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juobs
Commit 241323d9 authored by Javier's avatar Javier
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Merge branch 'javier'

parents 54e7b8a7 92f6a225
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Showing with 768 additions and 267 deletions
Manifest.toml
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Project.toml
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......@@ -8,6 +8,6 @@ ADerrors = "5e92007d-7bf1-471c-8ceb-4591b8b567a9"
BDIO = "375f315e-f2c4-11e9-2ef9-134f02f79e27"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
Optim = "429524aa-4258-5aef-a3af-852621145aeb"
PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
src/juobs.jl
View file @ 241323d9
module juobs
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, Optim
import Statistics: mean
include("juobs_types.jl")
......@@ -8,7 +8,7 @@ include("juobs_reader.jl")
include("juobs_tools.jl")
include("juobs_obs.jl")
export read_mesons, read_ms1, read_ms, read_md
export read_mesons, read_ms1, read_ms, read_md, truncate_data!
export get_matrix, uwgevp_tot, energies, uwdot
export corr_obs, md_sea, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine
export meff, dec_const_pcvc, comp_t0
......
src/juobs_obs.jl
View file @ 241323d9
......@@ -14,12 +14,13 @@ corr_pp = corr_obs.(data)
m = meff(corr_pp[1], [50, 60], pl=false)
```
"""
function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bool=false, mu::Union{Vector{Float64}, Nothing}=nothing)
function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bool=false, mu::Union{Vector{Float64}, Nothing}=nothing,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
dim = length(corr)
aux = 0.5 .* log.((corr[2:dim-2] ./ corr[3:dim-1]).^2)
mass = plat_av(aux, plat)
uwerr(mass)
mass = plat_av(aux, plat, wpm)
if pl == true
isnothing(wpm) ? uwerr(mass) : uwerr(mass, wpm)
x = 1:length(aux)
y = value.(aux)
dy = err.(aux)
......@@ -65,7 +66,8 @@ m = meff(corr_pp[1], [50, 60], pl=false)
f = dec_const_pcvc(corr_pp[1], [50, 60], m, pl=false)
```
"""
function dec_const_pcvc(corr::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, mu::Vector{Float64}, y0::Int64 ; pl::Bool=true, data::Bool=false)
function dec_const_pcvc(corr::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, mu::Vector{Float64}, y0::Int64 ; pl::Bool=true, data::Bool=false,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
"""
compute the decay constant when the source is far from the boundaries
"""
......@@ -74,14 +76,21 @@ function dec_const_pcvc(corr::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, mu
aux = exp.((collect(1:dim) .- y0 ) .* [m for k in 1:dim])
R = ((aux .* corr_pp).^2).^0.25
R_av = plat_av(R, plat)
R_av = plat_av(R, plat, wpm)
f = sqrt(2) * (mu[1] + mu[2]) *R_av / m^1.5
uwerr(f)
if pl == true
if isnothing(wpm)
uwerr(f)
uwerr(R_av)
uwerr.(R)
else
uwerr(f, wpm)
uwerr(R_av, wpm)
uwerr.(R, wpm)
end
v = value(R_av)
e = err(R_av)
uwerr.(R)
figure()
fill_between(plat[1]:plat[2], v-e, v+e, color="green", alpha=0.75)
errorbar(1:length(R), value.(R), err.(R), fmt="x", color="black")
......@@ -138,10 +147,31 @@ t0_r = comp_t0(Y, [38, 58], L=32, rw=[rw1, rw2], pl=true)
```
"""
function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2)
function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false,
rw::Union{Matrix{Float64}, Nothing}=nothing, npol::Int64=2, ws::ADerrors.wspace=ADerrors.wsg,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
Ysl = Y.Ysl
t = Y.t
id = Y.id
replica = size.([Ysl], 1)
#Truncation
n_ws = findfirst(x-> x == id, ws.map_nob)
if !isnothing(n_ws)
ivrep_ws = ws.fluc[n_ws].ivrep
if length(ivrep_ws) != 1
error("Different number of replicas")
end
if replica[1] > ivrep_ws[1]
println("Automatic truncation in Ysl ", ivrep_ws[1], " / ", replica[1], ". R = 1")
Ysl = Ysl[1:ivrep_ws[1], :, :]
elseif replica[1] < ivrep_ws[1]
error("Automatic truncation failed. R = 1\nTry using truncate_data!")
end
end
Ysl = isnothing(rw) ? Ysl : apply_rw(Ysl, rw)
xmax = size(Ysl, 2)
......@@ -157,7 +187,7 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Un
end
end
x = t[nt0-dt0:nt0+dt0]
t2E = [plat_av(Y_aux[:, j], plat) for j=1:2*dt0+1] .* x.^2 / L^3
t2E = [plat_av(Y_aux[:, j], plat, wpm) for j=1:2*dt0+1] .* x.^2 / L^3
model(x, p) = get_model(x, p, npol)
......@@ -165,8 +195,14 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Un
fmin(x, p) = model(x, p) .- 0.3
t0 = root_error(fmin, t[nt0], par)
if pl
if isnothing(wpm)
uwerr(t0)
uwerr.(t2E)
else
uwerr(t0, wpm)
uwerr.(t2E, wpm)
end
v = value.(t2E)
e = err.(t2E)
......@@ -190,18 +226,38 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Un
return t0
end
function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false, rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2)
function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false,
rw::Union{Vector{Matrix{Float64}}, Nothing}=nothing, npol::Int64=2, ws::ADerrors.wspace=ADerrors.wsg,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
nr = length(Y)
Ysl = getfield.(Y, :Ysl)
t = getfield.(Y, :t)
t = t[1]
id = getfield.(Y, :id)
vtr = getfield.(Y, :vtr)
replica = length.(vtr)
replica = size.(Ysl, 1)
if !all(id .== id[1])
error("IDs are not equal")
end
#Truncation
n_ws = findfirst(x-> x == id[1], ws.map_nob)
if !isnothing(n_ws)
ivrep_ws = ws.fluc[n_ws].ivrep
if length(replica) != length(ivrep_ws)
error("Different number of replicas")
end
for k = 1:length(replica)
if replica[k] > ivrep_ws[k]
println("Automatic truncation in Ysl ", ivrep_ws[k], " / ", replica[k], ". R = ", k)
Ysl[k] = Ysl[k][1:ivrep_ws[k], :, :]
elseif replica[k] < ivrep_ws[k]
error("Automatic truncation failed. R = ", replica[k], "\nTry using truncate_data!")
end
end
end
Ysl = isnothing(rw) ? Ysl : apply_rw(Ysl, rw)
tmp = Ysl[1]
......@@ -219,7 +275,7 @@ function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false
end
end
x = t[nt0-dt0:nt0+dt0]
t2E = [plat_av(Y_aux[:, j], plat) for j=1:2*dt0+1] .* x.^2 / L^3
t2E = [plat_av(Y_aux[:, j], plat, wpm) for j=1:2*dt0+1] .* x.^2 / L^3
model(x, p) = get_model(x, p, npol)
......@@ -227,8 +283,14 @@ function comp_t0(Y::Vector{YData}, plat::Vector{Int64}; L::Int64, pl::Bool=false
fmin(x, p) = model(x, p) .- 0.3
t0 = root_error(fmin, t[nt0], par)
if pl
if isnothing(wpm)
uwerr(t0)
uwerr.(t2E)
else
uwerr(t0, wpm)
uwerr.(t2E, wpm)
end
v = value.(t2E)
e = err.(t2E)
......
src/juobs_reader.jl
View file @ 241323d9
......@@ -71,6 +71,7 @@ end
@doc raw"""
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)
This faction 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.
......@@ -83,6 +84,7 @@ read_mesons(path, "G5")
read_mesons(path, nothing, "G5")
read_mesons(path, "G5", "G5")
read_mesons(path, "G5", "G5", id=1)
read_mesons([path1, path2], "G5", "G5")
```
"""
function read_mesons(path::String, g1::Union{String, Nothing}=nothing, g2::Union{String, Nothing}=nothing; id::Union{Int64, Nothing}=nothing)
......@@ -156,6 +158,21 @@ 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)
res = read_mesons.(path, g1, g2, id=id)
nrep = length(res)
ncorr = length(res[1])
cdata = Vector{Vector{CData}}(undef, ncorr)
for icorr = 1:ncorr
cdata[icorr] = Vector{CData}(undef, nrep)
for r = 1:nrep
cdata[icorr][r] = res[r][icorr]
end
end
return cdata
end
function read_rw(path::String; v::String="1.2")
data = open(path, "r")
nrw = read(data, Int32)
......@@ -242,20 +259,20 @@ function read_md(path::String)
end
@doc raw"""
read_ms(path::String)
read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)
Reads openQCD ms dat files at a given path. This method return:
Reads openQCD ms dat files at a given path. This method return YData:
t(t): flow time values
Wsl(icfg, x0, t): the time-slice sums of the densities of the Wilson plaquette action
Ysl(icfg, x0, t): the time-slice sums of the densities of the Yang-Mills action
Qsl(icfg, x0, t): the time-slice sums of the densities of the topological charge
vtr: vector that contains trajectory number
id: ensmble id
Examples:
```@example
t, W, Y, Q = read_ms(path)
Y = read_ms(path)
```
"""
function read_ms(path::String; id::Union{Int64, Nothing}=nothing)
function read_ms(path::String; id::Union{Int64, Nothing}=nothing, dtr::Int64=1)
if isnothing(id)
bname = basename(path)
m = findfirst(r"[A-Z][0-9]{3}r[0-9]{3}", bname)
......@@ -273,27 +290,38 @@ function read_ms(path::String; id::Union{Int64, Nothing}=nothing)
ntr = Int32((fsize - 3*4 - 8) / datsize)
vntr = Vector{Int32}(undef, ntr)
if mod(ntr, dtr) != 0
error("ntr / dtr must be exact")
end
vntr = Vector{Int32}(undef, div(ntr, dtr))
# x0, t, cfg
Wsl = Array{Float64}(undef, ntr, tvals, nn + 1)
Ysl = Array{Float64}(undef, ntr, tvals, nn + 1)
Qsl = Array{Float64}(undef, ntr, tvals, nn + 1)
Wsl = Array{Float64}(undef, div(ntr, dtr), tvals, nn + 1)
Ysl = Array{Float64}(undef, div(ntr, dtr), tvals, nn + 1)
Qsl = Array{Float64}(undef, div(ntr, dtr), tvals, nn + 1)
k = 0
for itr = 1:ntr
vntr[itr] = read(data, Int32)
tmp = read(data, Int32)
if mod(itr, dtr) == 0
k += 1
vntr[k] = tmp
end
for iobs = 1:3
for inn = 0:nn
tmp = Vector{Float64}(undef, tvals)
read!(data, tmp)
tmp2 = Vector{Float64}(undef, tvals)
read!(data, tmp2)
if mod(itr, dtr) == 0
if iobs == 1
Wsl[itr, :, inn + 1] = tmp
Wsl[k, :, inn + 1] = tmp2
elseif iobs == 2
Ysl[itr, :, inn + 1] = tmp
Ysl[k, :, inn + 1] = tmp2
elseif iobs == 3
Qsl[itr, :, inn + 1] = tmp
Qsl[k, :, inn + 1] = tmp2
end
end
end
end
end
......@@ -301,3 +329,60 @@ function read_ms(path::String; id::Union{Int64, Nothing}=nothing)
t = Float64.(0:nn) .* dn .* eps
return YData(vntr, t, Ysl, id)
end
@doc raw"""
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})
Truncates the output of read_mesons and read_ms taking the first nc configurations.
Examples:
```@example
#Single replica
dat = read_mesons(path, "G5", "G5")
Y = read_ms(path)
truncate_data!(dat, nc)
truncate_data!(Y, nc)
#Two replicas
dat = read_mesons([path1, path2], "G5", "G5")
Y = read_ms.([path1_ms, path2_ms])
truncate_data!(dat, [nc1, nc2])
truncate_data!(Y, [nc1, nc2])
```
"""
function truncate_data!(data::YData, nc::Int64)
data.vtr = data.vtr[1:nc]
data.Ysl = data.Ysl[1:nc, :, :]
return nothing
end
function truncate_data!(data::Vector{YData}, nc::Vector{Int64})
truncate_data!.(data, nc)
return nothing
end
function truncate_data!(data::Vector{CData}, nc::Int64)
N = length(data)
for k = 1:N
data[k].vcfg = data[k].vcfg[1:nc]
data[k].re_data = data[k].re_data[1:nc, :]
data[k].im_data = data[k].im_data[1:nc, :]
end
return nothing
end
function truncate_data!(data::Vector{Vector{CData}}, nc::Vector{Int64})
N = length(data)
R = length(data[1])
for k = 1:N
for r = 1:R
data[k][r].vcfg = data[k][r].vcfg[1:nc[r]]
data[k][r].re_data = data[k][r].re_data[1:nc[r], :]
data[k][r].im_data = data[k][r].im_data[1:nc[r], :]
end
end
return nothing
end
\ No newline at end of file
src/juobs_tools.jl
View file @ 241323d9
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