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Commit 46964452 authored by Alessandro 's avatar Alessandro
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Merge remote-tracking branch 'origin/javier' into alessandro 

mergin javier into alessandro
parents f3531bef 225ac7af
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.gitignore
View file @ 46964452
......@@ -2,3 +2,5 @@
analysis/plat\.txt
*.pdf
analysis/*.txt
Manifest.toml
View file @ 46964452
......@@ -2,17 +2,23 @@
[[ADerrors]]
deps = ["BDIO", "FFTW", "FastGaussQuadrature", "ForwardDiff", "LaTeXStrings", "LinearAlgebra", "Nettle", "PGFPlotsX", "Plots", "Printf", "QuadGK", "Roots", "Statistics", "Test", "UnicodePlots"]
git-tree-sha1 = "f1c9954c17c0e87f185d532163e9e630efd12fe3"
repo-rev = "9c41ec2e161e4826bfe0752be8bf2a0bc025759c"
git-tree-sha1 = "2d3b701de1b206f497c632413b5a783fbd65d714"
repo-rev = "master"
repo-url = "https://gitlab.ift.uam-csic.es/alberto/aderrors.jl"
uuid = "5e92007d-7bf1-471c-8ceb-4591b8b567a9"
version = "0.1.0"
[[AbstractFFTs]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "8ed9de2f1b1a9b1dee48582ad477c6e67b83eb2c"
git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0"
uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
version = "1.0.0"
version = "1.0.1"
[[Adapt]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "ffcfa2d345aaee0ef3d8346a073d5dd03c983ebe"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.2.0"
[[ArgCheck]]
git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a"
......@@ -197,9 +203,9 @@ version = "4.3.1+4"
[[FFTW]]
deps = ["AbstractFFTs", "FFTW_jll", "IntelOpenMP_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Reexport"]
git-tree-sha1 = "c31e446bf3b12aad2ec8fc500fe19528c148d811"
git-tree-sha1 = "1b48dbde42f307e48685fa9213d8b9f8c0d87594"
uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
version = "1.3.1"
version = "1.3.2"
[[FFTW_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
......@@ -275,9 +281,9 @@ version = "6.1.2+6"
[[GR]]
deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"]
git-tree-sha1 = "b90b826782cb3ac5b7a7f41b3fd0113180257ed4"
git-tree-sha1 = "12d971c928b7ecf19b748a2c7df6a365690dbf2c"
uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71"
version = "0.53.0"
version = "0.55.0"
[[GR_jll]]
deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt_jll", "Zlib_jll", "libpng_jll"]
......@@ -287,9 +293,9 @@ version = "0.53.0+0"
[[GeometryBasics]]
deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
git-tree-sha1 = "a28d728c2d825285fe27f38ca322399d35d1a5b9"
git-tree-sha1 = "4d4f72691933d5b6ee1ff20e27a102c3ae99d123"
uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
version = "0.3.6"
version = "0.3.9"
[[Gettext_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"]
......@@ -309,10 +315,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
version = "1.0.0"
[[HTTP]]
deps = ["Base64", "Dates", "IniFile", "MbedTLS", "Sockets"]
git-tree-sha1 = "c7ec02c4c6a039a98a15f955462cd7aea5df4508"
deps = ["Base64", "Dates", "IniFile", "MbedTLS", "NetworkOptions", "Sockets", "URIs"]
git-tree-sha1 = "c9f380c76d8aaa1fa7ea9cf97bddbc0d5b15adc2"
uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
version = "0.8.19"
version = "0.9.5"
[[IOCapture]]
deps = ["Logging"]
......@@ -386,6 +392,18 @@ git-tree-sha1 = "3a0084cec7bf157edcb45a67fac0647f88fe5eaf"
uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
version = "0.14.7"
[[LazyArtifacts]]
deps = ["Pkg"]
git-tree-sha1 = "4bb5499a1fc437342ea9ab7e319ede5a457c0968"
uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3"
version = "1.3.0"
[[LeastSquaresOptim]]
deps = ["FiniteDiff", "ForwardDiff", "LinearAlgebra", "Optim", "Printf", "SparseArrays", "Statistics", "SuiteSparse"]
git-tree-sha1 = "b5a1931bf37616820c4ef71629b6308d67f0b393"
uuid = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891"
version = "0.8.1"
[[LibGit2]]
deps = ["Printf"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
......@@ -467,10 +485,10 @@ uuid = "2fda8390-95c7-5789-9bda-21331edee243"
version = "0.12.0"
[[MKL_jll]]
deps = ["IntelOpenMP_jll", "Libdl", "Pkg"]
git-tree-sha1 = "eb540ede3aabb8284cb482aa41d00d6ca850b1f8"
deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
git-tree-sha1 = "c253236b0ed414624b083e6b72bfe891fbd2c7af"
uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
version = "2020.2.254+0"
version = "2021.1.1+1"
[[MacroTools]]
deps = ["Markdown", "Random"]
......@@ -531,6 +549,11 @@ git-tree-sha1 = "b3b169cec36b850cfacbefc0b0a5f68a6089eb70"
uuid = "4c82536e-c426-54e4-b420-14f461c4ed8b"
version = "3.4.1+2"
[[NetworkOptions]]
git-tree-sha1 = "ed3157f48a05543cce9b241e1f2815f7e843d96e"
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
version = "1.2.0"
[[Ogg_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "a42c0f138b9ebe8b58eba2271c5053773bde52d0"
......@@ -614,9 +637,9 @@ uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
[[PlotThemes]]
deps = ["PlotUtils", "Requires", "Statistics"]
git-tree-sha1 = "c6f5ea535551b3b16835134697f0c65d06c94b91"
git-tree-sha1 = "a3a964ce9dc7898193536002a6dd892b1b5a6f1d"
uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
version = "2.0.0"
version = "2.0.1"
[[PlotUtils]]
deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"]
......@@ -626,9 +649,9 @@ version = "1.0.10"
[[Plots]]
deps = ["Base64", "Contour", "Dates", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"]
git-tree-sha1 = "4797acb266b8d9ff316f4581924e71c6709f152d"
git-tree-sha1 = "142dd04f5060c04de91cc10ca76dffb291a02426"
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
version = "1.10.1"
version = "1.10.6"
[[PositiveFactorizations]]
deps = ["LinearAlgebra"]
......@@ -679,9 +702,9 @@ version = "1.1.1"
[[RecipesPipeline]]
deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
git-tree-sha1 = "9ea2f5bf1b26918b16e9f885bb8e05206bfc2144"
git-tree-sha1 = "c4d54a78e287de7ec73bbc928ce5eb3c60f80b24"
uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
version = "0.2.1"
version = "0.3.1"
[[Reexport]]
deps = ["Pkg"]
......@@ -709,9 +732,9 @@ version = "0.2.2+1"
[[Roots]]
deps = ["Printf"]
git-tree-sha1 = "8f743e4f4368d1d753f3806bf635899dad6b4847"
git-tree-sha1 = "369e25546984dff5df351bc056fccc30de615080"
uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
version = "1.0.7"
version = "1.0.8"
[[SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
......@@ -777,10 +800,10 @@ uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
version = "0.9.6"
[[StructArrays]]
deps = ["DataAPI", "Tables"]
git-tree-sha1 = "ad1f5fd155426dcc879ec6ede9f74eb3a2d582df"
deps = ["Adapt", "DataAPI", "Tables"]
git-tree-sha1 = "26ea43b4be7e919a2390c3c0f824e7eb4fc19a0a"
uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
version = "0.4.2"
version = "0.5.0"
[[SuiteSparse]]
deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
......@@ -794,14 +817,19 @@ version = "1.0.0"
[[Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
git-tree-sha1 = "240d19b8762006ff04b967bdd833269ad642d550"
git-tree-sha1 = "a716dde43d57fa537a19058d044b495301ba6565"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.2.2"
version = "1.3.2"
[[Test]]
deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
[[URIs]]
git-tree-sha1 = "7855809b88d7b16e9b029afd17880930626f54a2"
uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
version = "1.2.0"
[[UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
......@@ -983,9 +1011,9 @@ version = "1.2.11+18"
[[Zstd_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "6f1abcb0c44f184690912aa4b0ba861dd64f11b9"
git-tree-sha1 = "2c1332c54931e83f8f94d310fa447fd743e8d600"
uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
version = "1.4.5+2"
version = "1.4.8+0"
[[libass_jll]]
deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
......
Project.toml
View file @ 46964452
......@@ -7,6 +7,7 @@ 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"
......
analysis/analysis_pcac.jl 0 → 100644
View file @ 46964452
using juobs, ADerrors, DelimitedFiles, PyPlot, LaTeXStrings
const path = "/home/javier/Lattice/charm/production_2"
const path_plat = "/home/javier/Lattice/juobs/analysis/plat.txt"
const ensembles = ["H400", "N202", "N200", "N203", "N300", "J303"]
const deg = [true, true, false, false, true, false]
const L = [32, 48, 48, 48, 48, 64]
const beta = [3.46 , 3.55, 3.55, 3.55, 3.70, 3.70]
const R = [["H400r001", "H400r002"], "N202r001", ["N200r000", "N200r001"], ["N203r000", "N203r001"], "N300r002", "J303r003"]
include("/home/javier/Lattice/juobs/analysis/functions.jl")
include("/home/javier/Lattice/juobs/constants/juobs_const.jl")
m_ll = Vector{uwreal}(undef, length(ensembles))
m_ss = Vector{uwreal}(undef, length(ensembles))
m_hh = Vector{Vector{uwreal}}(undef, length(ensembles))
mu_pp = Vector{Vector{Vector{Float64}}}(undef, length(ensembles))
for iens = 1:length(ensembles)
pp = read_dat(R[iens], "G5", "G5")
a0p = read_dat(R[iens], "G5", "G0G5")
rew = read_rew(R[iens])
pp_obs = corr_obs.(pp, L=L[iens], rw=rew)
a0p_obs = corr_obs.(a0p, L=L[iens], rw=rew)
mu_pp[iens] = getfield.(pp_obs, :mu)
m = comp_pcac(a0p_obs, pp_obs, deg[iens], ensembles[iens])
m_ll[iens] = get_ll(mu_pp[iens], m, deg[iens])
m_ss[iens] = deg[iens] ? m_ll[iens] : get_ss(mu_pp[iens], m, deg[iens])
m_hh[iens] = get_hh(mu_pp[iens], m, deg[iens])
end
mm = get_mu.(mu_pp, deg)
mul_pp = getindex.(mm, 1)
mus_pp = getindex.(mm, 2)
muh_pp = getindex.(mm, 3)
cot_ll = Vector{uwreal}(undef, length(ensembles))
cot_ss = Vector{uwreal}(undef, length(ensembles))
cot_hh = Vector{Vector{uwreal}}(undef, length(ensembles))
for iens = 1:length(ensembles)
cot_ll[iens] = za(beta[iens]) * m_ll[iens] / mul_pp[iens]
cot_ss[iens] = za(beta[iens]) * m_ss[iens] / mus_pp[iens]
cot_hh[iens] = fill(za(beta[iens]), 3) .* m_hh[iens] ./ muh_pp[iens]
end
\ No newline at end of file
analysis/functions.jl
View file @ 46964452
......@@ -8,14 +8,19 @@ function read_dat(rep::Vector{String}, g1::String="G5", g2::String="G5")
p = joinpath.(path, rep, "info")
f = [filter(x-> contains(x, ".dat"), readdir(p[k]))[1] for k = 1:length(p)]
f = joinpath.(p, f)
aux = read_mesons.(f, g1, g2)
res = []
for j = 1:length(aux[1])
aux2 = [aux[i][j] for i = 1:length(aux)]
push!(res, aux2)
return read_mesons(f, g1, g2)
end
function read_rew(rep::String)
p = joinpath(path, rep, "rew")
f = filter(x-> contains(x, ".dat"), readdir(p))
f = joinpath(p, f[1])
try
return read_ms1(f)
catch
return read_ms1(f, v="1.4")
end
return res
end
read_rew(rep::Vector{String}) = read_rew.(rep)
function get_mu(mu_list::Vector{Vector{Float64}}, deg::Bool)
mu_sorted = unique(sort(minimum.(mu_list)))
......@@ -48,6 +53,16 @@ function get_ls(mu_list, obs::Vector{uwreal}, deg::Bool)
end
end
function get_ss(mu_list, obs::Vector{uwreal}, deg::Bool)
mul, mus, muh = get_mu(mu_list, deg)
for k = 1:length(mu_list)
mu = mu_list[k]
if mus in mu && mu[1] == mu[2] #s-s
return obs[k]
end
end
end
function get_lh(mu_list, obs::Vector{uwreal}, deg::Bool)
mul, mus, muh = get_mu(mu_list, deg)
obs_lh = Vector{uwreal}(undef, 0)
......@@ -72,6 +87,17 @@ function get_sh(mu_list, obs::Vector{uwreal}, deg::Bool)
return obs_sh
end
function get_hh(mu_list, obs::Vector{uwreal}, deg::Bool)
mul, mus, muh = get_mu(mu_list, deg)
obs_hh = Vector{uwreal}(undef, 0)
for k = 1:length(mu_list)
mu = mu_list[k]
if mu[1] == mu[2] && !(mul in mu) && !(mus in mu)
push!(obs_hh, obs[k])
end
end
return obs_hh
end
function select_plateau(ens::String, mu_list, deg::Bool)
mul, mus, muh = get_mu(mu_list, deg)
f = readdlm(path_plat)
......@@ -116,6 +142,11 @@ function comp_meff(pp_obs::Vector{juobs.Corr}, deg::Bool, ens::String; pl::Bool=
plat = select_plateau(ens, mu_list, deg)
return meff.(pp_obs, plat, pl=pl)
end
function comp_pcac(a0p_obs::Vector{juobs.Corr}, pp_obs::Vector{juobs.Corr}, deg::Bool, ens::String; pl::Bool=false)
mu_list = getfield.(pp_obs, :mu)
plat = select_plateau(ens, mu_list, deg)
return mpcac.(a0p_obs, pp_obs, plat, pl=pl)
end
function comp_f(pp_obs::Vector{juobs.Corr}, m::Vector{uwreal}, deg::Bool, ens::String; pl::Bool=false)
mu_list = getfield.(pp_obs, :mu)
plat = select_plateau(ens, mu_list, deg)
......
docs/build/index.html
View file @ 46964452
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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="Wednesday 3 March 2021 11:34">Wednesday 3 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="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>
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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="Wednesday 3 March 2021 11:34">Wednesday 3 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="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>
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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="Wednesday 3 March 2021 11:34">Wednesday 3 March 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>
<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="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><script src="search_index.js"></script><script src="assets/search.js"></script></html>
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......@@ -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="Wednesday 3 March 2021 11:34">Wednesday 3 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="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>
docs/src/obs.md
View file @ 46964452
# Observables
```@docs
meff
mpcac
dec_const
dec_const_pcvc
comp_t0
```
......
src/juobs.jl
View file @ 46964452
module juobs
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, Optim
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, LeastSquaresOptim
import Statistics: mean
include("juobs_types.jl")
......@@ -10,7 +10,7 @@ include("juobs_obs.jl")
export read_mesons, read_ms1, read_ms, read_md, truncate_data!
export get_matrix, energies, uwdot, uweigvals, uweigvecs, uweigen, invert, getall_eigvals, getall_eigvecs
export corr_obs, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine
export meff, dec_const_pcvc, comp_t0
export corr_obs, corr_sym, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine
export meff, mpcac, dec_const, dec_const_pcvc, comp_t0
end # module
src/juobs_linalg.jl
View file @ 46964452
......@@ -126,7 +126,7 @@ function energies(evals::Union{Vector{Vector{uwreal}},Array{Array{uwreal}} }; wp
ratio = evals[t][i] / evals[t+1][i]
aux_en[t] = 0.5*log(ratio * ratio)
end
isnothing(wpm) ? uwerr.(aux_en) : uwerr.(aux_en, wpm)
isnothing(wpm) ? uwerr.(aux_en) : [uwerr(a, wpm) for a in aux_en]
eff_en[i] = copy(aux_en)
end
return eff_en
......@@ -179,7 +179,7 @@ evals = getall_eigvals(matrices, 5) #where t_0=5
Julia>
```
"""
function getall_eigvals(a::Vector{Matrix}, t0::Int64; iter=30 )
function getall_eigvals(a::Vector{Matrix{uwreal}}, t0::Int64; iter=30 )
n = length(a)
res = Vector{Vector{uwreal}}(undef, n)
[res[i] = uweigvals(a[i], a[t0]) for i=1:n]
......
src/juobs_obs.jl
View file @ 46964452
This diff is collapsed.
src/juobs_reader.jl
View file @ 46964452
......@@ -84,13 +84,13 @@ function read_CHeader(path::String; legacy::Bool=false)
end
@doc raw"""
read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{Int64, Nothing}=nothing, legacy::Bool=false)
read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false)
read_mesons(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{Int64, Nothing}=nothing, legacy::Bool=false)
read_mesons(path::Vector{String}, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{String, Nothing}=nothing, legacy::Bool=false)
This function read a mesons dat file at a given path and returns a vector of `CData` structures for different masses and Dirac structures.
Dirac structures `g1` and/or `g2` can be passed as string arguments in order to filter correaltors.
ADerrors id can be specified as argument. If is not specified, the `id` is fixed according to the ensemble name (example: "H400"-> id = 400)
ADerrors id can be specified as argument. If is not specified, the `id` is fixed according to the ensemble name (example: "H400"-> id = "H400")
*For the old version (without smearing, distance preconditioning and theta) set legacy=true.
......@@ -100,17 +100,18 @@ read_mesons(path)
read_mesons(path, "G5")
read_mesons(path, nothing, "G5")
read_mesons(path, "G5", "G5")
read_mesons(path, "G5", "G5", id=1)
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{Int64, 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)
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 = parse(Int64, bname[m[2:4]])
id = bname[m[1:4]]
#id = parse(Int64, bname[m[2:4]])
end
data = open(path, "r")
......@@ -123,8 +124,8 @@ function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union
fsize = filesize(path)
datsize = 4 + sum(c.dsize for c in c_header)*tvals*nnoise #datasize / ncnfg
ncfg = Int32((fsize-g_header.hsize-sum(c.hsize for c in c_header)) / datsize)
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)
......@@ -174,7 +175,7 @@ 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{Int64, Nothing}=nothing, legacy::Bool=false)
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)
nrep = length(res)
ncorr = length(res[1])
......@@ -277,28 +278,32 @@ function read_md(path::String)
end
@doc raw"""
read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)
read_ms(path::String; id::Union{String, Nothing}=nothing, dtr::Int64=1, obs::String="Y")
Reads openQCD ms dat files at a given path. This method return YData:
- `t(t)`: flow time values
- `Ysl(icfg, x0, t)`: the time-slice sums of the densities of the Yang-Mills action
- `obs(icfg, x0, t)`: the time-slice sums of the densities of the observable (Wsl, Ysl or Qsl)
- `vtr`: vector that contains trajectory number
- `id`: ensmble id
`dtr` = `dtr_cnfg` / `dtr_ms`, where `dtr_cnfg` is the number of trajectories computed before saving the configuration. `dtr_ms`
is the same but applied to the ms.dat file.
Examples:
```@example
Y = read_ms(path)
```
"""
function read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)
function read_ms(path::String; id::Union{String, Nothing}=nothing, dtr::Int64=1 , obs::String="Y")
if isnothing(id)
bname = basename(path)
m = findfirst(r"[A-Z][0-9]{3}r[0-9]{3}", bname)
id = parse(Int64, bname[m[2:4]])
id = bname[m[1:4]]
#id = parse(Int64, bname[m[2:4]])
end
data = open(path, "r")
......@@ -349,7 +354,17 @@ function read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)
end
close(data)
t = Float64.(0:nn) .* dn .* eps
return YData(vntr, t, Ysl, id)
if obs == "W"
return YData(vntr, t, Wsl, id)
elseif obs == "Y"
return YData(vntr, t, Ysl, id)
elseif obs == "Q"
return YData(vntr, t, Qsl, id)
else
println("obs = ", obs," is not valid")
return nothing
end
end
@doc raw"""
......@@ -380,7 +395,7 @@ truncate_data!(Y, [nc1, nc2])
"""
function truncate_data!(data::YData, nc::Int64)
data.vtr = data.vtr[1:nc]
data.Ysl = data.Ysl[1:nc, :, :]
data.obs = data.obs[1:nc, :, :]
return nothing
end
function truncate_data!(data::Vector{YData}, nc::Vector{Int64})
......
src/juobs_tools.jl
View file @ 46964452
......@@ -29,21 +29,6 @@ function apply_rw(data::Vector{<:Array{Float64}}, W::Vector{Matrix{Float64}})
return data_r
end
function dobsdp(a::uwreal, p::uwreal) # Compute da / dp
if count(p.prop .== true) != 1
error("I do not know how to compute this")
end
for i = 1:min(length(a.der), length(p.der))
if (p.prop[i] && a.prop[i])
return a.der[i] / p.der[i]
end
end
return 0.0
end
function check_corr_der(obs::Corr, derm::Vector{Corr})
g1 = Vector{String}(undef, 0)
g2 = Vector{String}(undef, 0)
......@@ -140,8 +125,36 @@ function corr_obs(cdata::Array{CData, 1}; real::Bool=true, rw::Union{Array{Array
return Corr(obs, cdata)
end
@doc raw"""
corr_sym(corrL::Corr, corrR::Corr, parity::Int64=1)
Computes the symmetrized correlator using the left correlador `corrL` and the right correlator `corrR`. The source position
of `corrR` must be `T - 1 - y0`, where `y0` is the source position of `corrL`.
```@example
pp_sym = corr_sym(ppL, ppR, +1)
a0p_sym = corr_sym(a0pL, a0pR, -1)
```
"""
function corr_sym(corrL::Corr, corrR::Corr, parity::Int64=1)
T = length(corrL.obs)
sym = [:kappa, :mu, :gamma]
if corrL.y0 != T - 1 - corrR.y0
error("Corr: Parameter mismatch")
end
for s in sym
if getfield(corrL, s) != getfield(corrR, s)
error("Corr: Parameter mismatch")
end
end
if abs(parity) != 1
error("incorrect value of parity (+- 1)")
end
#TODO: VECTORIZE
res = (corrL.obs[1:end] + parity * corrR.obs[end:-1:1]) / 2
return Corr(res, corrL.kappa, corrL.mu, corrL.gamma, corrL.y0)
end
#TODO: VECTORIZE, uwreal?
@doc raw"""
md_sea(a::uwreal, md::Vector{Matrix{Float64}}, ws::ADerrors.wspace=ADerrors.wsg)
......@@ -195,8 +208,8 @@ function md_sea(a::uwreal, md::Vector{Matrix{Float64}}, ws::ADerrors.wspace=ADer
if !all(id .== id[1])
error("ids do not match")
end
id = id[1]
id = ws.id2str[id[1]]
ivrep = getfield.(ws.fluc[p], :ivrep)
ivrep1 = fill(ivrep[1], length(ivrep))
if !all(ivrep .== ivrep1)
......@@ -208,6 +221,7 @@ function md_sea(a::uwreal, md::Vector{Matrix{Float64}}, ws::ADerrors.wspace=ADer
error("Nr obs != Nr md")
end
#md_aux as a Matrix + Automatic truncation
md_aux = md[1][:, 1:ivrep[1]]
for k = 2:length(md)
md_aux = cat(md_aux, md[k][:, 1:ivrep[k]], dims=2)
......@@ -215,27 +229,21 @@ function md_sea(a::uwreal, md::Vector{Matrix{Float64}}, ws::ADerrors.wspace=ADer
fluc_obs = getfield.(ws.fluc[p], :delta)
fluc_md = md_aux .- mean(md_aux, dims=2)
uwerr(a)
fluc_obs = mchist(a, id)
nrw = size(fluc_md, 1)
d = a.der[p]
nobs = sum(a.prop)
if nrw == 1
der1 = uwreal(0)
for k = 1:nobs
der1 = der1 - d[k] * uwreal(fluc_md[1, :] .* fluc_obs[k], id, ivrep)
end
der1 = uwreal(-fluc_md[1, :] .* fluc_obs, id, ivrep)
return (der1, der1)
elseif nrw == 2
der1 = uwreal(0)
der2 = uwreal(0)
for k = 1:nobs
der1 = der1 - d[k] * uwreal(fluc_md[1, :] .* fluc_obs[k], id, ivrep)
der2 = der2 - d[k] * uwreal(fluc_md[2, :] .* fluc_obs[k], id, ivrep)
end
der1 = uwreal(-fluc_md[1, :] .* fluc_obs, id, ivrep)
der2 = uwreal(-fluc_md[2, :] .* fluc_obs, id, ivrep)
return (der1, der2)
else
return nothing
end
end
@doc raw"""
......@@ -286,13 +294,13 @@ function md_val(a::uwreal, obs::Corr, derm::Vector{Corr})
corr = getfield(obs, :obs)
der = [dobsdp(a, corr[k]) for k = 1:length(corr)]
der = [derivative(a, corr[k]) for k = 1:length(corr)]
derm1, derm2 = derm
return (sum(der .* derm1.obs), sum(der .* derm2.obs))
end
function plat_av(obs::Vector{uwreal}, plat::Vector{Int64}, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
isnothing(wpm) ? uwerr.(obs) : uwerr.(obs, wpm)
isnothing(wpm) ? uwerr.(obs) : [uwerr(obs_aux, wpm) for obs_aux in obs]
w = 1 ./ err.(obs)[plat[1]:plat[2]].^2
av = sum(w .* obs[plat[1]:plat[2]]) / sum(w)
return av
......@@ -321,7 +329,7 @@ m2_phys = fitp[1] + fitp[2] * phi2_phys
```
"""
function lin_fit(x::Vector{<:Real}, y::Vector{uwreal}; wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
isnothing(wpm) ? uwerr.(y) : uwerr.(y, wpm)
isnothing(wpm) ? uwerr.(y) : [uwerr(yaux, wpm) for yaux in y]
par = lin_fit(x, value.(y), err.(y))
chisq(p, d) = sum((d .- p[1] .- p[2].*x).^2 ./ err.(y) .^2)
(fitp, csqexp) = fit_error(chisq, par, y)
......@@ -375,7 +383,7 @@ fit_routine(model, xdata, ydata, param=3, covar=true)
```
"""
function fit_routine(model::Function, xdata::Array{<:Real}, ydata::Array{uwreal}, param::Int64=3; wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
isnothing(wpm) ? uwerr.(ydata) : uwerr.(ydata, wpm)
isnothing(wpm) ? uwerr.(ydata) : [uwerr(yaux, wpm) for yaux in ydata]
yval = value.(ydata)
yer = err.(ydata)
......@@ -403,8 +411,8 @@ function fit_routine(model::Function, xdata::Array{uwreal}, ydata::Array{uwreal}
uwerr.(ydata)
uwerr.(xdata)
else
uwerr.(ydata, wpm)
uwerr.(xdata, wpm)
[uwerr(yaux, wpm) for yaux in ydata]
[uwerr(xaux, wpm) for xaux in xdata]
end
yval = value.(ydata)
......@@ -442,14 +450,18 @@ function fit_routine(model::Function, xdata::Array{uwreal}, ydata::Array{uwreal}
C = isnothing(wpm) ? [ADerrors.cov(aux[k]) for k = 1:Ndata] : [ADerrors.cov(aux[k], wpm) for k = 1:Ndata]
chisq_full_cov(p, d) = get_chi2_cov(model, d, C, p, Nalpha)
min_fun_cov(t) = chisq_full_cov(t, dat)
sol = optimize(min_fun_cov, vcat(fit.param, dat[1:Nalpha*Ndata]), method=LBFGS())
sol = optimize(min_fun_cov, vcat(fit.param, dat[1:Nalpha*Ndata]), LevenbergMarquardt())
(upar, chi2_exp) = isnothing(wpm) ? fit_error(chisq_full_cov, Optim.minimizer(sol), data) : fit_error(chisq_full_cov, Optim.minimizer(sol), data, wpm)
(upar, chi2_exp) = isnothing(wpm) ? fit_error(chisq_full_cov, sol.minimizer, data) : fit_error(chisq_full_cov, sol.minimizer, data, wpm)
println("Chisq / chiexp: ", min_fun_cov(sol.minimizer), " / ", chi2_exp, " (dof: ", length(ydata) - param,")")
else
chisq_full(p, d) = get_chi2(model, d, ddat, p, Nalpha)
min_fun(t) = chisq_full(t, dat)
sol = optimize(min_fun, vcat(fit.param, dat[1:Nalpha*Ndata]), method=LBFGS())
(upar, chi2_exp) = isnothing(wpm) ? fit_error(chisq_full, Optim.minimizer(sol), data) : fit_error(chisq_full, Optim.minimizer(sol), data, wpm)
sol = optimize(min_fun, vcat(fit.param, dat[1:Nalpha*Ndata]), LevenbergMarquardt())
(upar, chi2_exp) = isnothing(wpm) ? fit_error(chisq_full, sol.minimizer, data) : fit_error(chisq_full, sol.minimizer, data, wpm)
println("Chisq / chiexp: ", min_fun(sol.minimizer), " / ", chi2_exp, " (dof: ", length(ydata) - param,")")
end
#### chisq_full, min_fun out of conditional ->
......@@ -461,7 +473,6 @@ function fit_routine(model::Function, xdata::Array{uwreal}, ydata::Array{uwreal}
print("\n Fit parameter: ", i, ": ")
details(upar[i])
end
println("Chisq / chiexp: ", sol.minimum, " / ", chi2_exp, " (dof: ", length(ydata) - param,")")
return upar
end
......
src/juobs_types.jl
View file @ 46964452
......@@ -133,7 +133,7 @@ mutable struct CData
vcfg::Array{Int32}
re_data::Array{Float64}
im_data::Array{Float64}
id::Int64
id::String
CData(a, b, c, d, e) = new(a, b, c, d, e)
end
......@@ -167,13 +167,14 @@ mutable struct Corr
y0 = Int64(h[1].x0)
return new(a, kappa, mu, gamma, y0)
end
Corr(o::Vector{uwreal}, k::Vector{Float64}, m::Vector{Float64}, g::Vector{String}, y::Int64) = new(o, k, m, g, y)
end
mutable struct YData
vtr::Vector{Int32}
t::Vector{Float64}
Ysl::Array{Float64, 3}
id::Int64
obs::Array{Float64, 3}
id::String
YData(a, b, c, d) = new(a, b, c, d)
end
......@@ -214,4 +215,14 @@ end
function Base.show(io::IO, a::CData)
print(io, a.header)
end
function Base.show(io::IO, a::Corr)
fnames = fieldnames(Corr)
for k in fnames
f = getfield(a, k)
if k != :obs
print(io, "$k = $f\t")
end
end
end
\ No newline at end of file
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