Updated juobs_uwreal_const to use Ref{uwreal}

d3e648ea · Antonino D'Anna · 8fe484e9 · d3e648ea · d3e648ea · d3e648ea
Commit d3e648ea authored Feb 03, 2025 by Antonino D'Anna
39 changed files
--- a/.gitignore
+++ b/.gitignore
 analysis/plat\.txt
 *.pdf
 analysis/*.txt
--- a/Manifest.toml
+++ b/Manifest.toml
--- a/README.md
+++ b/README.md
 # juobs
 Analysis code (Julia)
\ No newline at end of file
--- a/analysis/analysis.jl
+++ b/analysis/analysis.jl
--- a/analysis/analysis_pcac.jl
+++ b/analysis/analysis_pcac.jl
 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
--- a/analysis/fits.log
+++ b/analysis/fits.log
--- a/analysis/functions.jl
+++ b/analysis/functions.jl
--- a/analysis/results.txt
+++ b/analysis/results.txt
 (H400)$Z^{tm}_M \mu_c \sqrt{8t_0} = $3.030909671357194 +/- 0.07903701818131038
 (H400)$M_D \sqrt{8t_0}= $3.9807556606105736 +/- 0.05781703939545818
 (H400)$M_Ds \sqrt{8t_0}= $3.9807556606105736 +/- 0.05781703939545818
 (H400)$M_D* \sqrt{8t_0}= $4.278934408455874 +/- 0.05001764960908615
 (H400)$M_Ds* \sqrt{8t_0}= $4.278934408455874 +/- 0.05001764960908615
 (H400)$f_D \sqrt{8t_0}= $0.5171340154200049 +/- 0.0030551745985989815
 (H400)$f_Ds \sqrt{8t_0}= $0.5171340154200049 +/- 0.0030551745985989815
 (N200)$Z^{tm}_M \mu_c \sqrt{8t_0} = $3.0777083812680863 +/- 0.07529964071401364
 (N200)$M_D \sqrt{8t_0}= $3.9484624535288577 +/- 0.056300551744400275
 (N200)$M_Ds \sqrt{8t_0}= $4.0641686659916445 +/- 0.05571406258479428
 (N200)$M_D* \sqrt{8t_0}= $4.2322082817565505 +/- 0.05089413966187937
 (N200)$M_Ds* \sqrt{8t_0}= $4.366150683510803 +/- 0.050567123757276136
 (N200)$f_D \sqrt{8t_0}= $0.4781332278412574 +/- 0.002533317431472261
 (N200)$f_Ds \sqrt{8t_0}= $0.5253557430045498 +/- 0.0019233408904497612
 (N203)$Z^{tm}_M \mu_c \sqrt{8t_0} = $3.069739432147581 +/- 0.07467450492462731
 (N203)$M_D \sqrt{8t_0}= $3.9619597653172356 +/- 0.05581411314938938
 (N203)$M_Ds \sqrt{8t_0}= $4.027646770204338 +/- 0.055472228755110334
 (N203)$M_D* \sqrt{8t_0}= $4.253505640330456 +/- 0.050187214812839276
 (N203)$M_Ds* \sqrt{8t_0}= $4.326727158575913 +/- 0.049836834652424916
 (N203)$f_D \sqrt{8t_0}= $0.488543655769974 +/- 0.0026562881901046583
 (N203)$f_Ds \sqrt{8t_0}= $0.5157212901463102 +/- 0.0021384519222027373
 (N300)$Z^{tm}_M \mu_c \sqrt{8t_0} = $2.997384760490272 +/- 0.07895636913539895
 (N300)$M_D \sqrt{8t_0}= $3.94373962398667 +/- 0.059571174171691506
 (N300)$M_Ds \sqrt{8t_0}= $3.94373962398667 +/- 0.059571174171691506
 (N300)$M_D* \sqrt{8t_0}= $4.291279319094004 +/- 0.04988459701774591
 (N300)$M_Ds* \sqrt{8t_0}= $4.291279319094004 +/- 0.04988459701774591
 (N300)$f_D \sqrt{8t_0}= $0.5032296543520727 +/- 0.003757345679706973
 (N300)$f_Ds \sqrt{8t_0}= $0.5032296543520727 +/- 0.003757345679706973
 (J303)$Z^{tm}_M \mu_c \sqrt{8t_0} = $3.13490498080823 +/- 0.08328602171541571
 (J303)$M_D \sqrt{8t_0}= $3.970055446897706 +/- 0.062204612871266905
 (J303)$M_Ds \sqrt{8t_0}= $4.113876464562304 +/- 0.06232345158893755
 (J303)$M_D* \sqrt{8t_0}= $4.199854539735192 +/- 0.05475423487017079
 (J303)$M_Ds* \sqrt{8t_0}= $4.399899824892723 +/- 0.05477252163421222
 (J303)$f_D \sqrt{8t_0}= $0.4649182529771295 +/- 0.004855221613601069
 (J303)$f_Ds \sqrt{8t_0}= $0.5220832840476 +/- 0.0031391370517194982
 $Z^{tm}_M \mu_c \sqrt{8t_0}$ = 3.289196404345117 +/- 0.16908049991604063
 muc(MeV) = 1571.5428436124926 +/- 74.65754166879076
 $M_D \sqrt{8t_0}$ = 4.034261174024082 +/- 0.12045227374006602
 m_D(MeV) = 1927.5268174700511 +/- 51.13372706582599
 $M_Ds \sqrt{8t_0}$ = 4.270003547803183 +/- 0.12354622671856343
 m_Ds(MeV) = 2040.1620009329038 +/- 52.898332267818304
 $M_D* \sqrt{8t_0}$ = 4.103105481644236 +/- 0.10100061920706542
 m_D_star(MeV) = 1960.4198909335223 +/- 42.35821470980299
 $M_Ds* \sqrt{8t_0}$ = 4.498614355722275 +/- 0.09456340196942646
 m_Ds_star(MeV) = 2149.3897985442322 +/- 37.956898903502925
 $f_D \sqrt{8t_0}$ = 0.4363276333625155 +/- 0.017871060655147757
 f_D(MeV) = 208.47267398669123 +/- 8.883408580389085
 $f_Ds \sqrt{8t_0}$ = 0.5263085789505523 +/- 0.011256710293275131
 f_Ds(MeV) = 251.46460688360165 +/- 6.054227498288841
--- a/constants/juobs_const.jl
+++ b/constants/juobs_const.jl
 const hc = 197.3269804 #MeV fm
 const ens_db = Dict(
    #"ens_id"=>[L, T, beta, dtr, vrw, trunc_cnfg]
    "H101"     => [32, 96, 3.4, 2, "1.2", [1001,1009]],
    "H102r001" => [32, 96, 3.4, 2, "2.0", [997]],
    "H102r002" => [32, 96, 3.4, 2, "2.0", [1008]],
    "H105"     => [32, 96, 3.4, 2, "2.0", [947,1042]],
    "H105r005" => [32, 96, 3.4, 1, "1.2", [837]],
    "H400"     => [32, 96, 3.46, 1, "1.2", [505,540]],
    "D450"     => [64, 128, 3.46, 1, ["2.0"], [1000]],
    "N202"     => [48, 128, 3.55, 2, "1.2", [899]],
    "N203"     => [48, 128, 3.55, 1, "2.0", [756,787]],
    "N200"     => [48, 128, 3.55, 1, "2.0", [856,856]],
    "D200"     => [64, 128, 3.55, 2, "2.0", [2001]],
    "E250"     => [96, 192, 3.55, 1, ["2.0"], [1009]],
    "N300"     => [48, 128, 3.70, 1, "1.2", [1521]],
    "N302"     => [48, 128, 3.70, 1, "1.2", [2201]],
    "J303"     => [64, 192, 3.70, 2, "2.0", [1073]],
    "E300"     => [96, 192, 3.70, 1, ["1.4"], [1139]],
    "J500"     => [64, 192, 3.85, 2, ["1.2", "1.4", "2.0"], [789,655,431]],
    "J501"     => [64, 192, 3.85, 1, ["1.2", "1.4", "2.0"], [1635,1142,1150]]
 )
 const db = Dict(
    "J501" => ["ts001_chunk1", "ts001_chunk3", "ts190_chunk1", "ts190_chunk2"],
    "J500" => ["ts001_chunk1", "ts001_chunk2", "ts190_chunk1", "ts190_chunk2"],
    "E250" => ["ts001", "ts097"],
    "E300" => ["ts001_chunk2", "ts001_chunk3", "ts190_chunk1"],#, "ts001_chunk1"],
    "D450" => ["ts001", "ts065_1", "ts065_2"]
 )
 const db_c = Dict(
    "J501" => ["ts001", "ts190"],
    "J500" => ["ts001_chunk1", "ts190_chunk2"],
    "E250" => ["ts001"],
    "E300" => ["ts001_chunk2"],#, "ts001_chunk1"]
    "D450" => ["ts001_1", "ts001_2"]
 )
 const sym_bool = Dict(
    "J501" => true,
    "J500" => true,
    "E250" => false,
    "E300" => false,
    "D450" => false
 )
 const flag_s = Dict(
    "J303r003" => [324,325,326],
    "H105r001" => [100,105,106],
    "H105r002" => [1],
    "H105r005" => [254, 255, 256, 257, 259, 260, 261, 264, 265, 266, 269, 280, 282, 283, 284, 285, 286, 287, 288, 289, 291, 299, 301, 313, 314, 315, 316, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342]
 )
 const ensemble_inv = Dict(
    "H101"     => 1,
    "H102r001" => 2,
    "H102r002" => 3,
    "H105"     => 4,
    "H105r005" => 5,
    "H400"     => 6,
    "D450"     => 7,
    "N202"     => 8,
    "N203"     => 9,
    "N200"     => 10,
    "D200"     => 11,
    "E250"     => 12,
    "N300"     => 13,
    "N302"     => 14,
    "J303"     => 15,
    "E300"     => 16,
    "J500"     => 17,
    "J501"     => 18
 )
\ No newline at end of file
--- a/constants/juobs_uwreal_const.jl
+++ b/constants/juobs_uwreal_const.jl
--- a/constants/path_csv.jl
+++ b/constants/path_csv.jl
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+++ b/docs/build/obs.html
--- a/docs/build/reader.html
+++ b/docs/build/reader.html
--- a/docs/build/search.html
+++ b/docs/build/search.html
 <!DOCTYPE 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><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.039/juliamono-regular.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/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"><a href="index.html">juobs Documentation</a></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> version 0.27.15 on <span class="colophon-date" title="Friday 1 July 2022 12:33">Friday 1 July 2022</span>. Using Julia version 1.6.5.</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>
--- a/docs/build/search_index.js
+++ b/docs/build/search_index.js
--- a/docs/build/tools.html
+++ b/docs/build/tools.html
--- a/docs/make.jl
+++ b/docs/make.jl
 using Documenter, juobs
 push!(LOAD_PATH, "../src")
 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))
--- a/docs/src/index.md
+++ b/docs/src/index.md
 # DOCUMENTATION
 ## Contents
 ```@contents
 Pages = ["reader.md", "tools.md", "obs.md", "linalg.md"]
 Depth = 3
 ```
--- a/docs/src/linalg.md
+++ b/docs/src/linalg.md
 # Linear Algebra
 ```@docs
 uweigvals
 uweigvecs
 uweigen
 get_matrix
 energies
 getall_eigvals
 getall_eigvecs
 ```
--- a/docs/src/obs.md
+++ b/docs/src/obs.md
 # Observables
 ```@docs
 meff
 mpcac
 dec_const
 dec_const_pcvc
 comp_t0
 ```
--- a/docs/src/reader.md
+++ b/docs/src/reader.md
 # Reader
 ```@docs
 read_mesons
 read_ms
 read_ms1
 read_md
 truncate_data!
 ```
--- a/docs/src/tools.md
+++ b/docs/src/tools.md
 # Tools
 ```@docs
 corr_obs
 corr_sym
 md_sea
 md_val
 lin_fit
 fit_routine
 bayesian_av
 ```
--- a/gevp tools/tools.jl
+++ b/gevp tools/tools.jl
--- a/src/Changelog.md
+++ b/src/Changelog.md
 This file should keep track of all the changes made on a brach since the last merging with master.
 On the master brach, it should keep track of all the major, potentially code-codebreaking, changes perform.
 This file should not be merged into master, but only kept as a reference within its own branch
 ### Antonino Branch
  - Changes before Dic 8 2024:
    - Added juobs_plot.jl with the plot routine: plot_data to plot uwreal and plot_func to plot a function.
    - Updated some documentation in juobs_reader.jl
    - Updated documentation in juobs_tools.jl
    - Updated documentation in juobs_type.jl 
  - Dic 8 2024: added functions plat_av to the existing one. This change should not be code-breaking, since it only add different version of the exising one. Now it is possible to pass a Vector or a Matrix W containing the weight to use in the plateau average. If W is a Matrix, a correlated fit is perform. If W is not given, then the old function is called. 
  - Dic 10 2024: mpcac function now follow the convention more clearly. documentation updated juobs_tools. 
                 pvalue function for uncorrelated data now accept a W vector. default value is Vector{Float64}(), and if W is not provided, it is computed as the inverse of the error squared of the data. 
\ No newline at end of file
--- a/src/juobs.jl
+++ b/src/juobs.jl
 module juobs
 using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, Optim, ForwardDiff
 using Base: Float64
 import Statistics: mean
 include("juobs_types.jl")
 include("juobs_linalg.jl")
 include("juobs_reader.jl")
 include("juobs_tools.jl")
 include("juobs_plots.jl")
 include("juobs_obs.jl")
 include("../constants/juobs_const.jl")
 include("../constants/path_csv.jl")
 export EnsInfo
 export ens_db, db, db_c, flag_s, sym_bool, ensemble_inv
 export read_mesons, read_mesons_correction, read_mesons_multichunks, read_mesons_correction_multichunks, read_ens_tm, read_ens_tm_sym, read_ens_TSM, read_ens_wil, read_ens_csv, get_corr_tm, get_corr_TSM, get_corr_TSM_multichunks, get_corr_wil, read_ms1, read_ms, read_md, get_YM, get_YM_dYM, truncate_data!, concat_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_obs_TSM, corr_sym, corr_sym_E250, corr_sym_D450, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av, pvalue
 export plot_data,plot_func, pvalue, fve, model_av, fit_alg
 export meff, mpcac, dec_const, dec_const_w, dec_const_w, dec_const_pcvc, comp_t0, get_m, get_m_pbc, get_mpcac, get_f_wil, get_f_wil_pbc, get_f_tm, get_f_tm_pbc, get_w0t0_plat
 end # module
--- a/src/juobs_linalg.jl
+++ b/src/juobs_linalg.jl
--- a/src/juobs_obs.jl
+++ b/src/juobs_obs.jl
--- a/src/juobs_plots.jl
+++ b/src/juobs_plots.jl
--- a/src/juobs_reader.jl
+++ b/src/juobs_reader.jl
--- a/src/juobs_tools.jl
+++ b/src/juobs_tools.jl
--- a/src/juobs_types.jl
+++ b/src/juobs_types.jl