source: palm/trunk/TUTORIAL/SOURCE/program_structure.tex @ 1229

% $Id: program_structure.tex 1227 2013-09-18 14:14:13Z raasch $
\input{header_tmp.tex}
%\input{../header_lectures.tex}

\usepackage[utf8]{inputenc}
\usepackage{ngerman}
\usepackage{pgf}
\usetheme{Dresden}
\usepackage{subfigure}
\usepackage{units}
\usepackage{multimedia}
\newcommand{\event}[1]{\newcommand{\eventname}{#1}}
\usepackage{xmpmulti}
\usepackage{tikz}
\usepackage{pdfcomment}
\usetikzlibrary{shapes,arrows,positioning}
\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
\usepackage{listings}
\lstset{language=[90]Fortran,
  basicstyle=\ttfamily \tiny,
  keywordstyle=\color{black},
  commentstyle=\color{black},
  morecomment=[l]{!\ }% Comment only with space after !
}


\institute{Institut fÌr Meteorologie und Klimatologie, Leibniz UniversitÀt 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.png}}

\title[PALM Program Structure]{PALM Program Structure}
\author{Siegfried Raasch}


% Notes:
% jede subsection bekommt einen punkt im menu (vertikal ausgerichtet.
% jeder frame in einer subsection bekommt einen punkt (horizontal ausgerichtet)
\begin{document}

\begin{frame}
\titlepage
\end{frame}

\section{PALM Program Structure}
\subsection{PALM Program Structure}

%Folie 01
\begin{frame}
   \begin{center}
      PALM - Program Structure
   \end{center}
\end{frame}

%Folie 02
\begin{frame}
   \frametitle{Contents}
   \begin{flushleft}
      This part gives a brief overview about the structure of the PALM code:
   \end{flushleft}
   \begin{itemize}
      \item<2->{Flow chart}
      \item<3->{Most important variables and how they are declared}
      \item<4->{Machine dependencies}
   \end{itemize}
\end{frame}

%Folie 03
\begin{frame}[fragile]
   \frametitle{PALM Code: General Features}
   \begin{itemize}
      \item<2->{PALM is written in FORTRAN90. Current version number is 3.9.}
      \item<3->{With some very minor exceptions, the code is using the FORTRAN standard, so it should compile without error on any FORTRAN90/95 compiler.}
      \item<4->{Data handling between subroutines is mostly done using FORTRAN90-modules instead of using parameter lists.
      \begin{minipage}{0.45\textwidth}
         \centering
         \begin{lstlisting}
SUBROUTINE parin
   USE control_parameters
   USE grid_variables
   .
   .
         \end{lstlisting}
      \end{minipage}
      \begin{minipage}{0.45\textwidth}
         \centering
         \begin{lstlisting}
SUBROUTINE parin( a, b, c, ... )
   INTEGER ::  a, b
   REAL    ::  c, ...
   .
   .
         \end{lstlisting}
      \end{minipage}
      \mbox{Most modules can be found in file .../trunk/SOURCE/modules.f90}}
   \end{itemize}
\end{frame}

%Folie 04
\begin{frame}
   \frametitle{PALM Code: General Features}
   \begin{itemize}
      \item<2->{Machine dependent code segments, e.g. calls for flushing of buffers (CALL FLUSH / CALL FLUSH\_), or calls of special software (e.g. netCDF or dvrp), which are available on some machines only, are activated using preprocessor directives.}
      \item<3->{The serial and parallel PALM version is also activated by preprocessor directives.}
      \item<4->{The code is splitted into several files, most of them containing just one subroutine, e.g. file ``parin.f90'' contains ``SUBROUTINE parin''.}
      \item<5->{The code includes an interface which can be used by users to add their own code extensions. Advantage: These code extensions can be reused (normally) for future PALM releases without requiring any changes.}
   \end{itemize}
\end{frame}

%Folie 05
\begin{frame}
   \frametitle{PALM Flow Chart (I)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=15pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=15pt, font=\tiny]
   \tikzstyle{line} = [draw, -]

   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [yellow] (PALM) {PALM};}
      \uncover<1->{\node [white2, right=0.2cm of PALM] (PALMspace) {};}
      
      \uncover<2->{\node [yellow, below=0.2cm of PALMspace] (initcoup) {init\_coupling};}
      \path<2-> [line] (PALM.south) |- (initcoup.west);

      \uncover<3->{\node [yellow, below=0.05cm of initcoup] (localtre) {local\_tremain\_ini};}
      \path<3-> [line] (PALM.south) |- (localtre.west);

      \uncover<4->{\node [yellow, below=0.05cm of localtre] (initdvrp) {init\_dvrp\_logging};}
      \path<4-> [line] (PALM.south) |- (initdvrp.west);

      \uncover<5->{\node [yellow, below=0.05cm of initdvrp] (parin) {parin};}
      \path<5-> [line] (PALM.south) |- (parin.west);
      \uncover<5->{\node [white, right=0.2cm of parin] (parinspace) {};}

         \uncover<5->{\node [yellow, below=0cm of parinspace] (readvar) {read\_var\_list};}
         \path<5-> [line,dashed] (parin.south) |- (readvar.west);

         \uncover<5->{\node [yellow, below=0.05cm of readvar] (packageparin) {package\_parin};}
         \path<5-> [line,dashed] (parin.south) |- (packageparin.west);

          \uncover<5->{\node [green, below=0.05cm of packageparin] (userparin) {user\_parin};}
          \path<5-> [line] (parin.south) |- (userparin.west);

      \uncover<6->{\node [yellow, below=1.4cm of parin] (initpeg) {init\_pegrid};}
      \path<6-> [line] (PALM.south) |- (initpeg.west);
      \uncover<6->{\node [white, right=0.2cm of initpeg] (initpegspace) {};}

      \uncover<7->{\node [yellow, below=0.05cm of initpeg] (initgrid) {init\_grid};}
      \path<7-> [line] (PALM.south) |- (initgrid.west);
      \uncover<7->{\node [white, right=0.2cm of initgrid] (initgridspace) {};}
      
         \uncover<7->{\node [green, below=0cm of initgridspace] (userinitgrid) {user\_init\_grid};}
         \path<7-> [line,dashed] (initgrid.south) |- (userinitgrid.west);

      \uncover<1->{\node [white, below=5.8cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (PALM.south) |- (continu2.north);

      \uncover<1->{\node [white, below=5.2cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);
   \end{tikzpicture}
\end{frame}

%Folie 06
\begin{frame}
   \frametitle{PALM Flow Chart (II)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.43\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.43\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green1} = [rectangle, draw, fill=green!20, text width=0.23\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]

   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

      \uncover<1->{\node [yellow, right=0.2cm of PALM] (checkpara) {check\_parameters};}
      \path<1-> [line] (PALM.south) |- (checkpara.west);
      \uncover<1->{\node [white, right=0.2cm of checkpara] (checkparaspace) {};}
      \uncover<1->{\node [white, right=0.365cm of checkpara] (checkparaspacelarge) {};}
  
          \uncover<2->{\node [green1, below=0cm of checkparaspacelarge] (usercheckdatapr) {user\_check\_data\_output\_pr};}
          \path<2-> [line] (checkpara.south) |- (usercheckdatapr.west);

          \uncover<2->{\node [green, below=0.52cm of checkparaspace] (usercheckdata) {user\_check\_data\_output};}
          \path<2-> [line] (checkpara.south) |- (usercheckdata.west);

          \uncover<2->{\node [yellow, below=0.05cm of usercheckdata] (initmasks) {init\_masks};}
          \path<2-> [line,dashed] (checkpara.south) |- (initmasks.west);

             \uncover<2->{\node [green, right=0.2cm of initmasks] (usercheckdata2) {user\_check\_data\_output};}
             \path<2-> [line] (initmasks.east) |- (usercheckdata2.west);

          \uncover<2->{\node [yellow, below=0.05cm of initmasks] (usercheckpara) {user\_check\_parameters};}
          \path<2-> [line] (checkpara.south) |- (usercheckpara.west);

      \uncover<3->{\node [yellow, below=1.9cm of checkpara] (init3d) {init\_3d\_model};}
      \path<3-> [line] (PALM.south) |- (init3d.west);
      \uncover<3->{\node [white, right=0.05cm of init3d] (init3dspace) {};}
      \uncover<3->{\node [whitelarge, right=0.05cm of init3d] (init3dspacelarge) {};}

         \uncover<4->{\node [yellowLarge, below=-0.05cm of init3dspacelarge] (init1d) {init\_1d\_model (calls various subroutines)};}
         \path<4-> [line,dashed] (init3d.south) |- (init1d.west);

         \uncover<4->{\node [yellow, below=0.5cm of init3dspace] (initslope) {init\_slope};}
         \path<4-> [line,dashed] (init3d.south) |- (initslope.west);

         \uncover<4->{\node [green, below=0.05cm of initslope] (userinit3d) {user\_init\_3d\_model};}
         \path<4-> [line,dashed] (init3d.south) |- (userinit3d.west);

         \uncover<4->{\node [yellow, below=0.05cm of userinit3d] (disturbh) {disturb\_heatflux};}
         \path<4-> [line,dashed] (init3d.south) |- (disturbh.west);

         \uncover<4->{\node [yellow, below=0.05cm of disturbh] (initrank) {init\_rankine};}
         \path<4-> [line,dashed] (init3d.south) |- (initrank.west);

            \uncover<4->{\node [yellow, right=0.05cm of initrank] (pres) {pres};}
            \path<4-> [line] (initrank.east) -- (pres.west);
            \uncover<4->{\node [white, below=-0.05cm of pres] (presspace) {};}

               \uncover<4->{\node [yellowsmall, right=0.05cm of presspace] (poisfft) {poisfft};}
               \path<4-> [line] (pres.east) -| (poisfft.north);

               \uncover<4->{\node [yellowsmall, right=0.05cm of poisfft] (sor) {sor};}
               \path<4-> [line] (pres.east) -| (sor.north);

               \uncover<4->{\node [yellowsmall, right=0.05cm of sor] (poismg) {poismg};}
               \path<4-> [line] (pres.east) -| (poismg.north);

         \uncover<4->{\node [yellow, below=0.05cm of initrank] (initpt) {init\_pt\_anomaly};}
         \path<4-> [line,dashed] (init3d.south) |- (initpt.west);

         \uncover<4->{\node [yellow, below=0.05cm of initpt] (randomfuncini) {random\_function\_ini};}
         \path<4-> [line] (init3d.south) |- (randomfuncini.west);

      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);

      \uncover<4->{\node [white2, below=6.6cm of checkpara] (continu3) {};}
      \path<4-> [line,dashed] (init3d.south) |- (continu3.north);

      \uncover<4->{\node [white2, below=6.0cm of checkpara] (continu4) {};}
      \path<4-> [line] (init3d.south) |- (continu4.north);

   \end{tikzpicture}
\end{frame}

%Folie 07
\begin{frame}
   \frametitle{PALM Flow Chart (III)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.43\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.43\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green1} = [rectangle, draw, fill=green!20, text width=0.23\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]

   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

       \uncover<1->{\node [yellow, right=0.2cm of PALM] (init3d) {init\_3d\_model};}
       \path<1-> [line] (PALM.south) |- (init3d.west);
       \uncover<1->{\node [white, right=0.05cm of init3d] (init3dspace) {};}
       \uncover<1->{\node [whitelarge, right=0.05cm of init3d] (init3dspacelarge) {};}

         \uncover<2->{\node [yellow, below=0.05cm of init3dspace] (read3d) {read\_3d\_binary};}
         \path<2-> [line,dashed] (init3d.south) |- (read3d.west);

            \uncover<2->{\node [green, right=0.05cm of read3d] (userreadrestart) {user\_read\_restart\_data};}
            \path<2-> [line] (read3d.east) -- (userreadrestart.west);

         \uncover<2->{\node [yellow, below=0.5cm of init3dspace] (initslope) {init\_slope};}
         \path<2-> [line,dashed] (init3d.south) |- (initslope.west);

         \uncover<2->{\node [yellow, below=0.05cm of initslope] (initadvec) {init\_advec};}
         \path<2-> [line] (init3d.south) |- (initadvec.west);

         \uncover<2->{\node [yellow, below=0.05cm of initadvec] (distfield) {disturb\_field};}
         \path<2-> [line,dashed] (init3d.south) |- (distfield.west);

         \uncover<2->{\node [yellow, below=0.05cm of distfield] (pres) {pres};}
         \path<2-> [line,dashed] (init3d.south) |- (pres.west);
         \uncover<2->{\node [white, below=-0.05cm of pres] (presspace) {};}

            \uncover<2->{\node [yellowsmall, right=0.05cm of presspace] (poisfft) {poisfft};}
            \path<2-> [line] (pres.east) -| (poisfft.north);

            \uncover<2->{\node [yellowsmall, right=0.05cm of poisfft] (sor) {sor};}
            \path<2-> [line] (pres.east) -| (sor.north);

            \uncover<2->{\node [yellowsmall, right=0.05cm of sor] (poismg) {poismg};}
            \path<2-> [line] (pres.east) -| (poismg.north);

         \uncover<2->{\node [green, below=0.05cm of pres] (userinitplant) {user\_init\_plant\_canopy};}
         \path<2-> [line,dashed] (init3d.south) |- (userinitplant.west);

         \uncover<2->{\node [yellow, below=0.05cm of userinitplant] (initdvrp) {init\_dvrp};}
         \path<2-> [line,dashed] (init3d.south) |- (initdvrp.west);

         \uncover<2->{\node [yellow, below=0.05cm of initdvrp] (initocean) {init\_ocean};}
         \path<2-> [line,dashed] (init3d.south) |- (initocean.west);

            \uncover<2->{\node [yellow, right=0.05cm of initocean] (eqnstsea) {eqn\_state\_seawater};}
            \path<2-> [line] (initocean.east) -| (eqnstsea.west);

         \uncover<2->{\node [yellow, below=0.05cm of initocean] (initcloudphys) {init\_cloud\_physics};}
         \path<2-> [line,dashed] (init3d.south) |- (initcloudphys.west);

        \uncover<2->{\node [yellow, below=0.05cm of initcloudphys] (lpminit) {lpm\_init};}
        \path<2-> [line,dashed] (init3d.south) |- (lpminit.west);
        \uncover<2->{\node [white, right=0.2cm of lpminit] (lpminspace) {};}

            \uncover<2->{\node [yellow, below=0.05cm of lpminspace] (lpmreadrestart) {lpm\_read\_restart\_file};}
            \path<2-> [line,dashed] (lpminit.south) |- (lpmreadrestart.west);

            \uncover<2->{\node [green, below=0.05cm of lpmreadrestart] (userlpmin) {user\_lpm\_init};}
            \path<2-> [line] (lpminit.south) |- (userlpmin.west);

      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);

      \uncover<2->{\node [white2, below=6.6cm of init3d] (continu3) {};}
      \path<2-> [line,dashed] (init3d.south) |- (continu3.north);

      \uncover<2->{\node [white2, below=6.0cm of init3d] (continu4) {};}
      \path<2-> [line] (init3d.south) |- (continu4.north);

   \end{tikzpicture}
\end{frame}

%Folie 08
\begin{frame}
   \frametitle{PALM Flow Chart (IV)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.43\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.43\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green1} = [rectangle, draw, fill=green!20, text width=0.23\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]

   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

       \uncover<2->{\node [yellow, right=0.2cm of PALM] (init3d) {init\_3d\_model};}
       \path<2-> [line] (PALM.south) |- (init3d.west);
       \uncover<2->{\node [white, right=0.05cm of init3d] (init3dspace) {};}
       \uncover<2->{\node [whitelarge, right=0.05cm of init3d] (init3dspacelarge) {};}

       \uncover<3->{\node [yellow, below=0.05cm of init3dspace] (lpminit) {lpm\_init};}
       \path<3-> [line,dashed] (init3d.south) |- (lpminit.west);
       \uncover<3->{\node [white, right=0.2cm of lpminit] (lpminspace) {};}

            \uncover<4->{\node [yellow, below=0.05cm of lpminspace] (lpmsortar) {lpm\_sort\_arrays};}
            \path<4-> [line,dashed] (lpminit.south) |- (lpmsortar.west);

            \uncover<5->{\node [yellow, below=0.05cm of lpmsortar] (dataoutpdvrp) {data\_output\_dvrp};}
            \path<5-> [line,dashed] (lpminit.south) |- (dataoutpdvrp.west);
            \uncover<5->{\node [white, right=0.2cm of dataoutpdvrp] (dataoutpdvrpspace) {};}

               \uncover<6->{\node [green, below=0.05cm of dataoutpdvrpspace] (usercoltap) {user\_dvrp\_coltab};}
               \path<6-> [line,dashed] (dataoutpdvrp.south) |- (usercoltap.west);

               \uncover<7->{\node [green, below=0.05cm of usercoltap] (userdataoutdvrp) {user\_data\_output\_dvrp};}
               \path<7-> [line] (dataoutpdvrp.south) |- (userdataoutdvrp.west);

       \uncover<8->{\node [green, below=1cm of lpminit] (userinit) {user\_init};}
       \path<8-> [line] (init3d.south) |- (userinit.west);

       \uncover<9->{\node [yellow, below=2.3cm of init3d] (header) {header};}
       \path<9-> [line] (PALM.south) |- (header.west);

          \uncover<10->{\node [green, right=0.05cm of header] (userheader) {user\_header};}
          \path<10-> [line] (header.east) |- (userheader.west);

       \uncover<11->{\node [yellow, below=0.05cm of header] (dataoutput2d) {data\_output\_2d};}
       \path<11-> [line,dashed] (PALM.south) |- (dataoutput2d.west);

          \uncover<12->{\node [green, right=0.05cm of dataoutput2d] (userdataoutput2d) {user\_data\_output\_2d};}
          \path<12-> [line] (dataoutput2d.east) |- (userdataoutput2d.west);

       \uncover<13->{\node [yellow, below=0.05cm of dataoutput2d] (dataoutput3d) {data\_output\_3d};}
       \path<13-> [line,dashed] (PALM.south) |- (dataoutput3d.west);

          \uncover<14->{\node [green, right=0.05cm of dataoutput3d] (userdataoutput3d) {user\_data\_output\_3d};}
          \path<14-> [line] (dataoutput3d.east) |- (userdataoutput3d.west);

       \uncover<15->{\node [yellow, below=0.05cm of dataoutput3d] (timeintegr) {time\_integration};}
       \path<15-> [line] (PALM.south) |- (timeintegr.west);
       \uncover<15->{\node [white, right=0.2cm of timeintegr] (timeintspace) {};}

          \uncover<16->{\node [yellow, below=0.05cm of timeintspace] (runcontr) {run\_control};}
          \path<16-> [line] (timeintegr.south) |- (runcontr.west);
          \uncover<16->{\node [white, right=0.2cm of runcontr] (runcontrspace) {};}

             \uncover<17->{\node [yellow, below=0.05cm of runcontrspace] (flowstat1) {flow\_statistics};}
             \path<17-> [line,dashed] (runcontr.south) |- (flowstat1.west);

                \uncover<18->{\node [green, right=0.05cm of flowstat1] (userstat1) {user\_statistics};}
                \path<18-> [line] (flowstat1.east) |- (userstat1.west);

          \uncover<19->{\node [yellow, below=0.5cm of runcontr] (surfcoup) {surface\_coupler};}
          \path<19-> [line,dashed] (timeintegr.south) |- (surfcoup.west);


      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);

   \end{tikzpicture}
\end{frame}


%Folie 09
\begin{frame}
   \frametitle{PALM Flow Chart (V)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green1} = [rectangle, draw, fill=green!20, text width=0.23\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{greenLarge} = [rectangle, draw, fill=green!20, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{linered} = [draw, color=red, -]
   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
   \tikzstyle{redsmall} = [rectangle, draw, align=center, fill=red!100, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{boxinfo} = [rectangle, align=center, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{whitebox} = [rectangle, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   
   %"align=center" hinzufÃŒgen, um in den boxen zu zentrieren.
   
   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

      \uncover<1->{\node [yellow, right=0.2cm of PALM] (timeintegr) {time\_integration};}
      \uncover<1->{\node [whitebox, right=0.3cm of PALM] (timeintegrline) {};}
      \path<1-> [line] (PALM.south) |- (timeintegr.west);
      \uncover<1->{\node [white, right=0.05cm of timeintegr] (timeintegrspace) {};}
      \uncover<1->{\node [whitelarge, right=0.05cm of timeintegr] (timeintegrspacelarge) {};}
      \uncover<1->{\node [Bigwhite, right=0.05cm of timeintegr] (timeintegrspacebox) {};}

         \uncover<1->{\node [yellow, below=-0.05cm of timeintegrspace] (timestep) {timestep};}
         \path<1-> [line] (timeintegr.south) |- (timestep.west);

            \uncover<1->{\node [yellow, right=0.05cm of timestep] (globminmax) {global\_min\_max};}
            \path<1-> [line] (timestep.east) |- (globminmax.west);

         \uncover<1->{\node [greenLarge, below=0.5cm of timeintegrspacelarge] (useractions) {user\_actions (before\_timestep)};}
         \path<1-> [line] (timeintegr.south) |- (useractions.west);

         \uncover<1->{\node [yellowLarge, below=0.05cm of useractions] (timestepscheme) {timestep\_scheme\_steering};}
         \path<1-> [line] (timeintegr.south) |- (timestepscheme.west);

         \uncover<1->{\node [Bigbox, below=1.3cm of timeintegrspacebox] (bigbox) {};}
%         \path<1-> [line] (timeintegr.south) |- (bigbox.west);
         \uncover<1->{\node [white, below=1.6cm of timeintegrline] (boxlinespace) {};}
         \path<1-> [line] (timeintegr.south) |- (boxlinespace.north);

            \uncover<1->{\node [yellowLarge, below=0.4cm of timestepscheme] (prognosticequve) {prognostic\_equations\_vector};}
            \uncover<1->{\node [yellowLarge, right=0.05cm of prognosticequve] (prognosticequca) {prognostic\_equations\_cache};}
%            \uncover<1->{\node [yellowLarge, below=0.05cm of prognosticequca] (prognosticequve) {prognostic\_equations\_vector};}
            \uncover<1->{\node [boxinfo, below=-0.025cm of prognosticequve] (Boxinfo) {For details, see \\ PALM Flow Chart (VIII).};}
            \path<1-> [linered] (boxlinespace.north) -| (prognosticequca.north);
            \path<1-> [line] (boxlinespace.north) -| (prognosticequve.north);
%            \uncover<1->{\node [redsmall, above=0.3cm of prognosticequca] (redadv) {standard\\advection};}

         \uncover<1->{\node [yellow, below=3.1cm of timeintegrspace] (lpm) {lpm};}
         \path<1-> [line,dashed] (timeintegr.south) |- (lpm.west) ;

            \uncover<1->{\node [yellowLarge, right=0.05cm of lpm] (lpmmore) {user\_lpm\_advec + more};}
            \path<1-> [line] (lpm.east) -- (lpmmore.west);

         \uncover<1->{\node [yellowLarge, below=2.15cm of timestepscheme] (interactiondrop) {interaction\_droplets\_ptq};}
         \path<1-> [line,dashed] (interactiondrop.west) -| (timeintegr.south);

         \uncover<1->{\node [yellow, below=0.65cm of lpm] (boundconds) {boundary\_conds};}
         \path<1-> [line,dashed] (boundconds.west) -| (timeintegr.south);

         \uncover<1->{\node [yellow, below=0.05cm of boundconds] (swaptimelevel) {swap\_timelevel};}
         \path<1-> [line] (swaptimelevel.west) -| (timeintegr.south);

         \uncover<1->{\node [yellow, below=0.05cm of swaptimelevel] (inflowturb) {inflow\_turbulence};}
         \path<1-> [line,dashed] (inflowturb.west) -| (timeintegr.south);

         \uncover<1->{\node [yellow, below=0.05cm of inflowturb] (distfield) {disturb\_field};}
         \path<1-> [line,dashed] (distfield.west) -| (timeintegr.south);

      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);
   \end{tikzpicture}
\end{frame}

%Folie 10
\begin{frame}
   \frametitle{PALM Flow Chart (VI)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{greenLarge} = [rectangle, draw, fill=green!20, text width=0.3\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{linered} = [draw, color=red, -]
   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
   \tikzstyle{redsmall} = [rectangle, draw, align=center, fill=red!100, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{boxinfo} = [rectangle, align=center, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{whitebox} = [rectangle, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   
   %"align=center" hinzufÃŒgen, um in den boxen zu zentrieren.
   
   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

      \uncover<1->{\node [yellow, right=0.2cm of PALM] (timeintegr) {time\_integration};}
      \path<1-> [line] (PALM.south) |- (timeintegr.west);
      \uncover<1->{\node [white, right=0.05cm of timeintegr] (timeintegrspace) {};}
      \uncover<1->{\node [whitelarge, right=0.05cm of timeintegr] (timeintegrspacelarge) {};}

         \uncover<1->{\node [yellow, below=-0.05cm of timeintegrspace] (pres) {pres};}
         \path<1-> [line] (timeintegr.south) |- (pres.west);
         \uncover<1->{\node [white, below=-0.05cm of pres] (presspace) {};}

            \uncover<1->{\node [yellowsmall, right=0.05cm of presspace] (poisfft) {poisfft};}
            \path<1-> [line] (pres.east) -| (poisfft.north);

            \uncover<1->{\node [yellowsmall, right=0.05cm of poisfft] (sor) {sor};}
            \path<1-> [line] (pres.east) -| (sor.north);

            \uncover<1->{\node [yellowsmall, right=0.05cm of sor] (poismg) {poismg};}
            \path<1-> [line] (pres.east) -| (poismg.north);

         \uncover<1->{\node [yellowLarge, below=0.8cm of timeintegrspacelarge] (calcliquidwatercontent) {calc\_liquid\_water\_content};}
         \path<1-> [line,dashed] (timeintegr.south) |- (calcliquidwatercontent.west);

         \uncover<1->{\node [yellow, below=0.9cm of pres] (computevpt) {compute\_vpt};}
         \path<1-> [line,dashed] (timeintegr.south) |- (computevpt.west);

         \uncover<1->{\node [yellow, below=0.05cm of computevpt] (prandtlfluxes) {prandtl\_fluxes};}
         \path<1-> [line,dashed] (timeintegr.south) |- (prandtlfluxes.west);

         \uncover<1->{\node [yellow, below=0.05cm of prandtlfluxes] (diffusivities) {diffusivities};}
         \path<1-> [line,dashed] (timeintegr.south) |- (diffusivities.west);

         \uncover<1->{\node [greenLarge, below=2.88cm of timeintegrspacelarge] (useractionsafter) {user\_actions (after\_integration)};}
         \path<1-> [line] (timeintegr.south) |- (useractionsafter.west);

         \uncover<1->{\node [yellow, below=0.575cm of diffusivities] (checkforrestart) {check\_for\_restart};}
         \path<1-> [line,dashed] (timeintegr.south) |- (checkforrestart.west);

            \uncover<1->{\node [yellow, right=0.05cm of checkforrestart] (localtremain) {local\_tremain};}
            \path<1-> [line] (checkforrestart.east) -- (localtremain.west);

         \uncover<1->{\node [yellow, below=1.1cm of diffusivities] (flowstatistics) {flow\_statistics};}
         \path<1-> [line,dashed] (timeintegr.south) |- (flowstatistics.west);

            \uncover<1->{\node [green, right=0.05cm of flowstatistics] (userstat) {user\_statistics};}
            \path<1-> [line] (flowstatistics.east) -- (userstat.west);

         \uncover<1->{\node [yellow, below=0.05cm of flowstatistics] (sumup3d) {sum\_up\_3d\_data};}
         \path<1-> [line,dashed] (timeintegr.south) |- (sumup3d.west);

            \uncover<1->{\node [greenLarge, right=0.05cm of sumup3d] (user3ddataav) {user\_3d\_data\_averaging};}
            \path<1-> [line] (sumup3d.east) -- (user3ddataav.west);

         \uncover<1->{\node [yellow, below=0.05cm of sumup3d] (calcspec) {calc\_spectra};}
         \path<1-> [line,dashed] (timeintegr.south) |- (calcspec.west);

            \uncover<1->{\node [green, right=0.05cm of calcspec] (userspec) {user\_spectra};}
            \path<1-> [line] (calcspec.east) -- (userspec.west);

      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);
   \end{tikzpicture}
\end{frame}

%Folie 11
\begin{frame}
   \frametitle{PALM Flow Chart (VII)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{greenLarge} = [rectangle, draw, fill=green!20, text width=0.3\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{linered} = [draw, color=red, -]
   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
   \tikzstyle{redsmall} = [rectangle, draw, align=center, fill=red!100, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{boxinfo} = [rectangle, align=center, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{whitebox} = [rectangle, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   
   %"align=center" hinzufÃŒgen, um in den boxen zu zentrieren.
   
   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

      \uncover<1->{\node [yellow, right=0.2cm of PALM] (timeintegr) {time\_integration};}
      \path<1-> [line] (PALM.south) |- (timeintegr.west);
      \uncover<1->{\node [white, right=0.05cm of timeintegr] (timeintegrspace) {};}
      \uncover<1->{\node [whitelarge, right=0.05cm of timeintegr] (timeintegrspacelarge) {};}

         \uncover<1->{\node [yellow, below=-0.05cm of timeintegrspace] (runcontr) {run\_control};}
         \path<1-> [line,dashed] (timeintegr.south) |- (runcontr.west);
         \uncover<1->{\node [white, right=0.2cm of runcontr] (runcontrspace) {};}

             \uncover<1->{\node [yellow, below=0.05cm of runcontrspace] (flowstat1) {flow\_statistics};}
             \path<1-> [line,dashed] (runcontr.south) |- (flowstat1.west);

                \uncover<1->{\node [green, right=0.05cm of flowstat1] (userstat1) {user\_statistics};}
                \path<1-> [line] (flowstat1.east) |- (userstat1.west);

         \uncover<1->{\node [yellow, below=1cm of timeintegrspace] (print1d) {print\_1d};}
         \path<1-> [line,dashed] (timeintegr.south) |- (print1d.west);

         \uncover<1->{\node [yellow, below=0.05cm of print1d] (dataoutp) {data\_output\_***};}
         \path<1-> [line,dashed] (timeintegr.south) |- (dataoutp.west);

         \uncover<1->{\node [greenLarge, below=2.15cm of timeintegrspacelarge] (useractionsaftert) {user\_actions (after\_timestep)};}
         \path<1-> [line] (timeintegr.south) |- (useractionsaftert.west);

      \uncover<1->{\node [white2, below=6.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=6.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);
   \end{tikzpicture}
\end{frame}


%Folie 12
\begin{frame}
   \frametitle{PALM Flow Chart (VIII)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.18\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.255\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, align=center, fill=yellow!20, text width=0.32\textwidth, minimum size=12pt, font=\scriptsize]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{linered} = [draw, color=red, -]
   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=1\textwidth, minimum size=183pt, font=\tiny]
   \tikzstyle{redsmall} = [rectangle, draw, align=center, fill=red!100, text width=0.18\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{boxinfo} = [rectangle, align=center, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{whitebox} = [rectangle, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{bigbox} = [rectangle, draw, fill=white!100, text width=0.21\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{bigbox2} = [rectangle, draw, align=center, fill=white!100, text width=0.29\textwidth, minimum size=12pt, font=\tiny]
   
   \tikzstyle{framebox} = [rectangle, draw, text width=0.2\textwidth, minimum size=104pt, font=\tiny]
   \tikzstyle{Endbox} = [rectangle, draw, fill=gray!20, text width=0.21\textwidth, minimum size=12pt, font=\tiny]

   
   %"align=center" hinzufÃŒgen, um in den boxen zu zentrieren.
   
   \begin{tikzpicture}[auto, node distance=0, >=stealth]

      \uncover<1->{\node [Bigbox] (bigbox) {};}
      \uncover<1->{\node [redsmall, above=-0.23cm of bigbox] (redadv) {standard advection};}

      \uncover<1->{\node [yellow, below=0.1cm of redadv] (calcmeanptprofile) {calc\_mean\_pt\_profile};}

%      \uncover<1->{\node [yellowLarge, left=0.5cm of calcmeanptprofile] (prognosticequationsnoopt) {prognostic\_equations\_noopt};}
      \uncover<1->{\node [yellowLarge, left=0.5cm of calcmeanptprofile] (prognosticequationscache) {prognostic\_equations\_cache};}
      \uncover<1->{\node [yellowLarge, right=0.5cm of calcmeanptprofile] (prognosticequationsvector) {prognostic\_equations\_vector};}

      \uncover<1->{\node [yellow, below=-0.05cm of calcmeanptprofile] (calcradiation) {calc\_radiation};}
      \uncover<1->{\node [yellow, below=-0.05cm of calcradiation] (impactoflatentheat) {impact\_of\_latent\_heat};}
      \uncover<1->{\node [yellow, below=-0.05cm of impactoflatentheat] (calcprecipitation) {calc\_precipitation};}
      \uncover<1->{\node [yellow, below=-0.05cm of calcprecipitation] (productioneinit) {production\_e\_init};}
      
      \uncover<1->{\node [whitesmall, left=-1.4cm of productioneinit] (productioneinitspace1) {};}
      \uncover<1->{\node [whitesmall, below=0cm of productioneinitspace1] (productioneinitspace2) {};}

      \uncover<1->{\node [bigbox, below=0.05cm of prognosticequationscache] (listingscache) {
         \texttt{\linespread {0.7}\selectfont\noindent
            DO i=nxl,nxr\\
            \quad DO j=nys,nyn\\
            \quad \quad CALL \textcolor{blue}{u-subr}\\
            \quad \quad CALL \textcolor{blue}{v-subr}\\
            \quad \quad CALL \textcolor{blue}{w-subr}\\
            \quad \quad CALL \textcolor{blue}{pt-subr}\\
            \quad \quad CALL \textcolor{blue}{q or s-subr}\\
            \quad \quad CALL \textcolor{blue}{e-subr}\\
            \quad ENDDO\\
            ENDDO\\
         }
      };}
      
      \uncover<1->{\node [bigbox, below=0.05cm of prognosticequationsvector] (listingsvector) {
         \texttt{\linespread {0.7}\selectfont\noindent
            CALL \textcolor{blue}{u-subr}\\
            CALL \textcolor{blue}{v-subr}\\
            .\\
            .\\
            .\\
%             !within subroutines:\\
%             DO i=nxl,nxr\\
%             \quad DO j=nys,nyn\\
%             \quad \quad DO k=nzb+1,nzt\\
%             \quad \quad \quad \quad ...\\
%             \quad \quad ENDDO\\
%             \quad ENDDO\\
%             ENDDO\\
         }
      };}
      \uncover<1->{\node [bigbox2, below=-0.25cm of productioneinitspace2] (foreachvariable) {
         \textcolor{blue}{
            \textbf{\underline{For each variable:}}\\
            u-, v-, w-component,\\
            pt, q or s, sa, e (SGS-TKE)
         }
      };}

      \uncover<1->{\node [whitesmall, right=-2.08cm of foreachvariable] (foreachvariablespace1) {};}
      \uncover<1->{\node [whitesmall, below=-0.18cm of foreachvariablespace1] (foreachvariablespace2) {};}

      \uncover<1->{\node [yellowlarge, below=0.05cm of foreachvariablespace2] (advecuvws) {advec\_\{uvws\}};}
      \path<1-> [line] (advecuvws.west) -| (foreachvariable.west);

      \uncover<1->{\node [yellowlarge, below=-0.05cm of advecuvws] (diffusionuvwse) {diffusion\_\{uvwse\}};}
      \path<1-> [line] (diffusionuvwse.west) -| (foreachvariable.west);

      \uncover<1->{\node [yellowlarge, below=-0.05cm of diffusionuvwse] (coriolis) {coriolis};}
      \path<1-> [line,dashed] (coriolis.west) -| (foreachvariable.west);

      \uncover<1->{\node [yellowlarge, below=-0.05cm of coriolis] (buoyancy) {buoyancy};}
      \path<1-> [line,dashed] (buoyancy.west) -| (foreachvariable.west);

      \uncover<1->{\node [yellowlarge, below=-0.05cm of buoyancy] (useractionstend) {\mbox{user\_actions (i,j,***-tendency)}};}
      \path<1-> [line] (useractionstend.west) -| (foreachvariable.west);

      \uncover<1->{\node [yellowlarge, below=-0.05cm of useractionstend] (productione) {production\_e};}
      \path<1-> [line,dashed] (productione.west) -| (foreachvariable.west);

      \uncover<1->{\node [framebox, below=-1.025cm of foreachvariable] (foreachvariableframe) {};}
      \uncover<1->{\draw [<-,line width=5pt, color=blue] (1,0.2) -- (1.5,1);}
      \uncover<1->{\draw [<-,line width=5pt, color=blue] (-1.54,0.2) -- (-2.04,1);}



      \uncover<2->{\node [Endbox, below=1.5cm of listingscache] (endboxcache) {
         \texttt{\linespread {0.7}\selectfont\noindent
            !within subroutines:\\
            DO k=nzb+1,nzt\\
            \quad \quad \textcolor{blue}{...}\\
            ENDDO\\
         }
      };}

      \uncover<2->{\node [Endbox, below=2.5cm of listingsvector] (endboxvec) {
         \texttt{\linespread {0.7}\selectfont\noindent
            !within subroutines:\\
            DO i = nxl, nxr \\
            \quad DO j = nys, nyn \\
            \quad \quad DO k=nzb+1,nzt\\
            \quad \quad \quad \textcolor{blue}{...}\\
            \quad \quad ENDDO \\
            \quad ENDDO \\
            ENDDO\\
         }
      };}

      \uncover<2->{\draw [<-,thick] (endboxcache.north) -- (listingscache.south);}
      \uncover<2->{\draw [<-,thick] (endboxvec.north) -- (listingsvector.south);}

   \end{tikzpicture}
\end{frame}

%Folie 13
\begin{frame}
   \frametitle{PALM Flow Chart (IX)}

   \tikzstyle{white} = [rectangle, text width=0.2\textwidth, font=\tiny]
   \tikzstyle{whitelarge} = [rectangle, text width=0.3\textwidth, font=\tiny]
   \tikzstyle{whitesmall} = [rectangle, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{white2} = [rectangle, text width=0]
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowsmall} = [rectangle, draw, fill=yellow!20, text width=0.08\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowlarge} = [rectangle, draw, fill=yellow!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{yellowLarge} = [rectangle, draw, fill=yellow!20, text width=0.3\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{green} = [rectangle, draw, fill=green!20, text width=0.2\textwidth, minimum size=13pt, font=\tiny]
   \tikzstyle{line} = [draw, -]
   \tikzstyle{linered} = [draw, color=red, -]
   \tikzstyle{Bigwhite} = [rectangle, text width=0.63\textwidth, minimum size=35pt, font=\tiny]
   \tikzstyle{Bigbox} = [rectangle, draw, fill=gray!20, text width=0.65\textwidth, minimum size=33pt, font=\tiny]
   \tikzstyle{redsmall} = [rectangle, draw, align=center, fill=red!100, text width=0.08\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{boxinfo} = [rectangle, align=center, text width=0.3\textwidth, minimum size=12pt, font=\tiny]
   \tikzstyle{whitebox} = [rectangle, text width=0.2\textwidth, minimum size=12pt, font=\tiny]
   
   %"align=center" hinzufÃŒgen, um in den boxen zu zentrieren.
   
   \begin{tikzpicture}[auto, node distance=0]
      \uncover<1->{\node [white2] (contino1) {};}
      \uncover<1->{\node [white2, below=0.26cm of contino1] (PALM) {};}

      \uncover<1->{\node [yellow, right=0.2cm of PALM] (timeintegr) {time\_integration};}
      \path<1-> [line] (PALM.south) |- (timeintegr.west);
      \uncover<1->{\node [white, right=0.05cm of timeintegr] (timeintegrspace) {};}
      \uncover<1->{\node [whitelarge, right=0.05cm of timeintegr] (timeintegrspacelarge) {};}
      \uncover<1->{\node [white, below=0.8cm of timeintegr] (boxlinespace) {};}
      \uncover<1->{\node [white, below=1.3cm of timeintegr] (boxlinespacedash) {};}
      \path<1-> [line] (timeintegr.south) |- (boxlinespace.north);
      \path<1-> [line,dashed] (timeintegr.south) |- (boxlinespacedash.north);


      \uncover<1->{\node [yellow, below=2cm of timeintegr] (write3dbinary) {write\_3d\_binary};}
      \path<1-> [line,dashed] (PALM.south) |- (write3dbinary.west);

         \uncover<1->{\node [yellow, right=0.05cm of write3dbinary] (writevarlist) {write\_var\_list};}
         \path<1-> [line] (write3dbinary.east) -- (writevarlist.west);

      \uncover<1->{\node [yellow, below=0.05cm of write3dbinary] (writeparticles) {lpm\_write\_restart\_file};}
      \path<1-> [line] (PALM.south) |- (writeparticles.west);

      \uncover<1->{\node [yellow, below=0.05cm of writeparticles] (header) {header};}
      \path<1-> [line] (PALM.south) |- (header.west);

         \uncover<1->{\node [green, right=0.05cm of header] (userheader) {user\_header};}
         \path<1-> [line] (header.east) -- (userheader.west);

      \uncover<1->{\node [green, below=0.05cm of header] (userlastactions) {user\_last\_actions};}
      \path<1-> [line] (PALM.south) |- (userlastactions.west);

      \uncover<1->{\node [yellow, below=0.05cm of userlastactions] (cpustatistics) {cpu\_statistics};}
      \path<1-> [line] (PALM.south) |- (cpustatistics.west);

      \uncover<1->{\node [white2, below=5.6cm of PALM] (continu2) {};}
      \path<1-> [line,dashed] (contino1.south) |- (continu2.north);

      \uncover<1->{\node [white2, below=5.0cm of PALM] (continu1) {};}
      \path<1-> [line] (PALM.south) |- (continu1.north);
   \end{tikzpicture}
\end{frame}

%Folie 14
\begin{frame}[fragile]
   \frametitle{Important Variables and Their Declaration}
   \begin{itemize}
      \item<2->{3D-arrays of prognostic variables are named $\Psi_m$, $\Psi$, and $\Psi_p$ for time level $t-\Delta t$, $t$, and $t+\Delta T$, respectively, with $\Psi = u$, $v$, $w$, $pt$, $q$, $e$, $sa$}
      \item<3->{They are by default declared as $\Psi$($z$,$y$,$x$) or $\Psi$($k$,$j$,$i$), e.g.\\
      \begin{minipage}{0.2\textwidth}
         with\\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)


nysg = nys - ngl,  nyng = nyn + ngl
nxlg = nxl - ngl,  nxrg = nxr + ngl
nzb, nzt (bottom, top)
nys, nyn (south, north)
nxl, nxr (left, right)
         \end{lstlisting}
      \end{minipage}\\
      as the index limits of the (sub-)domain. ngl is the number of ghost layers which depends on the advection scheme ( ngl = 3 for the default Wicker-Skamarock scheme)
      }
   \end{itemize}
\end{frame}

%Folie 15
\begin{frame}[fragile]
   \frametitle{Important Variables and Their Declaration}
   \begin{itemize}
      \item<1->{If only one processor is used, then\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
nxl = 0; nxr = nx
nys = 0; nyn = ny
         \end{lstlisting}
      \end{minipage}\\
      }
      \item<2->{For speed optimization, most of the 3D-variables are declared as pointers, e.g.\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
REAL, DIMENSION(:,:,:), POINTER ::  u, u_p, v, v_p, ...
         \end{lstlisting}
      \end{minipage}\\
      This does not affect the usage of these variables in the code in (almost) any way.
      }
   \end{itemize}
\end{frame}

%Folie 16
\begin{frame}[fragile]
   \frametitle{Some Other Frequently Used Variables}

\begin{table}[htbp]
  \centering
%  \caption{Add caption}
    \begin{tabular}{|l|l|p{0.22\linewidth}|l|}
    \hline
    variable & index bounds & meaning & comment\\
    \hline
    \hline
    \texttt{\tiny zu }   & \texttt{\tiny nzb:nzt+1 }& \tiny heights of the scalar (u,v) grid levels & \texttt{\tiny zu(0)=-zu(1)}\\
    \hline
    \texttt{\tiny zw }   & \texttt{\tiny nzb:nzt+1 }& \tiny heights of the w grid level & \texttt{\tiny zw(0)=0 }\\
    \hline
    \texttt{\tiny dzu }  & \texttt{\tiny 1:nzt+1 }& \tiny vertical grid spacings between scalar grid levels & \texttt{\tiny dzu(k)=zu(k)-zu(k-1)}\\
    \hline
    \texttt{\tiny ddzu } & \texttt{\tiny 1:nzt+1 }& \tiny inverse of grid spacings & \texttt{\tiny ddzu(k)=1.0/dzu(k)}\\
    \hline
    \texttt{\tiny dx  }  &       & {\tiny grid spacing along x} &  \\
    \hline
    \texttt{\tiny ddx }  &       & {\tiny inverse of dx} & \texttt{\tiny ddx=1.0/dx }\\
    \hline
    \texttt{\tiny current\_timestep\_number} &       & {\tiny timestep counter} &  \\
    \hline
    \texttt{\tiny simulated\_time }&       & {\tiny simulated time in seconds} &  \\
    \hline
    \end{tabular}%
%  \label{tab:addlabel}%
\end{table}%
\end{frame}


%Folie 17
\begin{frame}[fragile]
   \frametitle{Preprocessor Directives (I)}
   \begin{itemize}
      \item<1->{Preprocessor directives are special lines in the code which allows to compile alternative parts of the code depending on so-called \textbf{define-string} switches.\\ Code example:\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
#if defined( __abc )
CALL FLUSH( 9 )
#else
CALL FLUSH_( 9 )
#endif
         \end{lstlisting}
      \end{minipage}\\
      If now the compiler is called e.g.\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
ifort -cpp -D __abc ... (other options)
         \end{lstlisting}
      \end{minipage}\\
      then the line containing ``\texttt{\tiny CALL FLUSH( 9 )}'' is compiled. \\If the compiler call is\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
ifort -cpp ... (other options)
         \end{lstlisting}
      \end{minipage}\\
      the line containing ``\texttt{\tiny CALL FLUSH\_( 9 )}'' is compiled.
      }
   \end{itemize}
\end{frame}


%Folie 18
\begin{frame}[fragile]
   \frametitle{Preprocessor Directives (II)}
   \begin{itemize}
      \item<1->{The preprocessor directives require to include the compiler option ``\texttt{\scriptsize-cpp}'' in any way. Otherwise, the compilation will give error messages. \textbf{The option has to be given in the configuration file} 
                \texttt{\scriptsize .mrun.config} in the \texttt{\scriptsize \%cpp\_options} line. \textbf{Different compilers may require different options!}}\\

      \item<2->{Define-string switches can be combined using logical AND / OR operators \&\& / $\lvert \lvert$.\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
#if defined ( __abc  &&  __def )
         \end{lstlisting}
      \end{minipage}
      }
   \end{itemize}
\end{frame}


%Folie 19
\begin{frame}[fragile]
   \frametitle{Preprocessor Directives (III)}
   In the PALM code, define-string switches are used for following reasons:
   \begin{itemize}
      \item<2->{To switch between system dependent subroutines for:\\
      \begin{itemize}
         \item<2->{\texttt{\scriptsize \_\_ibm}} \quad IBM-Regatta systems\\
         \item<2->{\texttt{\scriptsize \_\_lc}}\;\: \quad Linux clusters (using Intel compiler ifort)\\
         \item<2->{\texttt{\scriptsize \_\_nec}} \quad NEC-SX systems\\
      \end{itemize}
      Switches are set automatically depending on mrun-option ``\texttt{\scriptsize-h}'', eg. ``\texttt{\scriptsize-h lcmine}'' sets ``\texttt{\scriptsize-D \_\_lc}''}
      \item<3->{To switch between the serial and the parallel code:\\
      \begin{itemize}
         \item<3->{\texttt{\scriptsize \_\_parallel}}
      \end{itemize}
      This switch is set by mrun-option ``\texttt{\scriptsize-K parallel}''.}
   \end{itemize}
\end{frame}


%Folie 20
\begin{frame}[fragile]
   \frametitle{Preprocessor Directives (IV)}
   In the PALM code, define-string switches are used for following reasons:
   \begin{itemize}
      \item<1->{To enable usage of special software packages which are not included in the compilation process by default\\
      \begin{itemize}
         \item<1->{\texttt{\scriptsize \_\_dvrp\_graphics}} \quad 3D visualization system\\
         \item<1->{\texttt{\scriptsize \_\_spectra}} \quad \quad \quad \quad calculation and output of power spectra\\
      \end{itemize}
      Switches are activated with mrun-option ``\texttt{\scriptsize-p}'', \mbox{eg. ``\texttt{\scriptsize-p} ``\texttt{\scriptsize spectra dvrp\_graphics}''''}}
   \end{itemize}
    {\small \quad\\ \quad\\ \quad}\\ \quad  \\ \quad %nicht fragen, was das soll!! Mir ist leider nichts bsseres eingefallen um den Satz unter der Überschrift deckungsgleich auf beiden Folien zu haben.
\end{frame}


%Folie 21
\begin{frame}[fragile]
   \frametitle{Preprocessor Directives (V)}
   \begin{itemize}
      \item<1->{Preprocessor directives are also used for string replacement in the code.\\ Example:\\A compiler call with preprocessor option\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
ifort -cpp -Dabcd=efgh
         \end{lstlisting}
      \end{minipage}
      will replace all strings ``\texttt{\scriptsize abcd}'' in the code with ``\texttt{\scriptsize efgh}'' \textbf{before} the code is compiled.\\
      This is used in PALM to change the MPI\_REAL datatypes (which are 4 Byte long by default), to 8 Bytes. The respective cpp-directives are given in the configuration file \texttt{\scriptsize .mrun.config.}:\\
      \begin{minipage}{0.2\textwidth}
         \quad \\\\
      \end{minipage}
      \begin{minipage}{0.7\textwidth}
         \centering
         \begin{lstlisting}
%cpp_options -cpp:-DMPI_REAL=MPI_DOUBLE_PRECISION:
             -DMPI_2REAL=MPI_2DOUBLE_PRECISION: ....
         \end{lstlisting}
      \end{minipage}
      }
   \end{itemize}
\end{frame}

\end{document}