Managing small and negative values · PALEOmodel Documentation"/><meta property="og:title" content="Managing small and negative values · PALEOmodel Documentation"/><meta property="twitter:title" content="Managing small and negative values · PALEOmodel Documentation"/><meta name="description" content="Documentation for PALEOmodel Documentation."/><meta property="og:description" content="Documentation for PALEOmodel Documentation."/><meta property="twitter:description" content="Documentation for PALEOmodel 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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data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" 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="../">PALEOmodel 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="../">PALEOmodel.jl</a></li><li><span class="tocitem">Design</span><ul><li><a class="tocitem" href="../MathematicalFormulation/">Mathematical formulation of the reaction-transport problem</a></li></ul></li><li><span class="tocitem">HOWTOs</span><ul><li><a class="tocitem" href="../HOWTOshowmodelandoutput/">Displaying model configuration and output from the Julia REPL</a></li><li class="is-active"><a class="tocitem" href>Managing small and negative values</a></li></ul></li><li><span class="tocitem">Reference</span><ul><li><a class="tocitem" href="../PALEOmodelSolvers/">PALEOmodel solvers</a></li><li><a class="tocitem" href="../PALEOmodelOutput/">PALEOmodel output</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">HOWTOs</a></li><li class="is-active"><a href>Managing small and negative values</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>Managing small and negative values</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/PALEOtoolkit/PALEOmodel.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/PALEOmodel.jl/blob/main/docs/src/HOWTOsmallnegativevalues.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="Managing-small-and-negative-values"><a class="docs-heading-anchor" href="#Managing-small-and-negative-values">Managing small and negative values</a><a id="Managing-small-and-negative-values-1"></a><a class="docs-heading-anchor-permalink" href="#Managing-small-and-negative-values" title="Permalink"></a></h1><p>It is common for biogeochemical reservoirs to both (i) be required to be non-negative, and (ii) approach zero (eg oxygen below the oxic layer in a sediment). This requires some explicit management to allow the numerical ODE / DAE solvers to operate stably and efficiently.</p><p>PALEO follows the recommended best practice for Sundials CVODE and other adaptive solvers (also including those in MATLAB), which is to allow -ve values within the error tolerance, and set rates to zero when this happens.</p><p>This is a FAQ for CVODE, <a href="https://computing.llnl.gov/projects/sundials/faq#cvode_negvals">https://computing.llnl.gov/projects/sundials/faq#cvode_negvals</a>, '... Remember that a small negative value in y returned by CVODE, with magnitude comparable to abstol or less, is equivalent to zero as far as the computation is concerned. .... '. See (<a href="../References/#Shampine2005">Shampine <em>et al.</em>, 2005</a>) for a detailed discussion.</p><p>There are three areas that need to be addressed:</p><ol><li>When calculating biogeochemical reaction rates that depend on <code>myvar</code>, use <code>max(myvar, 0.0)</code> or similar everywhere to set rates to zero for -ve values. Linear transport processes (eg diffusion, flux transport) should transport -ve values to maintain conservation properties.</li><li>Set the <code>abstol</code> solver option to control errors for near-zero values of state Variables, see <a href="../PALEOmodelSolvers/#DifferentialEquations-solvers">DifferentialEquations solvers</a>. The default value will often be too high. In some cases, it may be most efficient to tolerate -ve values, in other cases, it may be most efficient to control errors using a combination of <code>reltol</code> and <code>abstol</code> so that -ve values are not generated. The easiest way to set <code>abstol</code> in PALEO is to use <code>abstol=1e-5*PALEOmodel.get_statevar_norm(modeldata.solver_view_all)</code> to set to a small fraction (here 1e-5, experimentation will be needed) of the state variables' <code>norm_value</code> attributes (these are set in the .yaml configuration file). </li><li>Defend against -ve values when using plots with log scales by explicitly setting an axis lower limit eg <code>ylim=(1e-9, Inf)</code> (without this, the autoscaling will fail and possible produce strange-looking plots eg with inverted axes). See <a href="https://docs.juliaplots.org/latest/generated/attributes_axis/">https://docs.juliaplots.org/latest/generated/attributes_axis/</a></li></ol></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../HOWTOshowmodelandoutput/">« Displaying model configuration and output from the Julia REPL</a><a class="docs-footer-nextpage" href="../PALEOmodelSolvers/">PALEOmodel solvers »</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="Thursday 2 January 2025 21:53">Thursday 2 January 2025</span>. Using Julia version 1.6.7.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> |
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