%The first run of the AlCap experiment was performed at the $\pi$E1 beam line
%area, PSI from November 26 to December 23, 2013. The goal of the run was to
%measure protons rate and their spectrum following muon capture on aluminium.

The low energy muons from the $\pi$E1 beam line were stopped in thin aluminium
and silicon targets, and charged particles emitted were measured by two pairs
of silicon detectors inside of a vacuum vessel
(\cref{fig:alcap_setup_detailed}).  A stopped muon event is defined by
a group of upstream detectors and a muon veto plastic scintillator. 
The number of stopped muons is monitored by a germanium detector placed outside
of the vacuum chamber. In addition, several plastic scintillators were used to
provide veto signals for the silicon and germanium detectors. Two liquid
scintillators for neutron measurements were also tested in this run.  
\begin{figure}[btp] 
	\centering
	\includegraphics[width=0.55\textwidth]{figs/alcap_setup_detailed} 
	\caption{AlCap detectors: two silicon packages inside the vacuum vessel, 
    muon beam detectors including plastic scintillators and a wire chamber, 
    germanium detector and veto plastic scintillators.}
	\label{fig:alcap_setup_detailed} 
\end{figure} 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsubsection{Muon beam and vacuum chamber}
<<<<<<< Setup.tex
The muon beam of low energy at \SIrange{28}{45}{\MeV\per\cc}, and narrow
momentum spread of 3\% were used.
=======
One of the main requirements of the AlCap experiment was a low energy muon beam
with narrow momentum bite in order to achieve a high fraction of stopping muons
in the very thin targets. Muons with momenta from
\SIrange{28}{45}{\MeV\per c} and 3\% FWHM momentum bite were used. 
>>>>>>> 1.3

\Cref{fig:Rates} shows the measured muon rates
as a function of momentum for two different momentum bites.
\Cref{fig:Beam} shows an example of the resulting energy spectra recorded by
our silicon detector.
\begin{figure}[btp] 
	\centering
  \includegraphics[width=0.65\textwidth]{figs/Rates.png} 
  \caption{Measured muon rates at low momenta during the Run 2013. Beam rates
    at 1 \% FWHM momentum bite were about 3 times smaller than the rates at
    3 \% FWHM.}
	\label{fig:Rates} 
\end{figure}   

\begin{figure}[btp]
	\centering 
  \includegraphics[width=1.00\textwidth]{figs/beam.pdf} 
	\caption{Energy deposition at \SI{36.4}{/c} incident muon beam in an
    \SI{1500}{\micro\meter}-thick active target. The peak at low energy is due
    to beam electrons, the peaks at higher energies are due to muons. Momentum
    bite of 1 and 3\% FWHM on left and right hand side, respectively. The
    electron peak are the same in both plots as beam electrons are minimum
    ionisation particles and passed though the detector easily. The muon peak
    at the 3 \% FWHM momentum bite is notably broader than that at 1 \% FWHM
    setting.} 
  \label{fig:Beam} 
\end{figure}  

The targets and charged particle detectors are installed inside the vacuum
chamber as shown in \cref{fig:alcap_setup_detailed}.  The muon beam enters
from the right of \cref{fig:alcap_setup_detailed} and hits the target, which is
placed at the centre of the vacuum chamber and orientated at 45 degrees to the
beam axis.
The side walls and bottom flange of the vessel provide several
vacuum-feedthroughs for the high voltage and signal cables for the silicon and
scintillator detectors inside the chamber.
In addition, the chamber is equipped with several lead collimators
to quickly capture muons that do not stop in the actual target. 

For a safe operation of the silicon detector, a vacuum of \SI{e-4}{\milli\bar}
was necessary.  With the help of the vacuum group of PSI, we could consistently
reach the required vacuum level within 45 minutes after closure of the
chamber's top flange.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsubsection{Silicon detectors} 
The main detectors for charged particles measurement are four large area 
silicon detectors. The silicon detectors were grouped into two detector
packages located symmetrically at 90 degrees of the nominal muon beam path, SiL
and SiR in \cref{fig:alcap_setup_detailed}. Each arm consists of: one
$\Delta$E counter, a \SI{65}{\micro\meter}-thick silicon detector, divided into
4 quadrants; one E counter made from \SI{1500}{\micro\meter}-thick silicon; and
one plastic scintillator to identify electrons or high energy protons that
pass through the silicon. The area of each of these silicon detectors and the
scintillators is $50\times50 \textrm{mm}^2$. 
%There is a dead layer of
%\SI{0.5}{\micro\meter} on each side of the silicon detectors according to the
%manufacturer Micron Semiconductor
%\footnote{\url{http://www.micronsemiconductor.co.uk/}}.

%The detectors were named according to their positions relative to the muon
%view: the SiL package contains the thin
%detector SiL1 and thick detector SiL2; the SiR package has SiR1 and SiR2
%accordingly. Each quadrant of the thin detectors were also numbered from 1 to
%4, i.e. SiL1-1, SiL1-2, SiL1-3, SiL1-4, SiR1-1, SiR1-2, SiR1-3,
%SiR1-4.

Bias for the four silicon detectors was supplied by an ORTEC 710 NIM module,
which has a vacuum interlock input to prevent biasing before the safe vacuum
level has been reached. Typical voltage to fully depleted the detectors were
\SI{-300}{\volt} and \SI{-10}{\volt} for the thick and thin silicon detectors
respectively. The leakage currents at the operating voltages are less than
\SI{1.5}{\micro\ampere} for the thick detectors, and about
\SI{0.05}{\micro\ampere} for the thin ones (see \cref{fig:si_leakage}).
\begin{figure}[btp]
  \centering
    \includegraphics[width=0.85\textwidth]{figs/si_leakage}
  \caption{Leakage currents of the silicon detectors under bias.}
  \label{fig:si_leakage}
\end{figure}

The fact that a detector were fully depleted was checked by putting
a calibration source $^{241}\textrm{Am}$ at its ohmic side, and observing the
output
pulse height on an oscilloscope. One would expect that the maximum pulse height
increases as the bias is raised until the voltage of fully depleted. The effect
can also be seen on the pulse height spectrum as in
\cref{fig:sir2_bias_alpha}.
\begin{figure}[btp]
  \centering
    \includegraphics[width=0.75\textwidth]{figs/sir2_bias_alpha}
  \caption{$^{241}\textrm{Am}$ spectra in cases of fully depleted (top), and
    partly depleted (bottom).}
  \label{fig:sir2_bias_alpha}
\end{figure}

% subsubsection silicon_detectors (end)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsubsection{Upstream counters}
\label{sub:upstream_counters}
The upstream detector consists of three counters: a \SI{500}{\micro\meter}-thick
scintillator muon trigger counter ($\mu$SC); a muon anti-coincidence counter
($\mu$SCA) surrounding the trigger counter with a hole
of 35 \si{\milli\meter}\ in diameter to define the beam radius; and a multi-wire
proportional chamber ($\mu$PC) that uses 24 X wires and 24 Y wires at
2~\si{\milli\meter}~intervals. 

This set of detectors along with their read-out system
belong to the MuSun experiment, which operated at the same beam line just
before our run. Thanks to the MuSun group, the detectors were well-tuned and
ready to be used in our run without any modification.

% subsubsection upstream_counters (end)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

\subsubsection{Germanium detector}
%\begin{figure}[btp] 
	%\centering
	%\includegraphics[width=0.9\textwidth]{figs/neutron.png} 
	%\caption{Setup of two
	%liquid scintillators outside the vacuum envelope for neutron detection.}
	%\label{fig:neutron}
%\end{figure}
We used a germanium detector to normalise the number of stopped muons by
measuring characteristics muon X-rays from the target material. The primary
X-rays of interest are the 346.828~keV line for aluminium targets, and the
400.177 line for silicon targets. The energies and intensities of the X-rays
listed in \cref{tab:xray_ref} follow measurement results from
Measday and colleagues~\cite{MeasdayStocki.etal.2007}.
\begin{table}[btp]
  \begin{center}
    \begin{tabular}{c l l l l }
      \toprule
      \textbf{Elements}  & \textbf{Transition}
      & \textbf{Energy} & \textbf{Intensity}\\
      \midrule 
      $^{27}\textrm{Al}$ &  $2p-1s$ & $346.828 \pm 0.002$ & $79.8\pm 0.8$\\
         &  $3p-1s$ & $412.87  \pm 0.05$ &  $7.62\pm 0.15$\\
      \midrule
      $^{28}\textrm{Si}$ &  $2p-1s$ & $400.177 \pm 0.005$ & $80.3\pm 0.8$\\
       &  $3p-1s$ & $476.80 \pm 0.05$ & $7.40 \pm 0.20$\\
      \bottomrule
    \end{tabular}
  \end{center}
  \caption{Reference values of major muonic X-rays from aluminium and silicon.}
  \label{tab:xray_ref}
\end{table}

The germanium detector is
a GMX20P4-70-RB-B-PL, n-type, coaxial high purity germanium detector produced
by ORTEC. The detector was optimised for low energy gamma and X-rays
measurement with an ultra-thin entrance window of 0.5-mm-thick beryllium and
a 0.3-\si{\micro\meter}-thick ion implanted contact. The germanium crystal is
\SI{52.5}{\mm} in diameter, and \SI{55.3}{\mm} in length. The axial well has
a diameter of \SI{9.9}{\mm} and \SI{47.8}{\mm} deep.
%(\cref{fig:ge_det_dimensions}).

%\begin{figure}[btp]
  %\centering
    %\includegraphics[width=0.9\textwidth]{figs/ge_det_dimensions}
  %\caption{Dimensions of the germanium detector}
  %\label{fig:ge_det_dimensions}
%\end{figure}

The detector was installed outside of the vacuum chamber at 32 cm from the
target, viewing the target through a 10-mm-thick aluminium window, behind
a plastic scintillator counter used to veto electrons. Liquid nitrogen
necessary for the operation of the detector had to be refilled every 8 hours.

\subsubsection{Plastic and liquid scintillators}
\label{sub:plastic_scintillators}
Apart from the scintillators in the upstream group, there were four other
plastic scintillators used as veto counters for:
\begin{itemize}
  \item punch-through-the-target muons, ScVe
  \item electrons and other high energy charged particles for germanium
    detector (ScGe) and  silicon detectors (ScL and ScR)
\end{itemize}
The ScL, ScR and ScVe were installed inside the vacuum vessel and  were
optically connected to external PMTs by light-guides at the bottom flange. 

We also set up two liquid scintillation counters for neutron measurements in
preparation  for the next beam time where the neutron measurements will be
carried out.
% subsubsection plastic_scintillators (end)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsubsection{Front-end electronics and data acquisition system}
The front-end electronics of the AlCap experiment was simple since we employed
a trigger-less read out system with waveform digitisers and flash ADCs
(FADCs). As shown in \cref{fig:alcapdaq_scheme}, all plastic
scintillators signals were amplified by PMTs, then fed into the digitisers. The
signals from silicon and germanium detectors were preamplified, and
subsequently shaped by spectroscopy amplifiers and timing filter amplifiers
(TFAs) to provide energy and timing information.
\begin{figure}[btp]
  \centering
    \includegraphics[width=0.99\textwidth]{figs/alcapdaq_scheme}
  \caption{Schematic diagram of the electronics and DAQ used in the Run 2013}
  \label{fig:alcapdaq_scheme}
\end{figure}

The germanium detector has its own transistor reset preamplifier
installed very close to the germanium crystal. Two ORTEC Model 142
preamplifiers were used for the thick silicon detectors. The timing outputs of
the preamplifiers were fed into three ORTEC Model 579 TFAs.
We used an ORTEC Model 673 to shape the germanium signal with 6~\si{\micro\second}
shaping time.

A more modern-style electronics was used for thin silicon detectors where the
preamplifier, shaping and timing amplifiers were implemented on one compact
package, namely a Mesytec MSI-8 box. This box has 8 channels, each channel
consists of one preamplifier board and one shaper-and-timing filter board which
can be fine-tuned independently. The shaping time was set to 1~\si{\micro\second}\
for all channels.

The detector system produced signals that differs significantly in time scale,
ranging from very fast (about 40~\si{\nano\second}\ from scintillators) to very slow
(several \si{\micro\second}\ from shaping outputs of semiconductor detectors). This
lead to the use of several sampling frequencies from 17~\si{\mega\hertz}\ to
250~\si{\mega\hertz}, and three types of digitisers were employed:
\begin{itemize}
  \item custom-built 12-bit 170-MHz FADCs which was designed for the
    MuCap experiment. Each FADC board has the same dimensions as those of
    a single-width 6U VME module, but is hosted in a custom built crate due to
    its different power supply mechanical structure. The FADC communicates with
    a host computer through a 100-Mb/s Ethernet interface using a simple
    Ethernet-level protocol. The protocol only allows detecting
    incomplete data transfers but no retransmitting is possible due to the
    limited size of the module's output buffer. The FADCs accept clock signal
    at the frequency of  50~\si{\mega\hertz}\ then multiply that internally up to
    170~\si{\mega\hertz}.  Each channel on one board can run at different sampling
    frequency not dependent on other channels. The FADC has 8 single-ended
    LEMO inputs with 1~\si{\volt} pp dynamic range. 
  \item a 14-bit 100-MS/s CAEN VME FADC waveform digitiser model V1724. The
    module houses 8 channels with 2.25~Vpp dynamic range on single-ended MCX
    coaxial inputs. The digitiser features an optical link for transmission of
    data to its host computer. All of 8 channels run at the same sampling
    frequency and have one common trigger.
  \item a 12-bit 250-MS/s CAEN desktop waveform digitizer model DT5720. This
    digitiser is similar to the V1724, except for its form factor and maximum
    sampling frequency. Although there is an optical link available, the module
    is connected to its host computer through a USB 2.0 interface where data
    transfer rate of 30 MB/s was determined to be good enough in our run
    (actual data rate from this digitiser was typically about 5 MB/s during the
    run). Communication with both CAEN digitisers was based on CAEN's
    proprietary binary drivers and libraries.
\end{itemize}
All digitisers were driven by external clocks which were derived from the same
500-\si{\mega\hertz}\ master clock, a high precision RF signal generator Model SG382
of Stanford Research System.

The silicon detectors were read out by FADC boards feature network-based data
readout interface. To maximize the data throughput, each of the four FADC
boards was read out through separate network adapter. 
The CAEN digitisers were used to read out
the germanium detector (timing and energy, slow signals) or scintillator
detectors (fast signals). For redundancy, all beam monitors ($\mu$SC, $\mu$SCA
and $\mu$PC) were also read out by a CAEN time-to-digital converter (TDC)
model V767 which was kindly provided by the MuSun experiment. 

The Data Acquisition System (DAQ) of the AlCap experiment, so-called AlCapDAQ,
provided the readout of front-end electronics, event assembling, data logging,
hardware monitoring and control, and the run database of the experiment
(\cref{fig:alcapdaq_pcs}). It was based on the MIDAS framework~\footnote{
MIDAS is a general purpose DAQ software system developed at PSI and TRIUMF:\\
\url{http://midas.triumf.ca}} and consisted of two circuits, {\em i})
a detector circuit for synchronous data readout from the front-end electronics
instrumenting detectors, and {\em ii}) a slow control circuit for asynchronous
periodic hardware monitoring (vacuum, liquid nitrogen
filling).  The detector circuit consisted of three computers, two front-end
computers and one computer serving both as a front-end and as a back-end
processor. The slow circuit consisted of one computer. All computers were
running Linux operating system and connected into a private subnetwork. 

%\hl{TODO: storage and shift monitor}

\begin{figure}[btp]
  \centering
    \includegraphics[width=0.95\textwidth]{figs/alcapdaq_pcs}
  \caption{AlCapDAQ in the Run 2013. The {\ttfamily fe6} front-end is
    a VME single board computer belongs to the MuSun group, reads out the
    upstream detectors.}
  \label{fig:alcapdaq_pcs}
\end{figure}

The data were collected as dead-time-free time segments of 110~ms, called
``block'', followed by about 10-ms-long time intervals used to complete data
readout and synchronize the DAQ. Such data collection approach was chosen to
maximize the data readout efficiency. During each 110-ms-long period, signals
from each detector were digitized independently by threshold crossing. The data
segment of each detector data were first written into on-board memories of
front-end electronics and either read out in a loop (CAEN TDCs and CAEN
digitizers) or streamed (FADCs) into the computer memories. The thresholds were
adjusted as low as possible and individually for each detector.  The time
correlation between detectors would be established in the analysis stage.

At the beginning of each block, the time counter in each digitiser is reset to
ensure time alignment across all modules. The period of 110~ms was chosen to be:
{\em i}) long enough compared to the time scale of several \si{\micro\second}\
of the physics of interest, {\em ii}) short enough so that there is no timer
rollover on any digitiser (a FADC runs at its maximum speed of
\SI{170}{\mega\hertz} could handle up to about \SI{1.5}{\second} with its
28-bit time counter).

To ease the task of handling data, the data collecting period was divided into
short runs, each run stopped when the logger had recorded 2 GB of data.
The data size effectively made each run last for about 5 minutes. The DAQ
automatically started a new run with the same parameters after about 6 seconds.
The short period of each run also allows the detection, and helps to reduce the
influence of effects such as electronics drifting, temperature fluctuation.

