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juobs
Commit a89edbca authored by Antonino D'Anna's avatar Antonino D'Anna Committed by Alessandro
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md_val for new version 

Julien's most updated code has all valence derivatives with the sign changed, so md_val needs to flip the sign. Also, the reader does not write "_d1, _d2" in the derivatives anymore for the new data files, so md_val does not look for "_d1, _d2". You need to select by hand which correlators are your valence derivatives, looking at the log file e.g.
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Manifest.toml
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Project.toml
View file @ a89edbca
......@@ -6,6 +6,7 @@ version = "0.1.0"
[deps]
ADerrors = "5e92007d-7bf1-471c-8ceb-4591b8b567a9"
BDIO = "375f315e-f2c4-11e9-2ef9-134f02f79e27"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
LsqFit = "2fda8390-95c7-5789-9bda-21331edee243"
......
constants/juobs_const.jl
View file @ a89edbca
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]
......@@ -17,31 +17,52 @@ 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
......@@ -49,10 +70,11 @@ for i = 1:7
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
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
end
const ZM = cobs(ZM_data, C1, "ZM values")
......@@ -63,12 +85,93 @@ 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]
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]
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
constants/path_csv.jl 0 → 100644
View file @ a89edbca
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src/juobs.jl
View file @ a89edbca
module juobs
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, Optim
using ADerrors, PyPlot, LaTeXStrings, LinearAlgebra, LsqFit, Optim, ForwardDiff
using Base: Float64
import Statistics: mean
......@@ -8,10 +8,14 @@ include("juobs_linalg.jl")
include("juobs_reader.jl")
include("juobs_tools.jl")
include("juobs_obs.jl")
include("../constants/juobs_const.jl")
include("../constants/path_csv.jl")
export read_mesons, read_mesons_correction, read_ms1, read_ms, read_md, truncate_data!
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, 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 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, fve, model_av, fit_alg
export meff, mpcac, dec_const, 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
src/juobs_linalg.jl
View file @ a89edbca
......@@ -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
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src/juobs_reader.jl
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src/juobs_tools.jl
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src/juobs_types.jl
View file @ a89edbca
......@@ -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
......@@ -193,6 +193,42 @@ mutable struct YData
YData(a, b, c, d) = new(a, b, c, d)
end
@doc raw"""
EnsInfo(ens_id::String, info::Vector{Any})
Examples:
```@example
id = "H101"
ens = EnsInfo(id, ens_db[id])
```
"""
mutable struct EnsInfo
id::String
L::Int64
T::Int64
beta::Float64
ca::Float64
dtr::Int64
vrw::Union{String, Vector{String}}
cnfg::Vector{Int64}
function EnsInfo(ens_id::String, info::Vector{Any})
id = ens_id
L = info[1]
T = info[2]
beta = info[3]
dtr = info[4]
vrw = info[5]
cnfg = info[6]
p0 = 9.2056
p1 = -13.9847
g2 = 6 ./ beta
ca = - 0.006033 .* g2 .*( 1 .+exp.(p0 .+ p1./g2))
return new(id, L, T, beta, ca, dtr, vrw, cnfg)
end
end
function Base.show(io::IO, a::GHeader)
print(io, "ncorr = ", a.ncorr, "\t")
print(io, "nnoise = ", a.nnoise, "\t")
......
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