Index: trunk/paper/notes.tex
===================================================================
--- trunk/paper/notes.tex	(revision 99)
+++ trunk/paper/notes.tex	(revision 100)
@@ -1,3 +1,3 @@
-\documentclass[a4paper,11pt,oneside,twocolumn]{article}
+\documentclass[a4paper,11pt,oneside,onecolumn]{article}
 \usepackage[english]{babel}
 \usepackage[ansinew]{inputenc}
@@ -11,4 +11,5 @@
 \usepackage{latexsym}
 \usepackage{array}
+\usepackage{multicol}
 
 \usepackage{fancyhdr}
@@ -18,4 +19,6 @@
 \usepackage{ifpdf}
 \usepackage{cite}
+
+\newcommand{\dollar}{\$}
 
 \ifpdf
@@ -39,14 +42,9 @@
 \date{}
 
-
-% The \textsc{Delphes} software provides a framework for fast simulation of particle interactions in a generic high-energy physics collider detector containing a tracking system, electromagnetic and hadronic calorimeters, and a muon system. It is an object-oriented system writen using the C++ programming language. Using input files originating from a Monte-Carlo event generator such as \textsc{pythia} and \textsc{herwig}, \textsc{Delphes} creates ``high-level" analysis objects.\\ 
-% 
 \begin{document}
 
 
-\twocolumn[ 
 \maketitle
-% \begin{@twocolumnfalse}
-    \begin{onecolabstract}
+
 Knowing whether theoretical predictions are visible and measurable in a high energy experiment is always delicate, due to the
 complexity of the related detectors, data acquisition chain and software. We introduce here a new framework, \textsc{Delphes}, for fast simulation of
@@ -57,9 +55,6 @@
 An overview of \textsc{Delphes} is given as well as a few use-cases for illustration.
 \vspace{1cm}
-    \end{onecolabstract}
-% \end{@twocolumnfalse}
-]
+
 \saythanks
-
 
 \section{Introduction}
@@ -91,9 +86,8 @@
 \begin{tabular}[!h]{lll}
 \hline
-Sub-system   & Card flag & $|\eta|^{max}$\\\hline
-Tracking     & {\verb MAX_TRACKER } & 2.5\\
-Calorimeters & {\verb MAX_CALO_CEN } & 3.0\\
-             & {\verb MAX_CALO_FWD } & 5.0\\
-Muon         & {\verb MAX_MU } & 2.4\\\hline
+Tracking     & {\verb CEN_max_tracker } & 2.5\\
+Calorimeters & {\verb CEN_max_calo_cen } & 3.0\\
+             & {\verb CEN_max_calo_fwd } & 5.0\\
+Muon         & {\verb CEN_max_mu } & 2.4\\\hline
 \end{tabular}
 \label{tab:defEta}
@@ -187,6 +181,6 @@
 \subsection{Tau identification}
 
-\begin{wrapfigure}{l}{0.5\columnwidth}
-\includegraphics[width=0.5\columnwidth]{Tau.eps}
+\begin{wrapfigure}{l}{0.3\columnwidth}
+\includegraphics[width=0.3\columnwidth]{Tau.eps}
 \caption{\small{detectorAng.eps}}
 \label{h_WW_ss_cut1}
@@ -197,9 +191,9 @@
 \subsubsection*{Electromagnetic collimation}
 
-To use the narrowness of the $\tau$-jet, the \textit{electromagnetic collimation} ($C_{\tau}^{em}$) is defined as the sum of the energy in a cone with $\Delta R = ${\verb TAU_CONE_ENERGIE } around the jet axis divided by the energy of the reconstructed jet. The energy in the small cone is calculated using the towers objects. To be taken into account a calorimeter tower should have a transverse energy above a given threshold {\verb M_SEEDTHRESHOLD}. A large fraction of the jet energy, denominated here with {\verb TAU_EM_COLLIMATION } is expected in this small cone. The quantity is represented in figure \ref{fig:tau1} for the default values (see table \ref{tab:tauRef})
+To use the narrowness of the $\tau$-jet, the \textit{electromagnetic collimation} ($C_{\tau}^{em}$) is defined as the sum of the energy in a cone with $\Delta R = ${\verb TAU_energy_scone } around the jet axis divided by the energy of the reconstructed jet. The energy in the small cone is calculated using the towers objects. To be taken into account a calorimeter tower should have a transverse energy above a given threshold {\verb JET_M_seed }. A large fraction of the jet energy, denominated here with {\verb TAU_energy_frac } is expected in this small cone. The quantity is represented in figure \ref{fig:tau1} for the default values (see table \ref{tab:tauRef}).
 
 \begin{figure}[!h]
 \begin{center}
-\includegraphics[width=0.8\columnwidth]{figures/Taujets1.eps}
+%\includegraphics[width=0.8\columnwidth]{figures/Taujets1.eps}
 \caption{\small{}}
 \label{fig:tau1}
@@ -211,5 +205,5 @@
 \begin{figure}[!h]
 \begin{center}
-\includegraphics[width=0.8\columnwidth]{figures/Taujets2.eps}
+%\includegraphics[width=0.8\columnwidth]{figures/Taujets2.eps}
 \caption{\small{}}
 \label{h_WW_ss_cut1}
@@ -217,5 +211,5 @@
 \end{figure}
 
-The tracking isolation for the $\tau$ identification requires that the number of tracks associated to a particle with $p_T >$ {\verb PT_TRACK_TAU } is one and only one in a cone with $\Delta R =$ {\verb TAU_CONE_TRACKS }. This cone should be entirely included in the tracker to be taken into account. This procedure selects taus decaying hadronically with a typical efficiency of $60\%$. Moreover, the minimal $p_T$ of the $\tau$-jet is required to be {\verb TAUJET_pt }(default value: 10~GeV).\\
+The tracking isolation for the $\tau$ identification requires that the number of tracks associated to a particle with $p_T >$ {\verb TAU_track_pt } is one and only one in a cone with $\Delta R =$ {\verb TAU_track_scone }. This cone should be entirely included in the tracker to be taken into account. This procedure selects taus decaying hadronically with a typical efficiency of $60\%$. Moreover, the minimal $p_T$ of the $\tau$-jet is required to be {\verb TAUJET_pt }(default value: 10~GeV).\\
 
 \begin{table}[!h]
@@ -224,9 +218,9 @@
 \hline
 Tau definition  & Card flag & Value\\\hline
-$\Delta R^{for~em}$     & {\verb TAU_CONE_ENERGIE } & 0.15\\
-min $E_{T}^{tower}$     & {\verb M_SEEDTHRESHOLD }  & 1.0~GeV\\
-$C_{\tau}^{em}$         & {\verb TAU_EM_COLLIMATION } & 0.95.\\
-$\Delta R^{for~tracks}$ & {\verb TAU_CONE_TRACKS } & 0.4\\
-min $p_T^{tracks}$      & {\verb PT_TRACK_TAU } & 2 GeV\\\hline
+$\Delta R^{for~em}$     & {\verb TAU_energy_scone } & 0.15\\
+min $E_{T}^{tower}$     & {\verb JET_M_seed }  & 1.0~GeV\\
+$C_{\tau}^{em}$         & {\verb TAU_energy_frac } & 0.95.\\
+$\Delta R^{for~tracks}$ & {\verb TAU_track_scone } & 0.4\\
+min $p_T^{tracks}$      & {\verb PTAU_track_pt } & 2 GeV\\\hline
 \end{tabular}
 \label{tab:tauRef}
@@ -244,8 +238,108 @@
 \section{Conclusion and perspectives}
 
+
+\newpage
+
+\appendix
+
+\section{User manual}
+
+The available code is a tar file which comes with everything you need to run the DELPHES package. Nevertheless in order to visualise the events with the FROG program, you need to install libraries as explained in {\it href="http://projects.hepforge.org/frog/}
+
+\subsection{Getting started}
+
+In order to run DELPHES on your system, first download is sources and compile it:\\
+\begin{quote}
+\begin{verbatim}
+me@mylaptop:~$ wget http://www.fynu.ucl.ac.be/users/s.ovyn/files/Delphes_V_*.*.tar 
+me@mylaptop:~$ tar -xvf Delphes_V_*.*. tar  
+me@mylaptop:~$ cd Delphes_V_*.* 
+me@mylaptop:~$ ./genMakefile.tcl >; Makefile 
+me@mylaptop:~$ make 
+\end{verbatim}
+\end{quote}    
+
+
+\subsection{Running Delphes on your events}
+
+\subsubsection{Setting the run configuration}
+
+The program is driven by two datacards (default cards are data/DataCardDet.dat and data/trigger.dat) which allow a large spectrum of running conditions. 
+{\b The run card }\\
+
+Contains all needed information to run DELPHES
+\begin{itemize}
+  
+\item The following parameters are available: detector parameters, including calorimeter and tracking coverage and resolution, transverse energy thresholds allowed for reconstructed objects, jet algorithm to use as well as jet parameters. 
+  
+\item Four flags, {\verb FLAG_bfield }, {\verb FLAG_vfd }, {\verb FLAG_trigger } and {\verb FLAG_frog } should be assigned to decide if the magnetic field propagation, the very forward detectors acceptance, the trigger selection and the preparation for FROG display respectively are running by DELPHES.
+  
+\item An example (the default detector card) can be found in {\verb files/DataCardDet.dat }
+\end{itemize}
+
+{\b The trigger card }\\
+Contains the definition of all trigger bits
+\begin{itemize}
+  
+\item Cuts can be applied on the transverse momentum of electrons, muons, jets, tau-jets, photons and transverse missing energy.
+\item Be careful that the following structured should be used: 
+  \begin{enumerate}
+  \item One trigger bit per line, the first entry in the line is the name of the trigger bit 
+  \item If the trigger bit uses the presence of multiple identical objects, their transverse momentum thresholds must be defined in decreasing order 
+  \item The different object requirements must be separated by a {\verb && } flag
+  \item Example of a trigger bit line:\\
+    \begin{quote}
+\begin{verbatim}	
+DoubleElec  >> ELEC1_PT: '20' && ELEC2_PT: '10'    
+\end{verbatim}
+    \end{quote}
+  \end{enumerate}
+\item An example (the default trigger card) can be found <a href="files/trigger.dat" title="Home">here</a></li>
+\end{itemize}
+
+\subsubsection{Running the code}
+Create the above cards (data/mydetector.dat and data/mytrigger.dat)
+Create a text file containing the list of input files that will be used by DELPHES (with extension *.lhe, *.root or *.hep)
+To run the code, type the following
+\begin{quote}
+\begin{verbatim}
+me@mylaptop:~$ ./Delphes inputlist.list OutputRootFileName.root data/mydetector.dat data/mytrigger.dat
+\end{verbatim}
+\end{quote}
+
+
+\subsection{Running an analysis on your Delphes events}
+
+Two examples of codes running on the output root file of DELPHES are coming with the package
+\begin{enumerate}
+\item The {\verb Examples/Analysis_Ex.cpp } code shows how to access the available reconstructed objects and the trigger information The two following arguments are required: a text file containing the input DELPHES root files to run, and the name of the output root file. To run the code:
+  \begin{quote}
+\begin{verbatim}
+./Analysis_Ex input_file.list output_file.root
+\end{verbatim}
+  \end{quote}
+  
+\item The {\verb Examples/Trigger_Only.cpp } code permits to run the trigger selection separately from the general detector simulation on output DELPHES root files. An input DELPHES root file is mandatory as argument. The new tree containing the trigger information will be added in these file. The trigger datacard is also necessary. To run the code:
+  \begin{quote}
+\begin{verbatim}
+./Trigger_Only input_file.root data/trigger.dat
+\end{verbatim}
+  \end{quote}
+  
+\end{enumerate}
+
+\subsection{Running the FROG event display}
+
+\begin{itemize}
+\item If the { \verb FLAG_frog } was switched on, two files were created during the run of DELPHES: {\verb DelphesToFrog.vis } and {\verb DelphesToFrog.geom }. They contain all the needed information to run frog.
+\item To display the events and the geometry, you first need to compile FROG. Go to the {\verb Utilities/FROG } and type {\verb make }.
+\item Go back into the main directory and type {\verb ./Utilities/FROG/frog }.
+\end{itemize}
+
 \begin{thebibliography}{99}
+  
 \bibitem{Delphes} \textsc{Delphes}, hepforge:
 \end{thebibliography}
-\appendix
+
 Attention : in SmearUtil::NumTracks, the function arguments 'Eta' and 'Phi' have been switched. Previously, 'Phi' was before 'Eta', now 'Eta' comes in front. This is for consistency with the other functions in SmearUtil. Check your routines, when using NumTracks !
 
