Index: palm/trunk/TUTORIAL/SOURCE/exercise_cbl.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/exercise_cbl.tex	(revision 949)
+++ palm/trunk/TUTORIAL/SOURCE/exercise_cbl.tex	(revision 954)
@@ -56,6 +56,6 @@
 \end{frame}
 
-\section{Exercise 1: Convection Between Plates}
-\subsection{Exercise 1: Convective Between Plates}
+\section{Exercise}
+\subsection{Exercise}
 
 % Folie 2
@@ -207,5 +207,60 @@
 \end{frame}
 
-
-
+% Folie 8
+\section{Results}
+\subsection{Results}
+
+\begin{frame}
+   \frametitle{$xy$-cross sections (instantaneous)}
+   \begin{center}
+      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_100.eps}
+      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_500.eps}\\
+      \includegraphics[width=0.42\textwidth]{exercise_cbl_figures/xy_w_750.eps}
+   \end{center}
+\end{frame}
+
+% Folie 9
+\begin{frame}
+   \frametitle{$xz$-cross sections ($\unit[900]{s}$ average)}
+   \begin{center}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y250m.eps}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y500m.eps}\\
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y750m.eps}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/xz_w_y1000m.eps}
+   \end{center}
+\end{frame}
+
+% Folie 10
+\begin{frame}
+   \frametitle{Vertical profiles (I)}
+   \begin{center}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_pt.eps}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt.eps}
+   \end{center}
+\end{frame}
+
+% Folie 11
+\begin{frame}
+   \frametitle{LES?}
+   \begin{center}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt2.eps}
+      \includegraphics[width=0.55\textwidth]{exercise_cbl_figures/pr_wpt_resolved.eps}
+   \end{center}
+\end{frame}
+
+% Folie 12
+\begin{frame}
+   \frametitle{Time series (I)}
+   \begin{center}
+      \includegraphics[width=1.0\textwidth]{exercise_cbl_figures/ts.eps}
+   \end{center}
+\end{frame}
+
+% Folie 13
+\begin{frame}
+   \frametitle{Time series (II)}
+   \begin{center}
+      \includegraphics[width=1.0\textwidth]{exercise_cbl_figures/ts2.eps}
+   \end{center}
+\end{frame}
 \end{document}
Index: palm/trunk/TUTORIAL/SOURCE/exercise_neutral.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/exercise_neutral.tex	(revision 954)
+++ palm/trunk/TUTORIAL/SOURCE/exercise_neutral.tex	(revision 954)
@@ -0,0 +1,184 @@
+% $Id$
+\input{header_tmp.tex}
+%\input{../header_lectures.tex}
+
+\usepackage[utf8]{inputenc}
+\usepackage{ngerman}
+\usepackage{pgf}
+\usetheme{Dresden}
+\usepackage{subfigure}
+\usepackage{units}
+\usepackage{tabto}
+\usepackage{multimedia}
+\usepackage{hyperref}
+\newcommand{\event}[1]{\newcommand{\eventname}{#1}}
+\usepackage{xmpmulti}
+\usepackage{tikz}
+\usetikzlibrary{shapes,arrows,positioning}
+\usetikzlibrary{decorations.markings}             %neues paket
+\usetikzlibrary{decorations.pathreplacing}        %neues paket
+\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{multicol}
+\usepackage{pdfcomment}
+\usepackage{graphicx}
+\usepackage{listings}
+\lstset{showspaces=false,language=fortran,basicstyle=
+        \ttfamily,showstringspaces=false,captionpos=b}
+
+\institute{Institut fÃŒr Meteorologie und Klimatologie, Leibniz UniversitÃ€t Hannover}
+\date{last update: \today}
+\event{PALM Seminar}
+\setbeamertemplate{navigation symbols}{}
+
+\setbeamertemplate{footline}
+  {
+    \begin{beamercolorbox}[rightskip=-0.1cm]&
+     {\includegraphics[height=0.65cm]{imuk_logo.pdf}\hfill \includegraphics[height=0.65cm]{luh_logo.pdf}}
+    \end{beamercolorbox}
+    \begin{beamercolorbox}[ht=2.5ex,dp=1.125ex,
+      leftskip=.3cm,rightskip=0.3cm plus1fil]{title in head/foot}
+      {\leavevmode{\usebeamerfont{author in head/foot}\insertshortauthor} \hfill \eventname \hfill \insertframenumber \; / \inserttotalframenumber}
+    \end{beamercolorbox}
+    \begin{beamercolorbox}[colsep=1.5pt]{lower separation line foot}
+    \end{beamercolorbox}
+  }
+%\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
+
+\title[Exercise 2: Neutrally Stratified  Boundary Layer]{Exercise 2: Neutrally Stratified  Boundary Layer}
+\author{Siegfried Raasch}
+
+\setbeamersize{text margin left=.2cm,text margin right=.2cm}
+
+\begin{document}
+\footnotesize
+% Folie 1
+\begin{frame}
+\titlepage
+\end{frame}
+
+\section{Exercise}
+\subsection{Exercise}
+
+% Folie 2
+\begin{frame}
+   \frametitle{Exercise 2: Neutrally Stratified  Atmospheric Boundary Layer}
+   \begin{itemize}
+      \item The simulation should be for a neutrally stratified atmospheric boundary layer.
+      \item<2-> The flow should be driven by a constant large-scale pressure gradient, i.e. a geostrophic wind.
+      \item<3-> At the end of the simulation, turbulence as well as the mean flow should be in a stationary state.
+   \end{itemize}
+   \onslide<4->\textbf{Simulation features:}
+    \begin{itemize}
+          \item<4-> geostrophic wind:  \tabto{3cm} $u_\mathrm{g} = \unit[5]{m\ s^{-1}}, v_\mathrm{g} = \unit[0]{m\ s^{-1}}$
+          \item<5-> initial velocity:  \tabto{3cm} try constant velocity ($u = u_\mathrm{g}, v = v_\mathrm{g}$, everywhere)\\ 
+                    \tabto{3cm} or a mean vertical profile created by the 1D-model
+          \item<6-> roughness length:  \tabto{3cm} $z_0 = \unit[0.1]{m}$
+    \end{itemize}
+\onslide<7->Please choose domain size, grid size and time to be simulated appropriately.
+\end{frame}
+
+% Folie 3
+\begin{frame}
+   \frametitle{Questions to be Answered:}
+    \begin{itemize}
+       \item<1-> How long do you have to simulate until turbulence / mean flow become stationary?
+       \vspace{1em}
+       \item<2-> How do the horizontally and temporally averaged vertical velocity and momentum flux profiles look like?
+       \vspace{1em}
+       \item<3-> Is it really a large-eddy simulation, i.e. are the subgrid-scale fluxes much smaller than the resolved-scale fluxes?
+       \vspace{1em}
+       \item<4-> How does the turbulence spectra of $u$, $v$, $w$, along $x$ and along $y$ look like?\\
+                 Can you identify the inertial subrange?
+    \end{itemize}
+\end{frame}
+
+% Folie 4
+ \begin{frame}
+    \frametitle{Hints (I)}
+     \begin{itemize}
+        \item<1-> Please remember hints given for the previous exercise!
+        \item<2-> \textbf{Initial profiles:}
+        \begin{itemize}
+           \tiny
+           \item<3-> The 1D-model (\texttt{\textcolor{blue}{initializing\_actions} = 'set\_1d-model\_profiles'}) is mainly controlled by parameters \texttt{\textcolor{blue}{end\_time\_1d}} and \texttt{\textcolor{blue}{damp\_level\_1d}}. Please keep in mind that the profiles from the 1D-model should also be in a stationary state.
+           \vspace{0.5em}
+            \item<3-> Output of vertical profile data generated by the 1D-model is controlled by parameter \texttt{\textcolor{blue}{dt\_pr\_1d}}. It is in ASCII-format and it is written into a separate file. You can include the profiles of the 1D-model, which are used to initialize the 3D-model, in the standard profile data output of the 3D-model (which is controlled by parameter \texttt{\textcolor{blue}{data\_output\_pr}}) by adding a \texttt{'\#'} sign to the respective output quantitiy, e.g. \texttt{\textcolor{blue}{data\_output\_pr} = '\#u'}.
+           \vspace{0.5em}
+            \item<3-> For the 1D-model, please set \texttt{\textcolor{blue}{mixing\_length} = 'blackadar'} and \texttt{\textcolor{blue}{dissipation\_1d} = 'detering'} in order to get a correct mean boundary layer wind profile. The default settings of these parameters would switch the turbulence parameterization of the 1D-model to the SGS-parameterization of the 3D-LES-model, which represents only the SGS-parts of turbulence. However, for this exercise the 1D-model has to parameterize all scales of turbulence (i.e. it should be used as a RANS-model).
+        \end{itemize}
+
+        \item<4-> \textbf{Stationary state:}
+        \begin{itemize}
+           \tiny
+           \item<4-> You probably will find it difficult to get the mean flow to a stationary state (for the 1D-model as well as for the 3D-model. Can you identify the mechanism responsible for this? Try parameters \texttt{\textcolor{blue}{damp\_level\_1d}} (for the 1D-model) and \texttt{\textcolor{blue}{rayleigh\_damping\_factor}} (for the 3D-model; this is a \texttt{d3par}-parameter!) to overcome this problem.
+           \vspace{0.5em}
+           \item<5-> You can switch on a Galilei-transformation in order to save CPU-time (see parameter \texttt{\textcolor{blue}{galilei\_transformation}}).
+        \end{itemize}
+
+     \end{itemize}
+ \end{frame}
+
+% Folie 5
+ \begin{frame}
+    \frametitle{Hints (II)}
+     \begin{itemize}
+        \item<1-> \textbf{Spectra:}
+        \begin{itemize}
+           \scriptsize
+           \item<2-> Output of spectra requires to switch on the spectra-package using \textbf{mrun}-option \texttt{-p}:\\
+                     \texttt{mrun ... -p spectra}
+           \vspace{0.5em}
+           \item<3-> Spectra output is controlled by parameters \texttt{\textcolor{blue}{data\_output\_sp}}, \texttt{\textcolor{blue}{dt\_dosp}}, etc. These package-parameters have to be given     in a separate NAMELIST-block which has to follow the \texttt{d3par}-block:\\
+                     \texttt{\&d3par end\_time = ... /}\\
+                     \texttt{\&spectra\_par data\_output\_sp = ... /}\\
+        \end{itemize}
+     \end{itemize}
+ \end{frame}
+
+% Folie 6
+\section{Results}
+\subsection{Results}
+
+% Folie 7
+\begin{frame}
+   \frametitle{Time series of TKE}
+   \begin{center}
+      \includegraphics[width=1.0\textwidth]{exercise_neutral_figures/ts.eps}
+   \end{center}
+\end{frame}
+
+% Folie 8
+\begin{frame}
+   \frametitle{Vertical profiles of $\overline{w'u'}$, $\overline{w'v'}$}
+   \begin{center}
+      \includegraphics[width=0.50\textwidth]{exercise_neutral_figures/pr_wu.eps}
+      \includegraphics[width=0.50\textwidth]{exercise_neutral_figures/pr_wv.eps}\\
+   \end{center}
+\end{frame}
+
+% Folie 9
+\begin{frame}
+   \frametitle{Vertical profiles of $\overline{w'u'}$, $\overline{w'v'}$}
+   \begin{center}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/pr_wu_sgs.eps}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/pr_wv_sgs.eps}\\
+      \vspace{-0.3em}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/pr_wu_resolved.eps}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/pr_wv_resolved.eps}\\
+   \end{center}
+\end{frame}
+
+% Folie 10
+\begin{frame}
+   \frametitle{Spectra of $u$, $v$ and $w$}
+      \hspace{-1em}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/sp_u.eps}
+      \hspace{-2em}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/sp_v.eps}
+      \hspace{-2em}
+      \includegraphics[width=0.36\textwidth]{exercise_neutral_figures/sp_w.eps}
+\end{frame}
+
+\end{document}
Index: palm/trunk/TUTORIAL/SOURCE/particle_model.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/particle_model.tex	(revision 949)
+++ palm/trunk/TUTORIAL/SOURCE/particle_model.tex	(revision 954)
@@ -412,7 +412,4 @@
             \node[text width=6em] at (2.8,-2.1) {\scriptsize Calculation of particle trajectories begins (default value: 0.0)};
       
-      
-      
-      
             \onslide<3->
             \draw[->, ultra thick, color=red] (5,0.5) -- (5,-0.5);
@@ -420,6 +417,4 @@
             \node at (3.75,0.3) {\scriptsize \texttt{dt\underline{ }prel}};
             \draw[<->, thick, color=blue] (2.5,0.6) -- (4.95,0.6); 
-      
-      
       
             \onslide<4->
@@ -867,5 +862,5 @@
    \small
    \vspace{1mm}
-   The position of a particle is found by integrating $ \dfrac{dX_{\text{particle}}}{dt} = \vec{V}_{\text{particle}}$\\
+   The position of a particle is found by integrating $ \dfrac{d \vec{X}_{\text{particle}}}{dt} = \vec{V}_{\text{particle}}$\\
    \vspace{2mm}
    \onslide<2->Transferring the LES concept ...
@@ -982,5 +977,5 @@
    Assumption: subgrid scale turbulence locally isotropic\\
    \vspace{6mm}
-   $dV_{\text{sub}_i} = - \dfrac{3 f_s C_0}{4} \dfrac{V_{\text{sub}_i}}{e_s} dt + \dfrac{1}{3} \left( \dfrac{\partial e_s}{\partial x_i} + \dfrac{3}{2 e_s} \dfrac{d e_s}{dt} V_{\text{sub}_i}\right) dt + \sqrt{f_s C_0 \varepsilon}\, d\xi_i$\\
+   $dV_{\text{sub}_i} = - \dfrac{3 f_s C_0 \varepsilon}{4} \dfrac{V_{\text{sub}_i}}{e_s} dt + \dfrac{1}{3} \left( \dfrac{\partial e_s}{\partial x_i} + \dfrac{3}{2 e_s} \dfrac{d e_s}{dt} V_{\text{sub}_i}\right) dt + \sqrt{f_s C_0 \varepsilon}\, d\xi_i$\\
    \vspace{2mm}
    $f_s = \dfrac{\langle 2 e_s / 3 \rangle}{\langle 2 e_s / 3 \rangle + \langle \left( \sigma^2_{\text{res}U} + \sigma^2_{\text{res}V} + \sigma^2_{\text{res}W} \right) /3 \rangle}$\\
@@ -1266,5 +1261,5 @@
       \node (0) at (0,0) {};
       \node[draw, right=0.0cm of 0] {In case of cloud droplets: calculate the liquid water content};
-      \uncover<2->{\node[draw, right=0.0cm of 0, yshift=-0.6cm] {user defined setting of particle attributes (subroutine user\underline{ }particle\underline{ }attributes)};}
+      \uncover<2->{\node[draw, right=0.0cm of 0, yshift=-0.6cm] {user defined setting of particle attributes (subroutine \texttt{user\underline{ }particle\underline{ }attributes})};}
       \uncover<3->{\node[draw, right=0.0cm of 0, yshift=-1.2cm] {if necessary, add actual positions to the particle tails};}
       \uncover<4->{\node[draw, right=0.0cm of 0, yshift=-1.8cm] {write particle statistics on file \texttt{PARTICLE\underline{ }INFOS} (ASCII format)};  }    
@@ -1350,5 +1345,5 @@
    \includegraphics[scale=0.5]{particle_model_figures/footprint3_2.png}
    \begin{itemize}
-      \item particles are released every 2min over a period of 30min at z=70m in the total model domain ($\rightarrow$ 7 * 106 particles)
+      \item particles are released every 2min over a period of 30min at z=70m in the total model domain ($\rightarrow$ 7 * $10^6$ particles)
       \item particles are measured at z=72.5m, 77.5m, 100.0m
    \end{itemize}
Index: palm/trunk/TUTORIAL/SOURCE/program_control.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/program_control.tex	(revision 949)
+++ palm/trunk/TUTORIAL/SOURCE/program_control.tex	(revision 954)
@@ -1,5 +1,5 @@
 % $Id$
 \input{header_tmp.tex}
-%\input{header_lectures.tex}
+%\input{header_LECTURE.tex}
 
 \usepackage[utf8]{inputenc}
@@ -290,5 +290,5 @@
       errors have occurred!}}
    \par\bigskip
-   \includegraphics[width=1.6\textwidth]{program_control_figures/run_control_file.png}
+   \includegraphics[width=\textwidth]{program_control_figures/run_control_file.png}
    \normalsize
 \end{frame}
Index: palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex
===================================================================
--- palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex	(revision 949)
+++ palm/trunk/TUTORIAL/SOURCE/runs_with_mrun.tex	(revision 954)
@@ -42,4 +42,5 @@
     \end{beamercolorbox}
   }
+
 %\logo{\includegraphics[width=0.3\textwidth]{luhimuk_logo.pdf}}
 
@@ -64,9 +65,11 @@
       \texttt{ksh}-syntax) which can be used to compile and run programs, including 
       the handling of input/output files.
+      \vspace{4mm}
       \item<2-> The \texttt{mrun}-command has a number of options to control the 
       program execution\\
-         \quad \footnotesize \texttt{mrun -d example\_cbl -h lcsgih -K parallel -X8 -T2 ...}\\
+         \quad \footnotesize \texttt{mrun -d example\underline{ }cbl -h lcsgih -K parallel -X8 -T2 ...}\\
          \normalsize All options including a short description can be displayed by entering\\
          \quad \footnotesize \texttt{mrun ?}
+      \vspace{4mm}
       \item<3-> \normalsize The shellscript execution is also controlled by a configuration file with default name \texttt{.mrun.config} 
    \end{itemize}
@@ -75,10 +78,9 @@
 % Folie 3
 \begin{frame}
-   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\scriptsize]
-   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, 
-   font=\scriptsize]
-   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\scriptsize]
-   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\scriptsize]
-   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\scriptsize]
+   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.1\textwidth, font=\tiny]
+   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.22\textwidth, font=\tiny]
+   \tikzstyle{info} = [rectangle, text width=0.15\textwidth, font=\tiny]
+   \tikzstyle{white} = [rectangle, text width=0.7\textwidth, font=\tiny]
+   \tikzstyle{dummy} = [rectangle, text width=0.3\textwidth, font=\tiny]
    \tikzstyle{line} = [draw, -]
    \tikzstyle{alert} = [rectangle, draw, text width=0.77\textwidth, font=\scriptsize]
@@ -86,11 +88,13 @@
    \scriptsize
    \frametitle{Carrying Out Runs Using \texttt{mrun}}
-   Carrying out a program run typically needs two steps:\\
-   1. compilation\\
-   \quad \texttt{f90  ...  file1.f90 file2.f90 ...}\\
-   \onslide<2-> 2. execution\\
-   \quad \texttt{a.out}\\
+   \textbf{Carrying out a program run typically needs two steps:}\\
    \vspace{1mm}
-   \onslide<3->Besides, a program needs input data and creates output data:\\
+   \quad 1. compilation\\
+   \qquad \texttt{f90  ...  file1.f90 file2.f90 ...}\\
+   \vspace{1mm}
+   \onslide<2->\quad 2. execution\\
+   \qquad \texttt{a.out}\\
+   \vspace{3mm}
+   \onslide<3->\textbf{Besides, a program needs input data and creates output data:}\\
    
    \onslide<4->\begin{tikzpicture}[auto, node distance=0]
@@ -98,6 +102,6 @@
       \node [dummy, right=0.1cm of first] (second) {};
       
-      \node [yellow, above=0.5cm of second] (third) {\textbf{parameter for steering}};
-      \node [yellow, below=0.5cm of third] (fourth) {\textbf{control output}};
+      \node [yellow, above=0.4cm of second] (third) {\textbf{parameter for steering}};
+      \node [yellow, below=0.4cm of third] (fourth) {\textbf{control output}};
       \node [yellow, below=0.3cm of fourth] (fifth) {\textbf{output for analysis}};
       
@@ -113,20 +117,19 @@
          \texttt{OPEN (11, FILE='PARIN', FORM='FORMATTED')}};}
       \uncover<5->{\node [white, right=0.25cm of fourth] (tenth) {
-         \texttt{OPEN (15, FILE='RUN\_CONTROL', FORM='FORMATTED')}};}
+         \texttt{OPEN (15, FILE='RUN\underline{ }CONTROL', FORM='FORMATTED')}};}
       \uncover<5->{\node [white, right=0.25cm of fifth] (eleventh) {
-         \texttt{OPEN (40, FILE=âDATA\_1D\_PR\_NETCDF', FORM='FORMATTED')}};}
+         \texttt{OPEN (40, FILE=âDATA\underline{ }1D\underline{ }PR\underline{ }NETCDF', FORM='FORMATTED')}};}
    \end{tikzpicture}
    
-   \vspace{1mm}
+   \vspace{3mm}
    \scriptsize
-   \onslide<6->\textcolor{red}{Problems: The user has to copy or rename output files, if 
+   \onslide<6->\textcolor{red}{\textbf{Problems:} The user has to copy or rename output files, if 
    he/she wants to run the program more than once and if he concurrently wants to keep 
-   the files from the former run(s).
+   the files from the former run(s).\\
    If he/she is using different input parameter files for steering, these files also have 
    to be copied into the working directory before the program is executed.}\\
-   \ \\
+   \vspace{1mm}
    \begin{tikzpicture}[auto, node distance=0] 
-      \uncover<7->{\node [alert] (alert) {\textcolor{red}{It is therefore very desirable 
-      to automate these tasks!}};}
+      \uncover<7->{\node [alert] (alert) {\textcolor{red}{\textbf{It is therefore very desirable to automate these tasks!}}};}
    \end{tikzpicture}
 \end{frame}
@@ -140,7 +143,6 @@
    
    \frametitle{\texttt{mrun}: Principal Mode of Operation (I)}
-   \texttt{mrun} runs a program (in our case the PALM model) by carrying out the 
-   following principle tasks in a sequential order:\\
-   \scriptsize
+   \scriptsize \texttt{mrun} \textbf{runs a program (in our case the PALM model) by carrying out the following principle tasks in a sequential order:}\\
+   \vspace{1mm}
    \begin{enumerate}
       \item<2-> Create a temporary working directory and change into this directory:\\
@@ -149,10 +151,10 @@
       \ \\
       The path of \texttt{<tempdir>} is given in the configuration file 
-      \texttt{.mrun.config} by the environment variable \texttt{tmp\_user\_catalog}, e.g.:\\
-	   \quad \texttt{\%tmp\_user\_catalog  /tmp \hspace{30mm} <hi>  parallel}\\
+      \texttt{.mrun.config} by the environment variable \texttt{tmp\underline{ }user\underline{ }catalog}, e.g.:\\
+	   \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /tmp \hspace{30mm} <hi>  parallel}\\
 	   \ \\
 	   \onslide<3-> On SGI-ICE: \\
-	   \quad \texttt{\%tmp\_user\_catalog  /gfs2/work/<username> 
-	   \hspace{5mm} <hi>  lcsgih parallel}
+	   \quad \texttt{\%tmp\underline{ }user\underline{ }catalog  /gfs2/work/<username> 
+	   \hspace{5mm} lcsgih parallel}
 	   \begin{center}
 	      \begin{tikzpicture}[auto, node distance=0] 
@@ -160,10 +162,13 @@
          \end{tikzpicture}
 	   \end{center}
+	   \vspace{2mm}
 	   \item<5-> Copy the input files from a directory of the user into this working directory:\\
-	   \scriptsize
-	   \onslide<6->\hspace{-15mm} \texttt{cp <user\_input\_file1> 
-	   /tmp/<username>.<randomnumber>/<temporary\_input\_file1>}\\
-      \hspace{-15mm} \texttt{cp <user\_input\_file2> 
-      /tmp/<username>.<randomnumber>/<temporary\_input\_file2>}
+	   \vspace{1mm}
+	   \onslide<6-> \tiny \quad \texttt{cp <user\underline{ }input\underline{ }file1> 
+	   /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file1>}\\
+      \quad \texttt{cp <user\underline{ }input\underline{ }file2> 
+      /tmp/<username>.<randomnumber>/<temporary\underline{ }input\underline{ }file2>}\\
+      \vspace{2mm}
+      \scriptsize
       \begin{center}
 	      \begin{tikzpicture}[auto, node distance=0] 
@@ -172,6 +177,6 @@
        
             \uncover<7->{\node [yellowsmall, above=0.1cm of green] (yellow2) {JOBS/};}
-            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\_version/};}
-            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\_cbl/};}
+            \uncover<7->{\node [yellow, left=0.2cm of yellow2] (yellow1) {current\underline{ }version/};}
+            \uncover<7->{\node [yellow, right=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
             \uncover<7->{\node [yellowsmall, right=0.2cm of yellow3] (yellow4) {INPUT/};}
             
@@ -208,7 +213,7 @@
       \begin{center}
 	      \begin{tikzpicture}[auto, node distance=0] 
-	         \uncover<2->{\node [yellow] (yellow) {current\_version/};}
+	         \uncover<2->{\node [yellow] (yellow) {current\underline{ }version/};}
 	         \uncover<1->{\node [dummy, right=0.0cm of yellow] (dummy1) {};}
-	         \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\_DEPOSITORY\_\textit{parallel}/};}
+	         \uncover<2->{\node [green, right=0.2cm of yellow] (green1) {MAKE\underline{ }DEPOSITORY\underline{ }\textit{parallel}/};}
 	         \uncover<1->{\node [dummy, right=0.2cm of green1] (dummy2) {};}
             \uncover<3->{\node [green, below=0.5cm of dummy1] (green2) {/tmp/$<$username$>$.$<$randomnumber$>$};}
@@ -240,11 +245,11 @@
    
    \frametitle{\texttt{mrun}: Principal Mode of Operation (III)}
-
+   \footnotesize 
 	\begin{enumerate}
       \setcounter{enumi}{5}
 	   \item<1-> Copy the output files from the working directory to a (permanent) directory of the user:\\
-       \scriptsize \hspace{-16mm} \texttt{cp /tmp/<username>.<randomnumber>/<temporary\_output\_file1> <user\_output\_file1>}\\
-      \hspace{-16mm} \texttt{cp /tmp/<username>.<randomnumber>/<temporary\_output\_file2> <user\_output\_file2>}\\
-      
+       \tiny \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file1> <user\underline{ }output\underline{ }file1>}\\
+      \quad \texttt{cp /tmp/<username>.<randomnumber>/<temporary\underline{ }output\underline{ }file2> <user\underline{ }output\underline{ }file2>}\\
+      \footnotesize 
       \begin{center}
 	      \begin{tikzpicture}[auto, node distance=0] 
@@ -256,7 +261,7 @@
             
             \uncover<2->{\node [yellow, left=0.2cm of dummy3] (yellow2) {OUTPUT/};}
-            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\_cbl/};}
+            \uncover<2->{\node [yellow, left=0.2cm of yellow2] (yellow3) {example\underline{ }cbl/};}
             \uncover<2->{\node [yellow, left=0.2cm of yellow3] (yellow4) {JOBS/};}
-            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\_version/};}
+            \uncover<2->{\node [yellow, left=0.2cm of yellow4] (yellow5) {current\underline{ }version/};}
                       	                     
 	         \uncover<2-3>{\node [green, left=5.0cm of dummy1] (green) {/tmp/$<$username$>$.$<$randomnumber$>$};}
@@ -278,4 +283,5 @@
 	   \item<3-> Delete the temporary working directory\\
       \quad \texttt{rm -rf /tmp/<username>.<randomnumber>}\\
+      \vspace{2mm}
       \onslide<5->\textcolor{red}{Question: How does \texttt{mrun} know which files have to be copied and where from or where to they have to be copied?}
 
@@ -293,5 +299,5 @@
    \frametitle{Steering File Copy by the Configuration File (I)}
    \scriptsize
-   \textbf{Copying of files is controlled by so called \textit{file connection statements}. They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\
+   \textbf{Copying of files is controlled by so called} \textit{file connection statements}. \textbf{They connect local files in the temporary working directory with permanent files residing in the directory of the user.}\\
    \vspace{1mm}
    Principle example of a file connection statement (for the PALM parameter file):
@@ -305,6 +311,6 @@
          \uncover<1->{\node [dummy, right=0.0cm of part2] (dummy2) {};}
          \uncover<1->{\node [small, right=0.2cm of part2] (part3) {\texttt{d3\#}};}
-	      \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\_version/JOB/INPUT}};}
-	      \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\_p3d}};}
+	      \uncover<1->{\node [large, right=0.0cm of part3] (part4) {\texttt{\~{}/palm/current\underline{ }version/JOB/INPUT}};}
+	      \uncover<1->{\node [small, right=0.0cm of part4] (part5) {\texttt{\underline{ }p3d}};}
 	      \uncover<1->{\node [small, right=0.2cm of part5] (part6) {\texttt{( \textcolor{red}{nc} )}};}
 	            
@@ -330,8 +336,8 @@
    
    \onslide<8->The full name of the permanent file results from the directory name, the suffix and the value of \texttt{mrun}-Option \texttt{-d}, which defines the so-called \textbf{base name} of all files handled by \texttt{mrun}:\\
-   \quad \texttt{mrun -d \textcolor{blue}{example\_cbl} ...}\\
+   \quad \texttt{mrun -d \textcolor{blue}{example\underline{ }cbl} ...}\\
    gives the filename\\
-   \quad \texttt{\~{}/palm/current\_version/JOB/INPUT/\textcolor{blue}{example\_cbl}\_p3d}\\
-   \quad \texttt{( ... /\textcolor{blue}{example\_cbl}\_p3d\textcolor{red}{.nc} )}
+   \quad \texttt{\~{}/palm/current\underline{ }version/JOB/INPUT/\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d}\\
+   \quad \texttt{( ... /\textcolor{blue}{example\underline{ }cbl}\underline{ }p3d\textcolor{red}{.nc} )}
    
 \end{frame}
@@ -342,26 +348,26 @@
    \scriptsize
    \onslide<1-> The \textbf{base name} can additionally be a part of the directory name 
-   by using \texttt{\$fname} in the directory column of the file connection statement:\\
-   \quad \texttt{PARIN in d3\# \~{}/palm/current\_version/JOBS/\$fname/INPUT \_p3d}\\
+   by using \textcolor{blue}{\texttt{\$fname}} in the directory column of the file connection statement:\\
+   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
    \ \\
    \onslide<2-> Using the call\\
-   \quad \texttt{mrun -d abcde ...}\\
+   \quad \texttt{mrun -d \textcolor{blue}{abcde} ...}\\
    the input file will be expected under\\
-   \quad \texttt{\~{}/palm/current\_version/JOBS/abcde/INPUT/abcde\_p3d }\\
+   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/\textcolor{blue}{abcde}/INPUT/\textcolor{blue}{abcde}\underline{ }p3d }\\
    \ \\
    \onslide<3-> In this way, all files handled by the \texttt{mrun}-call are stored in 
-   the same subdirectory (abcde/) and will have the same string (\texttt{abcde}) as 
-   part of their names, so they can be easily identified as ''belonging'' to the model 
+   the same subdirectory (\textcolor{blue}{abcde/}) and will have the same string (\texttt{\textcolor{blue}{abcde}}) as 
+   part of their names, so they can be easily identified as \grqq belonging\grqq\, to the model 
    run initiated by that \texttt{mrun} call.\\
    \ \\
    \onslide<4-> Instead of always writing the full path name (i.e. 
-   \texttt{\~{}/palm/current\_version/JOBS}), an environment variable can be declared for 
+   \texttt{\~{}/palm/current\underline{ }version/JOBS}), an environment variable can be declared for 
    this at the beginning of the configuration file and be used in the file 
    connection statements:\\
-   \quad \texttt{\%base\_data  \~{}/palm/current\_version/JOBS}\\
-   \quad \texttt{PARIN in d3\#  \$base\_data/\$fname/INPUT \_p3d}\\
+   \quad \texttt{\%base\underline{ }data  \~{}/palm/current\underline{ }version/JOBS}\\
+   \quad \texttt{PARIN in d3\#  \textcolor{blue}{\$base\underline{ }data}/\textcolor{blue}{\$fname}/INPUT \underline{ }p3d}\\
    \ \\
    \onslide<5-> This easily allows to change the directories for all input/output files 
-   by just changing the value of \texttt{base\_data}.
+   by just changing the value of \texttt{base\underline{ }data}.
    
 \end{frame}
@@ -374,20 +380,20 @@
    have to be activated by giving their activation string in the 
    \texttt{mrun}-option \texttt{-r}:\\
-   \quad \texttt{PARIN in d3\# \~{}/palm/current\_version/JOBS/\$fname/INPUT \_p3d}\\
+   \quad \texttt{PARIN in d3\# \~{}/palm/current\underline{ }version/JOBS/\$fname/INPUT \underline{ }p3d}\\
    \ \\
    \onslide<2-> The permanent file 
-   \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/INPUT/example\_cbl\_p3d} 
+   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/INPUT/example\underline{ }cbl\underline{ }p3d} 
    will only be copied to the local file PARIN by using the call:\\
-   \quad \texttt{mrun -d example\_cbl -r ''d3\#'' ...}\\
+   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\#\dq\, ...}\\
    \ \\
    \onslide<3-> \textbf{Example for an output file:}\\
    The file connection statement\\
-   \quad \texttt{DATA\_1D\_PR\_NETCDF out:loc pr\# 
-   \~{}/palm/current\_version/JOBS/\$fname/OUTPUT \_pr nc}\\
+   \quad \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF out:loc pr\# 
+   \~{}/palm/current\underline{ }version/JOBS/\$fname/OUTPUT \underline{ }pr nc}\\
    \onslide<4-> will copy (after program execution) the local file 
-   \texttt{DATA\_1D\_PR\_NETCDF} to the permanent file 
-   \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/OUTPUT/example\_cbl\_pr.nc} if
+   \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF} to the permanent file 
+   \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/example\underline{ }cbl\underline{ }pr.nc} if
    \texttt{mrun} is called with the options\\
-   \quad \texttt{mrun -d example\_cbl -r ''d3\# pr\#'' ...}
+   \quad \texttt{mrun -d example\underline{ }cbl -r \dq d3\# pr\#\dq\, ...}
    
 \end{frame}
@@ -401,18 +407,18 @@
    Instead, new, so-called file cycles are created.\\
    If an output file, e.g.\\
-   \quad \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/MONITORING/example\_cbl\_rc}\\
+   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc}\\
    \ \\
    has been created from a first call of \texttt{mrun} and if the same \texttt{mrun} 
    call is submitted again, the second call will not replace the file 
-   \texttt{example\_cbl\_rc}, but will create a new file with name:\\
-   \quad \texttt{\~{}/palm/current\_version/JOBS/example\_cbl/MONITORING/example\_cbl\_rc.1}\\
+   \texttt{example\underline{ }cbl\underline{ }rc}, but will create a new file with name:\\
+   \quad \texttt{\~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING/example\underline{ }cbl\underline{ }rc.1}\\
    \ \\
    \onslide<2->In case of netCDF-files, the file cycle number is inserted before 
    the netCDF-suffix .nc, e.g.\\
-   \quad \texttt{example\_cbl\_pr.1.nc}\\
+   \quad \texttt{example\underline{ }cbl\underline{ }pr.1.nc}\\
    \ \\
    \onslide<3->The implemented file cycle mechanism does not allow to use 
    any other dots "'."'  in the path or filename:\\
-   \quad \texttt{\~{}/palm/version\_3.6/JOBS/example.sbl/MONITORING/example.sbl\_rc}
+   \quad \texttt{\~{}/palm/version\underline{ }3.6/JOBS/example.sbl/MONITORING/example.sbl\underline{ }rc}
 \end{frame}
 
@@ -430,5 +436,5 @@
 PARIN                    in:job        d3f      $base_data/$fname/INPUT    _p3df
 TOPOGRAPHY_DATA          in:locopt     d3#:d3f  $base_data/$fname/INPUT    _topo
-BININ                    in:loc:flpe   d3f:rec  $base_data/$fname/RESTART  _d3d
+BININ                    in:loc:flpe   d3f      $base_data/$fname/RESTART  _d3d
 PARTICLE_RESTART_DATA_IN in:loc:flpe   prtf     $base_data/$fname/RESTART  _rprt
 DATA_1D_PR_NETCDF        in:locopt     prf      $base_data/$fname/OUTPUT   _pr     nc
@@ -468,7 +474,46 @@
 DATA_3D_NETCDF       out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d     nc
 DATA_3D_AV_NETCDF    out:loc:tr   3d#:3df   $base_data/$fname/OUTPUT  _3d_av  nc
-DATA_PRT_NETCDF      out:loc:pe   prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
+DATA_MASK_01_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01     nc
+DATA_MASK_01_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m01_av  nc
+DATA_MASK_02_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02     nc
+DATA_MASK_02_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m02_av  nc
+DATA_MASK_03_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03     nc
+DATA_MASK_03_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m03_av  nc
+DATA_MASK_04_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04     nc
+DATA_MASK_04_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m04_av  nc
+DATA_MASK_05_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05     nc
+DATA_MASK_05_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m05_av  nc
+DATA_MASK_06_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06     nc
+DATA_MASK_06_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m06_av  nc
+DATA_MASK_07_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07     nc
+DATA_MASK_07_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m07_av  nc
+DATA_MASK_08_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08     nc
+DATA_MASK_08_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m08_av  nc
+DATA_MASK_09_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09     nc
+DATA_MASK_09_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m09_av  nc
+DATA_MASK_10_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10     nc
+DATA_MASK_10_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m10_av  nc
+DATA_MASK_11_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11     nc
+DATA_MASK_11_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m11_av  nc
+DATA_MASK_12_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12     nc
+DATA_MASK_12_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m12_av  nc
+DATA_MASK_13_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13     nc
+DATA_MASK_13_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m13_av  nc
+DATA_MASK_14_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14     nc
+DATA_MASK_14_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m14_av  nc
+DATA_MASK_15_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15     nc
+DATA_MASK_15_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m15_av  nc
+DATA_MASK_16_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16     nc
+DATA_MASK_16_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m16_av  nc
+DATA_MASK_17_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17     nc
+DATA_MASK_17_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m17_av  nc
+DATA_MASK_18_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18     nc
+DATA_MASK_18_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m18_av  nc
+DATA_MASK_19_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19     nc
+DATA_MASK_19_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m19_av  nc
+DATA_MASK_20_NETCDF    out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20     nc
+DATA_MASK_20_AV_NETCDF out:loc:tr ma#:maf   $base_data/$fname/OUTPUT  _m20_av  nc
 DATA_PRT_NETCDF      out:loc:trpe prt#:prtf $base_data/$fname/OUTPUT  _prt    nc
-DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr
+DATA_DVR             out:loc:trpe dvr       $base_data/$fname/OUTPUT  _dvr 
 #
 DVRP_LOG          out:loc:tr   dv#       $base_data/$fname/MONITORING  _dvrp_log
@@ -504,41 +549,43 @@
 \begin{frame}
    \frametitle{PALM \textit{Interactive} Example Run Using \texttt{mrun}: Tracing the Run by the User}
-   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
-   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.42\textwidth, font=\scriptsize, minimum height=0.6cm]
-   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.45\textwidth, font=\scriptsize, minimum height=0.6cm]
-   \tikzstyle{notes} = [rectangle, text width=0.46\textwidth, font=\scriptsize, minimum height=0.6cm]
-   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\scriptsize, minimum height=0.6cm]
+   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
+   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.35\textwidth, font=\tiny, minimum height=0.6cm]
+   \tikzstyle{yellow_big} = [rectangle, draw, fill=yellow!20, text width=0.55\textwidth, font=\tiny, minimum height=0.6cm]
+   \tikzstyle{notes} = [rectangle, text width=0.26\textwidth, font=\tiny, minimum height=0.6cm]
+   \tikzstyle{dummy} = [rectangle, text width=0.01\textwidth, font=\tiny, minimum height=0.6cm]
    \vspace{-1.0cm}
    \begin{center}
 	   \begin{tikzpicture}[auto, node distance=0] 
-         \uncover<1->{\node [yellow] (box1) {start run on local machine:\\
-                                            \texttt{mrun -d example\_cbl -h lcmuk ...}};}
-         \uncover<1->{\node [dummy, right=0.2cm of box1] (dummy1) {};}
-         \uncover<2->{\node [notes, above=0.2cm of dummy1] (notes1) {temporary working directory is created,\\all required files are copied there};}
-         \uncover<3->{\node [green, right=0.2cm of dummy1] (box2) {follow runs messages on terminal};}
-         \uncover<4->{\node [green, below=0.2cm of box2] (box3) {
-         as soon as message
+         \uncover<1->{\node [yellow] (box1) {\textbf{start run on local machine:}\\
+                                            \texttt{mrun -d example\underline{ }cbl -h lcmuk ...}};}
+         \uncover<1->{\node [dummy, right=1.4cm of box1] (dummy1) {};}
+         \uncover<2->{\node [notes, above=-0.3cm of dummy1] (notes1) {temporary working directory is created, all required files are copied there};}
+         \uncover<3->{\node [green, right=1.4cm of dummy1] (box2) {\textbf{follow run messages on terminal}};}
+         \uncover<4->{\node [green, below=0.5cm of box2] (box3) {
+         \textbf{as soon as message}
          
-         \texttt{*** execution starts in directory\\ \quad ''<tempdir>''}
-
-         you can change to this directory (in a new terminal) and watch the progess of timesteps
+         \texttt{*** execution starts in directory\\ \quad \dq <tempdir>\dq\, }\\
+         \ \\
+         \textbf{you can change to this directory (in a new terminal) and watch the progess of timesteps}
 
          \texttt{cd <tempdir>}\\
-         \texttt{tail -f RUN\_CONTROL}
-
+         \texttt{tail -f RUN\underline{ }CONTROL}\\
+         \ \\
          However, this might be difficult in case of short run times, because the run may have finished before you have entered the commands!
          };}
-         \uncover<1->{\node [dummy, left=0.2cm of box3] (dummy2) {};}
-         \uncover<5->{\node [notes, below=1.7cm of dummy2] (notes2) {results are copied from temporary \\ working directory to the userâs permanent directory};}
-         \uncover<6->{\node [yellow_big, left=0.2cm of dummy2] (box4) {
-         check, if the output files have sucessfully been transferred to the permanent directory:\\
-         \texttt{cd \~{}/palm/current\_version/JOBS/\\ \quad example\_cbl/MONITORING}\\
+         \coordinate[below=0.3cm of box3] (A);
+         \uncover<1->{\node [dummy, left=0.3cm of box3] (dummy2) {};}
+         \uncover<5->{\node [notes, below=0.0cm of A, text width=0.35\textwidth] (notes2) {results are copied from temporary working directory to the userâs permanent directory};}
+         \uncover<6->{\node [yellow_big, left=2.5cm of A] (box4) {
+         \textbf{check, if the output files have sucessfully been transferred to the permanent directory:}\\
+         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/MONITORING}\\
          \texttt{ls -al}\\
-         \texttt{cd \~{}/palm/current\_version/JOBS/\\ \quad example\_cbl/OUTPUT}\\
+         \texttt{cd \~{}/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT}\\
          \texttt{ls -al}
 };}
-         \draw<2-> [->] (box1.east) -- (box2.west);    
-         \draw<4-> [->] (box2.south) -- (box3.north);   
-         \draw<5-> [->] (box3.west) -- (box4.east);   
+         \draw<2-> [->,color=blue] (box1.east) -- (box2.west);    
+         \draw<4-> [->,color=blue] (box2.south) -- (box3.north);  
+         \draw<5-> [-,color=blue] (box3.south) -- (A);  
+         \draw<5-> [->,color=blue] (A) -- (box4.east);   
 	   \end{tikzpicture}
 	\end{center}
@@ -554,10 +601,10 @@
 \tikzstyle{line} = [draw, -latex']
 \begin{itemize}
-   \item Reminder: Running batch jobs requires a directory \texttt{~/job\_queue} for the job protocol files on the local \underline{and} remote host.
+   \item Reminder: Running batch jobs requires a directory \texttt{~/job\underline{ }queue} for the job protocol files on the local \underline{and} remote host.
 \end{itemize}
 \begin{tikzpicture}[auto, node distance=0]
     \node [yellow] (first) {
        \textbf{start job on local machine:}\\
-       \texttt{mrun -d example\_cbl -h lcsgih ...}
+       \texttt{mrun -d example\underline{ }cbl -h lcsgih ...}
     };
 \uncover<2->{
@@ -578,11 +625,11 @@
     \node [green, below=0.2cm of second] (third) {
        \textbf{if job is running, you may follow its progress by watching the job protocol:} \\ 
-       \texttt{cd ~/job\_queue \\ tail lcmuk\_example\_cbl}
+       \texttt{cd ~/job\underline{ }queue \\ tail lcmuk\underline{ }example\underline{ }cbl}
     };
 }
 \uncover<5->{
     \node [green, below=0.2cm of third] (fourth) {
-       \textbf{when job is running, change to directory \texttt{<tmp\_usr\_catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\
-       \texttt{tail -f RUN\_CONTROL}
+       \textbf{when job is running, change to directory \texttt{<tmp\underline{ }usr\underline{ }catalog>} and try to find there the latest directory \texttt{<HLRN-username>.<randomnumber>} \\ change to this directory and execute}\\
+       \texttt{tail -f RUN\underline{ }CONTROL}
     };
 }
@@ -590,5 +637,5 @@
     \node [green, below=0.2cm of fourth] (fifth) {
        \textbf{when the job is finished, watch, if the job protocol is transferred to the local host without errors:}\\
-       \texttt{cd ~/job\_queue \\ cat last\_job\_transfer\_protocol}
+       \texttt{cd ~/job\underline{ }queue \\ cat last\underline{ }job\underline{ }transfer\underline{ }protocol}
     };
 }
@@ -603,10 +650,10 @@
     \node [yellow, left=3.5cm of fifth] (sixth) {
        \textbf{check, if the job protocol and all output files have successfully been transferred to the local machine:}\\
-       \texttt{cd ~/job\_queue \\ ls -al \\ cd ~/palm/current\_version/JOBS/example \\ ls -al *}
+       \texttt{cd ~/job\underline{ }queue \\ ls -al \\ cd ~/palm/current\underline{ }version/JOBS/example \\ ls -al *}
     };
 }
 \uncover<9->{
      \node [alert, below=0.5cm of first.south east] (alert) {
-        \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the qeueuing system! Manual adjustments may be required in the mrun and subjob script!}
+        \textcolor{red}{Attention: Commands for submitting jobs and the behaviour of job protocol files are depending on the queueing system! Manual adjustments may be required in the mrun and subjob script!}
      };
 }
@@ -649,5 +696,5 @@
          \uncover<3->{\node [yellow_small] (box1) {\$HOME/};}
          \uncover<3->{\node [yellow_small, right=0.2cm of box1] (box2) {palm/};}
-         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\_version/};}
+         \uncover<3->{\node [yellow, right=0.2cm of box2] (box3) {current\underline{ }version/};}
          \uncover<3->{\node [green_small, right=0.4cm of box3] (box4) {trunk/};}
          
@@ -661,5 +708,5 @@
          \uncover<5->{\node [notes, below=0.1cm of box3] (notes3) {\texttt{.mrun.config}};}
           
-         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\_FOR\_RUN\_$<$run\_identifier$>$};}
+         \uncover<3->{\node [green, below=0.2cm of box6] (box7) {SOURCES\underline{ }FOR\underline{ }RUN\underline{ }$<$run\underline{ }identifier$>$};}
          
          \uncover<1->{\node [dummy, left=1.5cm of box7] (dummy2) {};}
