v1.1

.gitignore

@@ -1,2 +1,9 @@
+# Python Caches
+*.pyc
+*__pycache__*/
+
+# Folders to ignore
+backgroundProfiles/
+tmp/
 results/
-parameters/old
+snSimulations/

.vscode/settings.json

@@ -4,12 +4,14 @@
     ],
     "cSpell.ignoreWords": [
         "Abbar",
+        "Athar",
         "DISTDIAG",
         "Emod",
         "Keil",
         "LSODA",
         "Termb",
         "Valeig",
+        "Xsdat",
         "cdist",
         "ebar",
         "figsize",

CHANGELOG

@@ -0,0 +1,13 @@
+# v1.1
+- Updated gitignore.
+- Converted `plotgraphsScript.sh` to python script (`plotGraphsAfterSimulation.py`). Remove `plotgraphsScript.sh`.
+- Added scripts;
+  1. SN post baryon density generator script from preSN file with added shockwave (`create_SN_tXsdat.py`).
+  2. Run script for random `ri_km` and `magneticField_polynomialDecayDistance` (`run_random_ri_magPolDecDist.py`).
+- Added `holdIntermediateData` option to technical parameters `technicalParameters.dat`.
+  - Added new functions without holding intermediate data `RHS.py`.
+  - Adopted `diffSolvers.py` for new `holdIntermediateData` variable.
+- Fixed in matter hamiltonian (wrong assignment of Ye and nb when reading data from a file.)
+- Minor changes in `plotgraphs.py`.
+- Add function to copy background profile to results folder (`writeFiles.py`, `collnuPy.py`).
+- Change all "STATUS" strings/variables to "INFO" in all code.

LICENSE

@@ -300,7 +300,7 @@ or household purposes, or (2) anything designed or sold for incorporation
 into a dwelling.  In determining whether a product is a consumer product,
 doubtful cases shall be resolved in favor of coverage.  For a particular
 product received by a particular user, "normally used" refers to a
-typical or common use of that class of product, regardless of the status
+typical or common use of that class of product, regardless of the INFO
 of the particular user or of the way in which the particular user
 actually uses, or expects or is expected to use, the product.  A product
 is a consumer product regardless of whether the product has substantial

collNuPy.py

@@ -33,7 +33,7 @@
 # ============================
 # Colors For Printing
 class tLog:
-    STATUS  = '\033[94m'+'[STATUS]    '+'\033[0m'
+    INFO  = '\033[94m'+'[INFO]    '+'\033[0m'
     OK      = '\033[92m'+'[OK]        '+'\033[0m'
     WARNING = '\033[93m'+'[WARNING]   '+'\033[0m'
     ERROR   = '\033[91m'+'[ERROR]     '+'\033[0m'
@@ -51,7 +51,7 @@ class tLog:
         osCommand.makedirs(RESULTS_DIR)
         print(tLog.OK+"Results Folder Created.")
     else:
-        print(tLog.STATUS+"Results Folder Already Exists.")
+        print(tLog.INFO+"Results Folder Already Exists.")
     # ============================
 
     # ============================
@@ -95,14 +95,14 @@ class tLog:
 
     # ============================
     # Save final human readable data
-    # TODO: Comment out print after wrote the functions
+    # TODO: Comment out print after you wrote the functions
     if init.technicalParametersDic['output_humanReadable']:
         DATA_FOLDER_TXT= RESULTS_SIMULATION_DIR+ 'data/txt/'
         if not osCommand.path.exists(DATA_FOLDER_TXT):
             osCommand.makedirs(DATA_FOLDER_TXT)
             print(tLog.OK+"TXT Data Folder Created.")
         else:
-            print(tLog.STATUS+"TXT Data Folder Already Exists.")
+            print(tLog.INFO+"TXT Data Folder Already Exists.")
         # ============================
         # rhoFlavAll.txt
         write2file.rhoFlavAll_txt(init,DATA_FOLDER_TXT+'rhoFlavAll.txt', rhoFlavAll)
@@ -121,6 +121,11 @@ class tLog:
             #print(tLog.OK+"Saved: eigVal_eigVec.txt.")
     # ============================
 
+    # ============================
+    # Copy background profile file(s)
+    write2file.saveBackgroundProfiles(init, COLLECTIVE_NU_OSC_DIR+'backgroundProfiles/', DATA_FOLDER_NPZ)
+    # ============================
+
     # ============================
     # Save final plots
     if init.technicalParametersDic['plotGraphs']:
@@ -142,6 +147,6 @@ class tLog:
     osCommand.system('find . | grep -E "(__pycache__|.pyc|.pyo$)" | xargs rm -rf')
     print(tLog.OK+"Unused Files and Folders Removed.")
     #! ============================
-    print(tLog.STATUS+'[FINISHED] =====> simulation'+str(simNum)+' <===== [FINISHED]\n')
+    print(tLog.INFO+'[FINISHED] =====> simulation'+str(simNum)+' <===== [FINISHED]\n')
     exit()
 # ============================

modules/RHS.py

@@ -12,7 +12,7 @@
 # ============================
 # Colors For Printing
 class tLog:
-    STATUS  = '\033[94m'+'[STATUS]    '+'\033[0m'
+    INFO  = '\033[94m'+'[INFO]    '+'\033[0m'
     OK      = '\033[92m'+'[OK]        '+'\033[0m'
     WARNING = '\033[93m'+'[WARNING]   '+'\033[0m'
     ERROR   = '\033[91m'+'[ERROR]     '+'\033[0m'
@@ -22,6 +22,20 @@ class tLog:
 # ============================
 # RHS For Neutrinos f(r,rho) !!Only LSODA!!
 # Two Flavor
+def rhs2Flav_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian(rhoAll, dist).totalHam2Flav_km_1()
+    # rhoAll must be in the form of [2, energyMod, totFlav*2, totFlav*2]
+
+    # Total Hamiltionian (totHam) [2, energyMod, totFlav, totFlav]
+    # For neutrinos     -> totHam[0]
+    # For antineutrinos -> totHam[1]
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+    return np.array([(-1j)* ((totHamAP[0] @ rhoAll[0])- (rhoAll[0] @ totHamAP[0]))\
+        , (-1j)*((totHamAP[1] @ rhoAll[1])- (rhoAll[1] @ totHamAP[1]))]).flatten()
 def rhs2Flav(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -38,10 +52,10 @@ def rhs2Flav(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================
@@ -58,6 +72,20 @@ def rhs2Flav(rhoAll, dist):
     return np.array([(-1j)* ((totHamAP[0] @ rhoAll[0])- (rhoAll[0] @ totHamAP[0]))\
         , (-1j)*((totHamAP[1] @ rhoAll[1])- (rhoAll[1] @ totHamAP[1]))]).flatten()
 # Three Flavor
+def rhs3Flav_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian(rhoAll, dist).totalHam3Flav_km_1()
+    # rhoAll must be in the form of [2, energyMod, totFlav*2, totFlav*2]
+
+    # Total Hamiltionian (totHam) [2, energyMod, totFlav, totFlav]
+    # For neutrinos     -> totHam[0]
+    # For antineutrinos -> totHam[1]
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+    return np.array([(-1j)* ((totHamAP[0] @ rhoAll[0])- (rhoAll[0] @ totHamAP[0]))\
+        , (-1j)*((totHamAP[1] @ rhoAll[1])- (rhoAll[1] @ totHamAP[1]))]).flatten()
 def rhs3Flav(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -74,10 +102,10 @@ def rhs3Flav(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================
@@ -94,6 +122,20 @@ def rhs3Flav(rhoAll, dist):
     return np.array([(-1j)* ((totHamAP[0] @ rhoAll[0])- (rhoAll[0] @ totHamAP[0]))\
         , (-1j)*((totHamAP[1] @ rhoAll[1])- (rhoAll[1] @ totHamAP[1]))]).flatten()
 # Four Flavor
+def rhs4Flav_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian(rhoAll, dist).totalHam4Flav_km_1()
+    # rhoAll must be in the form of [2, energyMod, totFlav*2, totFlav*2]
+
+    # Total Hamiltionian (totHam) [2, energyMod, totFlav, totFlav]
+    # For neutrinos     -> totHam[0]
+    # For antineutrinos -> totHam[1]
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+    return np.array([(-1j)* ((totHamAP[0] @ rhoAll[0])- (rhoAll[0] @ totHamAP[0]))\
+        , (-1j)*((totHamAP[1] @ rhoAll[1])- (rhoAll[1] @ totHamAP[1]))]).flatten()
 def rhs4Flav(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -110,10 +152,10 @@ def rhs4Flav(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================
@@ -134,6 +176,20 @@ def rhs4Flav(rhoAll, dist):
 # ============================
 # RHS For Neutrinos f(r,rho) !!Only LSODA!!
 # Two Flavor
+def rhs2Flav_bigRho_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian_BigRho(rhoAll, dist).totalHam2Flav_km_1()
+    # rhoAll must be in the form of [energyMod, totFlav*2, totFlav*2]
+    # Total Hamiltionian (totHam) [energyMod,totFlav*2,totFlav*2]
+    # totHam[N,0:totFlav,0:totFlav] => Neutrinos
+    # totHam[N,totFlav:totFlav*2,totFlav:totFlav*2] => Anti-Neutrinos
+    # totHam[N,0:totFlav,totFlav:totFlav*2] => Neutrino to Anti-neutrino
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+
+    return ((-1j)* ((totHamAP @ rhoAll)- (rhoAll @ totHamAP))).flatten()
 def rhs2Flav_bigRho(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -150,10 +206,10 @@ def rhs2Flav_bigRho(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================
@@ -170,6 +226,20 @@ def rhs2Flav_bigRho(rhoAll, dist):
 
     return ((-1j)* ((totHamAP @ rhoAll)- (rhoAll @ totHamAP))).flatten()
 # Three Flavor
+def rhs3Flav_bigRho_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian_BigRho(rhoAll, dist).totalHam3Flav_km_1()
+    # rhoAll must be in the form of [energyMod, totFlav*2, totFlav*2]
+    # Total Hamiltionian (totHam) [energyMod,totFlav*2,totFlav*2]
+    # totHam[N,0:totFlav,0:totFlav] => Neutrinos
+    # totHam[N,totFlav:totFlav*2,totFlav:totFlav*2] => Anti-Neutrinos
+    # totHam[N,0:totFlav,totFlav:totFlav*2] => Neutrino to Anti-neutrino
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+
+    return ((-1j)* ((totHamAP @ rhoAll)- (rhoAll @ totHamAP))).flatten()
 def rhs3Flav_bigRho(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -186,10 +256,10 @@ def rhs3Flav_bigRho(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================
@@ -206,6 +276,20 @@ def rhs3Flav_bigRho(rhoAll, dist):
 
     return ((-1j)* ((totHamAP @ rhoAll)- (rhoAll @ totHamAP))).flatten()
 # Four Flavor
+def rhs4Flav_bigRho_noInterData(rhoAll, dist):
+    # ============================
+    # Define the RHS
+    totHamAP = hamil.hamiltonian_BigRho(rhoAll, dist).totalHam4Flav_km_1()
+    # rhoAll must be in the form of [energyMod, totFlav*2, totFlav*2]
+    # Total Hamiltionian (totHam) [energyMod,totFlav*2,totFlav*2]
+    # totHam[N,0:totFlav,0:totFlav] => Neutrinos
+    # totHam[N,totFlav:totFlav*2,totFlav:totFlav*2] => Anti-Neutrinos
+    # totHam[N,0:totFlav,totFlav:totFlav*2] => Neutrino to Anti-neutrino
+
+    # Note: 3d array + 2d array gives a result that add all 2d array with each element of 3d array
+    # Take Commutator of density and Hamiltonian for each energy
+
+    return ((-1j)* ((totHamAP @ rhoAll)- (rhoAll @ totHamAP))).flatten()
 def rhs4Flav_bigRho(rhoAll, dist):
     # ============================
     # Show intermediate distance and hold the values
@@ -222,10 +306,10 @@ def rhs4Flav_bigRho(rhoAll, dist):
         # To show current time
         currentTimeDate = datetime.datetime.now()
         fileObject = open('distanceAndTime.log','a+')
-        # Do not color the [STATUS]
+        # Do not color the [INFO]
         print('Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"), file=fileObject)
         fileObject.close()
-        print(tLog.STATUS+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
+        print(tLog.INFO+'Current distance is %.7f' % dist, 'km and time :', currentTimeDate.strftime("%Y-%m-%d %H:%M:%S"))
     # ============================
 
     # ============================