Index: palm/trunk/DOC/app/chapter_4.5.1.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.1.html	(revision 54)
+++ palm/trunk/DOC/app/chapter_4.5.1.html	(revision 62)
@@ -1,5 +1,7 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
 <html><head>
-<meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.5.1</title> <meta content="StarOffice 7 (Win32)" name="GENERATOR"> <meta content="Siegfried Raasch" name="AUTHOR"> <meta content="20041022;12155949" name="CREATED"> <meta content="20041117;11232134" name="CHANGED"> <meta content="parallel LES model" name="KEYWORDS"> <style>
+<meta content="text/html; charset=windows-1252" http-equiv="CONTENT-TYPE"><title>PALM chapter 4.5.1</title>
+<meta content="StarOffice 7 (Win32)" name="GENERATOR">
+<meta content="Siegfried Raasch" name="AUTHOR"> <meta content="20041022;12155949" name="CREATED"> <meta content="20041117;11232134" name="CHANGED"> <meta content="parallel LES model" name="KEYWORDS"> <style>
 <!--
 @page { size: 21cm 29.7cm }
@@ -16,5 +18,6 @@
 self-describing, <span style="font-weight: bold;">portable</span>
 objects that can be accessed through a simple interface (protable means
-that NetCDF data files can be read on any machine regardless of where they
+that NetCDF data files can be read on any machine regardless of where
+they
 have been created). Array values may be accessed directly, without
 knowing details of how the data are stored. Auxiliary information about
@@ -26,5 +29,7 @@
 (see <a href="#ncdump">further below</a>).
 Many (public domain) graphic software has built in interfaces to read
-NetCDF datasets (e.g. <span style="font-weight: bold;">ferret</span> or <span style="font-weight: bold;">NCL</span>). The complete NetCDF documentation
+NetCDF datasets (e.g. <span style="font-weight: bold;">ferret</span>
+or <span style="font-weight: bold;">NCL</span>).
+The complete NetCDF documentation
 is available from the <a href="http://www.unidata.ucar.edu/packages/netcdf/docs.html">NetCDF
 homepage</a>. The NetCDF tutorial for FORTRAN90 can also be found
@@ -48,5 +53,6 @@
 different files. The following table gives an overview about the
 different kind of NetCDF output data offered by PALM. Beside the local
-names of the files, the table also lists the minimum parameter settings which
+names of the files, the table also lists the minimum parameter settings
+which
 are necessary to switch on the output, as well as the parameters to be
 used to control the output.<br><br><table style="text-align: left; width: 750px; height: 226px;" border="1" cellpadding="2" cellspacing="2"><tbody><tr><td align="left" valign="top"><span style="font-weight: bold;">kind of data</span></td><td align="left" valign="top"><span style="font-weight: bold;">local filename</span></td><td align="left" valign="top"><span style="font-weight: bold;">parameter settings necessary to
@@ -61,5 +67,6 @@
 <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a>
 (or <a href="chapter_4.2.html#skip_time_dopr">skip_time_dopr</a>),
-<a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">timeseries</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_TS_NETCDF">DATA_1D_TS_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_dots">dt_dots</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>, <a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">spectra</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_SP_NETCDF">DATA_1D_SP_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#comp_spectra_level">comp_spectra_level</a>,
+<a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">timeseries</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_TS_NETCDF">DATA_1D_TS_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_dots">dt_dots</a></td><td align="left" valign="top"><a href="chapter_4.2.html#data_output_format">data_output_format</a>,
+<a href="chapter_4.1.html#statistic_regions">statistic_regions</a></td></tr><tr><td align="left" valign="top">spectra</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_1D_SP_NETCDF">DATA_1D_SP_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#comp_spectra_level">comp_spectra_level</a>,
 <a href="chapter_4.2.html#data_output_sp">data_output_sp</a>,
 <a href="chapter_4.2.html#dt_data_output">dt_data_output</a>
@@ -148,5 +155,7 @@
 <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>, <a href="chapter_4.2.html#skip_time_data_output">skip_time_data_output</a>
 (or <a href="chapter_4.2.html#skip_time_data_output_av">skip_time_data_output_av</a>,
-or <a href="chapter_4.2.html#skip_time_do3d">skip_time_do3d</a>)</td></tr><tr><td align="undefined" valign="undefined">particle timeseries</td><td style="vertical-align: top;"><a href="chapter_3.4.html#DATA_1D_PTS_NETCDF">DATA_1D_PTS_NETCDF</a></td><td style="vertical-align: top;"><a href="chapter_4.2.html#dt_data_output">dt_data_output</a> (or <a href="chapter_4.2.html#dt_dopts">dt_dopts</a>)</td><td align="undefined" valign="undefined"></td></tr><tr><td align="left" valign="top">particle attributes</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_PRT_NETCDF">DATA_PRT_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_write_particle_data">dt_write_particle_data</a></td><td align="left" valign="top"></td></tr></tbody></table><br><br><span style="font-weight: bold;">Creating, contents and
+or <a href="chapter_4.2.html#skip_time_do3d">skip_time_do3d</a>)</td></tr><tr><td align="undefined" valign="undefined">particle
+timeseries</td><td style="vertical-align: top;"><a href="chapter_3.4.html#DATA_1D_PTS_NETCDF">DATA_1D_PTS_NETCDF</a></td><td style="vertical-align: top;"><a href="chapter_4.2.html#dt_data_output">dt_data_output</a>
+(or <a href="chapter_4.2.html#dt_dopts">dt_dopts</a>)</td><td align="undefined" valign="undefined"></td></tr><tr><td align="left" valign="top">particle attributes</td><td align="left" valign="top"><a href="chapter_3.4.html#DATA_PRT_NETCDF">DATA_PRT_NETCDF</a></td><td align="left" valign="top"><a href="chapter_4.2.html#dt_write_particle_data">dt_write_particle_data</a></td><td align="left" valign="top"></td></tr></tbody></table><br><br><span style="font-weight: bold;">Creating, contents and
 post-processing of a PALM NetCDF file</span><br><br>This
 section describes, step-by-step, the creation, storage, and
@@ -184,5 +193,6 @@
 output of time-averaged data, the string <span style="font-style: italic;">'_av'</span> has to be
 additionally appended to the respective name string (see <a href="chapter_4.2.html#data_output">data_output</a>).<br><br><br></li><li>
-<p style="line-height: 100%;">Instantaneous data are output in NetCDF
+<p style="line-height: 100%;">Instantaneous data are
+output in NetCDF
 format
 into the
@@ -213,6 +223,11 @@
 additional file suffix, should be the string <span style="font-style: italic;">'nc'</span>, because many
 application programs expect NetCDF files to have the file extension <span style="font-style: italic;">'.nc'</span>. (This
-additional suffix given in the 6th column is always put at the very end of the filename, even
-in case of cycle numbers.)<br><br>Time averaged data are output into local file&nbsp;<a href="chapter_3.4.html#DATA_2D_XY_AV_NETCDF">DATA_2D_XY_AV_NETCDF</a> which requires an additional file connection statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp; DATA_2D_XY_AV_NETCDF out:loc:tr&nbsp; xy#&nbsp; ~/$fname/OUTPUT/$fname&nbsp; _xy_av nc&nbsp;&nbsp; .</span><br></p></li><li>With
+additional suffix given in the 6th column is always put at the very end
+of the filename, even
+in case of cycle numbers.)<br><br>Time averaged data are
+output into local file&nbsp;<a href="chapter_3.4.html#DATA_2D_XY_AV_NETCDF">DATA_2D_XY_AV_NETCDF</a>
+which requires an additional file connection statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp;
+DATA_2D_XY_AV_NETCDF out:loc:tr&nbsp; xy#&nbsp;
+~/$fname/OUTPUT/$fname&nbsp; _xy_av nc&nbsp;&nbsp; .</span><br></p></li><li>With
 parallel runs and choice of <a href="chapter_4.2.html#data_output_2d_on_each_pe">data_output_2d_on_each_pe</a>
 = <i>.T.</i>
@@ -223,5 +238,6 @@
 PLOT2D_XY_0000). These files have FORTRAN binary format. After PALM has
 finished, their content is merged into the final local destination file
-DATA_2D_XY_NETCDF by the program <span style="font-family: monospace;">combine_plot_fields</span>.&nbsp;<span style="font-weight: bold;"></span>This is done by adding the following output command to the configuration file:<br><br><span style="font-family: monospace;">&nbsp; &nbsp;OC:[[$
+DATA_2D_XY_NETCDF by the program <span style="font-family: monospace;">combine_plot_fields</span>.&nbsp;<span style="font-weight: bold;"></span>This is done by
+adding the following output command to the configuration file:<br><br><span style="font-family: monospace;">&nbsp; &nbsp;OC:[[$
 ( echo $localhost | cut -c1-3 ) = imbh ]] &amp;&amp;
 combine_plot_fields.x &nbsp; &nbsp; .</span><br><br>Using
@@ -255,5 +271,6 @@
 display of NetCDF datasets. One of the easiest ways to display the PALM
 data is the <a style="font-family: monospace;" href="http://ferret.wrc.noaa.gov/Ferret/">ferret</a>
-graphical user interface (GUI). On the IMUK-Linux-cluster, this can be called by
+graphical user interface (GUI). On the IMUK-Linux-cluster, this can be
+called by
 executing the command<br><br><span style="font-family: monospace;">&nbsp; &nbsp;ferret
 -gui &nbsp; &nbsp; .</span><br><br><span style="font-family: monospace;">ferret</span> is also
@@ -268,7 +285,10 @@
 as soon as available.<br><br><br></li><li><a name="netcdf_example_program"></a>One
 of the most flexible general ways for postprocessing NetCDF data
-is&nbsp;reading these data into a FORTRAN program. The&nbsp;<font color="#000000"></font><a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a> shows how to read 2d or 3d NetCDF datasets created by PALM. Compiling this program requires that the
+is&nbsp;reading these data into a FORTRAN program. The&nbsp;<a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a> shows
+how to read 2d or 3d NetCDF datasets created by PALM. Compiling this
+program requires that the
 NetCDF library is installed (if neccessary, please ask your system
-administrator). Some compilation instructions are given in the header of the
+administrator). Some compilation instructions are given in the header
+of the
 example program.<br><br><br></li><li>By
 default, each PALM job creates its own NetCDF files. If permanent files
@@ -276,20 +296,34 @@
 higher cycle numbers will be created. However, in case of a job chain,
 it is possible to extend the NetCDF datasets created by the initial
-run&nbsp;with data from the restart run(s). As a result, data of all
+run&nbsp;with data from the restart run(s). As a result, data of
+all
 output times of the complete job chain are contained in one file and
 the number of data files to be handled by the user may be reduced
-significantly.<br>To extend a NetCDF dataset (created by a previous run
+significantly.<br>To extend a NetCDF dataset (created by a
+previous run
 of a job chain) with data from the current run requires that this
 dataset must be provided as an INPUT file. This may be difficult in
 case that PALM is running on a remote host because typically the output
-data files from the previous run have been already transferred by <span style="font-weight: bold;">mrun</span> to the local workstation with a file connection statement like<br><br><span style="font-family: monospace;">&nbsp;
-&nbsp;DATA_2D_XY_NETCDF &nbsp;out:loc:tr&nbsp;&nbsp;xy#:xyf
-&nbsp;~/palm/current_version/JOBS/$fname/OUTPUT &nbsp;_xy&nbsp; nc</span><br><br>and thus they are not available on the remote host any more. <br>A
+data files from the previous run have been already transferred by <span style="font-weight: bold;">mrun</span> to the local
+workstation with a file connection statement like<br><br><span style="font-family: monospace;">&nbsp;
+&nbsp;DATA_2D_XY_NETCDF
+&nbsp;out:loc:tr&nbsp;&nbsp;xy#:xyf
+&nbsp;~/palm/current_version/JOBS/$fname/OUTPUT
+&nbsp;_xy&nbsp; nc</span><br><br>and thus
+they are not available on the remote host any more. <br>A
 workaround for solving this problem is to create an additional copy of
 the output file on the remote machine by adding the file connection
-statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp; DATA_2D_XY_NETCDF&nbsp; out:loc&nbsp; xy#:xyf&nbsp; ~/palm/current_version/JOBS/$fname/OUTPUT&nbsp; _xy&nbsp; nc</span><br><br>This additional copy can then be accessed from a restart job as an input file using the file connection statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp; DATA_2D_XY_NETCDF&nbsp; in:locopt&nbsp;&nbsp;xyf&nbsp; ~/palm/current_version/JOBS/$fname/OUTPUT&nbsp; _xy&nbsp; nc</span><br><br>Here the file attribut <span style="font-family: monospace;">locopt</span>
+statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp;
+DATA_2D_XY_NETCDF&nbsp; out:loc&nbsp; xy#:xyf&nbsp;
+~/palm/current_version/JOBS/$fname/OUTPUT&nbsp; _xy&nbsp; nc</span><br><br>This
+additional copy can then be accessed from a restart job as an input
+file using the file connection statement<br><br><span style="font-family: monospace;">&nbsp;&nbsp;
+DATA_2D_XY_NETCDF&nbsp; in:locopt&nbsp;&nbsp;xyf&nbsp;
+~/palm/current_version/JOBS/$fname/OUTPUT&nbsp; _xy&nbsp; nc</span><br><br>Here
+the file attribut <span style="font-family: monospace;">locopt</span>
 (2nd column) guarantees that the job continues if a permanent file does
 not exist (e.g. in case of an initial run). Otherwise, the job would be
-aborted.<br>Although the dataset created by the last run of a job chain
+aborted.<br>Although the dataset created by the last run of a job
+chain
 will contain data from all selected time levels of the complete job
 chain, the main disadvantage of this workaround is that the datasets
@@ -297,11 +331,19 @@
 and may consume large disc space. They have to be deleted "by hand" by
 the user on the local machine as well as on the remote
-machine&nbsp;because they only contain redundant data from the earlier
-time levels which are already contained&nbsp;in the dataset created by
-the last job of the job chain.<br><br><span style="font-weight: bold;">Note:</span><br>Extension of PALM NetCDF datasets of 2d horizontal cross sections requires that parameters <a href="chapter_4.2.html#data-output">data_output</a> and <a href="chapter_4.2.html#section_xy">section_xy</a>&nbsp;
+machine&nbsp;because they only contain redundant data from the
+earlier
+time levels which are already contained&nbsp;in the dataset created
+by
+the last job of the job chain.<br><br><span style="font-weight: bold;">Note:</span><br>Extension
+of PALM NetCDF datasets of 2d horizontal cross sections requires that
+parameters <a href="chapter_4.2.html#data-output">data_output</a>
+and <a href="chapter_4.2.html#section_xy">section_xy</a>&nbsp;
 for the restart runs are set identical to the initial run. In case of a
 value mismatch between initial and restart runs, a warning is issued in
 the job protocol file and the dataset will contain only data from those
-timelevels calculated within the restart run.<br>Similar restrictions apply for all other PALM NetCDF datasets (i.e. profiles, vertical cross sections, volume data, etc.).</li></ol><br>&nbsp;<br><span style="font-weight: bold;"><a name="NetCDF_example"></a>Example of a PALM NetCDF dataset</span><br><br>The
+timelevels calculated within the restart run.<br>Similar
+restrictions apply for all other PALM NetCDF datasets (i.e. profiles,
+vertical cross sections, volume data, etc.).</li></ol><br>&nbsp;<br><span style="font-weight: bold;"><a name="NetCDF_example"></a>Example
+of a PALM NetCDF dataset</span><br><br>The
 NetCDF dataset described here contains data of instantaneous horizontal
 cross sections and has been created using the settings of the <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">example
@@ -309,21 +351,126 @@
 4.4</a>),
 i.e. it contains section data of the w-velocity-component and of the
-potential temperature for vertical grid levels with index <span style="font-family: monospace;">k = 2</span> and <span style="font-family: monospace;">k = 10</span>, selected by the respective parameter settings <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'pt_xy'</span>, and <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>. Output has been created after every 900 s (<a href="chapter_4.2.html#dt_data_output">dt_data_output</a> = <span style="font-style: italic;">900.0</span>). Because of <a href="chapter_4.2.html#end_time">end_time</a> = <span style="font-style: italic;">3600.0</span>, the file contains data of 4 time levels (t = 900, 1800, 2700, 3600 s).<br>Supposed that the name of the NetCDF dataset is <span style="font-family: monospace;">example_xy.nc</span>, an analysis of the file contents using the command<br><br><span style="font-family: monospace;">&nbsp; &nbsp;ncdump -c example_xy.nc</span><br><br>will create the following output. The original ncdump output is displayed using <span style="font-family: monospace;">fixed spacing</span>, additional explanations are given in <span style="font-style: italic; font-family: monospace;">italian</span>.<br><br><div style="margin-left: 40px;"><span style="font-family: monospace;">netcdf&nbsp;example_xy { &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! filename</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">dimensions: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! 41 gridpoints along x and y, 4 timelevels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; time = UNLIMITED ; // (4 currently) &nbsp; &nbsp;<span style="font-style: italic;">! unlimited means that&nbsp;additional time levels can be added (e.g. by</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp;<span style="font-style: italic;">! restart jobs)</span><br>&nbsp;&nbsp;&nbsp; zu_xy = 2 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! vertical dimension (2, because two cross sections are selected);</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; zw_xy = 2 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! there are two different vertical dimensions zu and zw because due</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; zu1_xy = 1 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! to the staggered grid the z-levels of variables are those of the</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-x = 41 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! u- or the w-component of the velocity</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; y = 41 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">variables: &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! precision, dimensions, and units of the variables</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double time(time) ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! the variables containing the time levels and grid point coordinates</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; time:units = "seconds" ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! have the same names as the respective dimensions</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double zu_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; zu_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double zw_xy(zw_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; zw_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double zu1_xy(zu1_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; zu1_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double ind_z_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; ind_z_xy:units = "gridpoints" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double x(x) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; x:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; double y(y) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; y:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; float w_xy(time, zw_xy, y, x) ; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! array of the vertical velocity; it has 4 dimensions: x and y,</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; w_xy:long_name = "w_xy" ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! because it is a horizontal cross section, zw_xy, which defines</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; w_xy:units = "m/s" ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! the vertical levels of the sections, and time, for the time levels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; float pt_xy(time, zu_xy, y, x) ; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! array of the potential temperature, which is defined on the u-grid</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; pt_xy:long_name = "pt_xy" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; pt_xy:units = "K" ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">// global attributes:</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; :Conventions = "COARDS" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
-&nbsp;&nbsp;&nbsp; :title = "PALM&nbsp;&nbsp; 3.0&nbsp; run:
-example.00&nbsp; host: ibmh&nbsp; 13-04-06 15:12:43" ; &nbsp;<span style="font-style: italic;">! PALM run-identifier</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; :VAR_LIST = ";w_xy;pt_xy;" ; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! the list of output quantities contained in this dataset;</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp;<span style="font-style: italic;">! this global attribute can be used by FORTRAN programs to identify</span><br>&nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
-&nbsp;<span style="font-style: italic;">! and read the quantities contained in the file</span><br>data:</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;time = 905.3, 1808.98, 2711.98, 3603.59 ; <span style="font-style: italic;">! values of the four time levels</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zu_xy = 75, 475 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! heights of the two selected cross sections (u-grid)</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zw_xy = 100, 500 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zu1_xy = 25 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;x = 0, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, &nbsp; <span style="font-style: italic;">! x-coordinates of the gridpoints</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 2000 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;y = 0, 50, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp; 2000 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">}</span><br></div><br>If the option <span style="font-family: monospace;">-c</span> is omitted in the <span style="font-family: monospace;">ncdump</span> call, then also the complete grid point data of all quantities are output to the terminal.<br><br>The &nbsp;<a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a><span style="font-weight: bold;"></span> shows how to read this 2d
+potential temperature for vertical grid levels with index <span style="font-family: monospace;">k = 2</span> and <span style="font-family: monospace;">k = 10</span>,
+selected by the respective parameter settings <a href="chapter_4.2.html#data_output">data_output</a> = <span style="font-style: italic;">'w_xy'</span>, <span style="font-style: italic;">'pt_xy'</span>, and <a href="chapter_4.2.html#section_xy">section_xy</a> = <span style="font-style: italic;">2</span>, <span style="font-style: italic;">10</span>. Output has been
+created after every 900 s (<a href="chapter_4.2.html#dt_data_output">dt_data_output</a>
+= <span style="font-style: italic;">900.0</span>).
+Because of <a href="chapter_4.2.html#end_time">end_time</a>
+= <span style="font-style: italic;">3600.0</span>,
+the file contains data of 4 time levels (t = 900, 1800, 2700, 3600 s).<br>Supposed
+that the name of the NetCDF dataset is <span style="font-family: monospace;">example_xy.nc</span>,
+an analysis of the file contents using the command<br><br><span style="font-family: monospace;">&nbsp; &nbsp;ncdump
+-c example_xy.nc</span><br><br>will create the
+following output. The original ncdump output is displayed using <span style="font-family: monospace;">fixed spacing</span>,
+additional explanations are given in <span style="font-style: italic; font-family: monospace;">italian</span>.<br><br><div style="margin-left: 40px;"><span style="font-family: monospace;">netcdf&nbsp;example_xy {
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! filename</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">dimensions: &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp;<span style="font-style: italic;">!
+41 gridpoints along x and y, 4 timelevels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+time = UNLIMITED ; // (4 currently) &nbsp; &nbsp;<span style="font-style: italic;">! unlimited means
+that&nbsp;additional time levels can be added (e.g. by</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp;<span style="font-style: italic;">! restart jobs)</span><br>&nbsp;&nbsp;&nbsp;
+zu_xy = 2 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp;<span style="font-style: italic;">!
+vertical dimension (2, because two cross sections are selected);</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+zw_xy = 2 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp;<span style="font-style: italic;">!
+there are two different vertical dimensions zu and zw because due</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+zu1_xy = 1 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; <span style="font-style: italic;">!
+to the staggered grid the z-levels of variables are those of the</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+x = 41 ; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! u- or the w-component of the
+velocity</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+y = 41 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">variables: &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; <span style="font-style: italic;">!
+precision, dimensions, and units of the variables</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double time(time) ; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! the variables containing the
+time levels and grid point coordinates</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; time:units = "seconds" ; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! have the same names as the
+respective dimensions</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double zu_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; zu_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double zw_xy(zw_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; zw_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double zu1_xy(zu1_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; zu1_xy:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double ind_z_xy(zu_xy) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; ind_z_xy:units = "gridpoints" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double x(x) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; x:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+double y(y) ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; y:units = "meters" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+float w_xy(time, zw_xy, y, x) ; &nbsp; &nbsp; &nbsp;
+&nbsp;<span style="font-style: italic;">! array of the
+vertical velocity; it has 4 dimensions: x and y,</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; w_xy:long_name = "w_xy" ; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;<span style="font-style: italic;">! because it is a horizontal
+cross section, zw_xy, which defines</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; w_xy:units = "m/s" ; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! the vertical levels of the
+sections, and time, for the time levels</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+float pt_xy(time, zu_xy, y, x) ; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! array of the potential
+temperature, which is defined on the u-grid</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; pt_xy:long_name = "pt_xy" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; pt_xy:units = "K" ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">// global attributes:</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; :Conventions = "COARDS" ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; :title = "PALM&nbsp;&nbsp;
+3.0&nbsp; run:
+example.00&nbsp; host: ibmh&nbsp; 13-04-06 15:12:43" ;
+&nbsp;<span style="font-style: italic;">! PALM
+run-identifier</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+&nbsp;&nbsp;&nbsp; :VAR_LIST = ";w_xy;pt_xy;" ; &nbsp;
+&nbsp; &nbsp; <span style="font-style: italic;">!
+the list of output quantities contained in this dataset;</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp;<span style="font-style: italic;">! this global
+attribute can be used by FORTRAN programs to identify</span><br>&nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp;<span style="font-style: italic;">! and read the
+quantities contained in the file</span><br>data:</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;time = 905.3,
+1808.98, 2711.98, 3603.59 ; <span style="font-style: italic;">!
+values of the four time levels</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zu_xy = 75, 475 ;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <span style="font-style: italic;">! heights of the two selected
+cross sections (u-grid)</span></span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zw_xy = 100, 500 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;zu1_xy = 25 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;x = 0, 50, 100,
+150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, &nbsp; <span style="font-style: italic;">! x-coordinates of the gridpoints</span></span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300,
+1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950,
+</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+2000 ;</span><br style="font-family: monospace;"><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;y = 0, 50, 100,
+150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300,
+1350, </span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+1400, 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950,
+</span><br style="font-family: monospace;"><span style="font-family: monospace;">&nbsp;&nbsp;&nbsp;
+2000 ;</span><br style="font-family: monospace;"><span style="font-family: monospace;">}</span><br></div><br>If
+the option <span style="font-family: monospace;">-c</span>
+is omitted in the <span style="font-family: monospace;">ncdump</span>
+call, then also the complete grid point data of all quantities are
+output to the terminal.<br><br>The &nbsp;<a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/read_palm_netcdf_data.f90"><font color="#000080">example program</font></a><span style="font-weight: bold;"></span> shows how to read
+this 2d
 horizontal cross section dataset from a FORTRAN program (<a href="#netcdf_example_program">see above</a>).<br><hr>
-<p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.5.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.2.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p>
-<p style="line-height: 100%;"><span style="font-style: italic;">Last
-change:</span> 08/02/07 (SR)&nbsp;</p>
+<p style="line-height: 100%;"><br><font color="#000080"><font color="#000080"><a href="chapter_4.5.html"><font color="#000080"><img name="Grafik1" src="left.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img name="Grafik2" src="up.gif" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.2.html"><font color="#000080"><img style="border: 2px solid ; width: 32px; height: 32px;" alt="" name="Grafik3" src="right.gif"></font></a></font></font></p><p style="line-height: 100%;"><span style="font-style: italic;">Last
+change:</span> $Id$&nbsp;</p>
 </body></html>
