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Ignore:
Timestamp:
Sep 18, 2013 1:19:19 PM (11 years ago)
Author:
fuhrmann
Message:

several updates in the tutorial

File:
1 edited

Legend:

Unmodified
Added
Removed

  • palm/trunk/TUTORIAL/SOURCE/user_defined_code.tex

    r1080 r1226  
    1515\usepackage{tikz}
    1616\usetikzlibrary{shapes,arrows,positioning}
    17 \usetikzlibrary{decorations.markings}             %neues paket
    18 \usetikzlibrary{decorations.pathreplacing}        %neues paket
     17%\usetikzlibrary{decorations.markings}             %neues paket
     18%\usetikzlibrary{decorations.pathreplacing}        %neues paket
    1919\def\Tiny{\fontsize{4pt}{4pt}\selectfont}
    2020\usepackage{amsmath}
    … …  
    7070   \textbf{Problem:}
    7171   \begin{itemize}
    72       \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.
     72      \item<3-> If a new PALM version is released (current release is 3.9) and the user wants to use it, he would have to add his modifications to the new release again.
    7373   \end{itemize}   
    7474   \vspace{3mm}
    … …  
    8585\begin{frame}
    8686   \frametitle{General Structure of the User-Interface}
     87   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
    8788   \scriptsize
    8889   \begin{itemize}
    … …  
    9293   \end{itemize}
    9394   \onslide<3->
    94    \centering
    95    \includegraphics[scale=0.3]{user_defined_code_figures/user_last_actions.png}\\   
     95   \begin{center}
     96   \begin{tikzpicture}[auto]
     97      \node[yellow]{~\texttt{SUBROUTINE user\_last\_actions} \\
     98                    \par\medskip
     99                    \texttt{!------------------------------------------------------------------------------!}\\
     100                    \texttt{!}\\
     101                    \texttt{! Description:}\\
     102                    \texttt{! ------------}\\
     103                    \texttt{! Execution of user-defined actions at the end of a job.}\\
     104                    \texttt{!------------------------------------------------------------------------------!}\\
     105                    \par\medskip
     106                    ~~~~\texttt{USE control\_parameters}\\
     107                    ~~~~\texttt{USE user}\\
     108                    \par\medskip
     109                    ~~~~\texttt{IMPLICIT NONE}\\
     110                    \par\medskip
     111                    \texttt{!}\\
     112                    \texttt{!-- Here the user-defined actions at the end of a job follow.}\\
     113                    \texttt{!-- Sample for user-defined output:}\\
     114                    \vspace{0.5mm}
     115                    ~~~~\texttt{IF ( write\_binary(1:4) == 'true' )  THEN}\\
     116                    \vspace{0.5mm}
     117                    \texttt{!~~~~~~~IF ( ALLOCATED( u2\_av ) )  THEN}\\
     118                    \vspace{0.5mm}
     119                    \texttt{!~~~~~~~~~~WRITE ( 14 )  'u2\_av~~~~~~~~~~~~~~~';  WRITE ( 14 )  u2\_av}\\
     120                    \vspace{0.5mm}
     121                    \texttt{!~~~~~~~ENDIF}\\
     122                    \par\medskip
     123                    ~~~~~~~\texttt{WRITE ( 14 )  '*** end user ***~~~~'}\\
     124                    \par\medskip
     125                    ~~~~\texttt{ENDIF}\\
     126                    \par\medskip
     127                    ~\texttt{END SUBROUTINE user\_last\_actions}};
     128   \end{tikzpicture}
     129   \end{center}
     130%   \includegraphics[scale=0.3]{user_defined_code_figures/user_last_actions.png}\\   
    96131\end{frame}
    97132
    … …  
    99134\begin{frame}
    100135   \frametitle{Embedding of User-Interface Routines}
     136   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
    101137   \scriptsize
    102138   \begin{itemize}
    … …  
    106142   \end{itemize}
    107143   \onslide<2->
    108    \centering
    109    \includegraphics[scale=0.33]{user_defined_code_figures/embedding.png}\\
     144   \begin{center}
     145      \begin{tikzpicture}[auto]
     146         \node[yellow]{~\texttt{...}\\
     147                       \vspace{0.5mm}
     148                       \texttt{!}\\
     149                       \texttt{!-- If required, final user-defined actions, and}\\
     150                       \texttt{!-- last actions on the open files and close files. Unit 14 was opened}\\
     151                       \texttt{!-- in write\_3d\_binary but it is closed here, to allow writing on this}\\
     152                       \texttt{!-- unit in routine user\_last\_actions.}\\
     153                       \vspace{0.5mm}
     154                       ~~~~\texttt{CALL cpu\_log( log\_point(4), 'last actions', 'start' )}\\
     155                       ~~~~\texttt{DO  i = 0, io\_blocks-1}\\
     156                       ~~~~~~~\texttt{IF ( i == io\_group )  THEN}\\
     157                       ~~~~~~~~~~\texttt{\textcolor{blue}{CALL user\_last\_actions}}\\
     158                       \vspace{0.5mm}
     159                       ~~~~~~~~~~\texttt{IF ( write\_binary(1:4) == 'true' )  CALL close\_file( 14 )}\\
     160                       ~~~~~~~\texttt{ENDIF}\\
     161                       \vspace{0.5mm}
     162                       \texttt{\#if defined( \_\_parallel )}\\
     163                       ~~~~~~~\texttt{CALL MPI\_BARRIER( comm2d, ierr )}\\
     164                       \vspace{0.5mm}
     165                       \texttt{\#endif}\\
     166                       \vspace{0.5mm}
     167                       ~~~~\texttt{ENDDO}\\
     168                       \vspace{0.5mm}
     169                       ~~~~\texttt{CALL close\_file( 0 )}\\
     170                       \vspace{0.5mm}
     171                       ~~~~\texttt{CALL close\_dvrp}\\
     172                       ~~~~\texttt{CALL cpu\_log( log\_point(4), 'last actions', 'stop' )}\\
     173                       \vspace{1mm}
     174                       ~\texttt{...}\\
     175                       \vspace{1mm}
     176                       \texttt{!}\\
     177                       \texttt{!-- Take final CPU-time for CPU-time analysis}\\
     178                       ~~~~\texttt{CALL cpu\_log( log\_point(1), 'total', 'stop' )}\\
     179                       ~~~~\texttt{CALL cpu\_statistics}\\
     180                       \texttt{\#if defined( \_\_parallel )}\\
     181                       ~~~~\texttt{CALL MPI\_FINALIZE( ierr )}\\
     182                       \vspace{0.5mm}
     183                       \texttt{\#endif}\\
     184                       \par\medskip
     185                       ~\texttt{END PROGRAM palm}};
     186      \end{tikzpicture}
     187   \end{center}
     188
     189%   \includegraphics[scale=0.33]{user_defined_code_figures/embedding.png}\\
    110190\end{frame}
    111191
    … …  
    119199      % Define colours
    120200      \tikzstyle{green} = [draw, fill=green!30, text width=7.1em, text centered, minimum height=1.6em]
     201      \tikzstyle{green1} = [draw, fill=green!30, text width=12em, text centered, minimum height=1.6em]
     202      \tikzstyle{green2} = [draw, fill=green!30, text width=10em, text centered, minimum height=1.6em]
    121203      \tikzstyle{yellow} = [draw, fill=yellow!30, text width=7.1em, text centered, minimum height=1.6em]
    122204      \tikzstyle{orange} = [draw, fill=orange!60, text width=7.1em, text centered]
    123205     
    124206      % Define coordinates and draw nodes     
    125       \node[green, text width=5em] (PALM) at (0,0.1) {PALM};
     207      \node[yellow, text width=5em] (PALM) at (0,0.1) {PALM};
    126208
    127209      \coordinate (A) at (0,-0.7);
    128 
    129       \node[green, right=0.6cm of A] (parin) {parin};
    130      
    131       \coordinate[below=0.3cm of parin] (B);
    132       \coordinate[below=0.9cm of parin] (C);
    133       \coordinate[below=1.5cm of parin] (D);
    134      
    135       \node[green, right=0.6cm of B] (read) {read\_var\_list};
    136       \node[green, right=0.6cm of C] (package) {package\_parin};
    137       \node[yellow, right=0.6cm of D] (userparin) {user\_parin};
    138      
    139       \coordinate[below=3cm of PALM] (E);     
    140       \coordinate[below=3.6cm of PALM] (F);   
    141       \coordinate[below=4.2cm of PALM] (G);     
    142       \coordinate[below=4.8cm of PALM] (H);
    143       \coordinate[below=5.6cm of PALM] (I);
    144       \coordinate[below=7.4cm of PALM] (J);             
    145                
    146       \node[green, right=0.6cm of E] (initpegrid) {init\_pegrid};     
    147       \node[green, right=0.6cm of F] (initgrid) {init\_grid};
    148       \node[yellow, right=0.9cm of initgrid] (userinitgrid) {user\_init\_grid};
    149      
    150       \node[green, right=0.6cm of G] (checkparameters) {check\_parameters};       
    151       \node[yellow, right=0.9cm of checkparameters, text width=9.5em] (usercheckdataoutput) {user\_check\_data\_output};
    152       \node[green, right=0.6cm of H] (header) {header};
    153       \node[green, right=0.6cm of I] (init3dmodel) {init\_3d\_model};       
    154       \node[yellow, right=0.9cm of header] (userheader) {user\_header};
    155            
    156       \node[orange, right=0.6cm of J] (timeint) {time\_integration};       
    157      
    158       \coordinate[below=0.3cm of init3dmodel] (K);   
    159       \coordinate[below=0.9cm of init3dmodel] (L);       
    160      
    161       \node[green, right=0.6cm of K] (initparticles) {init\_particles};       
    162       \node[yellow, right=0.9cm of initparticles] (userinitparticles) {user\_init\_particles};   
    163       \node[yellow, right=0.6cm of L] (userinit) {user\_init};       
    164      
    165       % Draw lines
    166       \draw[-, thick] (PALM) -- (0,-7.8);
    167       \draw[dotted, thick] (0,-8.2) -- (0,-7.8);
    168       \draw[-, thick] (A) -- (parin);
    169       \draw[-, thick] (parin) -- (D); 
    170       \draw[dashed, thick] (B) -- (read);
    171       \draw[dashed, thick] (C) -- (package);
    172       \draw[-, thick] (D) -- (userparin);
    173       \draw[-, thick] (E) -- (initpegrid);
    174       \draw[-, thick] (F) -- (initgrid);
    175       \draw[-, thick] (G) -- (checkparameters);
    176       \draw[-, thick] (H) -- (header);
    177       \draw[-, thick] (I) -- (init3dmodel);
    178       \draw[-, thick] (J) -- (timeint);
    179       \draw[dotted, thick] (init3dmodel) -- (K);
    180       \draw[-, thick] (K) -- (L);
    181       \draw[dashed, thick] (K) -- (initparticles);
    182       \draw[-, thick] (L) -- (userinit);
    183       \draw[-, thick] (initgrid) -- (userinitgrid);     
    184       \draw[-, thick] (checkparameters) -- (usercheckdataoutput);     
    185       \draw[-, thick] (header) -- (userheader);     
    186       \draw[-, thick] (initparticles) -- (userinitparticles);     
     210      \node[yellow, right=0.6cm of A] (parin) {parin};
     211
     212      \node[green, right=1mm of parin] (userparin) {user\_parin};
     213      \draw[-] (parin) -- (userparin);
     214
     215      \coordinate[below=0.6cm of A] (B);
     216      \node[yellow, right=0.6cm of B] (initgrid) {init\_grid};
     217
     218      \node[green, right=1mm of initgrid] (userinigrid) {user\_init\_grid};
     219      \draw[-] (initgrid) -- (userinigrid);
     220
     221      \coordinate[below=0.6cm of B] (C);
     222      \node[yellow, right=0.6cm of C] (checkparam) {check\_parameters};
     223
     224      \coordinate[below=0.3cm of checkparam] (D);
     225      \node[green1, right=0.6cm of D] (usercheckdataout) {user\_check\_data\_output/\_pr};
     226
     227      \coordinate[below=0.55cm of D] (E);
     228      \node[green1, right=0.6cm of E] (usercheckparam) {user\_check\_parameters};
     229
     230      \coordinate[below=1.7cm of C] (F);
     231      \node[yellow, right=0.6cm of F] (init3dmodel) {init\_3d\_model};
     232
     233      \coordinate[below=0.3cm of init3dmodel] (G);
     234      \node[green2, right=0.6cm of G] (userinit3d) {user\_init\_3d\_model};
     235
     236      \coordinate[below=0.55cm of G] (H);
     237      \node[yellow, right=0.6cm of H] (read3dbin) {read\_3d\_binary};
     238
     239      \coordinate[below=0.3cm of read3dbin] (I);
     240      \node[green1, right=0.6cm of I] (userreadrestart) {user\_read\_restart\_data};
     241
     242      \coordinate[below=1.15cm of H] (J);
     243      \node[green1, right=0.6cm of J] (userinitplan) {user\_init\_plant\_canopy};
     244
     245      \coordinate[below=0.6cm of J] (K);
     246      \node[yellow, right=0.6cm of K] (lpminit) {lpm\_init};
     247
     248      \node[green, right=1mm of lpminit] (userlpminit) {user\_lpm\_init};
     249      \draw[-] (lpminit) -- (userlpminit);     
     250
     251      \coordinate[below=0.6cm of K] (L);
     252      \node[green, right=0.6cm of L] (userinit) {user\_init};
     253
     254      \coordinate[below=4.05cm of F] (M);
     255      \node[yellow, right=0.6cm of M] (header) {header};
     256
     257      \node[green, right=1mm of header] (userheader) {user\_header};
     258      \draw[-] (header) -- (userheader);     
     259%     
     260       % Draw lines
     261       \draw[-, thick] (PALM) -- (0,-7.8);
     262       \draw[dotted, thick] (0,-8.2) -- (0,-7.8);
     263       \draw[-] (A) -- (parin);
     264       \draw[-] (B) -- (initgrid);
     265       \draw[-] (C) -- (checkparam);
     266       \draw[-] (checkparam.south) |- (usercheckdataout.west);
     267       \draw[-] (checkparam.south) |- (usercheckparam.west);
     268       \draw[-] (F) -- (init3dmodel);
     269       \draw[-,dashed] (init3dmodel.south) |- (userinit3d.west);
     270       \draw[-,dashed] (init3dmodel.south) |- (read3dbin.west);
     271       \draw[-] (read3dbin.south) |- (userreadrestart.west);
     272       \draw[-,dashed] (init3dmodel.south) |- (userinitplan);
     273       \draw[-,dashed] (init3dmodel.south) |- (lpminit);
     274       \draw[-] (init3dmodel.south) |- (userinit);
     275       \draw[-] (M) -- (header);   
    187276     
    188277   \end{tikzpicture}
    … …  
    197286      % Define colours
    198287      \tikzstyle{green} = [draw, fill=green!30, text width=7.1em, text centered, minimum height=1.6em]
     288      \tikzstyle{green1} = [draw, fill=green!30, text width=10em, text centered, minimum height=1.6em]
    199289      \tikzstyle{yellow} = [draw, fill=yellow!30, text width=7.1em, text centered, minimum height=1.6em]
    200290      \tikzstyle{orange} = [draw, fill=orange!60, text width=7.1em, text centered]
    … …  
    214304      \coordinate[right=3.8cm of D] (E);
    215305                 
    216       \node[yellow, right=0.6cm of B, text width=14em] (useractions1) {\textcolor{blue}{user\_actions\_(\textit{'before\_timestep'})}};   
     306      \node[green, right=0.6cm of B, text width=14em] (useractions1) {\textcolor{blue}{user\_actions\_(\textit{'before\_timestep'})}};   
    217307         
    218308      \node[orange1, below=0.2cm of D] (progeq) {prognostic\_equations};   
    … …  
    220310      \node[draw, fill=red, text width=4em] at (8.6,-0.8) {\textcolor{white}{standard advection}};
    221311               
    222       \node[yellow, right=0.3cm of progframe, text width=14em] (useractions2) {\textcolor{blue}{user\_actions\_(\textit{'*\_tendency'})}};
     312      \node[green, right=0.3cm of progframe, text width=14em] (useractions2) {\textcolor{blue}{user\_actions\_(\textit{'*\_tendency'})}};
    223313     
    224314     
    … …  
    229319
    230320                             
    231       \node[green, right=0.6cm of F] (advecparticles) {advec\_particles};
    232       \node[yellow, right=0.9cm of advecparticles, text width=10em] (userparticlesattributes) {user\_particles\_attributes};
    233       \node[green, right=0.6cm of G] (exchangehoriz) {exchange\_horiz}; 
    234       \node[green, right=0.0cm of exchangehoriz] (asselin) {asselin\_filter};     
    235       \node[green, right=0.6cm of H] (swaptimelevel) {swap\_timelevel};
    236       \node[green, right=0.6cm of I] (pres) {pres};
     321      \node[yellow, right=0.6cm of F] (lpm) {lpm};
     322      \node[green, right=0.9cm of lpm, text width=10em] (userlpmadvec) {user\_lpm\_advec};
     323      \node[yellow, right=0.6cm of G] (exchangehoriz) {exchange\_horiz}; 
     324%      \node[yellow, right=0.0cm of exchangehoriz] (asselin) {asselin\_filter};     
     325      \node[yellow, right=0.6cm of H] (swaptimelevel) {swap\_timelevel};
     326      \node[yellow, right=0.6cm of I] (pres) {pres};
    237327     
    238328      \coordinate[below=0.3cm of pres] (J);   
    … …  
    244334      \coordinate[below=8.8cm of timeint] (P);     
    245335                 
    246       \node[green, right=0.6cm of K] (prandtlfluxes) {prandtl\_fluxes};   
    247       \node[yellow, right=0.6cm of L, text width=14em] (useractions3) {\textcolor{blue}{user\_actions\_(\textit{'after\_integration'})}};             
    248       \node[green, right=0.6cm of M] (diffusivities) {diffusivities};             
    249       \node[green, right=0.0cm of diffusivities] {check\_for\_restart};     
    250       \node[green, right=0.6cm of N] (flowstat) {flow\_statistics};
    251       \node[green, right=0.0cm of flowstat] (runcontrol) {run\_control}; 
    252       \node[yellow, below=0.2cm of flowstat] (userstat) {user\_statistics}; 
    253       \node[yellow, right=0.6cm of O, text width=14em] (useractions4) {\textcolor{blue}{user\_actions\_(\textit{'after\_timestep'})}};
    254       \node[green, right=0.6cm of P] (timestep) {timestep};             
    255 
    256       \node[green, right=0.2cm of runcontrol] (dataoutput) {data\_output\_***};
    257       \node[yellow, right=0.2cm of dataoutput] (userdvrpcoltab) {user\_dvrp\_coltab};
     336%      \node[yellow, right=0.6cm of K] (prandtlfluxes) {prandtl\_fluxes};   
     337      \node[green, right=0.6cm of K, text width=14em] (useractions3) {\textcolor{blue}{user\_actions\_(\textit{'after\_integration'})}};             
     338%      \node[yellow, right=0.6cm of L] (diffusivities) {diffusivities};             
     339%      \node[yellow, right=0.6cm of L] (checkrestart) {check\_for\_restart};     
     340      \node[yellow, right=0.6cm of L] (flowstat) {flow\_statistics};
     341      \node[green, right=0.6cm of flowstat] (userstat2) {user\_statistics}; 
     342
     343      \node[yellow, right=0.6cm of M] (sum3ddata) {sum\_up\_3d\_data}; 
     344      \node[green1, right=0.6cm of sum3ddata] (user3ddataav) {user\_3d\_data\_averaging};
     345
     346      \node[green, right=0.6cm of O, text width=14em] (useractions4) {\textcolor{blue}{user\_actions\_(\textit{'after\_timestep'})}};
     347%      \node[yellow, right=0.6cm of P] (timestep) {timestep};             
     348
     349      \node[yellow, right=0.2cm of user3ddataav] (dataoutput) {data\_output\_***};
     350      \node[green, right=0.2cm of dataoutput] (userdvrpcoltab) {user\_dvrp\_coltab};
    258351      \coordinate[below=0.2cm of dataoutput] (Q);   
    259352      \coordinate[right=0.4cm of Q] (R);   
    260353      \coordinate[right=3.0cm of R] (S);
    261354         
    262       \node[yellow, below=0.2cm of R, text width=9em] (output2d) {user\_data\_output\_2d};
    263       \node[yellow, below=0.2cm of S, text width=9em] (output3d) {user\_data\_output\_3d};
     355      \node[green, below=0.2cm of R, text width=9em] (output2d) {user\_data\_output\_2d};
     356      \node[green, below=0.2cm of S, text width=9em] (output3d) {user\_data\_output\_3d};
    264357     
    265358
    … …  
    276369      \draw[->, thick, color=red] (E) -- (progeqfast);       
    277370      \draw[-, thick] (progframe) -- (useractions2);
    278       \draw[-, thick] (F) -- (advecparticles);   
    279       \draw[-, thick] (userparticlesattributes) -- (advecparticles);   
     371      \draw[-, thick] (F) -- (lpm);   
     372      \draw[-, thick] (userlpmadvec) -- (lpm);   
    280373      \draw[-, thick] (G) -- (exchangehoriz);
    281374      \draw[-, thick] (H) -- (swaptimelevel);
    282375      \draw[-, thick] (I) -- (pres);     
    283376      \draw[dotted, thick] (pres) -- (J);
    284       \draw[-, thick] (K) -- (prandtlfluxes);   
    285       \draw[-, thick] (L) -- (useractions3);     
    286       \draw[-, thick] (M) -- (diffusivities); 
    287       \draw[-, thick] (N) -- (flowstat); 
    288       \draw[-, thick] (userstat) -- (flowstat); 
     377%      \draw[-, thick] (K) -- (prandtlfluxes);   
     378      \draw[-, thick] (K) -- (useractions3);     
     379      \draw[-, thick] (L) -- (flowstat); 
     380      \draw[-, thick] (M) -- (sum3ddata); 
     381      \draw[-, thick] (sum3ddata) -- (user3ddataav);
     382
     383      \draw[-, thick] (userstat2) -- (flowstat); 
    289384      \draw[-, thick] (O) -- (useractions4);
    290       \draw[-, thick] (P) -- (timestep);   
     385%      \draw[-, thick] (O) -- (timestep);   
    291386      \draw[-, thick] (dataoutput) -- (Q);
    292387      \draw[-, thick] (S) -- (Q);
    … …  
    320415      \coordinate[below=2.5cm of PALM] (D); 
    321416     
    322       \node[green, right=0.6cm of D] (write3dbinary) {write\_3d\_binary};
    323       \node[green, right=0.9cm of write3dbinary] (writevarlist) {write\_var\_list};   
     417      \node[yellow, right=0.6cm of D] (write3dbinary) {write\_3d\_binary};
     418      \node[yellow, right=0.9cm of write3dbinary] (writevarlist) {write\_var\_list};   
    324419       
    325420      \coordinate[below=3.5cm of PALM] (E);
    326421      \coordinate[below=4.1cm of PALM] (F);
    327422      \coordinate[below=4.7cm of PALM] (G);
    328       \node[green, right=0.6cm of E] (header) {header};     
    329       \node[yellow, right=0.6cm of F] (userlastactions) {user\_last\_actions};   
    330       \node[green, right=0.6cm of G] (cpustat) {cpu\_statistics};               
     423      \node[yellow, right=0.6cm of E] (header) {header};     
     424      \node[green, right=0.6cm of F] (userlastactions) {user\_last\_actions};   
     425      \node[yellow, right=0.6cm of G] (cpustat) {cpu\_statistics};               
    331426      % Draw lines
    332427      \draw[-, thick] (PALM) -- (G);
    … …  
    351446           \textbf{Name} & \textbf{Arguments} & \textbf{Called from} & \textbf{Task}\\
    352447           \hline
    353            \texttt{user\_3d\_data\_averaging} & \texttt{mode}, \texttt{variable} & \texttt{sum\_up\_3d\_data} & temporal averaging for user-defined quantities\\
     448           \texttt{user\_3d\_data\_averaging} & \texttt{mode}, \texttt{variable} & \texttt{average\_3d\_data} + \texttt{sum\_up\_3d\_data} & temporal averaging for user-defined quantities\\
    354449           \hline
    355450           \texttt{user\_actions} \texttt{user\_actions} & \texttt{location} \,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\,\, \texttt{i}, \texttt{j}, \texttt{location} & \texttt{time\_integration} +
    … …  
    358453           \texttt{user\_dummy (user\_additional \_routines.f90)} & - - - & - - - & for additional subroutines defined by the user\\
    359454           \hline
    360            \texttt{user\_advec\_particles} & - - - & \texttt{advec\_particles} & modification of particles after advection\\
    361            \hline
    362            \texttt{user\_check\_data\_output} & \texttt{variable}, \texttt{unit} & \texttt{check\_parameters} & check the user-defined output quantities\\
     455           \texttt{user\_check\_data\_output} & \texttt{variable}, \texttt{unit} & \texttt{check\_parameters} + \texttt{init\_masks}& check the user-defined output quantities\\
    363456           \hline
    364457           \texttt{user\_check\_data\_output\_pr} & \texttt{variable}, \texttt{var\_count}, \texttt{unit} & \texttt{check\_parameters} & check the user-defined profile output quantities\\
    … …  
    366459           \texttt{user\_check\_parameters} & - - - & \texttt{check\_parameters} & check user-defined variables\\
    367460           \hline         
    368            \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\\
     461           \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\\       
    369462           \hline         
    370463           \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\\
    … …  
    377470           \hline
    378471           \texttt{user\_dvrp\_coltab} & \texttt{mode}, \texttt{variable} & \texttt{data\_output\_dvrp} & defining color tables for particles\\   
    379            \hline         
     472           \hline
     473           \texttt{user\_header} & \texttt{io} & \texttt{header} & output user variables to header\\
     474           \hline
     475           \texttt{user\_init} & - - - & \texttt{init\_3d\_model} & e.g. reading from restart file\\
     476           \hline
    380477   \end{tabular}
    381478
    … …  
    391488           \textbf{Name} & \textbf{Arguments} & \textbf{Called from} & \textbf{Task}\\
    392489           \hline
    393            \texttt{user\_header} & \texttt{io} & \texttt{header} & output user variables to header\\
    394            \hline
    395            \texttt{user\_init} & - - - & \texttt{init\_3d\_model} & e.g. reading from restart file\\
    396            \hline
    397490           \texttt{user\_init\_3d\_model} & - - - & \texttt{init\_3d\_model} & special initializations\\
    398491           \hline
    399            \texttt{user\_init\_grid} & \texttt{gls}, \texttt{nzb\_local} & \texttt{init\_grid} & defining a special topography\\
     492           \texttt{user\_init\_grid} & \texttt{gls} & \texttt{init\_grid} & defining a special topography\\
    400493           \hline         
    401            \texttt{user\_init\_particles} & - - - & \texttt{init\_particles} & defining initial particle sources\\
    402            \hline                 
    403494           \texttt{user\_init\_plant\_canopy} & - - - & \texttt{init\_3d\_model} & setting of leaf area density and canopy drag coefficient\\
    404495           \hline
    405496           \texttt{user\_last\_actions} & - - - & \texttt{palm} & e.g. output for restart runs\\
    406            \hline         
     497           \hline
     498           \texttt{user\_lpm\_advec} & - - - & \texttt{lpm} & modification of particles after advection \\
     499           \hline
     500           \texttt{user\_lmp\_init} & - - - & \texttt{lpm\_init} & defining initial particle sources \\
     501           \hline
     502           \texttt{user\_lpm\_set\_attributes} & - - - & \texttt{lpm} & defining particles attributes \\
     503           \hline
    407504           \texttt{MODULE user (user\_module.f90)} & - - - & - - - & contains user defined variables\\
    408505           \hline                 
    409506           \texttt{user\_parin} &  & \texttt{parin} & reading user variables\\     
    410            \hline         
    411            \texttt{user\_particle\_attributes} & - - - & \texttt{advec\_particles} & defining particles attributes\\       
    412            \hline
     507           \hline 
    413508           \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\\         
    414509           \hline                 
    415            \texttt{user\_spectra} & \texttt{mode}, \texttt{m}, \texttt{pr} & \texttt{data\_output\_spectra} & output/calculation of additional user-defined quantities\\           
     510           \texttt{user\_spectra} & \texttt{mode}, \texttt{m}, \texttt{pr} & \texttt{calc\_spectra} + \texttt{data\_output\_spectra} & output/calculation of additional user-defined quantities\\         
    416511           \hline         
    417512           \texttt{user\_statistics} & \texttt{mode}, \texttt{sr}, \texttt{tn} & \texttt{flow\_statistics} & calculating additional horizontal averages + time series quantities\\             
    … …  
    429524\begin{frame}
    430525   \frametitle{Data Access / Exchange}
     526   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.6\textwidth, font=\tiny]
    431527   \footnotesize
    432528   \begin{itemize}
    … …  
    436532         \item<3-> by including the respective PALM modules in the user-interface subroutines.\\
    437533         \begin{center}
    438             \includegraphics[scale=0.3]{user_defined_code_figures/data_access_exchange.png}
     534%           \includegraphics[scale=0.3]{user_defined_code_figures/data_access_exchange.png}
     535            \begin{tikzpicture}[auto]
     536               \node[yellow]{\texttt{SUBROUTINE user\_actions( location )} \\
     537                             \par\medskip
     538                             ~~~~~\texttt{\textcolor{blue}{USE arrays\_3d}} \\
     539                             ~~~~~\texttt{\textcolor{blue}{USE control\_parameters}} \\
     540                             ~~~~~\texttt{\textcolor{blue}{USE cpulog}} \\
     541                             ~~~~~\texttt{\textcolor{blue}{USE indices}} \\
     542                             ~~~~~\texttt{\textcolor{blue}{USE interfaces}} \\
     543                             ~~~~~\texttt{\textcolor{blue}{USE pegrid}} \\
     544                             ~~~~~\texttt{\textcolor{red}{USE user}} \\
     545                             \par\medskip
     546                             ~~~~~\texttt{IMPLICIT NONE} \\
     547                             \par\medskip
     548                             ~~~~~\texttt{CHARACTER (LEN=$^\ast$) ::  location} \\
     549                             \par\medskip
     550                             ~~~~~\texttt{INTEGER ::  i, j, k}};
     551            \end{tikzpicture}
    439552         \end{center}
    440553      \end{itemize}
    … …  
    451564\begin{frame}
    452565   \frametitle{Usage of \texttt{user\underline{ }actions} (I)}
     566   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
    453567   \scriptsize
    454568   \begin{itemize}
    455569      \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.
    456       \vspace{2mm}
     570      \vspace{1.8mm}
    457571      \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.\\
    458572   \ \\
    … …  
    461575        \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:
    462576   \end{itemize}
    463    \vspace{-2mm}
     577   \vspace{-3mm}
    464578   \begin{center}
    465       \includegraphics[scale=0.33]{user_defined_code_figures/user_actions_1.png}
     579   \begin{tikzpicture}[auto]
     580      \node[yellow] {\texttt{DO  i = nxl, nxr} \\
     581                     ~~~\texttt{DO  j = nys, nyn} \\
     582                     \texttt{...} \\
     583                     ~~~~~~\texttt{CALL diffusion\_u( i, j )}\\
     584                     ~~~~~~\texttt{CALL coriolis( i, j, 1 )} \\
     585                     \texttt{...}\\
     586                     ~~~~~~\texttt{\textcolor{blue}{CALL user\_actions( i, j, 'u-tendency' )}}\\
     587                     \texttt{!} \\
     588                     \texttt{!-- Prognostic equation for u-velocity component} \\
     589                     ~~~~~~\texttt{DO  k = nzb\_u\_inner(j,i)+1, nzt} \\
     590                     ~~~~~~~~~\texttt{u\_p(k,j,i) = u(k,j,i) + dt\_3d * ( tsc(2) * tend(k,j,i) + \&} \\
     591                     \hspace{4.08cm} \texttt{tsc(3) * tu\_m(k,j,i) )       \&} \\
     592                     \hspace{2.93cm} \texttt{- tsc(5) * rdf(k) * ( u(k,j,i) - ug(k) )}\\
     593                     ~~~~~~\texttt{ENDDO} \\
     594                     \texttt{...}};
     595   \end{tikzpicture}
    466596   \end{center}
     597%    \begin{center}
     598%       \includegraphics[scale=0.33]{user_defined_code_figures/user_actions_1.png}
     599%    \end{center}
    467600\end{frame}
    468601
    … …  
    470603\begin{frame}
    471604   \frametitle{Usage of \texttt{user\underline{ }actions} (II)}
     605   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
    472606   \scriptsize
    473607   \begin{itemize}
    … …  
    475609   \end{itemize}
    476610   \begin{center}
    477       \includegraphics[scale=0.35]{user_defined_code_figures/user_actions_2.png}
     611      \begin{tikzpicture}[auto]
     612         \node[yellow]{~\texttt{SUBROUTINE user\_actions( location )}\\
     613                       \texttt{...}\\
     614                       \texttt{!}\\
     615                       \texttt{!--    Here the user-defined actions follow}\\
     616                       \texttt{!--    No calls for single grid points are allowed at locations before and}\\
     617                       \texttt{!--    after the timestep, since these calls are not within an i,j-loop}\\
     618                       ~~~~~~~\texttt{SELECT CASE ( location )}\\
     619                       \texttt{...}\\
     620                       ~~~~~~~~~~\texttt{CASE ( 'after\_timestep' )}\\
     621                       \texttt{!}\\
     622                       \texttt{!-- Enter actions to be done after every timestep here}\\
     623                       \par\medskip
     624                       ~~~~~~~~~~\texttt{CASE ( 'u-tendency' )}\\
     625                       \texttt{!}\\
     626                       \texttt{!-- Enter actions to be done in the u-tendency term here}\\
     627                       ~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO i = nxl, nxr}}\\
     628                       ~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO j = nys, nyn}}\\
     629                       ~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{DO k = nxb+1, nzt}}\\
     630                       ~~~~~~~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{tend(k,j,i) = tend(k,j,i) - const * u(k,j,i) ...}}\\
     631                       ~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
     632                       ~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
     633                       ~~~~~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
     634                       \par\bigskip
     635                       ~~~~~~~~~~\texttt{CASE ( 'v-tendency' )}\\
     636                       \texttt{...}};
     637      \end{tikzpicture}
     638%      \includegraphics[scale=0.35]{user_defined_code_figures/user_actions_2.png}
    478639   \end{center}
    479640\end{frame}
    … …  
    482643\begin{frame}[t]
    483644   \frametitle{Usage of \texttt{user\underline{ }actions} (III)}
     645   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.5\textwidth, font=\Tiny]
    484646   \scriptsize
    485647   \begin{columns}[T]
    … …  
    507669   \uncover<4->{%
    508670   \begin{tikzpicture}[remember picture, overlay]
    509       \node [shift={(8.3 cm,3.0cm)}]  at (current page.south west)
    510          {%
    511          \begin{tikzpicture}[remember picture, overlay]
    512             \node[text width=14em] at (0,0) {\includegraphics[scale=0.3]{user_defined_code_figures/user_actions_3.png}};
    513          \end{tikzpicture}
    514          };
     671      \node [yellow,shift={(9.2 cm,3.0cm)}]  at (current page.south west){~\texttt{SUBROUTINE user\_actions\_ij( i, j, location )}\\
     672                                                                          \par\medskip
     673                                                                          ~~~\texttt{USE control\_parameters}\\
     674                                                                          ~~~\texttt{USE pegrid}\\
     675                                                                          ~~~\texttt{USE user}\\
     676                                                                          \par\medskip
     677                                                                          ~~~\texttt{IMPLICIT NONE}\
     678                                                                          \par\medskip
     679                                                                          ~~~\texttt{CHARACTER (LEN=*) ::  location}\\
     680                                                                          \par\medskip
     681                                                                          ~~~\texttt{INTEGER ::  i, idum, j}\\
     682                                                                          \par\medskip
     683                                                                          \texttt{!}\\
     684                                                                          \texttt{!--    Here the user-defined actions follow}\\
     685                                                                          \vspace{0.5mm}
     686                                                                          ~~~\texttt{SELECT CASE ( location )}\\
     687                                                                          \par\medskip
     688                                                                          ~~~~~~\texttt{CASE ( 'u-tendency' )}\\
     689                                                                          \texttt{!}\\
     690                                                                          \texttt{!--Enter actions to be done in the u-tendency term here}\\
     691                                                                          ~~~~~~~~~\texttt{\textcolor{blue}{DO k = nzb+1, nzt-1}}\\
     692                                                                          ~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{tend(k,j,i) = tend(k,j,i) + ...}}\\
     693                                                                          ~~~~~~~~~\texttt{\textcolor{blue}{ENDDO}}\\
     694                                                                          \par\medskip
     695                                                                          ~~~~~~\texttt{CASE ( 'v-tendency' )}};
     696%          {%
     697%          \begin{tikzpicture}[remember picture, overlay]
     698% %            \node[text width=14em] at (0,0) {\includegraphics[scale=0.3]{user_defined_code_figures/user_actions_3.png}};
     699%          \end{tikzpicture}
     700%          };
    515701    \end{tikzpicture}}
    516702   
    … …  
    520706\begin{frame}
    521707   \frametitle{Steering the User-Interface}
     708   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\Tiny]
    522709   \scriptsize
    523710   \begin{columns}[T]
    … …  
    530717         \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.
    531718         \begin{center}
    532             \includegraphics[scale=0.3]{user_defined_code_figures/steering_1.png}
     719%            \includegraphics[scale=0.3]{user_defined_code_figures/steering_1.png}
     720            \begin{tikzpicture}
     721               \node[yellow]{~\texttt{MODULE user}\\
     722                             \vspace{0.4mm}
     723                             \texttt{...}\\
     724                             \vspace{0.4mm}
     725                             ~\texttt{REAL \hspace{0.4cm}:: ~~\textcolor{blue}{foo = 0.0}}\\
     726                             \vspace{0.4mm}
     727                             \texttt{...}\\
     728                             \vspace{0.4mm}
     729                             ~\texttt{END MODULE user}};
     730            \end{tikzpicture}
    533731         \end{center}
    534732         \vspace{1mm}
    535733         \item<2-> Add the variable to the NAMELIST \texttt{/userpar/}. This NAMELIST already contains four predefined variables.
    536734         \begin{center}
    537             \includegraphics[scale=0.3]{user_defined_code_figures/steering_2.png}
     735%            \includegraphics[scale=0.3]{user_defined_code_figures/steering_2.png}
     736            \begin{tikzpicture}
     737               \node[yellow]{~\texttt{SUBROUTINE user\_parin}\\
     738                             \vspace{0.4mm}
     739                             \texttt{...}\\
     740                             \vspace{0.4mm}
     741                             ~~~~~\texttt{NAMELIST ~~/userpar/ ~~ data\_output\_pr\_user, data\_output\_user,}\\
     742                             \vspace{0.4mm}
     743                             \hspace{3cm}\texttt{\textcolor{blue}{foo}, region}\\
     744                             \vspace{0.4mm}
     745                             \texttt{...}\\
     746                             \vspace{0.4mm}
     747                             ~\texttt{END SUBROUTINE user\_parin}};
     748            \end{tikzpicture}
    538749         \end{center}
    539750         \vspace{1mm}
    540751         \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.         
    541752         \begin{center}
    542             \includegraphics[scale=0.3]{user_defined_code_figures/steering_3.png}
     753%            \includegraphics[scale=0.3]{user_defined_code_figures/steering_3.png}
     754            \begin{tikzpicture}
     755               \node[yellow]{~\texttt{\&inipar ~~~ nx = ... ~~/}\\
     756                             \vspace{0.4mm}
     757                             ~\texttt{\&d3par ~~~ end\_time = 3600.0, ... ~~/}\\
     758                             \par\smallskip
     759                             ~\texttt{\textcolor{blue}{\&userpar ~~foo = 12345.6 ~~/}}};
     760            \end{tikzpicture}
    543761         \end{center}
    544762         \vspace{1mm}
    … …  
    575793\begin{frame}
    576794   \frametitle{User-Defined Data for Restart Runs (I)}
     795   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.7\textwidth, font=\tiny]
    577796   \scriptsize
    578797   \begin{itemize}
    … …  
    583802   \end{itemize}
    584803   \begin{center}
    585       \includegraphics[scale=0.3]{user_defined_code_figures/restart_1.png}
     804%      \includegraphics[scale=0.3]{user_defined_code_figures/restart_1.png}
     805      \begin{tikzpicture}[auto]
     806         \node[yellow]{~\texttt{SUBROUTINE user\_last\_actions}\\
     807                       \texttt{...}\\
     808                       ~~~~~\texttt{\textcolor{blue}{WRITE ( 14 )  'foo \hspace{2cm}';  WRITE ( 14 )  foo}}\\
     809                       ~~~~~\texttt{\textcolor{blue}{WRITE ( 14 )  'bar \hspace{2cm}';  WRITE ( 14 )  bar}}
     810                       \par\smallskip
     811                       ~~~~~\texttt{WRITE ( 14 ) '*** end user *** \hspace{0.66cm}'}
     812                       \par\smallskip
     813                       ~\texttt{END SUBROUTINE user\_last\_actions}};
     814      \end{tikzpicture}
    586815   \end{center}
    587816\end{frame}
    … …  
    590819\begin{frame}
    591820   \frametitle{User-Defined Data for Restart Runs (II)}
     821   \tikzstyle{yellow} = [rectangle, draw, fill=yellow!30, text width=0.95\textwidth, font=\tiny]
    592822   \scriptsize
    593823   \begin{itemize}
    594824      \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}:
    595825   \end{itemize}
     826   \vspace{-2.7mm}
    596827   \begin{center}
    597       \includegraphics[scale=0.3]{user_defined_code_figures/restart_2.png}
     828%      \includegraphics[scale=0.3]{user_defined_code_figures/restart_2.png}
     829      \begin{tikzpicture}
     830         \node[yellow]{\texttt{~SUBROUTINE user\_read\_restart\_data( i, nxlfa, nxl\_on\_file, nxrfa, nxr\_on\_file, \&} \\
     831                       \hspace{3.84cm}\texttt{nynfa, nyn\_on\_file, nysfa, nys\_on\_file,    \&} \\
     832                       \hspace{3.84cm}\texttt{offset\_xa, offset\_ya, overlap\_count,       \&} \\
     833                       \hspace{3.84cm}\texttt{tmp\_2d, tmp\_3d )}\\
     834                       \texttt{...} \\
     835                       ~~~~~\texttt{IF ( initializing\_actions == 'read\_restart\_data' )  THEN}\\
     836                       ~~~~~~~~~\texttt{READ ( 13 )  field\_char} \\
     837                       ~~~~~~~~~\texttt{DO  WHILE ( TRIM( field\_char )  '*** end user ***' )}\\
     838                       \par\smallskip
     839                       ~~~~~~~~~~~~~\texttt{nxlf = nxlfa(i,k)}
     840                       \texttt{...} \\
     841                       ~~~~~~~~~~~~~\texttt{SELECT CASE ( TRIM( field\_char ) )}\\
     842                       \par\smallskip
     843                       ~~~~~~~~~~~~~~~~~\texttt{CASE ( '\textcolor{blue}{foo}' )} \\
     844                       ~~~~~~~~~~~~~~~~~~~~~\texttt{IF ( .NOT. ALLOCATED( \textcolor{blue}{foo} ) ) THEN}\\
     845                       ~~~~~~~~~~~~~~~~~~~~~~~~~\texttt{ALLOCATE( \textcolor{blue}{foo}(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )}\\
     846                       ~~~~~~~~~~~~~~~~~~~~~\texttt{ENDIF}\\
     847                       ~~~~~~~~~~~~~~~~~~~~~\texttt{IF ( k == 1 )  READ ( 13 )  tmp\_3d}\\
     848                       ~~~~~~~~~~~~~~~~~~~~~\texttt{\textcolor{blue}{foo}(:,nysc-nbgp:nync+nbgp,nxlc-nbgp:nxrc+nbgp) = \&} \\
     849                       \hspace{4.5cm}\texttt{tmp\_3d(:,nysf-nbgp:nynf+nbgp,nxlf-nbgp:nxrf+nbgp)}\\
     850                       \texttt{...}\\
     851                       ~~~~~~~~~~~~~\texttt{END SELECT}\\
     852                       \par\smallskip
     853                       ~~~~~~~~~\texttt{ENDDO}
     854                       \par\smallskip
     855                       ~~~~~~~~~\texttt{READ ( 13 )  field\_char}\\
     856                       \par\smallskip
     857                       ~~~~~~~~~\texttt{ENDDO}\\
     858                       ~~~~~\texttt{ENDIF}\\
     859                       \par\smallskip
     860                       ~\texttt{END SUBROUTINE user\_read\_restart\_data}};
     861      \end{tikzpicture}
    598862   \end{center}
    599863\end{frame}
    … …  
    610874            \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.:\\
    611875            \tiny
     876            \par\smallskip
    612877                 \quad \texttt{cd \~{ }/palm/current\underline{ }version}\\
    613878                 \quad \texttt{mkdir -p USER\underline{ }CODE/example\underline{ }cbl}\\
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