From d11d7528e591336e3cb5a3f8c47312c4f6d22a25 Mon Sep 17 00:00:00 2001
From: shivesh <s.p.mandalia@qmul.ac.uk>
Date: Wed, 28 Feb 2018 12:13:24 -0600
Subject: Initial Commit

---
 plot_llh/MinimalTools.py | 166 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 166 insertions(+)
 create mode 100644 plot_llh/MinimalTools.py

(limited to 'plot_llh/MinimalTools.py')

diff --git a/plot_llh/MinimalTools.py b/plot_llh/MinimalTools.py
new file mode 100644
index 0000000..4ae8360
--- /dev/null
+++ b/plot_llh/MinimalTools.py
@@ -0,0 +1,166 @@
+import numpy as np
+from PhysConst import PhysicsConstants
+
+def eigenvectors(M):
+        """ Calculates the eigenvectors and eigenvalues ordered by eigenvalue size
+
+        @type  M     : matrix
+        @param M     : matrix M
+
+        @rtype       : list
+        @return      : [eigenvalues list, eigenvector list]
+        """
+        D,V = np.linalg.eig(M)
+        DV = []
+        VT = V.T
+        for i,eigenvalue in enumerate(D):
+            DV.append([eigenvalue,VT[i]]) 
+
+        DV = sorted(DV,key = lambda x : x[0].real)#np.abs(x[0].real))
+
+        V2 = []
+        D2 = []
+        for e in DV:
+            V2.append(e[1])
+            D2.append(e[0])
+        return D2,V2
+
+# General Rotation Matrix
+def R(i,j,cp,param):
+        """ Rotation Matrix
+        Calculates the R_ij rotations. Also incorporates CP-phases when necesary.
+        @type   i       :   int
+        @param  i       :   i-column.
+        @type   j       :   int
+        @param  j       :   j-row.
+        @type   cp      :   int
+        @param  cp      :   if cp = 0 : no CP-phase. else CP-phase = CP_array[cp]
+
+        @rtype          :   numpy.array
+        @return         :   returns the R_ij rotation matrix.
+        """
+        # if cp = 0 -> no complex phase
+        # R_ij, i<j
+        if(j<i):
+            # no funny business
+            l = i
+            i = j
+            j = l
+
+        # rotation matrix generator
+        R = np.zeros([param.numneu,param.numneu],complex)
+        # diagonal terms
+        for k in np.arange(0,param.numneu,1):
+            if(k != i-1 and k != j-1):
+                R[k,k] = 1.0
+            else :
+                R[k,k] = param.c[i,j]
+        # non-diagonal terms
+        if(cp != 0):
+            sd = np.sin(param.dcp[cp])
+            cd = np.cos(param.dcp[cp])
+            faseCP = complex(cd,sd)
+        else:
+            faseCP = complex(1.0,0.0)
+
+        R[i-1,j-1] = param.s[i,j]*faseCP.conjugate()
+        R[j-1,i-1] = -param.s[i,j]*faseCP
+        return R
+
+def calcU(param):
+        """ Defining the mixing matrix parametrization.
+        @type   param   :   PhysicsConstants
+        @param  param   :   set of physical parameters to be used.
+
+        @rtype          :   None
+        @return         :   Sets mixing matrix.
+        """
+        if(param.numneu == 2):
+	        return self.R(1,2,0,param)
+        elif(param.numneu == 3):
+            return np.dot(R(2,3,0,param),np.dot(R(1,3,1,param),R(1,2,0,param)))
+        elif(param.numneu == 4):
+            return np.dot(R(3,4,0,param),np.dot(R(2,4,2,param),np.dot(R(1,4,0,param),np.dot(R(2,3,0,param),np.dot(R(1,3,1,param),R(1,2,0,param))))))
+        elif(param.numneu == 5):
+            return np.dot(R(4,5,0,param),np.dot(R(3,5,0,param),np.dot(R(2,5,0,param),np.dot(R(1,5,3,param),np.dot(R(3,4,0,param),np.dot(R(2,4,0,param),np.dot(R(1,4,2,param),np.dot(R(2,3,0,param),np.dot(R(1,3,1,param),R(1,2,0,param))))))))))
+        elif(param.numneu == 6):
+            # 3+3 twin-sterile-neutrino model
+            return np.dot(R(3,6,0,param),np.dot(R(2,5,0,param),np.dot(R(1,4,0,param),np.dot(R(2,3,0,param),np.dot(R(1,3,1,param),R(1,2,0,param))))))
+        else:
+            print "Sorry, too many neutrinos. Not yet implemented! =(."
+            quit()
+
+        # antineutrino case
+        if param.neutype == "antineutrino" :
+            return self.U.conjugate()
+
+
+
+def massM2(param):
+    """ Mass term in the neutrino mass basis.
+
+    @type   param   :   PhysicsConstants
+    @param  param   :   set of physical parameters to be used.
+
+    @rtype          :   numpy array
+    @return         :   mass matrix in mass basis.
+    """
+    M2 = np.zeros([param.numneu,param.numneu],complex)
+    for k in np.arange(1,param.numneu,1):
+        M2[k,k] = param.dmsq[k+1]
+    return M2
+
+def flavorM2(param):
+    """ Mass term in the neutrino flavor basis.
+
+    @type   param   :   PhysicsConstants
+    @param  param   :   set of physical parameters to be used.
+
+    @rtype          :   numpy array
+    @return         :   mass matrix in flavor basis.
+    """
+    U = calcU(param)
+    return np.dot(U,np.dot(massM2(param),U.conjugate().T))
+
+class LVP(PhysicsConstants):
+    def __init__(self):
+        super(LVP,self).__init__()
+        self.th12 = 0.0
+        self.th13 = 0.0
+        self.th23 = 0.0
+        self.delta1 = 0.0
+        self.deltaCP = 0.0
+        super(LVP,self).Refresh()
+
+        # LVS
+        self.LVS21 = 0.0	                #
+        self.LVS31 = 0.0                    #
+        self.LVS41 = 0.0                    #
+        self.LVS51 = 0.0                    #
+        self.LVS61 = 0.0                    #
+        # SQUARED MASS DIFFERENCE MATRIX
+        self.LVS = np.zeros([self.numneumax+2],float)
+        self.LVS[2] = self.LVS21
+        self.LVS[3] = self.LVS31
+        self.LVS[4] = self.LVS41
+        self.LVS[5] = self.LVS51
+        self.LVS[6] = self.LVS61
+
+    def Refresh(self):
+        super(LVP,self).Refresh()
+        LVS = self.LVS
+        LVS[2] = self.LVS21
+        LVS[3] = self.LVS31
+        LVS[4] = self.LVS41
+        LVS[5] = self.LVS51
+        LVS[6] = self.LVS61
+
+def DiagonalMatrixLV(param):
+    DD = np.zeros([param.numneu,param.numneu],complex)
+    for k in np.arange(1,param.numneu,1):
+        DD[k,k] = param.LVS[k+1]
+    return DD
+
+def LVTerm(LVparam):
+    U = calcU(LVparam)
+    return np.dot(U,np.dot(DiagonalMatrixLV(LVparam),U.conjugate().T))
-- 
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