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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Library Reference · Decapodes.jl</title><meta name="title" content="Library Reference · Decapodes.jl"/><meta property="og:title" content="Library Reference · Decapodes.jl"/><meta property="twitter:title" content="Library Reference · Decapodes.jl"/><meta name="description" content="Documentation for Decapodes.jl."/><meta property="og:description" content="Documentation for Decapodes.jl."/><meta property="twitter:description" content="Documentation for Decapodes.jl."/><script data-outdated-warner src="../assets/warner.js"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" 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href="../bc/bc_debug/">Misc Features</a></li><li><a class="tocitem" href="../ascii/">ASCII Operators</a></li><li><a class="tocitem" href="../canon/">Canonical Models</a></li><li class="is-active"><a class="tocitem" href>Library Reference</a><ul class="internal"><li><a class="tocitem" href="#Decapodes"><span>Decapodes</span></a></li></ul></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>Library Reference</a></li></ul><ul class="is-hidden-tablet"><li 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class="docs-heading-anchor-permalink" href="#Library-Reference" title="Permalink"></a></h1><h2 id="Decapodes"><a class="docs-heading-anchor" href="#Decapodes">Decapodes</a><a id="Decapodes-1"></a><a class="docs-heading-anchor-permalink" href="#Decapodes" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Decapodes.compile-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}, Vector{Decapodes.AllocVecCall}, Set{Symbol}, Int64, DataType, Decapodes.AbstractGenerationTarget, Bool}" href="#Decapodes.compile-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}, Vector{Decapodes.AllocVecCall}, Set{Symbol}, Int64, DataType, Decapodes.AbstractGenerationTarget, Bool}"><code>Decapodes.compile</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">compile(d::SummationDecapode, inputs::Vector{Symbol}, alloc_vectors::Vector{AllocVecCall}, optimizable_dec_operators::Set{Symbol}, dimension::Int, stateeltype::DataType, code_target::AbstractGenerationTarget, preallocate::Bool)</code></pre><p>Function that compiles the computation body. <code>d</code> is the input Decapode, <code>inputs</code> is a vector of state variables and literals, <code>alloc_vec</code> should be empty when passed in, <code>optimizable_dec_operators</code> is a collection of all DEC operator symbols that can use special in-place methods, <code>dimension</code> is the dimension of the problem (usually 1 or 2), <code>stateeltype</code> is the type of the state elements (usually Float32 or Float64), <code>code_target</code> determines what architecture the code is compiled for (either CPU or CUDA), and <code>preallocate</code> which is set to <code>true</code> by default and determines if intermediate results can be preallocated..</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/AlgebraicJulia/Decapodes.jl/blob/e6ff9e9d90d7fbe8cbc1ed4c085872ad9f6306a6/src/simulation.jl#L373-L381">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Decapodes.compile_env-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}, Set{Symbol}, Decapodes.AbstractGenerationTarget}" href="#Decapodes.compile_env-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}, Set{Symbol}, Decapodes.AbstractGenerationTarget}"><code>Decapodes.compile_env</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">compile_env(d::SummationDecapode, dec_matrices::Vector{Symbol}, con_dec_operators::Set{Symbol}, code_target::AbstractGenerationTarget)</code></pre><p>This creates the symbol to function linking for the simulation output. Those run through the <code>default_dec</code> backend expect both an in-place and an out-of-place variant in that order. User defined operations only support out-of-place.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/AlgebraicJulia/Decapodes.jl/blob/e6ff9e9d90d7fbe8cbc1ed4c085872ad9f6306a6/src/simulation.jl#L226-L231">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Decapodes.gensim-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}}" href="#Decapodes.gensim-Tuple{DiagrammaticEquations.decapodeacset.SummationDecapode, Vector{Symbol}}"><code>Decapodes.gensim</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">gensim(user_d::SummationDecapode, input_vars::Vector{Symbol}; dimension::Int=2, stateeltype::DataType = Float64, code_target::AbstractGenerationTarget = CPUTarget(), preallocate::Bool = true)</code></pre><p>Generates the entire code body for the simulation function. The returned simulation function can then be combined with a mesh, provided by <code>CombinatorialSpaces</code>, and a function describing symbol to operator mappings to return a simulator that can be used to solve the represented equations given initial conditions.</p><p><strong>Arguments:</strong></p><p><code>user_d</code>: The user passed Decapode for which simulation code will be generated. (This is not modified) </p><p><code>input_vars</code> is the collection of variables whose values are known at the beginning of the simulation. (Defaults to all state variables and literals in the Decapode)</p><p><strong>Keyword arguments:</strong></p><p><code>dimension</code>: The dimension of the problem. (Defaults to <code>2</code>)(Must be <code>1</code> or <code>2</code>)</p><p><code>stateeltype</code>: The element type of the state forms. (Defaults to <code>Float64</code>)(Must be <code>Float32</code> or <code>Float64</code>)</p><p><code>code_target</code>: The intended architecture target for the generated code. (Defaults to <code>CPUTarget()</code>)(Use <code>CUDATarget()</code> for NVIDIA CUDA GPUs)</p><p><code>preallocate</code>: Enables(<code>true</code>)/disables(<code>false</code>) pre-allocated caches for intermediate computations. Some functions, such as those that determine Jacobian sparsity patterns, or perform auto-differentiation, may require this to be disabled. (Defaults to <code>true</code>)</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/AlgebraicJulia/Decapodes.jl/blob/e6ff9e9d90d7fbe8cbc1ed4c085872ad9f6306a6/src/simulation.jl#L681-L702">source</a></section></article><pre class="documenter-example-output"><code class="nohighlight hljs ansi">[ Info: Page built in 2 seconds.
[ Info: This page was last built at 2024-08-21T00:17:12.832.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../canon/">« Canonical Models</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 1.6.0 on <span class="colophon-date" title="Wednesday 21 August 2024 00:27">Wednesday 21 August 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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