The paper itself involves the following
├── main.tex # The TeX file for the paper
├── assets # The Figures for the paper
│ ├── akhmedovOscPlt.pdf
│ ├── castle-wall-1.pdf
│ ├── castle-wall-2.pdf
│ ├── castle-wall.pdf
│ ├── castlewall-profile.pdf
│ ├── interference-reduction-three-modes-neutrino.pdf
│ ├── interference-reduction-three-modes-rabi.pdf
│ ├── interference-reduction-three-modes.pdf
│ ├── interference-reduction.pdf
│ ├── interference.png
│ ├── legacy-rabiOscillationsNeutrinoCoincidence.pdf
│ ├── placeholder.jpg
│ ├── rabi-isospin-rotating-frame.ggb
│ ├── rabi-isospin-rotating-frame.pdf
│ ├── rabi-isospin-static-frame.ggb
│ ├── rabi-isospin-static-frame.pdf
│ ├── rabi-oscillations-energy-gap-change.eps
│ ├── rabi-oscillations-energy-gap-change.pdf
│ ├── rabiOscillationsNeutrinoCoincidence-single-frequency.pdf
│ └── resonance-freq-example-1-added-new-slow-perturbation-destruction-compare-rotating-field.png
└── ref.bib # Reference
Other files are the supplementary materials
├── README.md
├── data
│ ├── plots.ipynb # The code for the plots
│ ├── assets
│ │ └── writing-paper-rabi-neutrino
│ │ ├── akhmedovConditionDeviationPlt.png
│ │ ├── akhmedovOscPlt.png
│ │ └── castle-wall-matter-profile-0.8-0.88.png
│ ├── castle-wall
│ │ ├── probAkhmedovRabiTheoryList-0.003Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-0.02.csv
│ │ ├── probAkhmedovRabiTheoryList-0.03Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-0.04.csv
│ │ ├── probAkhmedovRabiTheoryList-0.08.csv
│ │ ├── probAkhmedovRabiTheoryList-0.1.csv
│ │ ├── probAkhmedovRabiTheoryList-0.2.csv
│ │ ├── probAkhmedovRabiTheoryList-0.4.csv
│ │ ├── probAkhmedovRabiTheoryList-0.5.csv
│ │ ├── probAkhmedovRabiTheoryList-0.6.csv
│ │ ├── probAkhmedovRabiTheoryList-0.8.csv
│ │ ├── probAkhmedovRabiTheoryList-1..csv
│ │ ├── probAkhmedovRabiTheoryList-3\ Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-3.0649052682562883Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-3.065Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-3Pi-divied-by-2.csv
│ │ ├── probAkhmedovRabiTheoryList-3Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-4Pi.csv
│ │ ├── probAkhmedovRabiTheoryList-Pi-divied-by-250.csv
│ │ ├── solAkhList-0.003Pi.csv
│ │ ├── solAkhList-0.02.csv
│ │ ├── solAkhList-0.03Pi.csv
│ │ ├── solAkhList-0.04.csv
│ │ ├── solAkhList-0.08.csv
│ │ ├── solAkhList-0.1.csv
│ │ ├── solAkhList-0.2.csv
│ │ ├── solAkhList-0.4.csv
│ │ ├── solAkhList-0.5.csv
│ │ ├── solAkhList-0.6.csv
│ │ ├── solAkhList-0.8.csv
│ │ ├── solAkhList-1..csv
│ │ ├── solAkhList-3\ Pi.csv
│ │ ├── solAkhList-3.0649052682562883Pi.csv
│ │ ├── solAkhList-3.065Pi.csv
│ │ ├── solAkhList-3Pi-divied-by-2.csv
│ │ ├── solAkhList-3Pi.csv
│ │ ├── solAkhList-4Pi.csv
│ │ └── solAkhList-Pi-divied-by-250.csv
│ ├── castle-wall-1.pdf
│ ├── castle-wall-2.pdf
│ ├── castle-wall.pdf
│ ├── castlewall-profile.pdf
│ ├── data
│ ├── interference
│ │ ├── interference-three-modes-interferencePyGridLines.csv
│ │ ├── interference-three-modes-interferencePyUpperFrameTicks.csv
│ │ ├── interference1-three-modes-k1-1-k2-0.1-a1-0.0001-a2-0.01.csv
│ │ ├── interference1-three-modes-k1-1-k2-1oPi-a1-0.0001-a2-0.01.csv
│ │ ├── interference1-three-modes-ks1-1-k2-1oPi-a1-0.000035-a2-0.0083666.csv
│ │ ├── interference1-three-modes-ks1-1-k2-1oPi-a1-0.0001-a2-0.01.csv
│ │ ├── interference1-three-modes-ks1-1-k2-1oPi-a1-0.0001-a2-0.0141421.csv
│ │ ├── interference2-three-modes-k1-1-k2-0.0001-a1-0.0001-a2-0.01.csv
│ │ ├── interference2-three-modes-k1-1-k2-1o10000Pi-a1-0.000035-a2-0.0083666.csv
│ │ ├── interference2-three-modes-k1-1-k2-1o10000Pi-a1-0.0001-a2-0.0141421.csv
│ │ ├── interference2-three-modes-k1-1-k2-1o1000Pi-a1-0.0001-a2-0.01.csv
│ │ ├── interference2-three-modes-k1-1-k2-1o1000Pi-a1-0.0001-a2-0.0141421.csv
│ │ ├── interference3-three-modes-k1-1-k2-0.0001-k3-1o1000Pi-a1-0.0001-a2-0.01-a3-0.01.csv
│ │ ├── interference3-three-modes-k1-1-k2-1o10000Pi-k3-1o5432-a1-0.000035-a2-0.0083666-a3-0.0083666.csv
│ │ ├── interference3-three-modes-k1-1-k2-1o10000Pi-k3-1o5432-a1-0.0001-a2-0.0141421-a3-0.0141421.csv
│ │ ├── interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.01-a3-0.01.csv
│ │ ├── interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.0141421-a3-0.0141421.csv
│ │ ├── interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.0141421-a3-0.0141421qvalues-data-list-each-modes.csv
│ │ ├── paper-interference-a1-a2-0.0001-0.01-k1-k2-1.-0.1.csv
│ │ ├── paper-interference-a1-a2-0.0001-0.01-k1-k2-1.-10..csv
│ │ ├── paper-interference-a1-a2-0.0001-0.05-k1-k2-1.-0.1.csv
│ │ ├── paper-interference-a1-a2-0.0001-0.05-k1-k2-1.-10..csv
│ │ ├── paper-interference-theory-amplitude-2016-10-18.csv
│ │ ├── rabi-interference-three-modes-interferencePyGridLines.csv
│ │ ├── rabi-interference-three-modes-interferencePyGridLinesZeros.csv
│ │ ├── rabi-interference1-three-modes-k1-1-a1-0.0001.csv
│ │ ├── rabi-interference1-three-modes-k1-1-k2-1oPi-a1-0.0001-a2-0.0141421.csv
│ │ ├── rabi-interference1-three-modes-k1-1-k2-1oPi-a1-0.0001-a2-0.05.csv
│ │ ├── rabi-interference1-three-modes-k1-1-k2-1oPi-a1-0.0001-a2-0.141421.csv
│ │ ├── rabi-interference2-three-modes-k1-1-k2-1o1000Pi-a1-0.0001-a2-0.0141421.csv
│ │ ├── rabi-interference2-three-modes-k1-1-k2-1o1000Pi-a1-0.0001-a2-0.05.csv
│ │ ├── rabi-interference2-three-modes-k1-1-k2-1o1000Pi-a1-0.0001-a2-0.141421.csv
│ │ ├── rabi-interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.0141421-a3-0.0141421.csv
│ │ ├── rabi-interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.05-a3-0.05.csv
│ │ ├── rabi-interference3-three-modes-k1-1-k2-1o1000Pi-k3-1o543-a1-0.0001-a2-0.141421-a3-0.141421.csv
│ │ ├── sol10List-a1-0.000035-k1-1.csv
│ │ ├── sol11List-a1-a2-0.000035-0.01-k1-k2-1-0.01.csv
│ │ ├── sol12List-a1-a2-0.00001-0.000141421-k1-k2-1-0.01.csv
│ │ ├── sol12List-a1-a2-0.000035-0.000264575-k1-k2-1-0.01.csv
│ │ ├── sol12List-a1-a2-0.000035-0.00035-k1-k2-1-0.01.csv
│ │ ├── sol12List-a1-a2-0.000035-0.02-k1-k2-1-0.01.csv
│ │ ├── sol12List-a1-a2-0.0001-0.000447214-k1-k2-1-0.01.csv
│ │ ├── sol14List-a1-a2-0.00001-0.00774597-k1-k2-1-0.01.csv
│ │ ├── sol14List-a1-a2-0.000035-0.0144914-k1-k2-1-0.01.csv
│ │ ├── sol14List-a1-a2-0.000035-0.015-k1-k2-1-0.01.csv
│ │ ├── sol14List-a1-a2-0.0001-0.0244949-k1-k2-1-0.01.csv
│ │ ├── sol15List-a2-0.00447214-k2-0.01.csv
│ │ ├── sol15List-a2-0.0083666-k2-0.01.csv
│ │ ├── sol15List-a2-0.0141421-k2-0.01.csv
│ │ ├── theory10List-a1-0.000035-k1-1.csv
│ │ ├── theory11List-a1-a2-0.000035-0.01-k1-k2-1-0.01.csv
│ │ ├── theory12List-a1-a2-0.00001-0.000141421-k1-k2-1-0.01.csv
│ │ ├── theory12List-a1-a2-0.000035-0.000264575-k1-k2-1-0.01.csv
│ │ ├── theory12List-a1-a2-0.000035-0.00035-k1-k2-1-0.01.csv
│ │ ├── theory12List-a1-a2-0.000035-0.02-k1-k2-1-0.01.csv
│ │ ├── theory12List-a1-a2-0.0001-0.000447214-k1-k2-1-0.01.csv
│ │ ├── theory14List-a1-a2-0.00001-0.00774597-k1-k2-1-0.01.csv
│ │ ├── theory14List-a1-a2-0.000035-0.0144914-k1-k2-1-0.01.csv
│ │ ├── theory14List-a1-a2-0.000035-0.015-k1-k2-1-0.01.csv
│ │ ├── theory14List-a1-a2-0.0001-0.0244949-k1-k2-1-0.01.csv
│ │ ├── theory15List-a2-0.00447214-k2-0.01.csv
│ │ ├── theory15List-a2-0.0083666-k2-0.01.csv
│ │ └── theory15List-a2-0.0141421-k2-0.01.csv
│ ├── interference-reduction-three-modes-neutrino.pdf
│ ├── interference-reduction-three-modes-rabi.pdf
│ ├── interference-reduction-three-modes.pdf
│ ├── interference-reduction.pdf
│ ├── interference.pdf
│ ├── rabiOscillationsNeutrinoCoincidence-single-frequency-1.pdf
│ ├── rabiOscillationsNeutrinoCoincidence-single-frequency.pdf
│ ├── single-frequency
│ │ ├── paper-single-frequency-simple-a1-0.0001-k1-0.9999.csv
│ │ ├── paper-single-frequency-simple-a1-0.0001-k1-0.99998.csv
│ │ ├── paper-single-frequency-simple-a1-0.0001-k1-0.99999.csv
│ │ ├── paper-single-frequency-simple-a1-0.0001-k1-1.csv
│ │ ├── paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.9999.csv
│ │ ├── paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.99998.csv
│ │ ├── paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.99999.csv
│ │ └── paper-single-frequency-simple-theory-prob-a1-0.0001-k1-1.csv
│ ├── sol10PList.csv
│ ├── theory10List.csv
│ └── writing-paper-rabi-neutrino.ipynb
├── outline.tex
├── rabi_neutrino_oscillations-0.10.1.pdf
├── rabi_neutrino_oscillations-0.10.1.zip
├── rabi_neutrino_oscillations-0.9.1.pdf
├── rabi_neutrino_oscillations-0.9.1.zip
├── rabi_neutrino_oscillations-0.9.2.pdf
├── rabi_neutrino_oscillations-0.9.2.zip
├── rabi_neutrino_oscillations-0.9.3.pdf
├── rabi_neutrino_oscillations-0.9.3.zip
├── rabi_neutrino_oscillations-0.9.4.pdf
├── rabi_neutrino_oscillations-0.9.4.zip
├── rabi_neutrino_oscillations-0.9.5.pdf
├── rabi_neutrino_oscillations-0.9.6.pdf
├── tikz-plot.tex
└── PITCHME.md # Preserved for an elevator speech version of the work.
For 0.10.1 tag, the data used are all in the data folder.
Single frequency (Fig.1)
Theory
single-frequency/paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.9999.csv
single-frequency/paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.99998.csv
single-frequency/paper-single-frequency-simple-theory-prob-a1-0.0001-k1-1.csv
Numerical
single-frequency/paper-single-frequency-simple-a1-0.0001-k1-0.9999.csv
single-frequency/paper-single-frequency-simple-a1-0.0001-k1-0.99998.csv
single-frequency/paper-single-frequency-simple-a1-0.0001-k1-1.csv
Destruction effect (Fig.2)
interference/paper-interference-a1-a2-0.0001-0.01-k1-k2-1.-0.1.csv
interference/paper-interference-a1-a2-0.0001-0.01-k1-k2-1.-10..csv
interference/paper-interference-a1-a2-0.0001-0.05-k1-k2-1.-0.1.csv
interference/paper-interference-a1-a2-0.0001-0.05-k1-k2-1.-10..csv
interference/paper-interference-theory-amplitude-2016-10-18.csv # the data for the gridlines, which are the predictions of amplitudes using Rabi formula
Castle wall (Fig.4)
castle-wall/solAkhList-0.4.csv
castle-wall/probAkhmedovRabiTheoryList-0.4.csv
A transpose is used to counter the difference between python and Mathematica. For example,
theory1List = np.transpose( np.genfromtxt( 'single-frequency/paper-single-frequency-simple-theory-prob-a1-0.0001-k1-0.9999.csv', delimiter=",") )
So that we can simply plot out the list
plt.plot(theory1List[0][0::4],theory1List[1][0::4],'r-',\
markersize=ftsz*0.4, linewidth=2, fillstyle='full',\
markeredgecolor='red', markeredgewidth=0.0)
The full verions of the code is included in plot.ipynb.