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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>IndividualDisplacements.jl · IndividualDisplacements</title><link href="https://fonts.googleapis.com/css?family=Lato|Roboto+Mono" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.11.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.11.1/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="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"/><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">IndividualDisplacements</span></div><form class="docs-search" action="search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href>IndividualDisplacements.jl</a><ul class="internal"><li><a class="tocitem" href="#API-Guide-1"><span>API Guide</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"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>IndividualDisplacements.jl</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>IndividualDisplacements.jl</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/docs/src/index.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="IndividualDisplacements.jl-1"><a class="docs-heading-anchor" href="#IndividualDisplacements.jl-1">IndividualDisplacements.jl</a><a class="docs-heading-anchor-permalink" href="#IndividualDisplacements.jl-1" title="Permalink"></a></h1><p><strong>IndividualDisplacements.jl</strong> computes elementary point displacements over a gridded Earth domain (e.g. a climate model C-grid). A typical application is the simulation and analysis of materials moving through atmospheric flows (e.g. dust or chemicals) or oceanic flows (e.g. plastics or planktons).</p><p>Inter-operability with popular climate model grids and their representation in <a href="https://github.com/JuliaClimate/MeshArrays.jl">MeshArrays.jl</a> is a central element. The package can also read and plot trajectory simulation output from e.g. the <a href="https://mitgcm.readthedocs.io/en/latest/?badge=latest">MITgcm</a>. It was originally developed using <a href="https://eccov4.readthedocs.io/en/latest/">ECCOv4</a> and <a href="https://cbiomes.readthedocs.io/en/latest/">CBIOMES</a> ocean model simulations (<a href="https://doi.org/10.5194/gmd-8-3071-2015">Forget et al. 2015</a>).</p><p>The <code>VelComp!</code> and <code>VelComp</code> functions compute the velocity of tracked points. <code>tests/runtests.jl</code> uses solid body rotation as a benchmark (see below).</p><p><img src="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/master/examples/SolidBodyRotation.png" width="50%"></p><h2 id="API-Guide-1"><a class="docs-heading-anchor" href="#API-Guide-1">API Guide</a><a class="docs-heading-anchor-permalink" href="#API-Guide-1" title="Permalink"></a></h2><ul><li><a href="#IndividualDisplacements.ReadDisplacements-Tuple{String,DataType}"><code>IndividualDisplacements.ReadDisplacements</code></a></li><li><a href="#IndividualDisplacements.VelComp-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}"><code>IndividualDisplacements.VelComp</code></a></li><li><a href="#IndividualDisplacements.VelComp!-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}"><code>IndividualDisplacements.VelComp!</code></a></li><li><a href="#IndividualDisplacements.VelCopy-Tuple{Any,Any,DataFrames.DataFrame,Any}"><code>IndividualDisplacements.VelCopy</code></a></li><li><a href="#IndividualDisplacements.example1-Tuple{}"><code>IndividualDisplacements.example1</code></a></li><li><a href="#IndividualDisplacements.example2-Tuple{}"><code>IndividualDisplacements.example2</code></a></li><li><a href="#IndividualDisplacements.example2_setup-Tuple{}"><code>IndividualDisplacements.example2_setup</code></a></li><li><a href="#IndividualDisplacements.myread-Tuple{String,MeshArrays.gcmarray}"><code>IndividualDisplacements.myread</code></a></li></ul><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.ReadDisplacements-Tuple{String,DataType}" href="#IndividualDisplacements.ReadDisplacements-Tuple{String,DataType}"><code>IndividualDisplacements.ReadDisplacements</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">ReadDisplacements(dirIn::String,prec::DataType)</code></pre><p>Read displacements from MITgcm output file using MeshArrays and return as a DataFrame.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/read.jl#L16-L21">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.VelComp!-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}" href="#IndividualDisplacements.VelComp!-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}"><code>IndividualDisplacements.VelComp!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">VelComp!(du,u,p::Dict,tim)</code></pre><p>Interpolate velocity from gridded fields (after exchange on u0,v0) and return position increment <code>du</code> (i.e. <code>x,y,fIndex</code>).</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/compute.jl#L2-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.VelComp-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}" href="#IndividualDisplacements.VelComp-Tuple{Array{Float64,1},Array{Float64,1},Dict,Any}"><code>IndividualDisplacements.VelComp</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">VelComp(du,u,p::Dict,tim)</code></pre><p>Interpolate velocity from gridded fields and return position increment <code>du</code></p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/compute.jl#L59-L63">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.VelCopy-Tuple{Any,Any,DataFrames.DataFrame,Any}" href="#IndividualDisplacements.VelCopy-Tuple{Any,Any,DataFrames.DataFrame,Any}"><code>IndividualDisplacements.VelCopy</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">VelCopy(du,u,p::DataFrame,t)</code></pre><p>Interpolate velocity from MITgcm float_trajectories output and return position increment <code>du</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/read.jl#L2-L7">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.example1-Tuple{}" href="#IndividualDisplacements.example1-Tuple{}"><code>IndividualDisplacements.example1</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">example1()</code></pre><p>Global ocean case – just reading from file for now.</p><pre><code class="language-none">df=IndividualDisplacements.example1()
p=dirname(pathof(IndividualDisplacements))
include(joinpath(p,"plot_pyplot.jl"))
PyPlot.figure(); PlotMapProj(df,300); gcf()</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/examples.jl#L2-L14">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.example2-Tuple{}" href="#IndividualDisplacements.example2-Tuple{}"><code>IndividualDisplacements.example2</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia">example2()</code></pre><p>Reproducing <code>MITgcm/verification/flt_example/</code> case. This is based on an extended and modified configuration of the standard MITgcm test case.</p><pre><code class="language-none">(df,ref,sol)=IndividualDisplacements.example2();
p=dirname(pathof(IndividualDisplacements))
include(joinpath(p,"plot_pyplot.jl"))
PyPlot.figure(); PlotBasic(df,300,100000.0); gcf()
using Plots
Plots.plot(sol[1,:],sol[2,:],linewidth=5,lc=:black, title="One Trajectory Example",
xaxis="x",yaxis="y",label="Julia Solution") # legend=false
pl=Plots.plot!(ref[1,:],ref[2,:],lw=3,ls=:dash,lc=:red,label="MITgcm Solution")</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/examples.jl#L21-L39">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.example2_setup-Tuple{}" href="#IndividualDisplacements.example2_setup-Tuple{}"><code>IndividualDisplacements.example2_setup</code></a> — <span class="docstring-category">Method</span></header><section><div><p>example2_setup()</p><p>Read gridded variables from file using MeshArrays and return result in uvetc Dictionary.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/examples.jl#L72-L77">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="IndividualDisplacements.myread-Tuple{String,MeshArrays.gcmarray}" href="#IndividualDisplacements.myread-Tuple{String,MeshArrays.gcmarray}"><code>IndividualDisplacements.myread</code></a> — <span class="docstring-category">Method</span></header><section><div><p>myread()</p><p>Read a gridded variable from 2x2 tile files. This is used in <code>example2_setup()</code> with <code>flt_example/</code></p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/JuliaClimate/IndividualDisplacements.jl/blob/10da6986b486b77dab5e49b7b7e6c4d32e632822/src/examples.jl#L132-L137">source</a></section></article></article></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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Tuesday 11 February 2020 03:15">Tuesday 11 February 2020</span>. Using Julia version 1.2.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>