Home


About us
PALM
PALM-4U
Installation
Release notes
Documentation
Getting Help
Gallery
Developers area

Ignore:
Timestamp:
Jan 2, 2015 11:35:51 AM (9 years ago)
Author:
boeske
Message:

several updates in the tutorial

File:
1 edited

Legend:

Unmodified
Added
Removed

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

    r1080 r1515  
    7979   \small
    8080   \begin{itemize}     
    81            \item<1-> Interpreted language designed specifically for scientific data processing and visualization, free available
    82            \item<2-> Portable: it is running on many different operating systems including Solaris, AIX, IRIX, Linux, MacOSX, DecAlpha, Cygwin/Windows
    83       \item<3-> It's a powerful tool for file input and output, visualization and data analysis (but please \textbf{avoid the excessive usage of loops}, as NCL is an interpreted language) $\rightarrow$ integrated processing environment
     81      \item<1-> Interpreted language designed specifically for scientific
     82                data processing and visualization, freely available
     83      \item<2-> Portable: it is running on many different operating systems
     84                including AIX, Linux, MacOSX, Cygwin/Windows
     85      \item<3-> It's a powerful tool for file input and output, visualization
     86                and data analysis (but please \textbf{avoid the excessive usage
     87                of loops}, as NCL is an interpreted language) $\rightarrow$
     88                integrated processing environment
    8489   \end{itemize} 
    8590   \centering
    … …  
    9499   \begin{itemize}     
    95100           \item<1-> Supports calling C and FORTRAN extended routines
    96            \item<1-> Over 600 functions and procedures for visualization and data analysis are provided with NCL
     101           \item<1-> Over 600 functions and procedures for visualization and
     102                     data analysis are provided with NCL
    97103           \item<2-> Interactive mode: \texttt{\$ ncl}\\
    98104      \texttt{ncl 0>}
    99105      \item<3-> each line is interpreted as it is entered
    100       \item<1-> Batch mode: \texttt{\$ ncl ncl\underline{ }script.ncl}\\
     106      \item<4-> Batch mode: \texttt{\$ ncl ncl\underline{ }script.ncl}\\
    101107      interpreter of complete scripts, variables within the NCL script can\\
    102108      be steered by providing additional parameters with the ncl call\\
    … …  
    140146   \small
    141147   \begin{itemize}     
    142            \item<1-> Detailed information is available under\\
    143       \underline{http://www.ncl.ucar.edu/Download/index.shtml}
    144            \item<1-> Request an Earth System Grid account
    145       \underline{http://www.earthsystemgrid.org/}
    146            \item<2-> Download the appropriate binaries e.g. \texttt{A.tar.gz} for your system e.g. to \texttt{\$HOME}
     148      \item<1-> Detailed information is available under\\
     149                \underline{http://www.ncl.ucar.edu/Download/index.shtml}
     150      \item<1-> Request an Earth System Grid account
     151                \underline{http://www.earthsystemgrid.org/}
     152      \item<2-> Download the appropriate binaries e.g. \texttt{A.tar.gz}
     153                for your system e.g. to \texttt{\$HOME}
    147154      \item<2-> \texttt{\% gunzip \$HOME/A.tar.gz}
    148155      \item<2-> \texttt{\% mkdir -p /usr/local}\\
    … …  
    158165   \footnotesize
    159166   \begin{itemize}     
    160            \item<1-> Set the \texttt{NCARG\underline{ }ROOT} environment variable and your search path to where NCL/NCARG resides\\
    161            csh: \texttt{setenv NCARG\underline{ }ROOT /usr/local/}\\
    162            \hspace{1.6em} \texttt{setenv PATH /usr/local/bin:\$PATH}\\
    163            bash/ksh: \texttt{export NCARG\underline{ }ROOT=/usr/local/}\\
    164            \hspace{4.1em} \texttt{export PATH=/usr/local/bin:\$PATH}\\
    165            \vspace{3mm}
    166       \item<2-> Set the DISPLAY environment variable to indicate where to display graphics as for any X11 Windows application that you run\\
    167       e.g. ksh: \texttt{export DISPLAY=localhost:13.0}, or use \texttt{ssh -X} to tunnel X-communication.\\
     167      \item<1-> Set the \texttt{NCARG\underline{ }ROOT} environment variable and
     168                your search path to where NCL/NCARG resides\\
     169                csh: \texttt{setenv NCARG\underline{ }ROOT /usr/local/}\\
     170                \hspace{1.6em} \texttt{setenv PATH /usr/local/bin:\$PATH}\\
     171                bash/ksh: \texttt{export NCARG\underline{ }ROOT=/usr/local/}\\
     172                \hspace{4.1em} \texttt{export PATH=/usr/local/bin:\$PATH}\\
     173      \vspace{3mm}
     174      \item<2-> Set the DISPLAY environment variable to indicate where to
     175                display graphics as for any X11 Windows application that you
     176                run\\
     177                e.g. ksh: \texttt{export DISPLAY=localhost:13.0}, or use
     178                \texttt{ssh -X} to tunnel X-communication.\\
    168179      \vspace{3mm}
    169180      \item<3-> Test your NCL installation\\
    170       \quad \texttt{\% ng4ex gsun01}\\
    171       NCL script gsun01n.ncl is copied to your working directory and run through NCL. An X11 window should pop up.
     181                \quad \texttt{\% ng4ex gsun01}\\
     182                NCL script gsun01n.ncl is copied to your working directory and
     183                run through NCL. An X11 window should pop up.
    172184   \end{itemize} 
    173185
    … …  
    179191   \footnotesize
    180192   \begin{itemize}     
    181            \item<1-> Together with the PALM installation you have also received four NCL scripts, a configuration file and a manual; they can be found in the directory\\
    182            \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS/NCL/}
    183       \item<2-> All standard netCDF data output of PALM can be visualized by one of the scripts:
    184       \begin{itemize}
    185          \scriptsize
    186          \item[-]<2-> \texttt{cross\underline{ }sections.ncl} (2D/3D data, e.g. contour or vector plots)
    187          \item[-]<2-> \texttt{profiles.ncl} (profile data)
    188          \item[-]<2-> \texttt{timeseries.ncl} (time series data)
    189          \item[-]<2-> \texttt{spectra.ncl} (spectra data)
    190       \end{itemize} 
    191       \item<3-> To run these NCL scripts you can use the shell script \texttt{palmplot} which can be found in the directory\\
    192       \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS}
    193       \item<4-> The output of the plots can be changed with several parameters; these parameters can be either written in the prompt (when calling the shell script \texttt{palmplot}) or modified within the configuration file \texttt{.ncl.config}
     193      \item<1-> Together with the PALM installation you have also received four NCL scripts, a configuration file and a manual; they can be found in the directory\\
     194                \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS/NCL/}
     195      \item<2-> All standard netCDF data output of PALM can be visualized by one
     196                of the scripts:
     197                \begin{itemize}
     198                   \scriptsize
     199                   \item[-]<2-> \texttt{cross\underline{ }sections.ncl}
     200                                (2D/3D data, e.g. contour or vector plots)
     201                   \item[-]<2-> \texttt{profiles.ncl} (profile data)
     202                   \item[-]<2-> \texttt{timeseries.ncl} (time series data)
     203                   \item[-]<2-> \texttt{spectra.ncl} (spectra data)
     204                \end{itemize} 
     205      \item<3-> To run these NCL scripts you can use the shell script
     206                \texttt{palmplot} which can be found in the directory\\
     207                \texttt{\$HOME/palm/current\underline{ }version/trunk/SCRIPTS}
     208      \item<4-> The output of the plots can be changed with several parameters;
     209                these parameters can be either written in the prompt
     210                (when calling the shell script \texttt{palmplot}) or set
     211                within the configuration file \texttt{.ncl.config}
    194212   \end{itemize} 
    195213
    … …  
    203221   \small
    204222   \begin{itemize}     
    205            \item[-]<1-> Please create a personal configuration file by copying the default configuration file \texttt{.ncl.config.default} to the PALM working directory \texttt{\$HOME/palm/current\underline{ }version} and naming it \texttt{.ncl.config}
    206            \item[-]<2-> \texttt{.ncl.config} is used by NCL directly, thus the parameters have to be written according to the rules of the scripting language NCL
    207            \item[-]<3-> The configuration file contains all steering parameters with a short description and can be modified to personal needs
     223      \item[-]<1-> Please create a personal configuration file by copying
     224                   the default configuration file
     225                   \texttt{.ncl.config.default} to the PALM working
     226                   directory \texttt{\$HOME/palm/current\underline{ }version}
     227                   and naming it \texttt{.ncl.config}
     228      \item[-]<2-> \texttt{.ncl.config} is used by NCL directly, thus the
     229                   parameters have to be written according to the rules of the
     230                   scripting language NCL
     231      \item[-]<3-> The configuration file contains all steering parameters with
     232                   a short description and can be adjusted to personal needs
    208233   \end{itemize} 
    209234
    … …  
    217242   \footnotesize
    218243   \begin{itemize}     
    219            \item[-]<1-> The shell script is used as follows:\\
    220       \texttt{palmplot <plot\underline{ }identifier>}
    221       \item[-]<1-> \texttt{<plot\underline{ }identifier>} has to be \texttt{xy}, \texttt{xz}, \texttt{yz}, \texttt{pr}, \texttt{sp} or \texttt{ts} depending on the data to be plotted
     244      \item[-]<1-> The shell script is used as follows:\\
     245                   \texttt{palmplot <plot\underline{ }identifier>}
     246      \item[-]<1-> \texttt{<plot\underline{ }identifier>} has to be \texttt{xy},
     247                   \texttt{xz}, \texttt{yz}, \texttt{pr}, \texttt{sp} or
     248                   \texttt{ts} depending on the data to be plotted
    222249   \end{itemize}     
    223250   \vspace{3mm}
    224    \onslide<2->\begin{tabular}{ccc}
    225       \textbf{plot\underline{ }identifier} & \textbf{data used} & \textbf{ncl script}\\
    226            xy & instantaneous or time-averaged xy or 3D data & cross\underline{ }sections.ncl\\
    227            xz & instantaneous or time-averaged xz or 3D data & cross\underline{ }sections.ncl\\
    228            yz & instantaneous or time-averaged yz or 3D data & cross\underline{ }sections.ncl\\
    229            pr & profile or 3D data & profiles.ncl\\
    230            sp & spectra data & spectra.ncl\\
    231            ts & time series data & timeseries.ncl\\
     251   \onslide<2->
     252      \begin{tabular}{ccc}
     253         \textbf{plot\underline{ }identifier} & \textbf{data used} & \textbf{ncl script}\\
     254         xy & instantaneous or time-averaged xy or 3D data & cross\underline{ }sections.ncl\\
     255         xz & instantaneous or time-averaged xz or 3D data & cross\underline{ }sections.ncl\\
     256         yz & instantaneous or time-averaged yz or 3D data & cross\underline{ }sections.ncl\\
     257         pr & profile or 3D data & profiles.ncl\\
     258         sp & spectra data & spectra.ncl\\
     259         ts & time series data & timeseries.ncl\\
    232260   \end{tabular}
    233261
    … …  
    241269   \footnotesize
    242270   \begin{itemize}     
    243            \item[-]<1-> To change the output of the plot you can also use:\\
    244       \scriptsize \texttt{palmplot \textbf{plot\underline{ }identifier} parameter=value parameter=string ...}
     271      \item[-]<1-> To change the output of the plot you can also use:\\
     272                   \scriptsize
     273                   \texttt{palmplot \textbf{plot\underline{ }identifier}
     274                   parameter=value parameter=string ...}
    245275      \footnotesize \\
    246276      \vspace{2mm}
    247       \item[-]<2-> A list of all available parameters can be found in the configuration file \texttt{.ncl.config} or in the documentation:\\
    248       \uncover<3->{\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist}}\\
     277      \item[-]<2-> A list of all available parameters can be found in the
     278                   configuration file \texttt{.ncl.config} or in the
     279                   documentation:\\
     280                   \uncover<3->{\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist}}\\
    249281      \vspace{2mm}
    250       \item[-]<4-> Parameters specified in the prompt override parameters given in the configuration file\\
     282      \item[-]<4-> Parameters specified in the prompt override parameters given
     283                   in the configuration file\\
    251284      \vspace{2mm}
    252       \item[-]<5-> String parameters which can contain lists (\texttt{var}, \texttt{c\underline{ }var}, \texttt{vec1}, \texttt{vec2}, \texttt{plotvec}) have to be set in single quotes and the list itself has to be separated by blanks, e.g. \texttt{var='pt u w'}\\
     285      \item[-]<5-> String parameters which can contain lists (\texttt{var},
     286                   \texttt{c\underline{ }var}, \texttt{vec1}, \texttt{vec2},
     287                   \texttt{plotvec}) have to be set in single quotes and the
     288                   list itself has to be separated by blanks, e.g.
     289                   \texttt{var='pt u w'}\\
    253290      \vspace{2mm}
    254       \item[-]<1-> A short introduction for using the shell script is given by typing\\
    255       \texttt{palmplot ?}
     291      \item[-]<6-> A short introduction for using the shell script is given by
     292                   typing\\
     293                   \texttt{palmplot ?}
    256294   \end{itemize}     
    257295
    … …  
    260298% Folie 12
    261299\begin{frame}
    262    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (I)}
    263    \small
    264    \begin{itemize}     
    265            \item<1-> Starting the example run with the command\\
    266            \vspace{2mm}
    267       \texttt{mrun -d example\underline{ }cbl ... -r 'd3\# pr\# ts\# xy\# xz\#'}\\
    268       \vspace{2mm}
    269       results in the following output files in\\
    270       \vspace{2mm}
    271       \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}:\\
    272       \texttt{example\underline{ }cbl\underline{ }pr.nc}, \texttt{example\underline{ }cbl\underline{ }xy.nc}, \texttt{example\underline{ }cbl\underline{ }xz.nc},\\
    273       \texttt{example\underline{ }cbl\underline{ }ts.nc}
     300   \frametitle{Application Example: Visualization of the Output of the Example
     301               Run (example\underline{ }cbl) (I)}
     302   \small
     303   \begin{itemize}     
     304      \item<1-> Starting the example run with the command\\
     305                \vspace{2mm}
     306                \texttt{mrun -d example\underline{ }cbl ... -r
     307                        'd3\# pr\# ts\# xy\# xz\#'}\\
     308                \vspace{2mm}
     309                results in the following output files in\\
     310                \vspace{2mm}
     311                \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}:\\
     312                \texttt{example\underline{ }cbl\underline{ }pr.nc}, \texttt{example\underline{ }cbl\underline{ }xy.nc}, \texttt{example\underline{ }cbl\underline{ }xz.nc},\\
     313                \texttt{example\underline{ }cbl\underline{ }ts.nc}
    274314      \item<2-> Example: Visualization of the time series data\\
    275       \vspace{2mm}
    276       Goal: Output as eps-file \texttt{timeseries.eps} (by default the plot would be output to an X11 window)
     315                \vspace{2mm}
     316                Goal: Output as eps-file \texttt{timeseries.eps} (by default the
     317                plot would be output to an X11 window)
    277318   \end{itemize}     
    278319
    … …  
    281322% Folie 13
    282323\begin{frame}
    283    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (II)}
    284    \small
    285    \begin{itemize}     
    286            \item<1-> In order to reach the goal you can either ...
     324   \frametitle{Application Example: Visualization of the Output of the Example
     325               Run (example\underline{ }cbl) (II)}
     326   \small
     327   \begin{itemize}     
     328      \item<1-> In order to reach the goal you can either ...
    287329      \item<1-> ... Change to the directory\\
    288       \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}\\
    289       and use the shell script with the command\\
    290       \vspace{2mm}
    291       \texttt{palmplot ts file\underline{ }1=example\underline{ }cbl\underline{ }ts.nc format\underline{ }out=eps file\underline{ }out=timeseries}\\
    292       \vspace{2mm}
    293       Thus, the script \texttt{timeseries.ncl} is called and some of the parameters in the configuration file \texttt{.ncl.config} are directly set by specifying the related parameters in the command line,\\
    294       \vspace{2mm}
    295       \onslide<2-> e.g. \texttt{file\underline{ }1 = <netCDF file>} \textbf{(Note: the input file has always to be specified!)}, \texttt{file\underline{ }out = <output file>}
     330                \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}\\
     331                and use the shell script with the command\\
     332                \vspace{2mm}
     333                \texttt{palmplot ts file\underline{ }1=example\underline{ }cbl\underline{ }ts.nc format\underline{ }out=eps file\underline{ }out=timeseries}\\
     334                \vspace{2mm}
     335                Thus, the script \texttt{timeseries.ncl} is called and some of the parameters in the configuration file \texttt{.ncl.config} are directly set by specifying the related parameters in the command line,\\
     336                \vspace{2mm}
     337                \onslide<2-> e.g. \texttt{file\underline{ }1 = <netCDF file>}
     338                \textbf{(Note: the input file has always to be specified!)}, \texttt{file\underline{ }out = <output file>}
    296339   \end{itemize}     
    297340
    … …  
    300343% Folie 14
    301344\begin{frame}
    302    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (III)}
     345   \frametitle{Application Example: Visualization of the Output of the Example
     346               Run (example\underline{ }cbl) (III)}
    303347   \footnotesize
    304348   ... or you can modify the configuration file \texttt{.ncl.config}, e.g.\\
    … …  
    318362% Folie 15
    319363\begin{frame}
    320    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (IV)}
     364   \frametitle{Application Example: Visualization of the Output of the Example
     365               Run (example\underline{ }cbl) (IV)}
    321366   \footnotesize
    322367   \begin{itemize}
    323       \item<1-> Both ways will lead to the creation of a new file called \texttt{timeseries.eps} in the directory\\
    324       \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}
     368      \item<1-> Both ways will create a new file called \texttt{timeseries.eps}
     369                in the directory\\
     370               \texttt{\$HOME/palm/current\underline{ }version/JOBS/example\underline{ }cbl/OUTPUT/}
    325371   \end{itemize}
    326372   \centering
    327    \onslide<2->\includegraphics[scale=0.4]{ncl_figures/vis1.png}
     373   \onslide<2->\includegraphics[scale=0.25]{ncl_figures/vis1.png}
    328374   
    329375\end{frame}
    … …  
    331377% Folie 16
    332378\begin{frame}
    333    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (V)}
     379   \frametitle{Application Example: Visualization of the Output of the Example
     380               Run (example\underline{ }cbl) (V)}
    334381   \footnotesize
    335382   \begin{itemize}
    … …  
    341388   \end{itemize}
    342389   \centering
    343    \onslide<2->\includegraphics[scale=0.7]{ncl_figures/vis2.png}
     390   \onslide<2->\includegraphics[scale=0.3]{ncl_figures/vis2.png}
    344391   
    345392\end{frame}
    … …  
    348395\begin{frame}[t]
    349396   \tikzstyle{plain} = [rectangle, text width=0.27\textwidth, font=\small]
    350    \frametitle{Application Example: Visualization of the Output of the Example Run (example\underline{ }cbl) (VI)}
     397   \frametitle{Application Example: Visualization of the Output of the Example
     398               Run (example\underline{ }cbl) (VI)}
    351399   \footnotesize
    352400   Plot profiles with the command\\
    … …  
    367415      \node at (current page.north west){%
    368416      \begin{tikzpicture}[overlay]
    369          \node[plain,anchor=west] at (72mm,-51.5mm) {\includegraphics[scale=0.32]{ncl_figures/vis3.png}};
     417         \node[plain,anchor=west] at (72mm,-51.5mm)
     418              {\includegraphics[scale=0.32]{ncl_figures/vis3.png}};
    370419      \end{tikzpicture}
    371420      };
    … …  
    379428   \small
    380429   \begin{itemize}     
    381            \item<1-> The other NCL scripts delivered with PALM can be used in a similar way, however the parameters that can be specified differ from script to script
    382            \item<2-> There are plenty of parameters for each script. Please have a look to the NCL documentation (\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist}) for detailed information
    383       \item<1-> If one of the program aborts and there is no comment, check the configuration file - the scripts should not abort with the default values. Be sure to use the right data type (e.g.: integer = 2; float = 2.0; double = 2.0d; string = \dq name\dq ) 
     430      \item<1-> The other NCL scripts delivered with PALM can be used in
     431                a similar way, however the parameters that can be specified
     432                differ from script to script
     433      \item<2-> There are plenty of parameters for each script. Please have a
     434                look to the NCL documentation
     435                (\texttt{http://palm.muk.uni-hannover.de/wiki/doc/app/nclparlist})
     436                for detailed information
     437      \item<3-> If one of the program aborts and there is no comment,
     438                check the configuration file - the scripts should not abort with
     439                the default values. Be sure to use the right data type
     440                (e.g.: integer = 2; float = 2.0; double = 2.0d;
     441                string = \dq name\dq ) 
    384442   \end{itemize}   
    385443\end{frame}
Note: See TracChangeset for help on using the changeset viewer.
                                                                                                                                                                                                                                                                                                                                                                               
  | Impressum | ©Leibniz Universität Hannover |