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Manifest.toml
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Project.toml
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......@@ -7,7 +7,6 @@ version = "0.1.0"
ADerrors = "5e92007d-7bf1-471c-8ceb-4591b8b567a9"
BDIO = "375f315e-f2c4-11e9-2ef9-134f02f79e27"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
Optim = "429524aa-4258-5aef-a3af-852621145aeb"
......
docs/build/index.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>Home · 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 class="is-active"><a class="tocitem" href="index.html">Home</a><ul class="internal"><li><a class="tocitem" href="#Contents"><span>Contents</span></a></li></ul></li><li><a class="tocitem" href="reader.html">Reader</a></li><li><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="index.html">Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Home</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="DOCUMENTATION"><a class="docs-heading-anchor" href="#DOCUMENTATION">DOCUMENTATION</a><a id="DOCUMENTATION-1"></a><a class="docs-heading-anchor-permalink" href="#DOCUMENTATION" title="Permalink"></a></h1><h2 id="Contents"><a class="docs-heading-anchor" href="#Contents">Contents</a><a id="Contents-1"></a><a class="docs-heading-anchor-permalink" href="#Contents" title="Permalink"></a></h2><ul><li><a href="reader.html#Reader">Reader</a></li><li><a href="tools.html#Tools">Tools</a></li><li><a href="obs.html#Observables">Observables</a></li><li><a href="linalg.html#Linear-Algebra">Linear Algebra</a></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="reader.html">Reader »</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>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Home · 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 class="is-active"><a class="tocitem" href="index.html">Home</a><ul class="internal"><li><a class="tocitem" href="#Contents"><span>Contents</span></a></li></ul></li><li><a class="tocitem" href="reader.html">Reader</a></li><li><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="index.html">Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Home</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="DOCUMENTATION"><a class="docs-heading-anchor" href="#DOCUMENTATION">DOCUMENTATION</a><a id="DOCUMENTATION-1"></a><a class="docs-heading-anchor-permalink" href="#DOCUMENTATION" title="Permalink"></a></h1><h2 id="Contents"><a class="docs-heading-anchor" href="#Contents">Contents</a><a id="Contents-1"></a><a class="docs-heading-anchor-permalink" href="#Contents" title="Permalink"></a></h2><ul><li><a href="reader.html#Reader">Reader</a></li><li><a href="tools.html#Tools">Tools</a></li><li><a href="obs.html#Observables">Observables</a></li><li><a href="linalg.html#Linear-Algebra">Linear Algebra</a></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="reader.html">Reader »</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="Friday 17 September 2021 08:40">Friday 17 September 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
docs/build/linalg.html
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......@@ -78,4 +78,4 @@ evals = getall_eigvals(matrices, 5) #where t_0=5
Julia&gt;</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.getall_eigvecs" href="#juobs.getall_eigvecs"><code>juobs.getall_eigvecs</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">getall_eigvecs(a::Vector{Matrix}, delta_t; iter=30 )</code></pre><p>This function solves a GEVP problem, returning the eigenvectors, for a list of matrices.</p><p><span>$C(t_i)v_i = λ_i C(t_i-\delta_t) v_i$</span>, with i=1:lenght(a)</p><p>Here <code>delta_t</code> is the time shift within the two matrices of the problem, and is kept fixed. It takes as input:</p><ul><li><p><code>a::Vector{Matrix}</code> : a vector of matrices</p></li><li><p><code>delta_t::Int64</code> : the fixed time shift t-t_0</p></li><li><p><code>iter=30</code> : the number of iterations of the qr algorithm used to extract the eigenvalues </p></li></ul><p>It returns:</p><ul><li><code>res = Vector{Matrix{uwreal}}</code></li></ul><p>where each <code>res[i]</code> is a matrix with the eigenvectors as columns Examples:</p><pre><code class="language-">mat_array = get_matrix(diag, upper_diag)
evecs = getall_eigvecs(mat_array, 5)</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="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>
evecs = getall_eigvecs(mat_array, 5)</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="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="Friday 17 September 2021 08:40">Friday 17 September 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
docs/build/obs.html
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docs/build/reader.html
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......@@ -24,4 +24,4 @@ truncate_data!(Y, nc)
dat = read_mesons([path1, path2], &quot;G5&quot;, &quot;G5&quot;)
Y = read_ms.([path1_ms, path2_ms])
truncate_data!(dat, [nc1, nc2])
truncate_data!(Y, [nc1, nc2])</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="index.html">« Home</a><a class="docs-footer-nextpage" href="tools.html">Tools »</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>
truncate_data!(Y, [nc1, nc2])</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="index.html">« Home</a><a class="docs-footer-nextpage" href="tools.html">Tools »</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="Friday 17 September 2021 08:40">Friday 17 September 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
docs/build/search.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>Search · 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><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="search.html">Search</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="search.html">Search</a></li></ul></nav><div class="docs-right"><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><p id="documenter-search-info">Loading search...</p><ul id="documenter-search-results"></ul></article><nav class="docs-footer"><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="Friday 17 September 2021 08:40">Friday 17 September 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body><script src="search_index.js"></script><script src="assets/search.js"></script></html>
docs/build/search_index.js
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This diff is collapsed.
docs/build/tools.html
View file @ 7c0e8824
......@@ -50,4 +50,4 @@ m2_phys = fitp[1] + fitp[2] * phi2_phys</code></pre></div><a class="docs-sourcel
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>
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="Friday 17 September 2021 08:40">Friday 17 September 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
src/juobs.jl
View file @ 7c0e8824
module juobs
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, Optim
using Base: Float64
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, LeastSquaresOptim
import Statistics: mean
include("juobs_types.jl")
......@@ -9,9 +9,9 @@ include("juobs_reader.jl")
include("juobs_tools.jl")
include("juobs_obs.jl")
export read_mesons, read_ms1, read_ms, read_md, truncate_data!
export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_data!
export get_matrix, energies, uwdot, uweigvals, uweigvecs, uweigen, invert, getall_eigvals, getall_eigvecs, hess_reduce, uwcholesky, transpose, tridiag_reduction, make_positive_def, invert_covar_matrix
export corr_obs, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine
export corr_obs, corr_obs_TSM, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine
export meff, mpcac, dec_const, dec_const_pcvc, comp_t0
end # module
src/juobs_obs.jl
View file @ 7c0e8824
......@@ -494,23 +494,26 @@ function get_model(x, p, n)
return s
end
@doc raw"""
comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, info::Bool=false)
comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, info::Bool=false)
Computes `t0` using the energy density of the action `Ysl`(Yang-Mills action).
`t0` is computed in the plateau `plat`.
A polynomial interpolation in `t` is performed to find `t0`, where `npol` is the degree of the polynomial (linear fit by default)
The flag `pl` allows to show the plot.
The flag `pl` allows to show the plot.
The flag `info` provides extra output that contains information about the primary observables. The function returns the primary observables ``<WY>`` and ``<W>``
(it returns the observable <Y> if rw=nothing)
```@example
#Single replica
Y = read_ms(path)
rw = read_ms(path_rw)
t0 = comp_t0(Y, [38, 58], L=32)
t0_r = comp_t0(Y, [38, 58], L=32, rw=rw)
t0, Yobs = comp_t0(Y, [38, 58], L=32, info=true)
t0_r, WYobs, Wobs = comp_t0(Y, [38, 58], L=32, rw=rw, info=true)
#Two replicas
Y1 = read_ms(path1)
......@@ -525,7 +528,7 @@ t0_r = comp_t0(Y, [38, 58], L=32, rw=[rw1, rw2], pl=true)
"""
function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false,
rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2, ws::ADerrors.wspace=ADerrors.wsg,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, info::Bool=false)
Ysl = Y.obs
t = Y.t
......@@ -551,16 +554,27 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false,
end
end
Ysl = isnothing(rw) ? Ysl : apply_rw(Ysl, rw)
xmax = size(Ysl, 2)
nt0 = t0_guess(t, Ysl, plat, L)
dt0 = iseven(npol) ? Int64(npol / 2) : Int64((npol+1)/ 2)
Y_aux = Matrix{uwreal}(undef, xmax, 2*dt0+1)
if !isnothing(rw)
Ysl_r, W = apply_rw(Ysl, rw)
W_obs = uwreal(W, id)
WY_aux = Matrix{uwreal}(undef, xmax, 2*dt0+1)
end
for i = 1:xmax
k = 1
for j = nt0-dt0:nt0+dt0
Y_aux[i, k] = uwreal(Ysl[:, i, j], id)
if isnothing(rw)
Y_aux[i, k] = uwreal(Ysl[:, i, j], id)
else
WY_aux[i, k] = uwreal(Ysl_r[:, i, j], id)
Y_aux[i, k] = WY_aux[i, k] / W_obs
end
k = k + 1
end
end
......@@ -601,12 +615,18 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false,
title(string(L"$t/a^2 = $", t[nt0]))
display(gcf())
end
return t0
if info && !isnothing(rw)
return (t0, WY_aux, W_obs)
elseif info && isnothing(rw)
return (t0, Y_aux)
else
return t0
end
end
function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false,
rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2, ws::ADerrors.wspace=ADerrors.wsg,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing, info::Bool=false)
nr = length(Y)
Ysl = getfield.(Y, :obs)
......@@ -641,18 +661,32 @@ function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false
end
end
Ysl = isnothing(rw) ? Ysl : apply_rw(Ysl, rw)
tmp = Ysl[1]
[tmp = cat(tmp, Ysl[k], dims=1) for k = 2:nr]
[tmp = cat(tmp, Ysl[k], dims=1) for k=2:nr]
nt0 = t0_guess(t, tmp, plat, L)
xmax = size(tmp, 2)
dt0 = iseven(npol) ? Int64(npol / 2) : Int64((npol+1) / 2)
Y_aux = Matrix{uwreal}(undef, xmax, 2*dt0+1)
if !isnothing(rw)
Ysl_r, W = apply_rw(Ysl, rw)
tmp_r = Ysl_r[1]
tmp_W = W[1]
[tmp_r = cat(tmp_r, Ysl_r[k], dims=1) for k = 2:nr]
[tmp_W = cat(tmp_W, W[k], dims=1) for k = 2:nr]
W_obs = uwreal(tmp_W, id, replica)
WY_aux = Matrix{uwreal}(undef, xmax, 2*dt0+1)
end
for i = 1:xmax
k = 1
for j = nt0-dt0:nt0+dt0
Y_aux[i, k] = uwreal(tmp[:, i, j], id, replica)
if isnothing(rw)
Y_aux[i, k] = uwreal(tmp[:, i, j], id, replica)
else
WY_aux[i, k] = uwreal(tmp_r[:, i, j], id, replica)
Y_aux[i, k] = WY_aux[i, k] / W_obs
end
k = k + 1
end
end
......@@ -693,7 +727,13 @@ function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false
title(string(L"$t/a^2 = $", t[nt0]))
display(gcf())
end
return t0
if info && !isnothing(rw)
return (t0, WY_aux, W_obs)
elseif info && isnothing(rw)
return (t0, Y_aux)
else
return t0
end
end
function t0_guess(t::Vector{Float64}, Ysl::Array{Float64, 3}, plat::Vector{Int64}, L::Int64)
......
src/juobs_reader.jl
View file @ 7c0e8824
......@@ -101,7 +101,8 @@ read_mesons(path, "G5", "G5", id="H100")
read_mesons(path, "G5_d2", "G5_d2", legacy=true)
```
"""
function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false)
function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false,
nnoise_trunc::Union{Int64, Nothing}=nothing)
t1 = isnothing(g1) ? nothing : findfirst(x-> x==g1, gamma_name) - 1
t2 = isnothing(g2) ? nothing : findfirst(x-> x==g2, gamma_name) - 1
if isnothing(id)
......@@ -119,6 +120,8 @@ function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union
tvals = g_header.tvals
nnoise = g_header.nnoise
nnoise_trunc = isnothing(nnoise_trunc) ? nnoise : min(nnoise, nnoise_trunc)
fsize = filesize(path)
datsize = 4 + sum(getfield.(c_header, :dsize)) * tvals * nnoise #data_size / ncnfg
......@@ -144,13 +147,13 @@ function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union
tmp = Array{Float64}(undef, tvals*nnoise)
read!(data, tmp)
tmp2 = reshape(tmp, (nnoise, tvals))
tmp2 = mean(tmp2, dims=1)
tmp2 = mean(tmp2[1:nnoise_trunc, :], dims=1)
data_re[c, icfg, :] = tmp2[1, :]
elseif c_header[k].is_real == 0
tmp = Array{Float64}(undef, 2*tvals*nnoise)
read!(data, tmp)
tmp2 = reshape(tmp, (2, nnoise, tvals))
tmp2 = mean(tmp2, dims=2)
tmp2 = mean(tmp2[:, 1:nnoise_trunc, :], dims=2)
data_re[c, icfg, :] = tmp2[1, 1, :]
data_im[c, icfg, :] = tmp2[2, 1, :]
......@@ -172,8 +175,102 @@ function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union
return res
end
function read_mesons(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false)
res = read_mesons.(path, g1, g2, id=id, legacy=legacy)
function read_mesons(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false,
nnoise_trunc::Union{Int64, Nothing}=nothing)
res = read_mesons.(path, g1, g2, id=id, legacy=legacy, nnoise_trunc=nnoise_trunc)
nrep = length(res)
ncorr = length(res[1])
cdata = Vector{Vector{CData}}(undef, ncorr)
for icorr = 1:ncorr
cdata[icorr] = Vector{CData}(undef, nrep)
for r = 1:nrep
cdata[icorr][r] = res[r][icorr]
end
end
return cdata
end
function read_mesons_correction(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false,
nnoise_trunc::Union{Int64, Nothing}=nothing)
t1 = isnothing(g1) ? nothing : findfirst(x-> x==g1, gamma_name) - 1
t2 = isnothing(g2) ? nothing : findfirst(x-> x==g2, gamma_name) - 1
if isnothing(id)
bname = basename(path)
m = findfirst(r"[A-Z][0-9]{3}r[0-9]{3}", bname)
id = bname[m[1:4]]
#id = parse(Int64, bname[m[2:4]])
end
data = open(path, "r")
g_header = read_GHeader(path)
c_header = read_CHeader(path, legacy=legacy)
ncorr = g_header.ncorr
tvals = g_header.tvals
nnoise = g_header.nnoise
nnoise_trunc = isnothing(nnoise_trunc) ? nnoise : min(nnoise, nnoise_trunc)
fsize = filesize(path)
datsize = 4 + sum(getfield.(c_header, :dsize)) * tvals * nnoise #data_size / ncnfg
ncfg = div(fsize - g_header.hsize - sum(getfield.(c_header, :hsize)), datsize) #(total size - header_size) / data_size
corr_match = findall(x-> (x.type1==t1 || isnothing(t1)) && (x.type2==t2 || isnothing(t2)), c_header)
seek(data, g_header.hsize + sum(c.hsize for c in c_header))
res = Array{CData}(undef, div(length(corr_match), 2)) # Modification: total length is divided by 2
data_re = zeros(div(length(corr_match), 2), ncfg, tvals) # Modification: total length is divided by 2
data_im = zeros(div(length(corr_match), 2), ncfg, tvals) # Modification: total length is divided by 2
vcfg = Array{Int32}(undef, ncfg)
for icfg = 1:ncfg
vcfg[icfg] = read(data, Int32)
c = 1
sgn = +1 # sign it changes at ncorr / 2. O_exact - O_sloppy
for k = 1:ncorr
if k in corr_match
if c_header[k].is_real == 1
tmp = Array{Float64}(undef, tvals*nnoise)
read!(data, tmp)
tmp2 = reshape(tmp, (nnoise, tvals))
tmp2 = mean(tmp2[1:nnoise_trunc, :], dims=1)
data_re[c, icfg, :] = data_re[c, icfg, :] + sgn * tmp2[1, :]
elseif c_header[k].is_real == 0
tmp = Array{Float64}(undef, 2*tvals*nnoise)
read!(data, tmp)
tmp2 = reshape(tmp, (2, nnoise, tvals))
tmp2 = mean(tmp2[:, 1:nnoise_trunc, :], dims=2)
data_re[c, icfg, :] = data_re[c, icfg, :] + sgn * tmp2[1, 1, :]
data_im[c, icfg, :] = data_im[c, icfg, :] + sgn * tmp2[2, 1, :]
end
c += 1
else
seek(data, position(data) + c_header[k].dsize*tvals*nnoise)
end
if k == div(ncorr, 2)
c = 1
sgn = -1
end
end
end
for c = 1:div(length(corr_match), 2)
res[c] = CData(c_header[corr_match[c]], vcfg, data_re[c, :, :], data_im[c, :, :], id)
end
close(data)
return res
end
function read_mesons_correction(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false,
nnoise_trunc::Union{Int64, Nothing}=nothing)
res = read_mesons_correction.(path, g1, g2, id=id, legacy=legacy, nnoise_trunc=nnoise_trunc)
nrep = length(res)
ncorr = length(res[1])
......
src/juobs_tools.jl
View file @ 7c0e8824
This diff is collapsed.
src/juobs_types.jl
View file @ 7c0e8824
......@@ -127,6 +127,15 @@ mutable struct CHeader
return a
end
end
function Base.:(==)(a::CHeader, b::CHeader)
for s in [:k1, :k2, :mu1, :mu2, :dp1, :dp2, :type1, :type2, :x0, :is_real, :theta1, :theta2]
if getfield(a, s) != getfield(b, s)
return false
end
end
return true
end
#Base.:(!=)(a::CHeader, b::CHeader) = !(a == b)
mutable struct CData
header::CHeader
......
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