source: palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex @ 1520

% $Id: user_defined_code.tex 1515 2015-01-02 11:35:51Z hoffmann $
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        \ttfamily,showstringspaces=false,captionpos=b}

\institute{Institute of Meteorology and Climatology, Leibniz UniversitÀt Hannover}
\selectlanguage{english}
\date{last update: \today}
\event{PALM Seminar}
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\title[The PALM User-Interface]{The PALM User-Interface}
\author{PALM group}

\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-> New releases of PALM (current release is 3.10) would require the user 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 the 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}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
   \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->
   \begin{center}
   \begin{tikzpicture}[auto]
      \node[yellow]{~\texttt{SUBROUTINE user\_last\_actions} \\
                    \par\medskip
                    \texttt{!------------------------------------------------------------------------------!}\\
                    \texttt{!}\\
                    \texttt{! Description:}\\
                    \texttt{! ------------}\\
                    \texttt{! Execution of user-defined actions at the end of a job.}\\
                    \texttt{!------------------------------------------------------------------------------!}\\
                    \par\medskip
                    ~~~~\texttt{USE control\_parameters}\\
                    ~~~~\texttt{USE kinds}\\
                    ~~~~\texttt{USE user}\\
                    \par\medskip
                    ~~~~\texttt{IMPLICIT NONE}\\
                    \par\medskip
                    \texttt{!}\\
                    \texttt{!-- Here the user-defined actions at the end of a job follow.}\\
                    \texttt{!-- Sample for user-defined output:}\\
                    \vspace{0.5mm}
                    ~~~~\texttt{IF ( write\_binary(1:4) == 'true' )  THEN}\\
                    \vspace{0.5mm}
                    \texttt{!~~~~~~~IF ( ALLOCATED( u2\_av ) )  THEN}\\
                    \vspace{0.5mm}
                    \texttt{!~~~~~~~~~~WRITE ( 14 )  'u2\_av~~~~~~~~~~~~~~~';  WRITE ( 14 )  u2\_av}\\
                    \vspace{0.5mm}
                    \texttt{!~~~~~~~ENDIF}\\
                    \par\medskip
                    ~~~~~~~\texttt{WRITE ( 14 )  '*** end user ***~~~~'}\\
                    \par\medskip
                    ~~~~\texttt{ENDIF}\\
                    \par\medskip
                    ~\texttt{END SUBROUTINE user\_last\_actions}};
   \end{tikzpicture}
   \end{center}
%   \includegraphics[scale=0.3]{user_defined_code_figures/user_last_actions.png}\\   
\end{frame}

% Folie 4
\begin{frame}
   \frametitle{Embedding of User-Interface Routines}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
   \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->
   \begin{center}
      \begin{tikzpicture}[auto]
         \node[yellow]{~\texttt{...}\\
                       \vspace{0.5mm}
                       \texttt{!}\\
                       \texttt{!-- If required, final user-defined actions, and}\\
                       \texttt{!-- last actions on the open files and close files. Unit 14 was opened}\\
                       \texttt{!-- in write\_3d\_binary but it is closed here, to allow writing on this}\\
                       \texttt{!-- unit in routine user\_last\_actions.}\\
                       \vspace{0.5mm}
                       ~~~~\texttt{CALL cpu\_log( log\_point(4), 'last actions', 'start' )}\\
                       ~~~~\texttt{DO  i = 0, io\_blocks-1}\\
                       ~~~~~~~\texttt{IF ( i == io\_group )  THEN}\\
                       ~~~~~~~~~~\texttt{\textcolor{blue}{CALL user\_last\_actions}}\\
                       \vspace{0.5mm}
                       ~~~~~~~~~~\texttt{IF ( write\_binary(1:4) == 'true' )  CALL close\_file( 14 )}\\
                       ~~~~~~~\texttt{ENDIF}\\
                       \vspace{0.5mm}
                       \texttt{\#if defined( \_\_parallel )}\\
                       ~~~~~~~\texttt{CALL MPI\_BARRIER( comm2d, ierr )}\\
                       \vspace{0.5mm}
                       \texttt{\#endif}\\
                       \vspace{0.5mm}
                       ~~~~\texttt{ENDDO}\\
                       \vspace{0.5mm}
                       ~~~~\texttt{CALL close\_file( 0 )}\\
                       \vspace{0.5mm}
                       ~~~~\texttt{CALL close\_dvrp}\\
                       ~~~~\texttt{CALL cpu\_log( log\_point(4), 'last actions', 'stop' )}\\
                       \vspace{1mm}
                       ~\texttt{...}\\
                       \vspace{1mm}
                       \texttt{!}\\
                       \texttt{!-- Take final CPU-time for CPU-time analysis}\\
                       ~~~~\texttt{CALL cpu\_log( log\_point(1), 'total', 'stop' )}\\
                       ~~~~\texttt{CALL cpu\_statistics}\\
                       \texttt{\#if defined( \_\_parallel )}\\
                       ~~~~\texttt{CALL MPI\_FINALIZE( ierr )}\\
                       \vspace{0.5mm}
                       \texttt{\#endif}\\
                       \par\medskip
                       ~\texttt{END PROGRAM palm}};
      \end{tikzpicture} 
   \end{center}

%   \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{green1} = [draw, fill=green!30, text width=12em, text centered, minimum height=1.6em]
      \tikzstyle{green2} = [draw, fill=green!30, text width=10em, 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[yellow, text width=5em] (PALM) at (0,0.1) {PALM};

      \coordinate (A) at (0,-0.7);
      \node[yellow, right=0.6cm of A] (parin) {parin};

      \node[green, right=1mm of parin] (userparin) {user\_parin};
      \draw[-] (parin) -- (userparin);

      \coordinate[below=0.6cm of A] (B);
      \node[yellow, right=0.6cm of B] (initgrid) {init\_grid};

      \node[green, right=1mm of initgrid] (userinigrid) {user\_init\_grid};
      \draw[-] (initgrid) -- (userinigrid);

      \coordinate[below=0.6cm of B] (C);
      \node[yellow, right=0.6cm of C] (checkparam) {check\_parameters};

      \coordinate[below=0.3cm of checkparam] (D);
      \node[green1, right=0.6cm of D] (usercheckdataout) {user\_check\_data\_output/\_pr};

      \coordinate[below=0.55cm of D] (E);
      \node[green1, right=0.6cm of E] (usercheckparam) {user\_check\_parameters};

      \coordinate[below=1.7cm of C] (F);
      \node[yellow, right=0.6cm of F] (init3dmodel) {init\_3d\_model};

      \coordinate[below=0.3cm of init3dmodel] (G);
      \node[green2, right=0.6cm of G] (userinit3d) {user\_init\_3d\_model};

      \coordinate[below=0.55cm of G] (H);
      \node[yellow, right=0.6cm of H] (read3dbin) {read\_3d\_binary};

      \coordinate[below=0.3cm of read3dbin] (I);
      \node[green1, right=0.6cm of I] (userreadrestart) {user\_read\_restart\_data};

      \coordinate[below=1.15cm of H] (J);
      \node[green1, right=0.6cm of J] (userinitplan) {user\_init\_plant\_canopy};

      \coordinate[below=0.6cm of J] (K);
      \node[yellow, right=0.6cm of K] (lpminit) {lpm\_init};

      \node[green, right=1mm of lpminit] (userlpminit) {user\_lpm\_init};
      \draw[-] (lpminit) -- (userlpminit);      

      \coordinate[below=0.6cm of K] (L);
      \node[green, right=0.6cm of L] (userinit) {user\_init};

      \coordinate[below=4.05cm of F] (M);
      \node[yellow, right=0.6cm of M] (header) {header};

      \node[green, right=1mm of header] (userheader) {user\_header};
      \draw[-] (header) -- (userheader);      
%      
       % Draw lines
       \draw[-, thick] (PALM) -- (0,-7.8); 
       \draw[dotted, thick] (0,-8.2) -- (0,-7.8);
       \draw[-] (A) -- (parin);
       \draw[-] (B) -- (initgrid);
       \draw[-] (C) -- (checkparam); 
       \draw[-] (checkparam.south) |- (usercheckdataout.west); 
       \draw[-] (checkparam.south) |- (usercheckparam.west); 
       \draw[-] (F) -- (init3dmodel);
       \draw[-,dashed] (init3dmodel.south) |- (userinit3d.west);
       \draw[-,dashed] (init3dmodel.south) |- (read3dbin.west);
       \draw[-] (read3dbin.south) |- (userreadrestart.west);
       \draw[-,dashed] (init3dmodel.south) |- (userinitplan);
       \draw[-,dashed] (init3dmodel.south) |- (lpminit);
       \draw[-] (init3dmodel.south) |- (userinit);
       \draw[-] (M) -- (header);   
      
   \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{green1} = [draw, fill=green!30, text width=10em, 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[green, 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\_vector};    
      \node[orange1, below=0.2cm of E] (progeqfast) {prognostic\_equations\_cache};
           
      \node[green, 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[yellow, right=0.6cm of F] (lpm) {lpm}; 
      \node[green, right=0.9cm of lpm, text width=10em] (userlpmadvec) {user\_lpm\_advec}; 
      \node[yellow, right=0.6cm of G] (exchangehoriz) {exchange\_horiz};  
%      \node[yellow, right=0.0cm of exchangehoriz] (asselin) {asselin\_filter};     
      \node[yellow, right=0.6cm of H] (swaptimelevel) {swap\_timelevel}; 
      \node[yellow, 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[yellow, right=0.6cm of K] (prandtlfluxes) {prandtl\_fluxes};    
      \node[green, right=0.6cm of K, text width=14em] (useractions3) {\textcolor{blue}{user\_actions\_(\textit{'after\_integration'})}};             
%      \node[yellow, right=0.6cm of L] (diffusivities) {diffusivities};              
%      \node[yellow, right=0.6cm of L] (checkrestart) {check\_for\_restart};      
      \node[yellow, right=0.6cm of L] (flowstat) {flow\_statistics};
      \node[green, right=0.6cm of flowstat] (userstat2) {user\_statistics};  

      \node[yellow, right=0.6cm of M] (sum3ddata) {sum\_up\_3d\_data};  
      \node[green1, right=0.6cm of sum3ddata] (user3ddataav) {user\_3d\_data\_averaging}; 

      \node[green, right=0.6cm of O, text width=14em] (useractions4) {\textcolor{blue}{user\_actions\_(\textit{'after\_timestep'})}}; 
%      \node[yellow, right=0.6cm of P] (timestep) {timestep};             

      \node[yellow, right=0.2cm of user3ddataav] (dataoutput) {data\_output\_***};
      \node[green, 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[green, below=0.2cm of R, text width=9em] (output2d) {user\_data\_output\_2d};
      \node[green, 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] (D) -- (E);
      \draw[->, thick] (E) -- (progeqfast);
      \draw[-, thick] (progeq) -- (D);      
      \draw[-, thick] (progframe) -- (useractions2); 
      \draw[-, thick] (F) -- (lpm);    
      \draw[-, thick] (userlpmadvec) -- (lpm);   
      \draw[-, thick] (G) -- (exchangehoriz);
      \draw[-, thick] (H) -- (swaptimelevel);
      \draw[-, thick] (I) -- (pres);     
      \draw[dotted, thick] (pres) -- (J);
%      \draw[-, thick] (K) -- (prandtlfluxes);   
      \draw[-, thick] (K) -- (useractions3);     
      \draw[-, thick] (L) -- (flowstat);  
      \draw[-, thick] (M) -- (sum3ddata);  
      \draw[-, thick] (sum3ddata) -- (user3ddataav);

      \draw[-, thick] (userstat2) -- (flowstat);  
      \draw[-, thick] (O) -- (useractions4); 
%      \draw[-, thick] (O) -- (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[yellow, right=0.6cm of D] (write3dbinary) {write\_3d\_binary};
      \node[yellow, 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[yellow, right=0.6cm of E] (header) {header};      
      \node[green, right=0.6cm of F] (userlastactions) {user\_last\_actions};    
      \node[yellow, 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{average\_3d\_data} + \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\_check\_data\_output} & \texttt{variable}, \texttt{unit} & \texttt{check\_parameters} + \texttt{init\_masks}& 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{two\_d} & \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
           \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
   \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\_init\_3d\_model} & - - - & \texttt{init\_3d\_model} & special initializations\\
           \hline
           \texttt{user\_init\_grid} & \texttt{gls} & \texttt{init\_grid} & defining a special topography\\
           \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{user\_lpm\_advec} & - - - & \texttt{lpm} & modification of particles after advection \\
           \hline
           \texttt{user\_lpm\_init} & - - - & \texttt{lpm\_init} & defining initial particle sources \\
           \hline
           \texttt{user\_lpm\_set\_attributes} & - - - & \texttt{lpm} & defining particles attributes \\
           \hline
           \texttt{MODULE user (user\_module.f90)} & - - - & - - - & contains user defined variables\\
           \hline                  
           \texttt{user\_parin} &  & \texttt{parin} & reading user variables\\     
           \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{calc\_spectra} + \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}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.6\textwidth, font=\tiny]
   \footnotesize
   \begin{itemize}
      \item<2-> \textbf{Between the standard PALM code and the user-interface:}\\
      \begin{itemize}
         \scriptsize
         \item<3-> by including the respective \textcolor{blue}{PALM modules} in the user-interface subroutines.\\
         \begin{center}
%           \includegraphics[scale=0.3]{user_defined_code_figures/data_access_exchange.png}
            \begin{tikzpicture}[auto]
               \node[yellow]{\texttt{SUBROUTINE user\_actions( location )} \\
                             \par\medskip
                             ~~~~~\texttt{\textcolor{blue}{USE arrays\_3d}} \\
                             ~~~~~\texttt{\textcolor{blue}{USE control\_parameters}} \\
                             ~~~~~\texttt{\textcolor{blue}{USE cpulog}} \\
                             ~~~~~\texttt{\textcolor{blue}{USE indices}} \\
                             ~~~~~\texttt{\textcolor{blue}{USE interfaces}} \\
                             ~~~~~\texttt{\textcolor{blue}{USE pegrid}} \\
                             ~~~~~\texttt{\textcolor{red}{USE user}} \\
                             \par\medskip
                             ~~~~~\texttt{IMPLICIT NONE} \\
                             \par\medskip
                             ~~~~~\texttt{CHARACTER (LEN=$^\ast$) ::  location} \\
                             \par\medskip
                             ~~~~~\texttt{INTEGER ::  i, j, k}};
            \end{tikzpicture}
         \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 (otherwise, the default code would depend on the user\\ interface).}
      \end{itemize}
   \end{itemize}

\end{frame}

% Folie 11
\begin{frame}
   \frametitle{Usage of \texttt{user\underline{ }actions} (I)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
   \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{1.8mm}
      \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 line within \texttt{prognostic\underline{ }equations}, where the tendencies for the u-component are calculated and integrated:
   \end{itemize}
   \vspace{-3mm}
   \begin{center}
   \begin{tikzpicture}[auto]
      \node[yellow] {\texttt{DO  i = nxl, nxr} \\
                     ~~~\texttt{DO  j = nys, nyn} \\
                     \texttt{...} \\
                     ~~~~~~\texttt{CALL diffusion\_u( i, j )}\\
                     ~~~~~~\texttt{CALL coriolis( i, j, 1 )} \\
                     \texttt{...}\\
                     ~~~~~~\texttt{\textcolor{blue}{CALL user\_actions( i, j, 'u-tendency' )}}\\
                     \texttt{!} \\
                     \texttt{!-- Prognostic equation for u-velocity component} \\
                     ~~~~~~\texttt{DO  k = nzb\_u\_inner(j,i)+1, nzt} \\
                     ~~~~~~~~~\texttt{u\_p(k,j,i) = u(k,j,i) + dt\_3d * ( tsc(2) * tend(k,j,i) + \&} \\
                     \hspace{4.08cm} \texttt{tsc(3) * tu\_m(k,j,i) )       \&} \\
                     \hspace{2.93cm} \texttt{- tsc(5) * rdf(k) * ( u(k,j,i) - ug(k) )}\\
                     ~~~~~~\texttt{ENDDO} \\
                     \texttt{...}};
   \end{tikzpicture}
   \end{center}
%    \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)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
   \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}
      \begin{tikzpicture}[auto]
         \node[yellow]{~\texttt{SUBROUTINE user\_actions( location )}\\
                       \texttt{...}\\
                       \texttt{!}\\
                       \texttt{!--    Here the user-defined actions follow}\\
                       \texttt{!--    No calls for single grid points are allowed at locations before and}\\
                       \texttt{!--    after the timestep, since these calls are not within an i,j-loop}\\
                       ~~~~~~~\texttt{SELECT CASE ( location )}\\
                       \texttt{...}\\
                       ~~~~~~~~~~\texttt{CASE ( 'after\_timestep' )}\\
                       \texttt{!}\\
                       \texttt{!-- Enter actions to be done after every timestep here}\\
                       \par\medskip
                       ~~~~~~~~~~\texttt{CASE ( 'u-tendency' )}\\
                       \texttt{!}\\
                       \texttt{!-- Enter actions to be done in the u-tendency term here}\\
                       ~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO i = nxl, nxr}}\\
                       ~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO j = nys, nyn}}\\
                       ~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO k = nxb+1, nzt}}\\
                       ~~~~~~~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{tend(k,j,i) = tend(k,j,i) - const * u(k,j,i) ...}}\\
                       ~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
                       ~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
                       ~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
                       \par\bigskip
                       ~~~~~~~~~~\texttt{CASE ( 'v-tendency' )}\\
                       \texttt{...}};
      \end{tikzpicture}
%      \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)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.5\textwidth, font=\Tiny]
   \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 executed in\\
            \texttt{prognostic\underline{ }equations\underline{ }cache}.
         \end{itemize}
      \end{column}
   \end{columns}
  
   \uncover<4->{%
   \begin{tikzpicture}[remember picture, overlay]
      \node [yellow,shift={(9.2 cm,3.0cm)}]  at (current page.south west){~\texttt{SUBROUTINE user\_actions\_ij( i, j, location )}\\
                                                                          \par\medskip
                                                                          ~~~\texttt{USE control\_parameters}\\
                                                                          ~~~\texttt{USE pegrid}\\
                                                                          ~~~\texttt{USE user}\\
                                                                          \par\medskip
                                                                          ~~~\texttt{IMPLICIT NONE}\
                                                                          \par\medskip
                                                                          ~~~\texttt{CHARACTER (LEN=*) ::  location}\\
                                                                          \par\medskip
                                                                          ~~~\texttt{INTEGER(iwp) ::  i, idum, j}\\
                                                                          \par\medskip
                                                                          \texttt{!}\\
                                                                          \texttt{!--    Here the user-defined actions follow}\\
                                                                          \vspace{0.5mm}
                                                                          ~~~\texttt{SELECT CASE ( location )}\\
                                                                          \par\medskip
                                                                          ~~~~~~\texttt{CASE ( 'u-tendency' )}\\
                                                                          \texttt{!}\\
                                                                          \texttt{!--Enter actions to be done in the u-tendency term here}\\
                                                                          ~~~~~~~~~\texttt{\textcolor{blue}{DO k = nzb+1, nzt-1}}\\
                                                                          ~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{tend(k,j,i) = tend(k,j,i) + ...}}\\
                                                                          ~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
                                                                          \par\medskip
                                                                          ~~~~~~\texttt{CASE ( 'v-tendency' )}};
%          {%
%          \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}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
   \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}
            \begin{tikzpicture}
               \node[yellow]{~\texttt{MODULE user}\\
                             \vspace{0.4mm}
                             \texttt{...}\\
                             \vspace{0.4mm}
                             ~\texttt{REAL(wp) \hspace{0.4cm}:: ~~\textcolor{blue}{foo = 0.0}}\\
                             \vspace{0.4mm}
                             \texttt{...}\\
                             \vspace{0.4mm}
                             ~\texttt{END MODULE user}};
            \end{tikzpicture}
         \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}
            \begin{tikzpicture}
               \node[yellow]{~\texttt{SUBROUTINE user\_parin}\\
                             \vspace{0.4mm}
                             \texttt{...}\\
                             \vspace{0.4mm}
                             ~~~~~\texttt{NAMELIST ~~/userpar/ ~~ data\_output\_pr\_user, data\_output\_user,}\\
                             \vspace{0.4mm}
                             \hspace{3cm}\texttt{\textcolor{blue}{foo}, region}\\
                             \vspace{0.4mm}
                             \texttt{...}\\
                             \vspace{0.4mm}
                             ~\texttt{END SUBROUTINE user\_parin}};
            \end{tikzpicture}
         \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_3.png}
            \begin{tikzpicture}
               \node[yellow]{~\texttt{\&inipar ~~~ nx = ... ~~/}\\
                             \vspace{0.4mm}
                             ~\texttt{\&d3par ~~~ end\_time = 3600.0, ... ~~/}\\
                             \par\smallskip
                             ~\texttt{\textcolor{blue}{\&userpar ~~foo = 12345.6 ~~/}}};
            \end{tikzpicture}
         \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)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
   \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}
      \begin{tikzpicture}[auto]
         \node[yellow]{~\texttt{SUBROUTINE user\_last\_actions}\\
                       \texttt{...}\\
                       ~~~~~\texttt{\textcolor{blue}{WRITE ( 14 )  'foo \hspace{2cm}';  WRITE ( 14 )  foo}}\\
                       ~~~~~\texttt{\textcolor{blue}{WRITE ( 14 )  'bar \hspace{2cm}';  WRITE ( 14 )  bar}}
                       \par\smallskip
                       ~~~~~\texttt{WRITE ( 14 ) '*** end user *** \hspace{0.66cm}'}
                       \par\smallskip
                       ~\texttt{END SUBROUTINE user\_last\_actions}};
      \end{tikzpicture}
   \end{center}
\end{frame}

% Folie 17
\begin{frame}
   \frametitle{User-Defined Data for Restart Runs (II)}
   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.95\textwidth, font=\tiny]
   \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}
   \vspace{-2.7mm}
   \begin{center}
%      \includegraphics[scale=0.3]{user_defined_code_figures/restart_2.png}
      \begin{tikzpicture}
         \node[yellow]{\texttt{~SUBROUTINE user\_read\_restart\_data( i, nxlfa, nxl\_on\_file, nxrfa, nxr\_on\_file, \&} \\
                       \hspace{3.84cm}\texttt{nynfa, nyn\_on\_file, nysfa, nys\_on\_file,    \&} \\
                       \hspace{3.84cm}\texttt{offset\_xa, offset\_ya, overlap\_count,       \&} \\
                       \hspace{3.84cm}\texttt{tmp\_2d, tmp\_3d )}\\
                       \texttt{...} \\
                       ~~~~~\texttt{IF ( initializing\_actions == 'read\_restart\_data' )  THEN}\\
                       ~~~~~~~~~\texttt{READ ( 13 )  field\_char} \\
                       ~~~~~~~~~\texttt{DO  WHILE ( TRIM( field\_char )  '*** end user ***' )}\\
                       \par\smallskip
                       ~~~~~~~~~~~~~\texttt{nxlf = nxlfa(i,k)}
                       \texttt{...} \\
                       ~~~~~~~~~~~~~\texttt{SELECT CASE ( TRIM( field\_char ) )}\\
                       \par\smallskip
                       ~~~~~~~~~~~~~~~~~\texttt{CASE ( '\textcolor{blue}{foo}' )} \\
                       ~~~~~~~~~~~~~~~~~~~~~\texttt{IF ( .NOT. ALLOCATED( \textcolor{blue}{foo} ) ) THEN}\\
                       ~~~~~~~~~~~~~~~~~~~~~~~~~\texttt{ALLOCATE( \textcolor{blue}{foo}(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )}\\
                       ~~~~~~~~~~~~~~~~~~~~~\texttt{ENDIF}\\
                       ~~~~~~~~~~~~~~~~~~~~~\texttt{IF ( k == 1 )  READ ( 13 )  tmp\_3d}\\
                       ~~~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{foo}(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) = \&} \\
                       \hspace{4.5cm}\texttt{tmp\_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)}\\
                       \texttt{...}\\
                       ~~~~~~~~~~~~~\texttt{END SELECT}\\
                       \par\smallskip
                       ~~~~~~~~~\texttt{ENDDO}
                       \par\smallskip
                       ~~~~~~~~~\texttt{READ ( 13 )  field\_char}\\
                       \par\smallskip
                       ~~~~~~~~~\texttt{ENDDO}\\
                       ~~~~~\texttt{ENDIF}\\
                       \par\smallskip
                       ~\texttt{END SUBROUTINE user\_read\_restart\_data}};
      \end{tikzpicture}
   \end{center}
\end{frame}

% Folie 18
\begin{frame}
   \frametitle{Using the User-Interface with \texttt{mrun}}
   \tiny
   \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.:\\
            \scriptsize
            \par\smallskip
                 \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{...}
            
            \item<3-> Set an additional path in the configuration file \texttt{.mrun.config} to allow \texttt{mrun} to find and include this file:\\
            \tiny
            \par\smallskip
                 \scriptsize \quad \texttt{\%add\underline{ }source\underline{ }path \hspace{1em} \$base\underline{ }directory/USER\underline{ }CODE/\$fname}
            \par\smallskip
                 \item<4-> Modify the interface routines according to your needs.
                 \item<5-> Start a PALM run by executing\\
            \par\smallskip
                 \scriptsize \quad      \texttt{mrun -d example\underline{ }cbl ...}\\
            \par\smallskip
                 \tiny
                 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}
         \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}