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juobs
Commit 92edc521 authored by ale's avatar ale
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Merge branch 'merging' into alejandro

parents c1cb07d7 d09bd022
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Manifest.toml
View file @ 92edc521
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constants/juobs_const.jl
View file @ 92edc521
using ADerrors
#PDG
const hc = 197.3269804 #MeV fm
const M_values = [1869.65, 2010.26, 1968.34, 2112.2, 2980.3, 3096.916, 5279.65] #MD, MD*, MDs, MDs*, \eta_c, J/\psi , MB (MeV)
const M_error = [0.05, 0.05, 0.07, 0.4, 1.2, 0.011, 0.12]
const M_values = [1869.65, 2010.26, 1968.34, 2112.2, 2980.3, 3096.916, 5279.65, 5366.3] #MD, MD*, MDs, MDs*, \eta_c, J/\psi , MB, MBs(MeV)
const M_error = [0.05, 0.05, 0.07, 0.4, 1.2, 0.011, 0.12, 0.6]
#1802.05243
const b_values = [3.40, 3.46, 3.55, 3.70, 3.85]
const ZM_data = [1.9684, 1.9935, 2.0253, 2.0630, 2.0814]
const ZM_error = [35, 27, 33, 38, 45] .* 1e-4
const ZM_tm_data = [2.6047, 2.6181, 2.6312, 2.6339, 2.6127]
const ZM_tm_error = [42, 33, 42, 48, 55] .* 1e-4
# 1808.09236
#1808.09236
const ZA_data = [0.75642, 0.76169, 0.76979, 0.78378, 0.79667]
const ZA_err = [72, 93, 43, 47, 47] .*1e-5
const ZV_data = [0.72259, 0.72845, 0.73886, 0.75574, 0.77074]
......@@ -17,41 +17,63 @@ const ZV_err = [74, 89, 46, 48, 49] .* 1e-5
#2005.01352
const ZS_over_ZP_data = [1.3497, 1.2914, 1.2317, 1.1709, 1.1343]
const ZS_over_ZP_err = [83, 64, 48, 23, 25 ] .* 1e-4
#1608.08900
const b_values2 = [3.40, 3.46, 3.55, 3.70]
const t0_data = [2.86, 3.659, 5.164, 8.595]
const t0_error = [11, 16, 18, 29] .* 1e-3
const t0_ph_value = [0.413]
const t0_ph_error = ones(1,1) .* 5e-3
## taking into account correlations in zm_tm
#2101.02694
# const b_values2 = [3.40, 3.46, 3.55, 3.70]
const t0_data = [2.846, 3.634, 5.140, 8.564, 14.064]
const t0_error = [8, 13, 21, 24, 63] .* 1e-3
# from AS analysis
const t0_ph_value = [0.4118]
const t0_ph_error = ones(1,1) .* 25e-4
#2101.10969
const RM_data = [2.335, 1.869, 1.523, 1.267, 1.149]
const RM_err = [31, 19, 14, 16, 18] .* 1e-3
#1906.03445 LCP1 for heavy quarks
const BA_MINUS_BP_data = [-0.324, -0.265, -0.196, -0.119, -0.073]
const BA_MINUS_BP_err = [17, 14, 14, 14, 12] .*1e-3
const ZDATA = [0.8981, 0.9468, 1.0015, 1.0612, 1.0971]
const ZERR = [35, 35, 30, 17, 18 ] .* 1e-4
#1802.05243 taking into account correlations in zm_tm
C = [[0.375369e-6, 0.429197e-6, -0.186896e-5] [0.429197e-6, 0.268393e-4, 0.686776e-4] [-0.186896e-5, 0.686776e-4, 0.212386e-3]]
z = cobs([0.348629, 0.020921, 0.070613], C, "z")
ZP(b) = z[1] + z[2] * (b - 3.79) + z[3] * (b - 3.79)^2
Mrat = uwreal([.9148, 0.0088], "M/mhad")
zm_tm_covar(b) = Mrat / ZP(b)
# same for zm wilson
CC = [[0.164635e-4, 0.215658e-4, -0.754203e-4] [0.215658e-4, 0.121072e-2, 0.308890e-2] [-0.754203e-4, 0.308890e-2, 0.953843e-2]]
zz = cobs([2.270073, 0.121644, -0.464575], CC, "zm")
z_covar(b) = value(Mrat) * (zz[1] + zz[2]*(b-3.79) + zz[3]*(b-3.79)^2)
## taking into account correlations in r_m
#Crm = [[3.699760, -2.198586, -1.476913e-3] [-2.198586, 1.306512, 8.776569e-4] [-1.476913e-3, 8.776569e-4, 5.895710e-7] ]
#c_i = cobs([-7.86078, 5.49175, -0.54078], Crm, "c_i in rm")
#rm(b::Float64) = 1.0 + 0.004630*(6/b)^4 * ((1. +c_i[1]*(6/b)^2 + c_i[2]*(6/b)^4) / (1. + c_i[3]*(6/b)^2))
##
#Cov matrices
const C1 = zeros(5, 5)
const C2 = zeros(5, 5)
const C3 = zeros(4, 4)
const C4 = zeros(7, 7)
const C3 = zeros(5, 5)
const C4 = zeros(8, 8)
const C5 = zeros(5, 5)
const C6 = zeros(5, 5)
const C7 = zeros(5, 5)
const C8 = zeros(5, 5)
const C9 = zeros(5, 5)
const C10 = zeros(5, 5)
for i = 1:7
for i = 1:8
C4[i, i] = M_error[i] ^ 2
if i<=5
C1[i, i] = ZM_error[i] ^ 2
C2[i, i] = ZM_tm_error[i] ^ 2
C5[i, i] = ZA_err[i] ^ 2
C6[i, i] = ZS_over_ZP_err[i] ^ 2
C7[i, i] = ZV_err[i] ^ 2
if i <= 4
C3[i, i] = t0_error[i] ^ 2
end
C7[i, i] = ZV_err[i] ^ 2
C8[i, i] = RM_err[i] ^2
C9[i,i] = BA_MINUS_BP_err[i] ^2
C10[i,i] = ZERR[i] ^2
C3[i, i] = t0_error[i] ^ 2
end
end
......@@ -63,12 +85,18 @@ const a_ = t0_ph ./ sqrt.(8 .* t0_)
const M = cobs(M_values, C4, "charmed meson masses")
const Za = cobs(ZA_data, C5, "ZA")
const Zv = cobs(ZV_data, C7, "ZV")
const ZS_over_ZP = cobs(ZS_over_ZP_data, C6, "ZS over ZP")
const ZS_over_ZP = cobs(ZS_over_ZP_data, C6, "ZS/ZP")
const RM = cobs(RM_data, C8, "rm")
const BA_BP = cobs(BA_MINUS_BP_data, C9, "ba-bp")
const ZZ = cobs(ZDATA, C10, "Z")
zm(beta::Float64) = ZM[b_values .== beta][1]
zm_tm(beta::Float64) = ZM_tm[b_values .== beta][1]
t0(beta::Float64) = t0_[b_values2 .== beta][1]
a(beta::Float64) = a_[b_values2 .== beta][1]
za(beta::Float64) = Za[b_values .== beta][1]
zv(beta::Float64) = Zv[b_values .== beta][1]
zs_over_zp(beta::Float64) = ZS_over_ZP[b_values .== beta][1]
\ No newline at end of file
zm(beta::Float64) = ZM[b_values .== beta][1]
zm_tm(beta::Float64) = ZM_tm[b_values .== beta][1]
t0(beta::Float64) = t0_[b_values .== beta][1]
a(beta::Float64) = a_[b_values .== beta][1]
za(beta::Float64) = Za[b_values .== beta][1]
zv(beta::Float64) = Zv[b_values .== beta][1]
zs_over_zp(beta::Float64) = ZS_over_ZP[b_values .== beta][1]
rm(beta::Float64) = RM[b_values .== beta][1]
ba_bp(beta::Float64) = BA_BP[b_values .== beta][1]
Z(beta::Float64) = ZZ[b_values .== beta][1]
\ No newline at end of file
src/juobs.jl
View file @ 92edc521
......@@ -12,6 +12,6 @@ include("juobs_obs.jl")
export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, 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, md_sea, md_val, plat_av, lin_fit, x_lin_fit, y_lin_fit, fit_routine, global_fit_routine, bayesian_av, pvalue
export meff, mpcac, dec_const, dec_const_pcvc, comp_t0
export meff, mpcac, dec_const, dec_const_w, dec_const_pcvc, comp_t0
end # module
src/juobs_linalg.jl
View file @ 92edc521
......@@ -62,7 +62,7 @@ function get_matrix(corr_diag::Vector{Vector{uwreal}}, corr_upper::Vector{Vector
if d != (n*(n-1) / 2)
error("Error get_matrix")
end
res = Vector{Matrix}(undef, time) # array with all the matrices at each time step.
res = Vector{Matrix{uwreal}}(undef, time) # array with all the matrices at each time step.
aux = Matrix{uwreal}(undef, n, n)
for t in 1:time
count=0
......@@ -180,10 +180,10 @@ matrices = [corr_diag, corr_upper]
Julia>
```
"""
function getall_eigvals(a::Vector{Matrix{uwreal}}, t0::Int64; iter=30 )
function getall_eigvals(a::Vector{Matrix{uwreal}}, t0::Int64; iter=5 )
n = length(a)
res = Vector{Vector{uwreal}}(undef, n)
[res[i] = uweigvals(a[i], a[t0]) for i=1:n]
[res[i] = uweigvals(a[i], a[t0], iter=iter) for i=1:n]
return res
end
......@@ -237,7 +237,7 @@ function uweigvals(a::Matrix{uwreal}, b::Matrix{uwreal}; iter = 5, diag::Bool=t
end
function uweigvals_dim_geq3(a::Matrix{uwreal}; iter = 5, diag::Bool=true)
n = size(a,1)
a = tridiag_reduction(a)
#a = tridiag_reduction(a)
for k in 1:iter
q_k, r_k = qr(a)
a = uwdot(r_k, q_k)
......@@ -281,7 +281,7 @@ mat_array = get_matrix(diag, upper_diag)
evecs = getall_eigvecs(mat_array, 5)
```
"""
function getall_eigvecs(a::Vector{Matrix}, delta_t; iter=5)
function getall_eigvecs(a::Vector{Matrix{uwreal}}, delta_t; iter=5)
n = length(a)-delta_t
res = Vector{Matrix{uwreal}}(undef, n)
[res[i] = uweigvecs(a[i+delta_t], a[i]) for i=1:n]
......@@ -315,20 +315,21 @@ res = uweigvecs(a) ##eigenvectors in column
res1 = uweigvecs(a,b) ## generalised eigenvectors in column
```
"""
function uweigvecs(a::Matrix{uwreal}; iter = 5)
function uweigvecs(a::Matrix{uwreal}; iter = 10)
n = size(a,1)
if n > 2
a, q = tridiag_reduction(a, q_mat=true)
end
# if n > 2
# a, q = tridiag_reduction(a, q_mat=true)
# end
u = idty(n)
for k in 1:iter
q_k, r_k = qr(a)
a = uwdot(r_k, q_k)
u = uwdot(u, q_k)
end
n > 2 ? (return uwdot(q,u)) : (return u)
#n > 2 ? (return uwdot(q,u)) : (return u)
return u
end
function uweigvecs(a::Matrix{uwreal}, b::Matrix{uwreal}; iter = 5)
function uweigvecs(a::Matrix{uwreal}, b::Matrix{uwreal}; iter = 10)
c = uwdot(invert(b), a)
#return uweigvecs(c, iter=iter)
n = size(c,1)
......@@ -691,9 +692,15 @@ end
"""
Return the transpose of a matrix or vector of uwreals
"""
function transpose(a::Matrix{uwreal})
function Base.transpose(a::Matrix{uwreal})
res = similar(a)
n = size(a, 1)
if size(a,1) == 1
return reshape(a, :,1)
elseif size(a,2) == 1
return reshape(a, 1,:)
end
for i in 1:n-1
for j in i+1:n
temp = a[i,j]
......@@ -705,7 +712,7 @@ function transpose(a::Matrix{uwreal})
res[n,n] = a[n,n]
return res
end
function transpose(vec::Vector{uwreal})
function Base.transpose(vec::Vector{uwreal})
res = deepcopy(vec)
return reshape(res,1,:)
end
......@@ -741,25 +748,37 @@ function idty(n::Int64)
return res
end
function make_positive_def(A::Matrix)
B = 0.5 * (A + A')
U, S, V = svd(B)
H = V * Diagonal(S) * V'
A_hat = 0.5 * (B + H)
A_hat = 0.5 * ( A_hat + A_hat')
k = 0
while !isposdef(A_hat)
mineig = minimum(eigvals(A_hat))
eps = 2.220446049250313e-16
A_hat = A_hat + (-mineig*k^2 .+ eps*Matrix(I, size(A)))
k+=1
end
return A_hat
function make_positive_def(A::Matrix; eps::Float64=10^(-14))
vals, vecs = eigen(Symmetric(A))
idx = findall(x-> x<0.0, vals)
vals[idx] .= eps
return Symmetric(vecs * Diagonal(vals) * vecs')
#B = 0.5 * (A + A')
#U, S, V = svd(B)
#H = V * Diagonal(S) * V'
#A_hat = 0.5 * (B + H)
#A_hat = 0.5 * ( A_hat + A_hat')
#k = 0
#while !isposdef(A_hat)
# mineig = minimum(eigvals(A_hat))
# eps = 2.220446049250313e-16
# A_hat = A_hat + (-mineig*k^2 .+ eps*Matrix(I, size(A)))
# k+=1
#end
#return A_hat
end
function invert_covar_matrix(A::Matrix)
function invert_covar_matrix(A::Matrix; eps::Float64=10^(-9))
F = svd(A)
cov_inv = F.V * Diagonal(1 ./F.S) * F.U'
s_diag = F.S
for i in 1:length(s_diag)
if s_diag[i] < eps
s_diag[i] = 0.0
else
s_diag[i] = 1 / s_diag[i]
end
end
cov_inv = F.V * Diagonal(s_diag) * F.U'
return cov_inv
end
......@@ -769,7 +788,80 @@ function more_penrose_inv(A::Matrix)
end
########################
# OPERATOR OVERLOADING
########################
function Base.:*(x::uwreal, y::Array{Any})
N = size(y, 1)
return fill(x, N) .* y
end
Base.:*(x::Array{Any}, y::uwreal) = Base.:*(y,x)
function Base.:*(x::uwreal, y::Array{Float64})
N = size(y, 1)
return fill(x, N) .* y
end
Base.:*(x::Array{Float64}, y::uwreal) = Base.:*(y,x)
function Base.:*(x::uwreal, y::Array{uwreal})
N = size(y, 1)
return fill(x, N) .* y
end
Base.:*(x::Array{uwreal}, y::uwreal) = Base.:*(y,x)
function Base.:+(x::uwreal, y::Vector{uwreal})
N = size(y, 1)
return fill(x, N) .+ y
end
function Base.:+(x::Float64, y::Vector{Float64})
N = size(y, 1)
return fill(x, N) .+ y
end
function Base.:+(x::Float64, y::Vector{uwreal})
N = size(y, 1)
return fill(x, N) .+ y
end
function Base.:-(x::Float64, y::Vector{Any})
N = size(y, 1)
return fill(x, N) .- y
end
function Base.:-(x::Float64, y::Vector{Float64})
N = size(y, 1)
return fill(x, N) .- y
end
function Base.:-(x::Float64, y::Vector{uwreal})
N = size(y, 1)
return fill(x, N) .- y
end
function Base.length(uw::uwreal)
return length(value(uw))
end
function Base.iterate(uw::uwreal)
return iterate(uw, 1)
end
function Base.iterate(uw::uwreal, state::Int64)
if state > length(uw)
return nothing
else
return uw[state], state +1
end
end
function Base.iterate(uw::Vector{uwreal})
return iterate(uw, 1)
end
function Base.iterate(uw::Vector{uwreal}, state::Int64)
if state > length(uw)
return nothing
else
return uw[state], state +1
end
end
function Base.getindex(uw::uwreal, ii::Int64)
idx = getindex(value(uw), ii)
return uw # uwreal([getindex(value(uw), kwargs...), err(uw)], " ")
end
function Base.abs2(uw::uwreal)
return (uw^2)^0.5
end
"""
Base.:*(x::uwreal, y::Matrix{uwreal})
......
src/juobs_obs.jl
View file @ 92edc521
This diff is collapsed.
src/juobs_reader.jl
View file @ 92edc521
......@@ -330,21 +330,130 @@ function read_rw(path::String; v::String="1.2")
return r_data
end
@doc raw"""
read_rw_openQCD2(path::String; print_info::Bool=false)
This function reads the reweighting factors generated with openQCD version 2.#.
The flag print_info if set to true print additional information for debugging
"""
function read_rw_openQCD2(path::String; print_info::Bool=false)
data = open(path, "r")
nrw = read(data, Int32)
nrw = Int32(nrw / 2)
nfct = Array{Int32}(undef, nrw)
read!(data, nfct)
nsrc = Array{Int32}(undef, nrw)
read!(data, nsrc)
null = read(data, Int32)
if null !== Int32(0)
error("In openQCD 2.0 this Int32 should be a zero.")
end
data_array = Array{Array{Float64}}(undef, nrw)
[data_array[k] = Array{Float64}(undef, 0) for k in 1:nrw]
vcfg = Vector{Int32}(undef, 0)
while !eof(data)
push!(vcfg, read(data, Int32))
if print_info
println("\n ######## cnfg: ", vcfg[end])
end
for k in 1:nrw
read_array_rwf_dat_openQCD2(data)
tmp_rw, n = read_array_rwf_dat_openQCD2(data)
tmp_nfct=1.0
for j in 1:n[1]
tmp_nfct *= mean((exp.(.-tmp_rw[j])))
end
push!(data_array[k], tmp_nfct)
end
end
return permutedims(hcat(data_array...), (2,1))
end
function read_array_rwf_dat_openQCD2(data::IOStream; print_info::Bool=false)
d = read(data, Int32)
n = Array{Int32}(undef, d)
read!(data, n)
size = read(data, Int32)
m = prod(n)
if print_info
println("d: ", d)
println("n: ", n)
println("size: ", size)
println("m: ", m)
end
if size == 4
types = Int32
elseif size == 8
types = Float64
elseif size == 16
types = Float64x2
else
error("No type with size=$(size) supported")
end
tmp_data = Array{types}(undef, m)
read!(data, tmp_data)
res = parse_array_openQCD2(d, n, tmp_data, quadprec=true)
return res, n
end
function parse_array_openQCD2(d, n, dat; quadprec=true)
if d != 2
error("dat must be a two-dimensional array")
end
res = Vector{Vector{Float64}}(undef, 0)
for k in range(1,n[1])
tmp = dat[(k-1)*n[2]+1:k*n[2]]
if quadprec
tmp2 = Vector{Float64}(undef, 0)
for j in range(start=1,step=2,stop=length(tmp))
push!(tmp2, tmp[j])
end
push!(res, tmp2)
else
push!(res, tmp)
end
end
return res
end
@doc raw"""
read_ms1(path::String; v::String="1.2")
Reads openQCD ms1 dat files at a given path. This method returns a matrix `W[irw, icfg]` that contains the reweighting factors, where
`irw` is the `rwf` 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.
The function is compatible with the output files of openQCD v=1.2, 1.4, 1.6 and 2.0. Version can be specified as argument.
Examples:
```@example
read_ms1(path)
read_ms1(path, v="1.4")
read_ms1(path, v="1.6")
read_ms1(path, v="2.0")
```
"""
function read_ms1(path::String; v::String="1.2")
if v == "2.0"
return read_rw_openQCD2(path)
end
r_data = read_rw(path, v=v)
nrw = length(r_data)
ncnfg = size(r_data[1])[3]
......@@ -417,6 +526,8 @@ function read_ms(path::String; id::Union{String, Nothing}=nothing, dtr::Int64=1
ntr = Int32((fsize - 3*4 - 8) / datsize)
if mod(ntr, dtr) != 0
println("ntr = ", ntr)
println("dtr = ", dtr)
error("ntr / dtr must be exact")
end
......@@ -573,7 +684,11 @@ function concat_data!(data1::Vector{Vector{CData}}, data2::Vector{Vector{CData}}
data1[k][r].vcfg = vcat(data1[k][r].vcfg, data2[k][r].vcfg)
data1[k][r].re_data = vcat(data1[k][r].re_data, data2[k][r].re_data)
data1[k][r].im_data = vcat(data1[k][r].im_data, data2[k][r].im_data)
idx = sortperm(data1[k][r].vcfg)
data1[k][r].vcfg = data1[k][r].vcfg[idx]
data1[k][r].re_data = data1[k][r].re_data[idx, :]
data1[k][r].im_data = data1[k][r].im_data[idx, :]
end
end
return nothing
end
\ No newline at end of file
end
src/juobs_tools.jl
View file @ 92edc521
This diff is collapsed.
src/juobs_types.jl
View file @ 92edc521
......@@ -182,7 +182,7 @@ mutable struct Corr
theta2 = h[1].theta2
return new(a, kappa, mu, gamma, y0, theta1, theta2)
end
Corr(o::Vector{uwreal}, k::Vector{Float64}, m::Vector{Float64}, g::Vector{String}, y::Int64) = new(o, k, m, g, y)
Corr(o::Vector{uwreal}, k::Vector{Float64}, m::Vector{Float64}, g::Vector{String}, y::Int64, th1::Vector{Float64}, th2::Vector{Float64} ) = new(o, k, m, g, y, th1, th2)
end
mutable struct YData
......
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