add scripts to apply neutrino oscillations to the atmospheric fluxes

This commit adds four scripts:

1. calculate-atmospheric-oscillations

This script uses an independent python package called nucraft to calculate the
neutrino oscillation probabilities for atmospheric neutrinos. These
probabilities are calculated as a function of energy and cosine of the zenith
angle and stored in text files.

2. apply-atmospheric-oscillations

This script combines the high energy 2D atmospheric neutrino flux from Barr and
the low energy 1D flux from Battistoni and then applies neutrino oscillations
to them. The results are then stored in new flux files that can be used with a
modified version of GENIE to simulate the oscillated atmospheric neutrino flux
from 10 MeV to 10 GeV.

3. plot-atmospheric-fluxes

This is a simple script to plot the atmospheric flux files produced by
apply-atmospheric-oscillations.

4. plot-atmospheric-oscillations

This is a simple script to plot the 2D neutrino oscillation probabilities.

1 files changed, 114 insertions, 0 deletions

diff --git a/utils/plot-atmospheric-oscillations b/utils/plot-atmospheric-oscillations
new file mode 100755
index 0000000..c24a776
--- /dev/null
+++ b/utils/plot-atmospheric-oscillations
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+"""
+Script to plot the probabilities for atmospheric neutrino oscillations. To run
+it:
+
+    $ ./plot-atmospheric-oscillations nue_osc_prob.txt
+"""
+from __future__ import print_function, division
+import numpy as np
+
+if __name__ == '__main__':
+    import argparse
+    from os.path import split, splitext
+
+    parser = argparse.ArgumentParser("script to plot atmospheric oscillations")
+    parser.add_argument("filenames", nargs='+', help="oscillation probability filenames")
+    parser.add_argument("--save", action="store_true", default=False, help="save plots")
+    args = parser.parse_args()
+
+    if args.save:
+        # default \textwidth for a fullpage article in Latex is 16.50764 cm.
+        # You can figure this out by compiling the following TeX document:
+        #
+        #    \documentclass{article}
+        #    \usepackage{fullpage}
+        #    \usepackage{layouts}
+        #    \begin{document}
+        #    textwidth in cm: \printinunitsof{cm}\prntlen{\textwidth}
+        #    \end{document}
+
+        width = 16.50764
+        width /= 2.54 # cm -> inches
+        # According to this page:
+        # http://www-personal.umich.edu/~jpboyd/eng403_chap2_tuftegospel.pdf,
+        # Tufte suggests an aspect ratio of 1.5 - 1.6.
+        height = width/1.5
+        FIGSIZE = (width,height)
+
+        import matplotlib.pyplot as plt
+
+        font = {'family':'serif', 'serif': ['computer modern roman']}
+        plt.rc('font',**font)
+
+        plt.rc('text', usetex=True)
+    else:
+        # on retina screens, the default plots are way too small
+        # by using Qt5 and setting QT_AUTO_SCREEN_SCALE_FACTOR=1
+        # Qt5 will scale everything using the dpi in ~/.Xresources
+        import matplotlib
+        matplotlib.use("Qt5Agg")
+
+        import matplotlib.pyplot as plt
+
+        # Default figure size. Currently set to my monitor width and height so that
+        # things are properly formatted
+        FIGSIZE = (13.78,7.48)
+
+        # Make the defalt font bigger
+        plt.rc('font', size=22)
+
+    for filename in args.filenames:
+        head, tail = split(filename)
+        root, ext = splitext(tail)
+
+        e, z, pnue, pnum, pnut = np.genfromtxt(filename).T
+
+        shape0 = len(np.unique(e))
+
+        ee = e.reshape((shape0,-1))
+        zz = z.reshape((shape0,-1))
+        pnue = pnue.reshape((shape0,-1))
+        pnum = pnum.reshape((shape0,-1))
+        pnut = pnut.reshape((shape0,-1))
+
+        levels = np.linspace(0,1,101)
+
+        plt.figure(figsize=FIGSIZE)
+        plt.contourf(ee,zz,pnue,levels=levels)
+        plt.gca().set_xscale('log')
+        plt.xlabel("Energy (GeV)")
+        plt.ylabel("Cos(Zenith)")
+        plt.colorbar()
+        plt.tight_layout()
+        if args.save:
+            plt.savefig("%s_nue.pdf" % root)
+            plt.savefig("%s_nue.eps" % root)
+        else:
+            plt.title(r"Probability to oscillate to $\nu_e$")
+        plt.figure(figsize=FIGSIZE)
+        plt.contourf(ee,zz,pnum,levels=levels)
+        plt.gca().set_xscale('log')
+        plt.xlabel("Energy (GeV)")
+        plt.ylabel("Cos(Zenith)")
+        plt.colorbar()
+        plt.tight_layout()
+        if args.save:
+            plt.savefig("%s_num.pdf" % root)
+            plt.savefig("%s_num.eps" % root)
+        else:
+            plt.title(r"Probability to oscillate to $\nu_\mu$")
+        plt.figure(figsize=FIGSIZE)
+        plt.contourf(ee,zz,pnut,levels=levels)
+        plt.gca().set_xscale('log')
+        plt.xlabel("Energy (GeV)")
+        plt.ylabel("Cos(Zenith)")
+        plt.colorbar()
+        plt.tight_layout()
+        if args.save:
+            plt.savefig("%s_nut.pdf" % root)
+            plt.savefig("%s_nut.eps" % root)
+        else:
+            plt.title(r"Probability to oscillate to $\nu_\tau$")
+
+    plt.show()