MANUAL OF VERSION 4.1 ......... DONE

git-svn-id: svn+ssh://svn.in2p3.fr/class@779 0e7d625b-0364-4367-a6be-d5be4a48d228

documentation/trunk/Manual/GeneralOverview.tex

@@ -368,7 +368,7 @@ Storage* MyStorage4 = new Storage(Logger);
 Pool* MyPool1 = new Pool(Logger, MyStorage1, 5*365.25*24*3600);
 
 // SeparationPlant separate U5 from U8 which goes in Storage 3 and 4.
-SeparationPlan* MySeparation1 = new SeparationPlant(Logger);
+SeparationPlant* MySeparation1 = new SeparationPlant(Logger);
 IsotopicVector IV_U8;
 IV_U8.Add(92, 238, 0, 1);
 MySeparationPlant1->SetBackEndDestination(MyStorage3, IV_U8, 0);
@@ -379,7 +379,7 @@ MySeparationPlant1->SetBackEndDestination(MyStorage4, IV_U5, 0);
 					
 
 // SeparationPlant separate Am Pu and U which goes respectively in myPool1, myStorage2 and mySeparationPlan1.
-SeparationPlan* MySeparation2 = new SeparationPlant(Logger);
+SeparationPlant* MySeparation2 = new SeparationPlant(Logger);
 IsotopicVector IV_MA;
 IV_MA.Add(95, 242, 1, 1.);
 MySeparationPlant2->SetBackEndDestination(MyPool1, IV_MA, 0);
@@ -757,7 +757,7 @@ gCLASS->SetTimeStep(365.25*24*3600/12); // monthly output
 
 
 \subsection{Reading a CLASS ouput}
-There is an easy way and an hard way to read CLASS outputs. The easy one is via the Graphical User Interface CLASSGui (see section~). This is an user friendly approach but as it is graphical it comes with its limitations. The hard way allows to access anything
+There is an easy way and an hard way to read CLASS outputs. The easy one is via the Graphical User Interface CLASSGui (see section~\ref{part:GUI}). This is an user friendly approach but as it is graphical it comes with its limitations. The hard way allows to access anything in your scenario evolution. This last approach requieres to write a specific .cxx file in which you can access any information you want by using the objects and methods of CLASS libraries. A detailed example of this approach can be found in \$CLASS\_PATH/example/ReadOuput.cxx. You are encouraged to read carefully the comments in this file to learn how to access the data you want. 
 
 
 

documentation/trunk/Manual/Introduction.tex

@@ -42,7 +42,7 @@ The CLASS package contains the followings :
  \subitem \textbf{Manual/}    : folder containing this user guide an its .tex sources
  \subitem \textbf{Doxygen/}   : folder containing the builded doxygen and its generation configuration 
 
-\item \textbf{example/} : folder containing simple examples of CLASS input
+\item \textbf{example/} : folder containing simple examples of CLASS input and an example of CLASS ouput reader
 
 \item \textbf{gui/} : folder containing sources of the graphical user interface for CLASS outputs
  \subitem \textbf{bin/}    : folder containing the CLASSGui binary (once comiled)
@@ -74,11 +74,11 @@ Experience in depletion codes and neutron transport codes.
 Make sure you have installed XCode and its command line tools (if not dowload and install from AppStore).\\ 
 Install \href{http://xquartz.macosforge.org/landing/}{XQuartz}\footnote{http://xquartz.macosforge.org/landing/}.\\
 We recommend NOT to use the clang compiler as there is no openmp library in it but the compilation should work with clang anyway\\
-TO INSTALL GNU COMPILER : You should install  \href{https://www.macports.org/install.php}{MacPorts}\footnote{https://www.macports.org/install.php} in order to get a gnu compiler.\\
-Then types this following command in terminal :\\
+TO INSTALL GNU COMPILER : You should install first \href{https://www.macports.org/install.php}{MacPorts}\footnote{https://www.macports.org/install.php} \\
+Then, types this following command in terminal :\\
 \begin{lstlisting}[style=terminal]
-sudo port install gcc48
-sudo port select --set gcc mp-gcc48
+sudo port install gcc5
+sudo port select --set gcc mp-gcc5
 \end{lstlisting}
 \item Root (CERN) :  
 CLASS uses Root to store output data. 
@@ -304,7 +304,7 @@ LOADING /Users/leniau/.tcshrc ... done
 \end{minipage}
 \end{center}
 
-Please report installation issue to the \href{https://forge.in2p3.fr/projects/classforge/issues/new}{forge}\footnote{https://forge.in2p3.fr/projects/classforge/issues/new}.
+Please report installation issues to the \href{https://forge.in2p3.fr/projects/classforge/issues/new}{forge}\footnote{https://forge.in2p3.fr/projects/classforge/issues/new}.
 
 \chapter{CLASS Execution}
 CLASS is a set of C++ libraries, there is no CLASS binary file. A CLASS executable has to be build by user using objects and methods defined in the CLASS package. \\
@@ -332,8 +332,8 @@ The following should show in your terminal :
     \begin{figure}[H]
     \centering
     \centerline{\includegraphics[scale=0.9]{CLASS_Run.png}}
-    \caption{CLASS logo}
-    \label{fig:CLASSLogo}
+    \caption{CLASS running in a shell}
+    \label{fig:CLASSRUN}
     \end{figure}
 
 

documentation/trunk/Manual/USEGUIDE.tex

@@ -43,6 +43,7 @@
 %% CHAPTER :	CLASSGUI
 %%%%%%%%%%%%%%%%%%%%%%%%%
 \part{CLASSGui : The results viewer}
+\label{part:GUI}
 To use the CLASSGui :
 \begin{center}
 \begin{minipage}{\textwidth}

documentation/trunk/Manual/bstyle.sty

@@ -15,7 +15,7 @@
 \usepackage{amssymb}
 \usepackage{mathrsfs}
 \usepackage{booktabs}
-\usepackage[colorlinks,linkcolor=blue]{hyperref}
+\usepackage[colorlinks=true, linkcolor=blue, urlcolor=red,  linktoc=all, citecolor=green]{hyperref}
 \usepackage{array}
 \usepackage{enumerate}
 \usepackage{epsfig}
@@ -42,13 +42,12 @@
 
 
 \hypersetup{
-    colorlinks=true, %set true if you want colored links
+  %  colorlinks=true, %set true if you want colored links
     linktoc=all,     %set to all if you want both sections and subsections linked
-    linkcolor=black,  %choose some color if you want links to stand out
+ %   linkcolor=black,  %choose some color if you want links to stand out
 }
 
 \usepackage{float}
-\usepackage{hyperref}
 \usepackage{xcolor}
 \usepackage{listings}     %Insérer du code source d'un pgm
 %\lstset{