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Commit d6bd07c8 authored by Alessandro 's avatar Alessandro
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corr_obs_TSM now supports different statistics between sloppy and correction... 

corr_obs_TSM now supports different statistics between sloppy and correction without neglecting the correlation. Extra flags idm_corr, idm_sl, nms have been added to allow this feature.
Documentation added
parent 85034d61
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Showing with 367 additions and 116 deletions
constants/juobs_const.jl
View file @ d6bd07c8
......@@ -23,14 +23,22 @@ 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
#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
## 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)
## 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)
......@@ -40,7 +48,7 @@ const C4 = zeros(7, 7)
const C5 = zeros(5, 5)
const C6 = zeros(5, 5)
const C7 = zeros(5, 5)
const C8 = zeros(5, 5)
for i = 1:7
C4[i, i] = M_error[i] ^ 2
if i<=5
......@@ -48,7 +56,8 @@ for i = 1:7
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
C7[i, i] = ZV_err[i] ^ 2
C8[i, i] = RM_err[i] ^2
if i <= 4
C3[i, i] = t0_error[i] ^ 2
end
......@@ -64,11 +73,13 @@ 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 RM = cobs(RM_data, C8, "rm")
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_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]
rm(beta::Float64) = RM[b_values .== beta][1]
\ No newline at end of file
src/juobs.jl
View file @ d6bd07c8
......@@ -12,6 +12,6 @@ include("juobs_obs.jl")
export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_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
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 @ d6bd07c8
......@@ -180,7 +180,7 @@ 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]
......@@ -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)
......@@ -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)
......@@ -741,25 +742,37 @@ 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
......
src/juobs_obs.jl
View file @ d6bd07c8
......@@ -23,9 +23,9 @@ function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bo
if pl
isnothing(wpm) ? uwerr(mass) : uwerr(mass, wpm)
x = 1:length(aux)
y = value.(aux)
y = abs.(value.(aux))
dy = err.(aux)
v = value(mass)
v = abs(value(mass))
e = err(mass)
figure()
......@@ -33,7 +33,9 @@ function meff(corr::Vector{uwreal}, plat::Vector{Int64}; pl::Bool=true, data::Bo
errorbar(x, y, dy, fmt="x", color="black")
ylabel(L"$m_\mathrm{eff}$")
xlabel(L"$x_0$")
ylim(v-100*e, v+100*e)
ylim(v-30*e, v+30*e)
# ylim(0.05, 0.075)
#xlim(64,length(y))
if !isnothing(kappa)
title(string(L"$\kappa_1 = $", kappa[1], L" $\kappa_2 = $", kappa[2]))
......@@ -92,10 +94,12 @@ function mpcac(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}; ca:
corr_a0p = -a0p[1:end]
corr_pp = pp[1:end]
der_a0p = (corr_a0p[3:end] .- corr_a0p[1:end-2]) / 2
if ca != 0.0
der_a0p = (corr_a0p[3:end] .- corr_a0p[1:end-2]) / 2
der2_pp = (corr_pp[1:end-4] - 2*corr_pp[3:end-2] + corr_pp[5:end])/4
der_a0p = der_a0p[2:end-1] + ca * der2_pp
else
der_a0p = (corr_a0p[4:end-1] .- corr_a0p[2:end-3]) / 2
end
#der_a0p = (corr_a0p[3:end] .- corr_a0p[1:end-2]) / 2
......@@ -132,7 +136,7 @@ function mpcac(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}; ca:
if !data
return mass
else
return (mass, aux)
return (mass, aux)
end
end
......@@ -199,16 +203,17 @@ f_ratio = dec_const(corr_a0pL, corr_a0pR, corr_ppL, corr_ppR, [50, 60], m, pl=tr
function dec_const(a0p::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, y0::Int64; ca::Float64=0.0, pl::Bool=true, data::Bool=false,
kappa::Union{Vector{Float64}, Nothing}=nothing, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
corr_a0p = -a0p
corr_pp = pp
T = length(corr_a0p)
corr_a0p = -a0p[2:end-1]
corr_pp = pp[2:end-1]
if ca != 0.0
der_pp = (corr_pp[3:end] - corr_pp[1:end-2]) / 2
corr_a0p = corr_a0p[2:end-1] + ca * der_pp
aux = exp.((collect(1:T-2) .- (T-1)/2) .* [m for k = 1:T-2])
T = length(corr_a0p)
aux = exp.((collect(1:T) .- (T)/2) .* [m for k = 1:T])
else
aux = exp.((collect(0:T-1) .- T/2) .* [m for k = 1:T])
T = length(corr_a0p)
aux = exp.((collect(1:T) .- T/2) .* [m for k = 1:T])
end
R = corr_a0p .* aux ./ [((corr_pp[T-y0])^2)^(1/4) for k = 1:length(corr_a0p)]
......@@ -369,7 +374,68 @@ end
function dec_const(vv::Corr, plat::Vector{Int64}, m::uwreal; pl::Bool=true, data::Bool=false,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
return dec_const(vv.obs, plat, m, vv.y0+1, kappa=vv.kappa, pl=pl, data=data, wpm=wpm)
return dec_const(vv.obs, plat, m, vv.y0, kappa=vv.kappa, pl=pl, data=data, wpm=wpm)
end
# this can be used also for pseudoscalar decay constants with wilson fermions
function dec_const_w(vv::Vector{uwreal}, pp::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, y0::Int64; ca::Float64=0.0, pl::Bool=true, data::Bool=false,
kappa::Union{Vector{Float64}, Nothing}=nothing, wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
corr_vv = vv[2:end-1]
corr_pp = pp[2:end-1]
T = length(corr_vv)
if ca != 0.0
der_pp = (corr_pp[3:end] - corr_pp[1:end-2]) / 2
corr_vv = corr_vv[2:end-1] + ca* der_pp
aux = exp.((collect(1:T-2) .- y0 ) .* fill(m, T-2))
else
#corr_vv = corr_vv[2:end-1]
aux = exp.((collect(1:T) .- y0 ) .* fill(m, T))
end
R = (aux .* corr_vv)
R_av = plat_av(R, plat, wpm)
f = sqrt(2 / m) * sqrt(R_av)
if pl
R .*= sqrt.(2 ./ [m for i in 1:length(R)])
uwerr.(R)
R_av *= sqrt(2/m)
isnothing(wpm) ? uwerr(R_av) : uwerr(R_av, wpm)
isnothing(wpm) ? uwerr(f) : uwerr(f, wpm)
x = 1:length(R)
y = value.(R)
dy = err.(R)
v = value(R_av)
e = err(R_av)
figure()
lbl = string(L"$af = $", sprint(show, f))
fill_between(plat[1]:plat[2], v-e, v+e, color="green", alpha=0.75, label=L"$R$")
errorbar(x, y, dy, fmt="x", color="black", label=lbl)
legend()
xlim(y0, y0 +plat[2] )
ylim(v-10*e, v+10*e)
ylabel(L"$af_{vec}$")
#ylabel(L"$R_\mathrm{av}$")
xlabel(L"$x_0$")
#title(L"$f_{B^*}$")
if !isnothing(kappa)
title(string( L"$\kappa_1 = $", kappa[1], L" $\kappa_2 = $", kappa[2]))
end
display(gcf())
#t = "ps_decay_$(kappa[1])_$(kappa[2]).pdf"
#savefig(joinpath("/Users/ale/Il mio Drive/phd/secondment/3pf test/analysis/plots",t))
end
if !data
return f
else
return f, R
end
end
function dec_const_w(vv::Corr, pp::Corr, plat::Vector{Int64}, m::uwreal; ca::Float64=0.0, pl::Bool=true, data::Bool=false,
wpm::Union{Dict{Int64,Vector{Float64}},Dict{String,Vector{Float64}}, Nothing}=nothing)
return dec_const_w(vv.obs, pp.obs, plat, m, vv.y0, ca=ca, kappa=vv.mu, pl=pl, data=data, wpm=wpm)
end
@doc raw"""
......@@ -424,6 +490,8 @@ function dec_const_pcvc(corr::Vector{uwreal}, plat::Vector{Int64}, m::uwreal, mu
errorbar(1:length(R), value.(R), err.(R), fmt="x", color="black", label=lbl)
ylabel(L"$R$")
xlabel(L"$x_0$")
xlim(y0,y0+plat[2])
ylim(v-10*e, v+10*e)
legend()
title(string(L"$\mu_1 = $", mu[1], L" $\mu_2 = $", mu[2]))
display(gcf())
......@@ -612,6 +680,7 @@ function comp_t0(Y::YData, plat::Vector{Int64}; L::Int64, pl::Bool=false,
fill_between(collect(plat[1]:plat[2]), v[t_pl]+e[t_pl], v[t_pl]-e[t_pl], alpha=0.75, color="green")
ylabel(L"$t^2E(x0, t)$")
xlabel(L"$x_0/a$")
ylim(v[t_pl]-20*e[t_pl], v[t_pl]+20*e[t_pl])
title(string(L"$t/a^2 = $", t[nt0]))
display(gcf())
end
......
src/juobs_tools.jl
View file @ d6bd07c8
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