source: palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex @ 982

% $Id: user_defined_code.tex 973 2012-08-07 16:03:47Z maronga $
\input{header_tmp.tex}
%\input{../header_lectures.tex}

\usepackage[utf8]{inputenc}
\usepackage{ngerman}
\usepackage{pgf}
\usetheme{Dresden}
\usepackage{subfigure}
\usepackage{units}
\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 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.pdf}}

\title[The PALM User-Interface]{The PALM User-Interface}
\author{Siegfried Raasch}

\begin{document}

% Folie 1
\begin{frame}
\titlepage
\end{frame}

\section{The PALM User-Interface}
\subsection{The PALM User-Interface}

% Folie 2
\begin{frame}
   \frametitle{Purpose of the User-Interface}
   \scriptsize
   \begin{itemize}
      \item<2-> The standard (default) PALM code cannot account for every specific demand of a user. In order to include these specific demands, the user would have to modify the standard code.
   \end{itemize}
   \vspace{2mm}
   \onslide<3->
   \textbf{Problem:}
   \begin{itemize}
      \item<3-> If a new PALM version is released (current release is 3.8) and the user wants to use it, he would have to add his modifications to the new release again.
   \end{itemize}   
   \vspace{3mm}
   \onslide<4->
   \textbf{Solution:}
   \begin{itemize}
      \item<4-> PALM offers a \grqq user-interface\grqq, i.e. a set of subroutines, where the user can add his modifications and which can be re-used for future releases of the standard PALM code.
      \item<5-> By using the user-interface, the standard code does not have to be modified by the user in most of all cases.
      \item<6-> The user-interface subroutines are almost \grqq empty\grqq\, by default. They are called from the standard PALM code but (with some very minor exceptions) do not contain any executable code.
   \end{itemize}   
\end{frame}

% Folie 3
\begin{frame}
   \frametitle{General Structure of the User-Interface}
   \scriptsize
   \begin{itemize}
      \item<1-> All routines can be found under \texttt{.../trunk/SOURCE}.
      \item<2-> There is one file for each routine. Filenames are \texttt{user\underline{ }*.f90}.\\
Example: \texttt{user\underline{ }last\underline{ }actions.f90}
   \end{itemize}
   \onslide<3->
   \centering
   \includegraphics[scale=0.3]{user_defined_code_figures/user_last_actions.png}\\   
\end{frame}

% Folie 4
\begin{frame}
   \frametitle{Embedding of User-Interface Routines}
   \scriptsize
   \begin{itemize}
      \item<1-> The user-interface routines are called from specific, well-defined locations in the standard PALM code.\\
   \ \\
   Example from \texttt{palm.f90}:
   \end{itemize}
   \onslide<2->
   \centering
   \includegraphics[scale=0.33]{user_defined_code_figures/embedding.png}\\
\end{frame}


% Folie 5
\begin{frame}
   \frametitle{Embedding of User-Interface Routines\\
   Flow Chart Overview (I): Initial Steps}
   \scriptsize
   \begin{tikzpicture}[scale=0.8, transform shape]
      % Define colours
      \tikzstyle{green} = [draw, fill=green!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{yellow} = [draw, fill=yellow!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{orange} = [draw, fill=orange!60, text width=7.1em, text centered]
      
      % Define coordinates and draw nodes      
      \node[green, text width=5em] (PALM) at (0,0.1) {PALM};

      \coordinate (A) at (0,-0.7);

      \node[green, right=0.6cm of A] (parin) {parin};
      
      \coordinate[below=0.3cm of parin] (B);
      \coordinate[below=0.9cm of parin] (C);
      \coordinate[below=1.5cm of parin] (D);
      
      \node[green, right=0.6cm of B] (read) {read\_var\_list};
      \node[green, right=0.6cm of C] (package) {package\_parin};
      \node[yellow, right=0.6cm of D] (userparin) {user\_parin};
      
      \coordinate[below=3cm of PALM] (E);      
      \coordinate[below=3.6cm of PALM] (F);    
      \coordinate[below=4.2cm of PALM] (G);      
      \coordinate[below=4.8cm of PALM] (H); 
      \coordinate[below=5.6cm of PALM] (I); 
      \coordinate[below=7.4cm of PALM] (J);             
                
      \node[green, right=0.6cm of E] (initpegrid) {init\_pegrid};      
      \node[green, right=0.6cm of F] (initgrid) {init\_grid}; 
      \node[yellow, right=0.9cm of initgrid] (userinitgrid) {user\_init\_grid}; 
      
      \node[green, right=0.6cm of G] (checkparameters) {check\_parameters};       
      \node[yellow, right=0.9cm of checkparameters, text width=9.5em] (usercheckdataoutput) {user\_check\_data\_output}; 
      \node[green, right=0.6cm of H] (header) {header}; 
      \node[green, right=0.6cm of I] (init3dmodel) {init\_3d\_model};       
      \node[yellow, right=0.9cm of header] (userheader) {user\_header}; 
            
      \node[orange, right=0.6cm of J] (timeint) {time\_integration};       
      
      \coordinate[below=0.3cm of init3dmodel] (K);   
      \coordinate[below=0.9cm of init3dmodel] (L);        
      
      \node[green, right=0.6cm of K] (initparticles) {init\_particles};       
      \node[yellow, right=0.9cm of initparticles] (userinitparticles) {user\_init\_particles};   
      \node[yellow, right=0.6cm of L] (userinit) {user\_init};       
     
      % Draw lines
      \draw[-, thick] (PALM) -- (0,-7.8); 
      \draw[dotted, thick] (0,-8.2) -- (0,-7.8);
      \draw[-, thick] (A) -- (parin);
      \draw[-, thick] (parin) -- (D);  
      \draw[dashed, thick] (B) -- (read);
      \draw[dashed, thick] (C) -- (package);
      \draw[-, thick] (D) -- (userparin); 
      \draw[-, thick] (E) -- (initpegrid);
      \draw[-, thick] (F) -- (initgrid);
      \draw[-, thick] (G) -- (checkparameters);
      \draw[-, thick] (H) -- (header);
      \draw[-, thick] (I) -- (init3dmodel);
      \draw[-, thick] (J) -- (timeint);
      \draw[dotted, thick] (init3dmodel) -- (K);
      \draw[-, thick] (K) -- (L);
      \draw[dashed, thick] (K) -- (initparticles);
      \draw[-, thick] (L) -- (userinit);
      \draw[-, thick] (initgrid) -- (userinitgrid);      
      \draw[-, thick] (checkparameters) -- (usercheckdataoutput);      
      \draw[-, thick] (header) -- (userheader);      
      \draw[-, thick] (initparticles) -- (userinitparticles);      
      
   \end{tikzpicture}
\end{frame}

% Folie 6
\begin{frame}
   \frametitle{Embedding of User-Interface Routines\\
   Flow Chart Overview (II): Time Integration Loop}
   \scriptsize
   \begin{tikzpicture}[scale=0.7, transform shape]
      % Define colours
      \tikzstyle{green} = [draw, fill=green!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{yellow} = [draw, fill=yellow!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{orange} = [draw, fill=orange!60, text width=7.1em, text centered]
      \tikzstyle{orange1} = [draw, fill=orange!80, text width=11em, text centered]      
      \definecolor{grey}{rgb}{0.25,0.25,0.25}

      % Define coordinates and draw nodes      
      \node[draw, text width=25em,minimum height=4.0em,fill=black!15] (progframe) at (5.75,-1.5) {};

      \coordinate (A) at (0,0);

      \node[orange, right=0.6cm of A] (timeint) {time\_integration};       
      
      \coordinate[below=0.3cm of timeint] (B);
      \coordinate[below=0.8cm of timeint] (C);   
      \coordinate[right=2cm of C] (D);   
      \coordinate[right=3.8cm of D] (E);
                 
      \node[yellow, right=0.6cm of B, text width=14em] (useractions1) {\textcolor{blue}{user\_actions\_(\textit{'before\_timestep'})}};    
         
      \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations};    
      \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_fast};
      \node[draw, fill=red, text width=4em] at (8.6,-0.8) {\textcolor{white}{standard advection}};
                
      \node[yellow, right=0.3cm of progframe, text width=14em] (useractions2) {\textcolor{blue}{user\_actions\_(\textit{'*\_tendency'})}}; 
      
      
      \coordinate[below=2.3cm of timeint] (F);
      \coordinate[below=2.9cm of timeint] (G);
      \coordinate[below=3.5cm of timeint] (H);
      \coordinate[below=4.1cm of timeint] (I);

                              
      \node[green, right=0.6cm of F] (advecparticles) {advec\_particles}; 
      \node[yellow, right=0.9cm of advecparticles, text width=10em] (userparticlesattributes) {user\_particles\_attributes}; 
      \node[green, right=0.6cm of G] (exchangehoriz) {exchange\_horiz};  
      \node[green, right=0.0cm of exchangehoriz] (asselin) {asselin\_filter};     
      \node[green, right=0.6cm of H] (swaptimelevel) {swap\_timelevel}; 
      \node[green, right=0.6cm of I] (pres) {pres};
      
      \coordinate[below=0.3cm of pres] (J);    
      \coordinate[below=5.1cm of timeint] (K);     
      \coordinate[below=5.7cm of timeint] (L);
      \coordinate[below=6.3cm of timeint] (M);
      \coordinate[below=6.9cm of timeint] (N);      
      \coordinate[below=8.2cm of timeint] (O); 
      \coordinate[below=8.8cm of timeint] (P);     
                  
      \node[green, right=0.6cm of K] (prandtlfluxes) {prandtl\_fluxes};    
      \node[yellow, right=0.6cm of L, text width=14em] (useractions3) {\textcolor{blue}{user\_actions\_(\textit{'after\_integration'})}};             
      \node[green, right=0.6cm of M] (diffusivities) {diffusivities};              
      \node[green, right=0.0cm of diffusivities] {check\_for\_restart};      
      \node[green, right=0.6cm of N] (flowstat) {flow\_statistics};
      \node[green, right=0.0cm of flowstat] (runcontrol) {run\_control};  
      \node[yellow, below=0.2cm of flowstat] (userstat) {user\_statistics};  
      \node[yellow, right=0.6cm of O, text width=14em] (useractions4) {\textcolor{blue}{user\_actions\_(\textit{'after\_timestep'})}}; 
      \node[green, right=0.6cm of P] (timestep) {timestep};             

      \node[green, right=0.2cm of runcontrol] (dataoutput) {data\_output\_***};
      \node[yellow, right=0.2cm of dataoutput] (userdvrpcoltab) {user\_dvrp\_coltab};
      \coordinate[below=0.2cm of dataoutput] (Q);   
      \coordinate[right=0.4cm of Q] (R);   
      \coordinate[right=3.0cm of R] (S); 
          
      \node[yellow, below=0.2cm of R, text width=9em] (output2d) {user\_data\_output\_2d};
      \node[yellow, below=0.2cm of S, text width=9em] (output3d) {user\_data\_output\_3d};
      


      \draw[dotted, thick] (0,0.05) -- (0,0.3);
      \draw[-, thick] (0,0.05) -- (0,-8.8);
      \draw[dotted, thick] (0,-9.2) -- (0,-8.8);
      \draw[-, thick] (A) -- (timeint);
      \draw[-, thick] (timeint) -- (P);
      \draw[-, thick] (B) -- (useractions1);
      \draw[-, thick] (C) -- (D);
      \draw[-, thick] (progeq) -- (D);      
      \draw[-, thick, color=red] (D) -- (E); 
      \draw[->, thick, color=red] (E) -- (progeqfast);        
      \draw[-, thick] (progframe) -- (useractions2); 
      \draw[-, thick] (F) -- (advecparticles);    
      \draw[-, thick] (userparticlesattributes) -- (advecparticles);   
      \draw[-, thick] (G) -- (exchangehoriz);
      \draw[-, thick] (H) -- (swaptimelevel);
      \draw[-, thick] (I) -- (pres);     
      \draw[dotted, thick] (pres) -- (J);
      \draw[-, thick] (K) -- (prandtlfluxes);   
      \draw[-, thick] (L) -- (useractions3);     
      \draw[-, thick] (M) -- (diffusivities);  
      \draw[-, thick] (N) -- (flowstat);  
      \draw[-, thick] (userstat) -- (flowstat);  
      \draw[-, thick] (O) -- (useractions4); 
      \draw[-, thick] (P) -- (timestep);   
      \draw[-, thick] (dataoutput) -- (Q); 
      \draw[-, thick] (S) -- (Q); 
      \draw[-, thick] (R) -- (output2d); 
      \draw[-, thick] (S) -- (output3d); 
   \end{tikzpicture}
\end{frame}


% Folie 7
\begin{frame}
   \frametitle{Embedding of User-Interface Routines\\
   Flow Chart Overview (III): Final Steps}
   \scriptsize
   \begin{tikzpicture}[scale=0.8, transform shape]
      % Define colours
      \tikzstyle{green} = [draw, fill=green!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{yellow} = [draw, fill=yellow!30, text width=7.1em, text centered, minimum height=1.6em]
      \tikzstyle{orange} = [draw, fill=orange!60, text width=7.1em, text centered]
      
      % Define coordinates and draw nodes      
      \node[green, text width=5em] (PALM) at (0,0.1) {PALM};

      \coordinate (A) at (0,-0.7);


      \node[orange, right=0.6cm of A] (timeint) {time\_integration};       
      \coordinate[below=0.5cm of timeint] (B);
      \coordinate[below=1.0cm of timeint] (C);   
     
      \coordinate[below=2.5cm of PALM] (D);  
     
      \node[green, right=0.6cm of D] (write3dbinary) {write\_3d\_binary};
      \node[green, right=0.9cm of write3dbinary] (writevarlist) {write\_var\_list};   
        
      \coordinate[below=3.5cm of PALM] (E); 
      \coordinate[below=4.1cm of PALM] (F); 
      \coordinate[below=4.7cm of PALM] (G); 
      \node[green, right=0.6cm of E] (header) {header};      
      \node[yellow, right=0.6cm of F] (userlastactions) {user\_last\_actions};    
      \node[green, right=0.6cm of G] (cpustat) {cpu\_statistics};                
      % Draw lines
      \draw[-, thick] (PALM) -- (G); 
      \draw[-, thick] (A) -- (timeint);
      \draw[-, thick] (B) -- (timeint);
      \draw[dotted, thick] (B) -- (C);
      \draw[dashed, thick] (D) -- (write3dbinary);
      \draw[-, thick] (write3dbinary) -- (writevarlist);
      \draw[-, thick] (E) -- (header);
      \draw[-, thick] (F) -- (userlastactions);
      \draw[-, thick] (G) -- (cpustat);

   \end{tikzpicture}
\end{frame}

% Folie 8
\begin{frame}
   \frametitle{Complete List of User-Interface Routines (I)}
   \tiny
   \begin{tabular}{|p{2.5cm}|p{2.4cm}|p{2.1cm}|p{3cm}|}
      \hline
           \textbf{Name} & \textbf{Arguments} & \textbf{Called from} & \textbf{Task}\\
           \hline
           \texttt{user\_3d\_data\_averaging} & \texttt{mode}, \texttt{variable} & \texttt{sum\_up\_3d\_data} & temporal averaging for user-defined quantities\\
           \hline
           \texttt{user\_actions} \texttt{user\_actions} & \texttt{location} \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\, \texttt{i}, \texttt{j}, \texttt{location} & \texttt{time\_integration} +
\texttt{prognostic\_equations} & e.g. additional forces to be included in the prognostic equations\\
           \hline
           \texttt{user\_dummy (user\_additional \_routines.f90)} & - - - & - - - & for additional subroutines defined by the user\\
           \hline
           \texttt{user\_advec\_particles} & - - - & \texttt{advec\_particles} & modification of particles after advection\\
           \hline
           \texttt{user\_check\_data\_output} & \texttt{variable}, \texttt{unit} & \texttt{check\_parameters} & check the user-defined output quantities\\
           \hline
           \texttt{user\_check\_data\_output\_pr} & \texttt{variable}, \texttt{var\_count}, \texttt{unit} & \texttt{check\_parameters} & check the user-defined profile output quantities\\
           \hline
           \texttt{user\_check\_parameters} & - - - & \texttt{check\_parameters} & check user-defined variables\\
           \hline          
           \texttt{user\_data\_output\_2d} & \texttt{av}, \texttt{variable}, \texttt{found}, \texttt{grid}, \texttt{local\_pf} & \texttt{data\_output\_2d} & output/calculation of additional user-defined quantities\\ 
           \hline          
           \texttt{user\_data\_output\_3d} & \texttt{av}, \texttt{variable}, \texttt{found}, \texttt{local\_pf}, \texttt{nz\_do} & \texttt{data\_output\_3d} & output/calculation of additional user-defined quantities\\
           \hline          
           \texttt{user\_data\_output\_dvrp} & \texttt{output\_variable}, \texttt{local\_pf} & \texttt{data\_output\_dvrp} & output of additional user-defined quantities\\
           \hline
           \texttt{user\_data\_output\_mask} & \texttt{av}, \texttt{variable}, \texttt{found}, \texttt{local\_pf} & \texttt{data\_output\_mask} & output of additional masked user-defined quantities\\
           \hline
           \texttt{user\_define\_netcdf\_grid} & \texttt{variable}, \texttt{found}, \texttt{grid\_x}, \texttt{grid\_y}, \texttt{grid\_z} & \texttt{netcdf} & defining the grid for additional output quantities\\
           \hline
           \texttt{user\_dvrp\_coltab} & \texttt{mode}, \texttt{variable} & \texttt{data\_output\_dvrp} & defining color tables for particles\\   
           \hline          
   \end{tabular}

\end{frame}

% Folie 9
\begin{frame}
   \frametitle{Complete List of User-Interface Routines (II)}
   \tiny
   \ \\
   \begin{tabular}{|p{2.5cm}|p{2.4cm}|p{2.1cm}|p{3cm}|}
      \hline
           \textbf{Name} & \textbf{Arguments} & \textbf{Called from} & \textbf{Task}\\
           \hline
           \texttt{user\_header} & \texttt{io} & \texttt{header} & output user variables to header\\
           \hline
           \texttt{user\_init} & - - - & \texttt{init\_3d\_model} & e.g. reading from restart file\\
           \hline
           \texttt{user\_init\_3d\_model} & - - - & \texttt{init\_3d\_model} & special initializations\\
           \hline
           \texttt{user\_init\_grid} & \texttt{gls}, \texttt{nzb\_local} & \texttt{init\_grid} & defining a special topography\\
           \hline          
           \texttt{user\_init\_particles} & - - - & \texttt{init\_particles} & defining initial particle sources\\
           \hline                  
           \texttt{user\_init\_plant\_canopy} & - - - & \texttt{init\_3d\_model} & setting of leaf area density and canopy drag coefficient\\
           \hline
           \texttt{user\_last\_actions} & - - - & \texttt{palm} & e.g. output for restart runs\\
           \hline          
           \texttt{MODULE user (user\_module.f90)} & - - - & - - - & contains user defined variables\\
           \hline                  
           \texttt{user\_parin} &  & \texttt{parin} & reading user variables\\     
           \hline          
           \texttt{user\_particle\_attributes} & - - - & \texttt{advec\_particles} & defining particles attributes\\       
           \hline
           \texttt{user\_read\_restart\_data} & \texttt{i}, \texttt{nxlfa}, \texttt{nxl\_on\_file}, \texttt{nxrfa}, \texttt{nxr\_on\_file}, \texttt{nynfa}, \texttt{nyn\_on\_file}, \texttt{nysfa}, \texttt{nys\_on\_file}, \texttt{offset\_xa}, \texttt{offset\_ya}, \texttt{overlap\_count}, \texttt{tmp\_2d}, \texttt{tmp\_3d} & \texttt{read\_3d\_binary} & reading user-defined 2d/3d-arrays from the restart file\\          
           \hline                  
           \texttt{user\_spectra} & \texttt{mode}, \texttt{m}, \texttt{pr} & \texttt{data\_output\_spectra} & output/calculation of additional user-defined quantities\\           
           \hline          
           \texttt{user\_statistics} & \texttt{mode}, \texttt{sr}, \texttt{tn} & \texttt{flow\_statistics} & calculating additional horizontal averages + time series quantities\\              
           \hline             
   \end{tabular}
   \ \\
   \ \\
   See PALM online documentation under \\
   \textbf{http://palm.muk.uni-hannover.de/wiki/doc/app/userint}\\
   for detailed explanations.

\end{frame}

% Folie 10
\begin{frame}
   \frametitle{Data Access / Exchange}
   \footnotesize
   \begin{itemize}
      \item<2-> \textbf{Between the standard PALM code and the user-interface:}\\
      \begin{itemize}
         \scriptsize
         \item<3-> by including the respective PALM modules in the user-interface subroutines.\\
         \begin{center}
            \includegraphics[scale=0.3]{user_defined_code_figures/data_access_exchange.png}
         \end{center} 
      \end{itemize}
      \item<4-> \textbf{Within the user-interface:}
      \begin{itemize}
         \scriptsize
         \item by the module \texttt{\textcolor{red}{user}} (file \texttt{user\underline{ }module.f90}),  which is used in every subroutine included in the interface.\\ \textbf{This module is (and should be) never used in the standard PALM code, in order to avoid data flow from the user interface to the\\ PALM default code!}
      \end{itemize}
   \end{itemize}

\end{frame}

% Folie 11
\begin{frame}
   \frametitle{Usage of \texttt{user\underline{ }actions} (I)}
   \scriptsize
   \begin{itemize}
      \item<1-> \texttt{user\underline{ }actions} is designed to add additional terms to the prognostic equations or to carry out special actions at the beginning or the end of each timestep.
      \vspace{2mm}
      \item<2-> Therefore, several calls of \texttt{user\underline{ }actions} can be found in the default PALM routines \texttt{time\underline{ }integration} and \texttt{prognostic\underline{ }equations}. The place from which it is called is communicated to the routine by a string-argument, e.g.\\
   \ \\
   \quad \texttt{CALL user\underline{ }actions ( 'u-tendency' )}\\
   \ \\
        \onslide<3-> It means that this call is from a place within \texttt{prognostic\underline{ }equations}, where the tendencies for the u-component are calculated and integrated:
   \end{itemize}
   \vspace{-2mm}
   \begin{center}
      \includegraphics[scale=0.33]{user_defined_code_figures/user_actions_1.png}
   \end{center}
\end{frame}

% Folie 12
\begin{frame}
   \frametitle{Usage of \texttt{user\underline{ }actions} (II)}
   \scriptsize
   \begin{itemize}
      \item Additional tendencies have to be included by the user at the respective code line in \texttt{user\underline{ }actions}:
   \end{itemize}
   \begin{center}
      \includegraphics[scale=0.35]{user_defined_code_figures/user_actions_2.png}
   \end{center}
\end{frame}

% Folie 13
\begin{frame}[t]
   \frametitle{Usage of \texttt{user\underline{ }actions} (III)}
   \scriptsize
   \begin{columns}[T]
      \begin{column}{1.15\textwidth}
         \begin{itemize}
            \item<1-> The different versions of \texttt{prognostic\underline{ }equations} (\texttt{prognostic\underline{ }equations\underline{ }cache}, \texttt{prognostic\underline{ }equations\underline{ }vector}) contain different calls of \texttt{user\underline{ }actions}:
            \item<2-> From \texttt{prognostic\underline{ }equations\underline{ }vector}: \hspace{0.6em}\texttt{CALL user\underline{ }actions ( 'u-tendency' )}
            \item<3-> From \texttt{prognostic\underline{ }equations},\\
            \texttt{prognostic\underline{ }equations\underline{ }cache}:\hspace{4em}\texttt{CALL user\underline{ }actions ( i, j, 'u-tendency' )}
            \vspace{3mm}
            \item<4-> In case that \texttt{prognostic\underline{ }equations}\\
            \texttt{prognostic\underline{ }equations\underline{ }cache} are\\
            used, the user has to add his code in\\
            the interface routine\\
            \texttt{user\underline{ }actions\underline{ }ij}:
            \vspace{3mm}
            \item<5-> Here, only the \texttt{k}-loop (vertical direction)\\
            has to be used, because loops over\\
            i and j are carried out in\\
            \texttt{prognostic\underline{ }equations\underline{ }cache}.
         \end{itemize}
      \end{column}
   \end{columns}
  
   \uncover<4->{%
   \begin{tikzpicture}[remember picture, overlay]
      \node [shift={(8.3 cm,3.0cm)}]  at (current page.south west)
         {%
         \begin{tikzpicture}[remember picture, overlay]
            \node[text width=14em] at (0,0) {\includegraphics[scale=0.3]{user_defined_code_figures/user_actions_3.png}};
         \end{tikzpicture}
         };
    \end{tikzpicture}}
   
\end{frame}

% Folie 14
\begin{frame}
   \frametitle{Steering the User-Interface}
   \scriptsize
   \begin{columns}[T]
      \begin{column}{1.1\textwidth}
         For steering the user-interface code, the user may want to add some additional variables and set their respective values within the parameter-file (e.g. \texttt{example\underline{ }cbl\underline{ }p3d}). This requires the following actions (example for a variable named \texttt{foo}):
      \end{column}
   \end{columns}
   \vspace{1mm}
      \begin{enumerate}
         \item<1-> Add the variable name to module \texttt{user} in order to define it and to make it available in all user-interface subroutines. Set a default value for this variable.
         \begin{center}
            \includegraphics[scale=0.3]{user_defined_code_figures/steering_1.png}
         \end{center}
         \vspace{1mm}
         \item<2-> Add the variable to the NAMELIST \texttt{/userpar/}. This NAMELIST already contains four predefined variables.
         \begin{center}
            \includegraphics[scale=0.3]{user_defined_code_figures/steering_2.png}
         \end{center}
         \vspace{1mm}
         \item<3-> Add the NAMELIST \texttt{\&userpar} to the parameter file (e.g. \texttt{example\underline{ }cbl\underline{ }p3d}) and assign a value to this variable.         
         \begin{center}
            \includegraphics[scale=0.3]{user_defined_code_figures/steering_1.png}
         \end{center}
         \vspace{1mm}
         \item<4-> Output the variable's value using \texttt{user\underline{ }header}.
      \end{enumerate}
      

\end{frame}

% Folie 15
\begin{frame}
   \frametitle{User-Defined Output}
   \scriptsize
   \begin{itemize}
      \item<2-> A very typical request of users is the calculation and output of quantities which are not part of PALM's standard output (e.g. a 3D-array of the resolved-scale vertical heat (temperature) flux).
      \vspace{2mm}
      \item<3-> The default user interface includes a number of subroutines which allow the calculation of user-defined quantities and output of these quantities as profiles, timeseries, 2d cross section or 3d volume data. These are e.g.\\
      \texttt{user\underline{ }check\underline{ }data\underline{ }output}, \texttt{user\underline{ }check\underline{ }data\underline{ }output\underline{ }pr},\\
      \texttt{user\underline{ }define\underline{ }netcdf\underline{ }grid}, \texttt{user\underline{ }statistics},\\
      \texttt{user\underline{ }3d\underline{ }data\underline{ }averaging}, \texttt{user\underline{ }data\underline{ }output\underline{ }2d},\\
      \texttt{user\underline{ }data\underline{ }output\underline{ }3d}.
      \vspace{2mm}
      \item<4-> The respective subroutines contain, as an example, code lines (written as comment lines) for calculating and output the square of the u-component velocity.
      \vspace{2mm}
      \item<5-> These quantities are output to PALM‘s standard netCDF files, i.e.\\ \texttt{DATA\underline{ }1D\underline{ }PR\underline{ }NETCDF}, \texttt{DATA\underline{ }1D\underline{ }TS\underline{ }NETCDF}, \texttt{DATA\underline{ }2D\underline{ }XY\underline{ }NETCDF} or \texttt{DATA\underline{ }3D\underline{ }NETCDF}.
      \vspace{2mm}
      \item<6-> The online documentation gives very detailed instructions about how to modify the interface in order to output user-defined quantities under\\
      \vspace{1mm}
      \textbf{http://palm.muk.uni-hannover.de/wiki/doc/app/userint/output}
   \end{itemize}
\end{frame}

% Folie 16
\begin{frame}
   \frametitle{User-Defined Data for Restart Runs (I)}
   \scriptsize
   \begin{itemize}
      \item It might be neccessary to save the values of user-defined variables at the end of a model run in order to use them for a restart run.\\
      \ \\
      This can be done using the routine \texttt{user\underline{ }last\underline{ }actions}.\\
      \grqq \texttt{14}\grqq\, is the file-id for the restart file (local filename \texttt{BINOUT}):
   \end{itemize}
   \begin{center}
      \includegraphics[scale=0.3]{user_defined_code_figures/restart_1.png}
   \end{center}
\end{frame}

% Folie 17
\begin{frame}
   \frametitle{User-Defined Data for Restart Runs (II)}
   \scriptsize
   \begin{itemize}
      \item Additionally, these variables have to be read from the restart file (file-id \grqq \texttt{13}\grqq\,, local filename \texttt{BININ}) by adding code to the routine \texttt{user\underline{ }read\underline{ }restart\underline{ }data}:
   \end{itemize}
   \begin{center}
      \includegraphics[scale=0.3]{user_defined_code_figures/restart_2.png}
   \end{center}
\end{frame}

% Folie 18
\begin{frame}
   \frametitle{Using the User-Interface with \texttt{mrun}}
   \scriptsize
   \begin{columns}[T]
      \begin{column}{1.1\textwidth}
         \vspace{-1mm}
         \textbf{Users can add their own (modified) user-interface to a PALM-run by carrying out the following steps:}
         \begin{enumerate}
            \item<2-> Copy the default (empty) user-interface files that you need (e.g. user\underline{ }module.f90, user\underline{ }parin.f90, user\underline{ }actions.f90) to a directory of your choice, e.g.:\\
            \tiny
                 \quad \texttt{cd \~{ }/palm/current\underline{ }version}\\
                 \quad \texttt{mkdir -p USER\underline{ }CODE/example\underline{ }cbl}\\
                 \quad \texttt{cp trunk/SOURCE/user\underline{ }module.f90  USER\underline{ }CODE/example\underline{ }cbl/user\underline{ }module.f90}\\
                 \quad \texttt{cp trunk/SOURCE/user\underline{ }parin.f90\hspace{1em}USER\underline{ }CODE/example\underline{ }cbl/user\underline{ }parin.f90}\\
            \quad \texttt{...}
            \scriptsize
            \vspace{-1mm}
            \item<3-> Set an additional path in the configuration file \texttt{.mrun.config} to allow \texttt{mrun} to find and include this file:\\
            \tiny
                 \quad \texttt{\%add\underline{ }source\underline{ }path \hspace{1em} \$base\underline{ }directory/USER\underline{ }CODE/\$fname}
                 \scriptsize
                 \item<4-> Modify the interface routines according to your needs.
                 \item<5-> Start a PALM run by executing\\
                 \tiny
                 \quad  \texttt{mrun -d example\underline{ }cbl ...}\\
                 \scriptsize
                 The files user\underline{ }*.f90 will be automatically compiled within the job / interactive run and will replace the respective PALM default user-interface files.
              \end{enumerate}
              \vspace{-2mm}
         \begin{itemize}
                 \item<6-> \textbf{The modified user-interface file cannot be pre-compiled by using} \texttt{mbuild}!
                 \item<7-> The above method allows to use different user-interfaces for different runs. Just store the respective interface-files in subdirectories \texttt{USER\underline{ }CODE/abcd}, \texttt{USER\underline{ }CODE/cdef}, etc. and start \texttt{mrun} with option \grqq \texttt{-d abcd}\grqq, \grqq \texttt{-d cdef}\grqq, etc.
         \end{itemize}

      \end{column}
   \end{columns} 
   
\end{frame}

\end{document}