refactor emcee scripts

1 files changed, 0 insertions, 390 deletions

diff --git a/plot_llh/PhysConst.py b/plot_llh/PhysConst.py
deleted file mode 100644
index 89a0be0..0000000
--- a/plot_llh/PhysConst.py
+++ /dev/null
@@ -1,390 +0,0 @@
-"""
-Author  : C.A. Arguelles
-Date    : 10/MAY/2011
-
-Contains Physics constants and global variables.
-
-Log :
-- Modified on 23/ABR/2012 by C.Arguelles
-    + Changed the definition of PhysicsConstants to
-    include an __init__ to separate the class global
-    properties from its instances.
-"""
-
-# python standard modules
-import numpy as np
-
-class PhysicsConstants(object):
-    
-    def __init__(self):
-        ## PHYSICS CONSTANTS
-        #===========================================================================
-        # NAME
-        #===========================================================================
-        
-        self.name = "STD"                    # Default values
-        self.linestyle = "solid"             # Default linestyle in plots
-        self.markerstyle = "*"               # Default marker style
-        self.colorstyle = "red"              # Default color style
-        self.savefilename = "output.dat"     # Default color style
-        
-        #===============================================================================
-        # ## MATH
-        #===============================================================================
-        self.PI=3.14159265		            # Pi
-        self.PIby2=1.5707963268	            # Pi/2
-        self.sqr2=1.4142135624	            # Sqrt[2]
-        self.ln2 = np.log(2.0)
-        
-        #===============================================================================
-        # ## EARTH 
-        #===============================================================================
-        self.EARTHRADIUS = 6371.0	        # [km] Earth radius
-        #===============================================================================
-        # ## SUN 
-        #===============================================================================
-        self.SUNRADIUS = 109*self.EARTHRADIUS     # [km] Sun radius 
-        
-        #===============================================================================
-        # # PHYSICAL CONSTANTS
-        #===============================================================================
-        self.GF = 1.16639e-23	            # [eV^-2] Fermi Constant 
-        self.Na = 6.0221415e+23 		        # [mol cm^-3] Avogadro Number
-        self.sw_sq = 0.2312                  # [dimensionless] sin(th_weinberg) ^2
-        self.G  = 6.67300e-11                # [m^3 kg^-1 s^-2]
-        self.alpha = 1.0/137.0               # [dimensionless] fine-structure constant 
-        
-        #===============================================================================
-        # ## UNIT CONVERSION FACTORS
-        #===============================================================================
-        # Energy
-        self.TeV = 1.0e12                    # [eV/TeV]
-        self.GeV = 1.0e9                     # [eV/GeV]
-        self.MeV = 1.0e6                     # [eV/MeV]
-        self.keV = 1.0e3                     # [eV/keV]
-        self.Joule = 1/1.60225e-19           # [eV/J]
-        # Mass
-        self.kg = 5.62e35                    # [eV/kg]
-        self.gr = 1e-3*self.kg               # [eV/g] 
-        # Time
-        self.sec = 1.523e15                  # [eV^-1/s]
-        self.hour = 3600.0*self.sec          # [eV^-1/h]
-        self.day = 24.0*self.hour            # [eV^-1/d]
-        self.year = 365.0*self.day           # [eV^-1/yr]
-        self.yearstosec = self.sec/self.year # [s/yr]
-        # Distance
-        self.meter = 5.076e6                 # [eV^-1/m]
-        self.cm = 1.0e-2*self.meter          # [eV^-1/cm]
-        self.km = 1.0e3*self.meter           # [eV^-1/km]
-        self.fermi = 1.0e-15*self.meter      # [eV^-1/fm]
-        self.angstrom = 1.0e-10*self.meter   # [eV^-1/A]
-        self.AU = 149.60e9*self.meter        # [eV^-1/AU]
-        self.parsec = 3.08568025e16*self.meter# [eV^-1/parsec]
-        # Integrated Luminocity # review
-        self.picobarn = 1.0e-36*self.cm**2   # [eV^-2/pb]
-        self.femtobarn = 1.0e-39*self.cm**2  # [eV^-2/fb]
-        # Presure
-        self.Pascal = self.Joule/self.meter**3 # [eV^4/Pa]
-        self.hPascal = 100.0*self.Pascal     # [eV^4/hPa]
-        self.atm = 101325.0*self.Pascal      # [eV^4/atm]
-        self.psi = 6893.0*self.Pascal        # [eV^4/psi]
-        # Temperature
-        self.kelvin = 1/1.1604505e4          # [eV/K]
-        # Angle
-        self.degree = self.PI/180.0          # [rad/degree]
-        # magnetic field
-        self.T = 0.000692445                 # [eV^2/T]
-        
-        # old notation
-        self.cm3toev3 = 7.68351405e-15       # cm^3-> ev^3
-        self.KmtoEv =5.0677288532e+9         # km -> eV
-        self.yearstosec = 31536.0e3          # years -> sec
-        
-        #===============================================================================
-        # ## NEUTRINO OSCILLATION PARAMETERS ##
-        #===============================================================================
-        
-        self.numneu = 3                      # number of neutrinos
-        self.numneumax = 6                   # maximum neutrino number
-        self.neutype = 'neutrino'
-        #neutype = 'antineutrino'
-        
-        # values updated according to 1209.3023 Table 1 FreeFluxes + RSBL
-        
-        # MIXING ANGLES
-       
-        self.th12 = 0.579639
-        self.th13 = 0.150098
-        self.th23 = self.PIby2/2.0
-        self.th14 = 0.0
-        self.th24 = 0.0
-        self.th34 = 0.0
-        self.th15 = 0.0
-        self.th25 = 0.0
-        self.th35 = 0.0
-        self.th45 = 0.0
-        self.th16 = 0.0
-        self.th26 = 0.0
-        self.th36 = 0.0
-        self.th46 = 0.0
-        self.th56 = 0.0
-        
-        # mixing angles matrix array
-        self.th = np.zeros([self.numneumax+1,self.numneumax+1],float)
-        self.th[1,2] = self.th12
-        self.th[1,3] = self.th13
-        self.th[2,3] = self.th23
-        self.th[1,4] = self.th14
-        self.th[2,4] = self.th24
-        self.th[3,4] = self.th34
-        self.th[1,5] = self.th15
-        self.th[2,5] = self.th25
-        self.th[3,5] = self.th35
-        self.th[4,5] = self.th45
-        self.th[1,6] = self.th16
-        self.th[2,6] = self.th26
-        self.th[3,6] = self.th36
-        self.th[4,6] = self.th46
-        self.th[5,6] = self.th56
-        
-        self.s12 = np.sin(self.th12)
-        self.c12 = np.cos(self.th12)
-        self.s13 = np.sin(self.th13)
-        self.c13 = np.cos(self.th13)
-        self.s23 = np.sin(self.th23)
-        self.c23 = np.cos(self.th23)
-        self.s14 = np.sin(self.th14)
-        self.c14 = np.cos(self.th14)
-        self.s24 = np.sin(self.th24)
-        self.c24 = np.cos(self.th24)
-        self.s34 = np.sin(self.th34)
-        self.c34 = np.cos(self.th34)
-        self.s15 = np.sin(self.th15)
-        self.c15 = np.cos(self.th15)
-        self.s25 = np.sin(self.th25)
-        self.c25 = np.cos(self.th25)
-        self.s35 = np.sin(self.th35)
-        self.c35 = np.cos(self.th35)
-        self.s45 = np.sin(self.th45)
-        self.c45 = np.cos(self.th45)
-        self.s16 = np.sin(self.th16)
-        self.c16 = np.cos(self.th16)
-        self.s26 = np.sin(self.th26)
-        self.c26 = np.cos(self.th26)
-        self.s36 = np.sin(self.th36)
-        self.c36 = np.cos(self.th36)
-        self.s46 = np.sin(self.th46)
-        self.c46 = np.cos(self.th46)
-        self.s56 = np.sin(self.th56)
-        self.c56 = np.cos(self.th56)    
-        
-        # cos(th_ij) matrix array
-        self.c = np.zeros([self.numneumax+1,self.numneumax+1],float)
-        self.c[1,2] = self.c12
-        self.c[1,3] = self.c13
-        self.c[1,4] = self.c14
-        self.c[2,3] = self.c23
-        self.c[2,4] = self.c24
-        self.c[3,4] = self.c34
-        self.c[1,5] = self.c15
-        self.c[2,5] = self.c25
-        self.c[3,5] = self.c35
-        self.c[4,5] = self.c45
-        self.c[1,6] = self.c16
-        self.c[2,6] = self.c26
-        self.c[3,6] = self.c36
-        self.c[4,6] = self.c46
-        self.c[5,6] = self.c56    
-        
-        # sin(th_ij) matrix array
-        self.s = np.zeros([self.numneumax+1,self.numneumax+1],float)
-        self.s[1,2] = self.s12
-        self.s[1,3] = self.s13
-        self.s[1,4] = self.s14
-        self.s[2,3] = self.s23
-        self.s[2,4] = self.s24
-        self.s[3,4] = self.s34
-        self.s[1,5] = self.s15
-        self.s[2,5] = self.s25
-        self.s[3,5] = self.s35
-        self.s[4,5] = self.s45
-        self.s[1,6] = self.s16
-        self.s[2,6] = self.s26
-        self.s[3,6] = self.s36
-        self.s[4,6] = self.s46
-        self.s[5,6] = self.s56    
-        
-        # CP PHASES
-        #self.delta21=3.3e-5
-        #self.delta32=3.1e-3
-        #self.delta31=self.delta32+self.delta21
-        #self.deltaCP=self.PIby2
-        
-        # CP Phases
-        self.deltaCP = 5.235987
-        self.delta1 = self.deltaCP
-        self.delta2 = 0.0
-        self.delta3 = 0.0
-        
-        # d-CP phases
-        self.dcp = np.zeros([self.numneumax-2+1],complex)
-        self.dcp[0] = 1.0
-        self.dcp[1] = self.delta1
-        self.dcp[2] = self.delta2
-        self.dcp[3] = self.delta3
-        
-        # SQUARED MASS DIFFERENCE
-        self.dm21sq = 7.50e-5	             # [eV^2]
-        self.dm31sq = 2.47e-3	             # [eV^2]
-        self.dm32sq = -2.43e-3               # [eV^2]
-        # STERILE 
-        self.dm41sq = 0.0                    # [eV^2]
-        self.dm51sq = 0.0                    # [eV^2]
-        self.dm61sq = 0.0                    # [eV^2]
-        # SQUARED MASS DIFFERENCE MATRIX
-        self.dmsq = np.zeros([self.numneumax+2],float)
-        self.dmsq[2] = self.dm21sq
-        self.dmsq[3] = self.dm31sq
-        self.dmsq[4] = self.dm41sq
-        self.dmsq[5] = self.dm51sq
-        self.dmsq[6] = self.dm61sq    
-        
-        self.dm2 = np.zeros([self.numneumax+1,self.numneumax+1],float)
-        self.dm2[1,2] = self.dm21sq
-        self.dm2[1,3] = self.dm31sq
-        self.dm2[2,3] = self.dm32sq
-        self.dm2[1,4] = self.dm41sq
-        self.dm2[1,5] = self.dm51sq
-        self.dm2[1,6] = self.dm61sq    
-        
-        # MIXING MATRIX
-        self.U = None
-        
-        #===============================================================================
-        # # PARTICLE MASSES
-        #===============================================================================
-        self.muon_mass = 0.10565 	     # [GeV]
-        self.neutron_mass = 0.939565         # [GeV]
-        self.proton_mass = 0.938272          # [GeV]
-        self.electron_mass = 0.510998910e-3  # [GeV]
-        
-        self.atomic_mass_unit = 1.660538e-24 # [g]
-        
-        ## names
-        self.electron = 0
-        self.muon = 1
-        self.tau = 2
-        self.sterile1 = 3
-        self.sterile2 = 4
-        self.sterile3 = 5
-    
-    #===============================================================================
-    # REFRESH
-    #===============================================================================
-    
-    def Refresh(self):
-        # Refresh angles
-        self.s12 = np.sin(self.th12)
-        self.c12 = np.cos(self.th12)
-        self.s13 = np.sin(self.th13)
-        self.c13 = np.cos(self.th13)
-        self.s23 = np.sin(self.th23)
-        self.c23 = np.cos(self.th23)
-        self.s14 = np.sin(self.th14)
-        self.c14 = np.cos(self.th14)
-        self.s24 = np.sin(self.th24)
-        self.c24 = np.cos(self.th24)
-        self.s34 = np.sin(self.th34)
-        self.c34 = np.cos(self.th34)
-        self.s15 = np.sin(self.th15)
-        self.c15 = np.cos(self.th15)
-        self.s25 = np.sin(self.th25)
-        self.c25 = np.cos(self.th25)
-        self.s35 = np.sin(self.th35)
-        self.c35 = np.cos(self.th35)
-        self.s45 = np.sin(self.th45)
-        self.c45 = np.cos(self.th45)
-        self.s16 = np.sin(self.th16)
-        self.c16 = np.cos(self.th16)
-        self.s26 = np.sin(self.th26)
-        self.c26 = np.cos(self.th26)
-        self.s36 = np.sin(self.th36)
-        self.c36 = np.cos(self.th36)
-        self.s46 = np.sin(self.th46)
-        self.c46 = np.cos(self.th46)
-        self.s56 = np.sin(self.th56)
-        self.c56 = np.cos(self.th56)                
-        
-        th = self.th
-        th[1,2] = self.th12
-        th[1,3] = self.th13
-        th[2,3] = self.th23
-        th[1,4] = self.th14
-        th[2,4] = self.th24
-        th[3,4] = self.th34
-        th[1,5] = self.th15
-        th[2,5] = self.th25
-        th[3,5] = self.th35
-        th[4,5] = self.th45
-        th[1,6] = self.th16
-        th[2,6] = self.th26
-        th[3,6] = self.th36
-        th[4,6] = self.th46
-        th[5,6] = self.th56        
-        # Refresh cos(th_ij)
-        c = self.c
-        c[1,2] = self.c12
-        c[1,3] = self.c13
-        c[1,4] = self.c14
-        c[2,3] = self.c23
-        c[2,4] = self.c24
-        c[3,4] = self.c34
-        c[1,5] = self.c15
-        c[2,5] = self.c25
-        c[3,5] = self.c35
-        c[4,5] = self.c45
-        c[1,6] = self.c16
-        c[2,6] = self.c26
-        c[3,6] = self.c36
-        c[4,6] = self.c46
-        c[5,6] = self.c56        
-        # Refresh sin(th_ij)
-        s = self.s
-        self.s[1,2] = self.s12
-        self.s[1,3] = self.s13
-        self.s[1,4] = self.s14
-        self.s[2,3] = self.s23
-        self.s[2,4] = self.s24
-        self.s[3,4] = self.s34
-        self.s[1,5] = self.s15
-        self.s[2,5] = self.s25
-        self.s[3,5] = self.s35
-        self.s[4,5] = self.s45
-        self.s[1,6] = self.s16
-        self.s[2,6] = self.s26
-        self.s[3,6] = self.s36
-        self.s[4,6] = self.s46
-        self.s[5,6] = self.s56                
-        # Refresh CP-Phases
-        dcp = self.dcp
-        dcp[0] = 1.0
-        dcp[1] = self.delta1
-        dcp[2] = self.delta2
-        dcp[3] = self.delta3
-        #dcp[4] = self.delta2        
-        # Refresh Square mass differences
-        dmsq = self.dmsq
-        dmsq[2] = self.dm21sq
-        dmsq[3] = self.dm31sq
-        dmsq[4] = self.dm41sq
-        dmsq[5] = self.dm51sq
-        dmsq[6] = self.dm61sq        
-        
-        dm2 = self.dm2
-        dm2[1,2] = self.dm21sq
-        dm2[1,3] = self.dm31sq
-        dm2[2,3] = self.dm32sq
-        dm2[1,4] = self.dm41sq
-        dm2[1,5] = self.dm51sq
-        dm2[1,6] = self.dm61sq
-