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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Observables · 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 class="is-active"><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="obs.html">Observables</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="obs.html">Observables</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="Observables"><a class="docs-heading-anchor" href="#Observables">Observables</a><a id="Observables-1"></a><a class="docs-heading-anchor-permalink" href="#Observables" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="juobs.meff" href="#juobs.meff"><code>juobs.meff</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bool=false )
meff(corr::Corr, plat::Vector{Int64}; pl::Bool=true, data::Bool=false)</code></pre><p>Computes effective mass for a given correlator corr at a given plateau <code>plat</code>. Correlator can be passed as an <code>Corr</code> struct or <code>Vector{uwreal}</code>.</p><p>The flags <code>pl</code> and <code>data</code> allow to show the plots and return data as an extra result.</p><pre><code class="language-">data = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
corr_pp = corr_obs.(data)
m = meff(corr_pp[1], [50, 60], pl=false)</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.dec_const_pcvc" href="#juobs.dec_const_pcvc"><code>juobs.dec_const_pcvc</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">dec_const_pcvc(corr::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, mu::Vector{Float64}, y0::Int64 ; pl::Bool=true, data::Bool=false)meff(corr::Corr, plat::Vector{Int64}; pl::Bool=true, data::Bool=false)
dec_const_pcvc(corr::Corr, plat::Vector{Int64}, m::uwreal; pl::Bool=true, data::Bool=false)</code></pre><p>Computes decay constant using the PCVC relation for twisted mass fermions. The decay constant is computed in the plateau <code>plat</code>. Correlator can be passed as an <code>Corr</code> struct or <code>Vector{uwreal}</code>. If it is passed as a uwreal vector, vector of twisted masses <code>mu</code> and source position <code>y0</code> must be specified.</p><p>The flags <code>pl</code> and <code>data</code> allow to show the plots and return data as an extra result.</p><pre><code class="language-">data = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
corr_pp = corr_obs.(data)
m = meff(corr_pp[1], [50, 60], pl=false)
f = dec_const_pcvc(corr_pp[1], [50, 60], m, pl=false)</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.comp_t0" href="#juobs.comp_t0"><code>juobs.comp_t0</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2)
comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2)</code></pre><p>Computes <code>t0</code> using the energy density of the action <code>Ysl</code>(Yang-Mills action). <code>t0</code> is computed in the plateau <code>plat</code>. A polynomial interpolation in <code>t</code> is performed to find <code>t0</code>, where <code>npol</code> is the degree of the polynomial (linear fit by default)</p><p>The flag <code>pl</code> allows to show the plot.</p><pre><code class="language-">#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)
#Two replicas
Y1 = read_ms(path1)
Y2 = read_ms(path2)
rw1 = read_ms(path_rw1)
rw2 = read_ms(path_rw2)
t0 = comp_t0([Y1, Y2], [38, 58], L=32, pl=true)
t0_r = comp_t0(Y, [38, 58], L=32, rw=[rw1, rw2], pl=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="tools.html">« Tools</a><a class="docs-footer-nextpage" href="linalg.html">Linear Algebra »</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="Wednesday 24 February 2021 11:46">Wednesday 24 February 2021</span>. Using Julia version 1.5.0.</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>Reader · 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 class="is-active"><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="reader.html">Reader</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="reader.html">Reader</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="Reader"><a class="docs-heading-anchor" href="#Reader">Reader</a><a id="Reader-1"></a><a class="docs-heading-anchor-permalink" href="#Reader" title="Permalink"></a></h1><article class="docstring"><header><a class="docstring-binding" id="juobs.read_mesons" href="#juobs.read_mesons"><code>juobs.read_mesons</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{Int64, Nothing}=nothing)
read_mesons(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{Int64, Nothing}=nothing)</code></pre><p>This function read a mesons dat file at a given path and returns a vector of <code>CData</code> structures for different masses and Dirac structures. Dirac structures <code>g1</code> and/or <code>g2</code> can be passed as string arguments in order to filter correaltors. ADerrors id can be specified as argument. If is not specified, the <code>id</code> is fixed according to the ensemble name (example: &quot;H400&quot;-&gt; id = 400)</p><p>Examples:</p><pre><code class="language-">read_mesons(path)
read_mesons(path, &quot;G5&quot;)
read_mesons(path, nothing, &quot;G5&quot;)
read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
read_mesons(path, &quot;G5&quot;, &quot;G5&quot;, id=1)
read_mesons([path1, path2], &quot;G5&quot;, &quot;G5&quot;)</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.read_ms" href="#juobs.read_ms"><code>juobs.read_ms</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)</code></pre><p>Reads openQCD ms dat files at a given path. This method return YData: </p><ul><li><p><code>t(t)</code>: flow time values</p></li><li><p><code>Ysl(icfg, x0, t)</code>: the time-slice sums of the densities of the Yang-Mills action </p></li><li><p><code>vtr</code>: vector that contains trajectory number</p></li><li><p><code>id</code>: ensmble id</p></li></ul><p>Examples:</p><pre><code class="language-">Y = read_ms(path)</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.read_ms1" href="#juobs.read_ms1"><code>juobs.read_ms1</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">read_ms1(path::String; v::String=&quot;1.2&quot;)</code></pre><p>Reads openQCD ms1 dat files at a given path. This method returns a matrix <code>W[irw, icfg]</code> that contains the reweighting factors, where <code>irw</code> is the <code>rwf</code> index and icfg the configuration number. The function is compatible with the output files of openQCD v=1.2, 1.4 and 1.6. Version can be specified as argument.</p><p>Examples:</p><pre><code class="language-">read_ms1(path)
read_ms1(path, v=&quot;1.4&quot;)
read_ms1(path, v=&quot;1.6&quot;)</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.read_md" href="#juobs.read_md"><code>juobs.read_md</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">read_md(path::String)</code></pre><p>Reads openQCD pbp.dat files at a given path. This method returns a matrix <code>md[irw, icfg]</code> that contains the derivatives <span>$dS/dm$</span>, where <span>$md[irw=1] = dS/dm_l$</span> and <span>$md[irw=2] = dS/dm_s$</span></p><p><span>$Seff = -tr(log(D+m))$</span></p><p><span>$dSeff/ dm = -tr((D+m)^-1)$</span></p><p>Examples:</p><pre><code class="language-">md = read_md(path)</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.truncate_data!" href="#juobs.truncate_data!"><code>juobs.truncate_data!</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia">truncate_data!(data::YData, nc::Int64)
truncate_data!(data::Vector{YData}, nc::Vector{Int64})
truncate_data!(data::Vector{CData}, nc::Int64)
truncate_data!(data::Vector{Vector{CData}}, nc::Vector{Int64})</code></pre><p>Truncates the output of <code>read_mesons</code> and <code>read_ms</code> taking the first <code>nc</code> configurations.</p><p>Examples:</p><pre><code class="language-">#Single replica
dat = read_mesons(path, &quot;G5&quot;, &quot;G5&quot;)
Y = read_ms(path)
truncate_data!(dat, nc)
truncate_data!(Y, nc)
#Two replicas
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="Wednesday 24 February 2021 11:46">Wednesday 24 February 2021</span>. Using Julia version 1.5.0.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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docs/build/search_index.js
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docs/build/tools.html 0 → 100644
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docs/make.jl
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using Documenter, juobs
push!(LOAD_PATH, "../src")
makedocs(sitename = "juobs Documentation")
makedocs(sitename = "juobs Documentation", doctest=true,
repo = "https://gitlab.ift.uam-csic.es/jugarrio/juobs",
pages = [
"Home" => "index.md",
"Reader" => "reader.md",
"Tools" => "tools.md",
"Observables" => "obs.md",
"Linear Algebra" => "linalg.md"],
format = Documenter.HTML(prettyurls=false))
docs/src/index.md
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# DOCUMENTATION
```@contents
```
## READER
```@docs
read_mesons
read_ms
read_ms1
read_md
truncate_data!
```
## Contents
## TOOLS
```@docs
corr_obs
md_sea
lin_fit
fit_routine
```@contents
Pages = ["reader.md", "tools.md", "obs.md", "linalg.md"]
Depth = 3
```
## LINEAR ALGEBRA
```@docs
uweigvals
uweigvecs
uweigen
get_matrix
energies
getall_eigvals
getall_eigvecs
```
## OBSERVABLES
```@docs
meff
dec_const_pcvc
comp_t0
```
docs/src/linalg.md 0 → 100644
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# Linear Algebra
```@docs
uweigvals
uweigvecs
uweigen
get_matrix
energies
getall_eigvals
getall_eigvecs
```
docs/src/obs.md 0 → 100644
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# Observables
```@docs
meff
dec_const_pcvc
comp_t0
```
docs/src/reader.md 0 → 100644
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# Reader
```@docs
read_mesons
read_ms
read_ms1
read_md
truncate_data!
```
docs/src/tools.md 0 → 100644
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# Tools
```@docs
corr_obs
md_sea
lin_fit
fit_routine
```
src/juobs_linalg.jl
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......@@ -254,7 +254,7 @@ This function computes the eigenvalues and the eigenvectors of a matrix of uwre
If a second matrix b is given as input, it returns the generalised eigenvalues and eigenvectors instead.
It takes as input:
- `a::Matrix{uwreal} : a matrix of uwreal
- `a::Matrix{uwreal}` : a matrix of uwreal
- `b::Matrix{uwreal}` : a matrix of uwreal, optional
......
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