update r15a_gamma report according to Jim's comments

r15a_1809_rate/r15a_gamma.tex

@@ -119,7 +119,9 @@ pulses from HPGe and \ce{LaBr3} detectors are shown in
     \includegraphics[width=1.0\textwidth]{figs/typical_pulses}
     \caption{Typical output pulses of HPGe and \ce{LaBr3} detectors: energy
       output HPGe high gain (top left), energy output HPGe low gain (top
-      right), timing output HPGe (bottom left), and \ce{LaBr3} (bottom right).}
+      right), timing output HPGe (bottom left), and \ce{LaBr3} (bottom right).
+      Each clock tick corresponds to \SI{10}{\ns} and \SI{2}{\ns} for top and
+      bottom plots, respectively.}
     \label{fig:typical_pulses}
   \end{figure}
 \end{center}
@@ -127,8 +129,9 @@ pulses from HPGe and \ce{LaBr3} detectors are shown in
 The timing pulses from the HPGe detector were not used in this analysis because
 they are too long and noisy (see bottom left \cref{fig:typical_pulses}).
 Energy of the HPGe detector is taken as amplitude of spectroscopy amplifier
-outputs, its timing is determined by the clock tick where the trace passing
+outputs, its timing is determined by the clock tick where the trace passes
-\SI{30}{\percent} of the amplitude. 
+\SI{30}{\percent} of the amplitude. The timing resolution is \SI{235}{\ns}
+using this method.
 
 \ce{LaBr3} pulses were passed through a moving average window filter (60
 samples wide), then integrated to obtain energy resolution. 
@@ -141,14 +144,16 @@ position. There was a separate run for background radiation.
 
 \cref{fig:uncalibrated_labr3_spectra} shows \ce{LaBr3}
 spectra with calibration sources \ce{^{88}Y}, \ce{^{60}Co}, and background
-radiation. It can be seen that the self activation from \ce{Ac} dominates the
+radiation. It can be seen that below \SI{1.5}{\MeV} region the self activation
-spectra. The \SI{1173}{\kilo\eV} peak barely shows up in \ce{^{60}Co}
+from \ce{^{138}La} shows up clearly, and above that products from the chain
-spectrum, while the \SI{1332}{\keV} peak is buried under the
+decay of \ce{^{227}Ac} dominate the spectrum. The \SI{1173}{\kilo\eV} peak
-\SI{1436}{\kilo\eV} peak from \ce{^{138}La}. The \SI{1836}{\kilo\eV}
+barely shows up in \ce{^{60}Co} spectrum, while the \SI{1332}{\keV} peak is
-peak of \ce{^{88}Y} and the annihilation peak \SI{511}{\kilo\eV} can be
+buried under the \SI{1436}{\kilo\eV} peak from \ce{^{138}La}. The
-distinguished, but the \SI{898}{\kilo\eV} has been distorted by the electrons
+\SI{1836}{\kilo\eV} peak of \ce{^{88}Y} and the annihilation peak
-and \SI{789}{\kilo\eV} gammas from the beta decay of \ce{^{138}La}. The energy
+\SI{511}{\kilo\eV} can be distinguished, but the \SI{898}{\kilo\eV} has been
-resolution (FWHM) at the \SI{1836}{\kilo\eV} peak was \SI{5.9}{\percent}.
+distorted by the electrons and \SI{789}{\kilo\eV} gammas from the beta decay of
+\ce{^{138}La}. The energy resolution (FWHM) at the \SI{1836}{\kilo\eV} peak was
+\SI{5.9}{\percent}.
 
 \begin{center}
   \begin{figure}[htbp]
@@ -162,6 +167,7 @@ resolution (FWHM) at the \SI{1836}{\kilo\eV} peak was \SI{5.9}{\percent}.
 \end{center}
 
 The HPGe spectra are much cleaner as shown in Figure~\ref{fig:hpge_ecal}.
+Energy resolutions are better than \SI{3.2}{\keV} for all calibrated peaks.
 \begin{center}
   \begin{figure}[htbp]
     \centering
@@ -215,12 +221,20 @@ $2p-1s$   & 346.8      & \num{7.26e-4}          &\num{4.73e-5}  \\
 \label{sub:labr3_spectra}
 The \ce{LaBr3} energy spectra for the Al dataset are presented in
 \cref{fig:labr3_all_al_runs}. The muonic $2p-1s$ peak shows up clearly in
-the prompt spectrum as expected. The \SI{1809}{\kilo\eV} peak can be
+the prompt spectrum as expected, the signal-to-background ratio is
-recognized, it has better
+\num{3.13(2)}. The \SI{1809}{\kilo\eV} peak can be
-signal-to-background ratio in the prompt spectrum than in the delay spectrum
+recognized, it has better signal-to-background ratio in the prompt spectrum
-(0.88 to 0.33). The background under the \SI{1809}{\kilo\eV} is dominated by
+than in the delay spectrum (0.88 to 0.33). The background under the
-the $\alpha$ decay of progenies from \ce{^{227}Ac}. I think that this
+\SI{1809}{\kilo\eV} is dominated by
-\ce{LaBr3} in the current set up is not suitable to use as a STM detector.
+the $\alpha$ decay of progenies from \ce{^{227}Ac}.
+
+It is clear that this
+\ce{LaBr3} detector in the current set up is not good enough to measure the
+\SI{1809}{\keV} line. The situation of the $2p-1s$ line is a little better, but
+more studies is needed to understand the background and possible interferences
+around the peak. On another note, there have been steady progress in
+manufacturing \ce{LaBr3} detectors, and better performance has been observed.
+
 \begin{center}
   \begin{figure}[htbp]
     \centering
@@ -288,7 +302,7 @@ Therefore the emission rate per nuclear capture is:
   R_{1808.7} = \frac{N_{1808.7}}{A_{1808.7} \times N_{\mu} \times 0.609} = 0.51 \pm 0.05,
 \end{equation}
 , where the factor 0.609 comes from the fact that only \SI{60.9}{\percent} of
-stopped muons are captured. This result is consistent with the rate reported
+stopped muons are captured. This result is consistent with the rate
-by Measday et al.
+\num{0.51(5)} reported by Measday et al.
 
 \end{document}

stm_study_201611/stm_study.bib

@@ -457,6 +457,19 @@
   Url                      = {http://www.sciencedirect.com/science/article/pii/0031916364904792}
 }
 
+@TechReport{Bartoszek2014,
+  Title                    = {{Mu2e Technical Design Report}},
+  Author                   = {Bartoszek, L. and others},
+  Year                     = {2014},
+
+  Archiveprefix            = {arXiv},
+  Collaboration            = {Mu2e},
+  Eprint                   = {1501.05241},
+  Primaryclass             = {physics.ins-det},
+  Reportnumber             = {FERMILAB-TM-2594, FERMILAB-DESIGN-2014-01},
+  Slaccitation             = {%%CITATION = ARXIV:1501.05241;%%}
+}
+
 @Article{BauerBortels.1990,
   Title                    = {Response of Si detectors to electrons, deuterons and alpha particles},
   Author                   = {Bauer, P and Bortels, G},

stm_study_201611/stm_study.tex

@@ -12,22 +12,40 @@
   detect-family=true,
   separate-uncertainty=true]{siunitx}
 % \usepackage{listings}
-\usepackage{xcolor}
+\usepackage[dvipsnames]{xcolor}
 \usepackage{upquote}
 \usepackage{minted}
 \usemintedstyle{perldoc}
 
 \usepackage[framemethod=tikz]{mdframed}
+\usepackage{adjustbox}
 
-\definecolor{greybg}{rgb}{0.25,0.25,0.25}
+% \definecolor{greybg}{rgb}{0.25,0.25,0.25}
-\definecolor{yellowbg}{rgb}{0.91, 0.84, 0.42}
+% \definecolor{yellowbg}{rgb}{0.91, 0.84, 0.42}
-\definecolor{bananamania}{rgb}{0.98, 0.91, 0.71}
+% \definecolor{bananamania}{rgb}{0.98, 0.91, 0.71}
 
-\mdfsetup{%
+\mdfdefinestyle{warning}{%
-  middlelinecolor=red,
+  linecolor=red!70,
-  middlelinewidth=1pt,
+  frametitle={Warning},
+  frametitlerule=true,
+  frametitlebackgroundcolor=orange!40,
+  backgroundcolor=orange!30,
+  innertopmargin=\topskip,
+  roundcorner=8pt,
+  linewidth=1pt,
+}
+% \mdtheorem[style=theoremstyle]{warning}{Warning}
+
+\mdfdefinestyle{listing}{%
+  linecolor=Aquamarine!50,
+  linewidth=1pt,
   backgroundcolor=yellow!40,
-  roundcorner=8pt}
+  roundcorner=8pt,
+  % frametitlerule=true,
+  % frametitlebackgroundcolor=yellow!50,
+  innertopmargin=\topskip,
+}
+% \mdtheorem[style=listing]{listing}{Listing}
 
 % \DeclareSIUnit\eVperc{\eV\per\clight}
 % \DeclareSIUnit\clight{\text{\ensuremath{c}}}
@@ -86,16 +104,16 @@ The study was done using Mu2e Offline version v6\textunderscore
 TS5 (see \cref{fig:stm_geo_all}), taking \texttt{cd3-beam-g4s2-mubeam.0728a}
 dataset as input. The dataset contains 5098 files, each corresponds to
 \num{1e6} proton-on-target (POT). The dataset were reused 16 times with
-different random seeds, where \SI{97}{\percent} of runs succeeded, equivalent
+different random seeds, where \SI{97.6}{\percent} of runs succeeded, equivalent
-to \num{8e11} POTs.
+to \num{7.96e10} POTs.
 
 \begin{figure}[htbp]
   \centering
   \includegraphics[width=1.0\textwidth]{figs/stm_geo_all}
-  \caption{Simulation geometry showing the DS region on the left, sweeper magnet,
+  \caption{Simulation geometry showing the Detector Solenoid region on the
-    FOV collimator, spot-size collimator, and the STM detectors on the right.
+    left, sweeper magnet, Field-Of-View collimator, Spot-Size collimator, and
-    Particles saved in the input files are shoot from the TS5 (orange circle),
+    the STM detectors on the right. Particles saved in the input files are
-    and transported to the STM region.}
+    shoot from the TS5 (orange circle), and transported to the STM region.}
   \label{fig:stm_geo_all}
 \end{figure}
 
@@ -112,6 +130,8 @@ the output file.
 \centering
 \caption{List of virtual detectors read out in this study}
 \label{tab:vds_list}
+\begin{adjustbox}{max width=\textwidth}
+  
 \begin{tabular}{@{}ccll@{}}
 \toprule
   &VDID & Location               & Abbreviation              \\
@@ -126,6 +146,7 @@ the output file.
 8 & 100 & Downstream of the FOV collimator      & STM\textunderscore FieldOfViewCollDnStr \\
 \bottomrule
 \end{tabular}
+\end{adjustbox}
 \end{table}
 
 \section{Simulation and analysis code}
@@ -135,13 +156,13 @@ The simulation and analysis code are located at:
 \url{/mu2e/app/users/namtran/STM_study_201611}.
 
 % \lstinputlisting[language=bash,frame=single]{listings/code_dir_tree.sh}
-\begin{mdframed}
+\begin{mdframed}[style=listing]
   \inputminted[fontsize=\footnotesize]{bash}{listings/code_dir_tree.sh}
 \end{mdframed}
 
 \texttt{step00} contains configuration files for this simulation and a script to
-submit all 5098 jobs (correspond to number of input files) to the FermiGrid.
+submit all 5098 jobs to the FermiGrid. It took about 14 hours to complete one
-It took about 14 hours to complete a job in average.
+job in average.
 
 The \texttt{analysis} folder contains a script 
 (\texttt{run\textunderscore statistics.sh}) which checks if a job has finished
@@ -151,25 +172,30 @@ make plots.
 
 \section{Results}
 \label{sec:results}
-\subsection{STM detector spectra}
+\begin{mdframed}[style=warning]
-\label{sub:stm_detector_spectra}
+Muonic X-rays and probabilities in the simulation are not correct (see
+\cref{sec:muonic_x_rays_in_geant4}).
+\end{mdframed}
 
-Energy spectrum of particles hitting STM detectors are presented in
+\subsection{STM detector energy spectra}
-\cref{fig:stm_det_ke}. There were not many hits, and only the annihilation
+\label{sub:stm_detector_spectra}
-peak stands out. Most of the particles are photons as shown in
+Energy spectrum of particles hitting STM detectors in the range
+\SIrange{0.1}{3.1}{\MeV} are presented in \cref{fig:stm_det_ke}. There were not many
+hits, and only the annihilation peak stands out. Most of the particles are
+photons as shown in
 \cref{fig:stm_det_ptype}.
 \begin{figure}[htbp]
   \centering
-  \includegraphics[width=0.7\textwidth]{figs/ke_det1UpStr}
+  \includegraphics[width=0.85\textwidth]{figs/ke_det1UpStr}
-  \includegraphics[width=0.7\textwidth]{figs/ke_det2UpStr}
+  \includegraphics[width=0.85\textwidth]{figs/ke_det2UpStr}
   \caption{Kinetic energy of particles hitting STM detectors 1 (top), and
     2 (bottom).}
   \label{fig:stm_det_ke}
 \end{figure}
 \begin{figure}[htbp]
   \centering
-  \includegraphics[width=0.7\textwidth]{figs/ke_pdg_det1UpStr}
+  \includegraphics[width=\textwidth]{figs/ke_pdg_det1UpStr}
-  \includegraphics[width=0.7\textwidth]{figs/ke_pdg_det2UpStr}
+  \includegraphics[width=\textwidth]{figs/ke_pdg_det2UpStr}
   \caption{Kinetic energy and type of particles hitting STM detectors 1 (top),
     and 2 (bottom).}
   \label{fig:stm_det_ptype}
@@ -179,32 +205,138 @@ peak stands out. Most of the particles are photons as shown in
 \label{sub:stm_detector_hit_rate_estimation}
 The average number of hits on a STM detector per POT is:
 \begin{equation}
-  \frac{888 + 888}{2 \times 8 \times 10^{11}} = 8.7 \times 10^{-9}. 
+  \frac{672 + 714}{2 \times 7.96 \times 10^{10}} = 8.7 \times 10^{-9}. 
+  \label{eqn:stm_hit_count}
 \end{equation}
-There are 3.1 POTs per proton bunch, so the number of hits per bunch is:
+There would be \num{3.1e7} POTs per proton bunch, so the number of hits each
+bunch is: 
 \begin{equation}
-  8.7 \times 10^{-9} \times 3.1 \times 10^7 = 0.27
+  8.7 \times 10^{-9} \times 3.1 \times 10^7 = 0.27.
 \end{equation}
 The instantaneous hit rate, assuming an interval of \SI{1695}{\ns} between
 bunches, is:
 \begin{equation}
-  \frac{0.27}{1695\times 10^{-9}} = \SI{159e3}{\Hz}
+  \frac{0.27}{1695\times 10^{-9}} = \SI{158.9e3}{\Hz}
 \end{equation}
 
-\section{Timing of hits on STM detector}
+The uncertainty on the hit rate estimation is \SI{2.6}{\percent} if
-\label{sec:timing_of_hits_on_stm_detector}
+only statistical uncertainty of the hit counting in \cref{eqn:stm_hit_count} is
+taken into account. This hit rate is too high for a HPGe detector to function
+well, so an attenuator would be installed upstream of the spot-size collimator
+to lower the hit rate to about \SI{10}{\kHz}.
 
-\section{Signal to background ratio}
+\subsection{Hit timing on STM detectors}
-\label{sec:signal_to_background_ratio}
+\label{sub:timing_of_hits_on_stm_detectors}
+Timing in the simulation starts from the birth of a primary proton, which means
+all events start at the same $t = 0$ time. In order to mimic the pulse
+structure of the proton beam (\SI{250}{\ns} pulse width, \SI{1695}{\ns} between
+pulses~\cite{Bartoszek2014}), the recorded times on each event are smeared by
+a Gaussian distribution with a $\sigma = 250 / 6 = \SI{41.7}{\ns}$.
+
+The hit timing as a function of kinetic energy for several virtual detectors
+are shown in \cref{fig:ke_time_4vds}. Most of hits arrive between
+\num{100} and \SI{400}{\ns} from the center of a proton pulse. Only a few of
+particles could hit the STM detectors, especially in the energy region around
+the $2p-1s$ peak, that it is hard to investigate the
+dependence between timing and energy of hits. Therefore I will only analyze the
+timing information of hits STM\_SpotSizeCollUpStr.
+
+\begin{figure}[htbp]
+  \centering
+  \includegraphics[width=1.0\textwidth]{figs/ke_time_4vds}
+  \caption{Hit timing as a function of kinetic energy at spot size
+    collimator upstream (top left) and down stream (top right), and two STM
+    detectors (bottom left and right).} 
+  \label{fig:ke_time_4vds}
+\end{figure}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\subsection{Signal to background ratio: $2p-1s$ peak at spot-size collimator
+  upstream}
+\label{sub:signal_to_background_ratio_2p_1s_peak_at_spot_size_collimator_upstream}
+The energy of muonic $2p-1s$ transition in aluminum is given as \SI{335}{\keV}
+by Geant4. Background is taken as the average counts for 10 bins around
+\SI{335}{\keV}, and signal strength is calculated by subtracting the background
+from the count under the peak. Energy spectra at spot-size
+collimator upstream (VD 101: STM\_SpotSizeCollUpStr) in \SI{50}{\ns} windows
+and their signal-to-background ratios are shown in
+\cref{fig:ke_SpotSizeCollUpStr_time_slices}.
+\begin{figure}[htbp]
+  \centering
+  \includegraphics[width=1.0\textwidth]{figs/ke_SpotSizeCollUpStr_time_slices}
+  \caption{Energy spectra at STM\_SpotSizeCollUpStr and signal-to-background
+    ratios in 50-ns time windows.}
+  \label{fig:ke_SpotSizeCollUpStr_time_slices}
+\end{figure}
+
+\subsection{Signal to background ratio: \SI{1809}{\keV} at spot-size collimator
+upstream}
+\label{sub:signal_to_background_ratio_1809_kev_at_spot_size_collimator_upstream}
 
-Muonic X-rays and probabilities in the simulation are not correct, see
-\cref{sec:muonic_x_rays_in_geant4}.
 
 %%%% Appendices
+\pagebreak
 \appendix
 \section{How to run the simulation and analyze data}
+%%%%%%%%%%%%%%%%%%%
 \label{sec:how_to_run_the_simulation_and_analyze_data}
+\subsection{Simulating beam flash}
+\label{sub:simulating_beam_flash}
+Simulation scripts are in:
+\url{/mu2e/app/users/namtran/STM_study_201611/step00}:
+\begin{itemize}
+  \item \url{fcl/step00.fcl}: configuration for this study (primary particles,
+    virtual detectors to be read out, particle filtering, ...)
+  \item \url{geom/geom.txt}: specify geometry settings (thickness
+    of shields, enabled virtual detectors, ...)
+  \item \url{submit.sh}: submit all jobs (5098) in the
+    \url{cd3-beam-g4s2-mubeam.0728a.list} to the grid 
+\end{itemize}
 
+\noindent Steps to run the simulation:
+\begin{itemize}
+  \item preparing user's code: follow Mu2e instruction to create an
+    \texttt{Offline} distribution (mine is at
+    \url{/mu2e/app/users/namtran/Offline}),
+
+  \item setting up \texttt{mu2e} environment \footnote{I used \texttt{mu2egrid}
+      version \texttt{v3\_02\_00} which supports \texttt{mu2eart} command}:
+    \begin{mdframed}[style=listing]
+      \inputminted[
+        fontsize=\scriptsize,
+        firstline=1,
+        lastline=11,
+        breaklines=true,
+        breakanywhere=true
+        ]{bash}{listings/runall.sh}
+    \end{mdframed}
+
+  \item submitting all jobs: 
+    \begin{mdframed}[style=listing]
+      \inputminted[
+        fontsize=\scriptsize,
+        firstline=13,
+        breaklines=true,
+        breakanywhere=true
+        ]{bash}{listings/runall.sh}
+    \end{mdframed}
+\end{itemize}
+
+\noindent Analysis code
+\url{/mu2e/app/users/namtran/STM_study_201611/analysis}:
+\begin{itemize}
+  \item \texttt{run\_statistics}: skims the log files (\texttt{mu2e.log} in
+    each subdirectory`) to make a list of successful runs, and collect CPU
+    time, random seeds. This script should be run first.
+
+  \item \texttt{main.cc}: the analysis code, it is rather simple now, only
+    exports a few histograms from virtual detector hits. Run \texttt{make}
+    to produce the executable \texttt{read\_vd}.
+  \item \texttt{read\_vd}: takes a list of simulation outputs as input to
+    produce a single ROOT file which contains several histograms.
+\end{itemize}
+
+%%%%%%%%%%%%%%%%%%%
 \section{Muonic X-rays in Geant4}
 \label{sec:muonic_x_rays_in_geant4}
 The muonic energy levels and transition probabilities were calculated using
@@ -216,7 +348,7 @@ a simple model described by Mukhopadhyay~\cite{Mukhopadhyay.1977}.
       % language=c++, firstline=64, lastline=93,firstnumber=64,
       % breaklines=true, breakatwhitespace=true,
       % frame=single]{listings/G4EmCaptureCascade.cc}
-      \begin{mdframed}
+      \begin{mdframed}[style=listing]
         \inputminted[
           breaklines=true,
           stepnumber=5,
@@ -227,7 +359,7 @@ a simple model described by Mukhopadhyay~\cite{Mukhopadhyay.1977}.
       \end{mdframed}
   \item Energy of K-shell muons are calculated from energy of K-shell
     electrons:
-      \begin{mdframed}
+      \begin{mdframed}[style=listing]
         \inputminted[
           breaklines=true,
           stepnumber=5,
@@ -238,7 +370,7 @@ a simple model described by Mukhopadhyay~\cite{Mukhopadhyay.1977}.
       \end{mdframed}
     \item Energies of muons on other shells are calculated by scaling from that
       of K-shell muons:
-      \begin{mdframed}
+      \begin{mdframed}[style=listing]
         \inputminted[
           breaklines=true,
           stepnumber=5,