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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Tools · juobs Documentation</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/5.15.0/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.0/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" 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">juobs Documentation</span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="index.html">Home</a></li><li><a class="tocitem" href="reader.html">Reader</a></li><li class="is-active"><a class="tocitem" href="tools.html">Tools</a></li><li><a class="tocitem" href="obs.html">Observables</a></li><li><a class="tocitem" href="linalg.html">Linear Algebra</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"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="tools.html">Tools</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="tools.html">Tools</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs" title="Edit on GitLab"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitLab</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="Tools"><a class="docs-heading-anchor" href="#Tools">Tools</a><a id="Tools-1"></a><a class="docs-heading-anchor-permalink" href="#Tools" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="juobs.corr_obs" href="#juobs.corr_obs"><code>juobs.corr_obs</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">corr_obs(cdata::CData; real::Bool=true, rw::Union{Array{Float64, 2}, Nothing}=nothing, L::Int64=1)

corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array{Float64, 2}, 1}, Nothing}=nothing, L::Int64=1)</code></pre><p>Creates a <code>Corr</code> struct with the given <code>CData</code> struct <code>cdata</code> (<code>read_mesons</code>) for a single replica. An array of <code>CData</code> can be passed as argument for multiple replicas.</p><p>The flag <code>real</code> select the real or imaginary part of the correlator. If <code>rw</code> is specified, the method applies reweighting. <code>rw</code> is passed as a matrix of Float64 (<code>read_ms1</code>) The correlator can be normalized with the volume factor if <code>L</code> is fixed.</p><pre><code class="language-">#Single replica
data = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
rw = read_ms1(path_rw)
corr_pp = corr_obs.(data)
corr_pp_r = corr_obs.(data, rw=rw)

#Two replicas
data = read_mesons([path_r1, path_r2], &quot;G5&quot;, &quot;G5&quot;)
rw1 = read_ms1(path_rw1)
rw2 = read_ms1(path_rw2)

corr_pp = corr_obs.(data)
corr_pp_r = corr_obs.(data, rw=[rw1, rw2])</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="juobs.md_sea" href="#juobs.md_sea"><code>juobs.md_sea</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">md_sea(a::uwreal, md::Vector{Matrix{Float64}}, ws::ADerrors.wspace=ADerrors.wsg)</code></pre><p>Computes the derivative of an observable A with respect to the sea quark masses.</p><p><span>$\frac{d &lt;A&gt;}{dm(sea)} = \sum_i \frac{\partial &lt;A&gt;}{\partial &lt;O_i&gt;}  \frac{d &lt;O_i&gt;}{d m(sea)}$</span></p><p><span>$\frac{d &lt;O_i&gt;}{dm(sea)} = &lt;O_i&gt; &lt;\frac{\partial S}{\partial m}&gt; - &lt;O_i \frac{\partial S}{\partial m}&gt;  = - &lt;(O_i - &lt;O_i&gt;) (\frac{\partial S}{\partial m} - &lt;\frac{\partial S}{\partial m}&gt;)&gt;$</span></p><p>where <span>$O_i$</span> are primary observables </p><p><code>md</code> is a vector that contains the derivative of the action <span>$S$</span> with respect to the sea quark masses for each replica. <code>md[irep][irw, icfg]</code></p><p><code>md_sea</code> returns a tuple of uwreal observables <span>$(dA/dm_l, dA/dm_s)|_{sea}$</span>,  where <span>$m_l$</span> and <span>$m_s$</span> are the light and strange quark masses.</p><pre><code class="language-">#Single replica
data = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
md = read_md(path_md)
rw = read_ms1(path_rw)

corr_pp = corr_obs.(data, rw=rw)
m = meff(corr_pp[1], plat)
m_mdl, m_mds = md_sea(m, [md], ADerrors.wsg)
m_shifted = m + 2 * dml * m_mdl + dms * m_mds

#Two replicas
data = read_mesons([path_r1, path_r2], &quot;G5&quot;, &quot;G5&quot;)
md1 = read_md(path_md1)
md2 = read_md(path_md2)

corr_pp = corr_obs.(data)
m = meff(corr_pp[1], plat)
m_mdl, m_mds = md_sea(m, [md1, md2], ADerrors.wsg)
m_shifted = m + 2 * dml * m_mdl + dms * m_mds</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="juobs.md_val" href="#juobs.md_val"><code>juobs.md_val</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">md_val(a::uwreal, obs::Corr, derm::Vector{Corr})</code></pre><p>Computes the derivative of an observable A with respect to the valence quark masses.</p><p><span>$\frac{d &lt;A&gt;}{dm(val)} = \sum_i \frac{\partial &lt;A&gt;}{\partial &lt;O_i&gt;}  \frac{d &lt;O_i&gt;}{d m(val)}$</span></p><p><span>$\frac{d &lt;O_i&gt;}{dm(val)} = &lt;\frac{\partial O_i}{\partial m(val)}&gt;$</span></p><p>where <span>$O_i$</span> are primary observables </p><p><code>md</code> is a vector that contains the derivative of the action <span>$S$</span> with respect to the sea quark masses for each replica. <code>md[irep][irw, icfg]</code></p><p><code>md_val</code> returns a tuple of <code>uwreal</code> observables <span>$(dA/dm_1, dA/dm_2)|_{val}$</span>,  where <span>$m_1$</span> and <span>$m_2$</span> are the correlator masses.</p><pre><code class="language-">data = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;, legacy=true)
data_d1 = read_mesons(path, &quot;G5_d1&quot;, &quot;G5_d1&quot;, legacy=true)
data_d2 = read_mesons(path, &quot;G5_d2&quot;, &quot;G5_d2&quot;, legacy=true)

rw = read_ms1(path_rw)

corr_pp = corr_obs.(data, rw=rw)
corr_pp_d1 = corr_obs.(data_d1, rw=rw)
corr_pp_d2 = corr_obs.(data_d2, rw=rw)
derm = [[corr_pp_d1[k], corr_pp_d2[k]] for k = 1:length(pp_d1)]

m = meff(corr_pp[1], plat)
m_md1, m_md2 = md_val(m, corr_pp[1], derm[1])
m_shifted = m + 2 * dm1 * m_md1 + dm2 * m_md2</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="juobs.lin_fit" href="#juobs.lin_fit"><code>juobs.lin_fit</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">lin_fit(x::Vector{&lt;:Real}, y::Vector{uwreal})</code></pre><p>Computes a linear fit of uwreal data points y. This method return uwreal fit parameters and chisqexpected.</p><pre><code class="language-">fitp, csqexp = lin_fit(phi2, m2)
m2_phys = fitp[1] + fitp[2] * phi2_phys</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="juobs.fit_routine" href="#juobs.fit_routine"><code>juobs.fit_routine</code></a><span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">fit_routine(model::Function, xdata::Array{&lt;:Real}, ydata::Array{uwreal}, param::Int64=3; wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)

fit_routine(model::Function, xdata::Array{uwreal}, ydata::Array{uwreal}, param::Int64=3; wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, covar::Bool=false)</code></pre><p>Given a model function with a number param of parameters and an array of <code>uwreal</code>, this function fit ydata with the given <code>model</code> and print fit information The method return an array <code>upar</code> with the best fit parameters with their errors. The flag <code>wpm</code> is an optional array of Float64 of lenght 4. The first three paramenters specify the criteria to determine the summation windows:</p><ul><li><p><code>vp[1]</code>: The autocorrelation function is summed up to <span>$t = round(vp[1])$</span>.</p></li><li><p><code>vp[2]</code>: The sumation window is determined using U. Wolff poposal with <span>$S_\tau = wpm[2]$</span></p></li><li><p><code>vp[3]</code>: The autocorrelation function <span>$\Gamma(t)$</span> is summed up a point where its error <span>$\delta\Gamma(t)$</span> is a factor <code>vp[3]</code> times larger than the signal.</p></li></ul><p>An additional fourth parameter <code>vp[4]</code>, tells ADerrors to add a tail to the error with <span>$\tau_{exp} = wpm[4]$</span>. Negative values of <code>wpm[1:4]</code> are ignored and only one component of <code>wpm[1:3]</code> needs to be positive. If the flag <code>covar</code>is set to true, <code>fit_routine</code> takes into account covariances between x and y for each data point.</p><pre><code class="language-">@. model(x,p) = p[1] + p[2] * exp(-(p[3]-p[1])*x)
@. model2(x,p) = p[1] + p[2] * x[:, 1] + (p[3] + p[4] * x[:, 1]) * x[:, 2]
fit_routine(model, xdata, ydata, param=3)
fit_routine(model, xdata, ydata, param=3, covar=true)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://gitlab.ift.uam-csic.es/jugarrio/juobs">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="reader.html">« Reader</a><a class="docs-footer-nextpage" href="obs.html">Observables »</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></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 23 March 2021 11:06">Tuesday 23 March 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>