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    19 <h4 style="line-height: 100%;"><font size="4">4.5.5 Plots of 3d volume
     2<html><head>
     3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
     4chapter 4.5.5</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041027;13094394"> <meta name="CHANGED" content="20041117;11561956"> <meta name="KEYWORDS" content="parallel LES model"> <style>
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     9
     10<body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.5
     11Plots of 3d volume
    2012data with AVS</font></h4>
    21 <p style="line-height: 100%;">In contrast to the plot output described
     13<p style="line-height: 100%;">In contrast to the plot
     14output described
    2215so far, which can be handled more or less automatically, the creation
    2316of
    24 plots with <b>AVS</b> requires programming a so-called network by
    25 using the <span style="font-weight: bold;">AVS</span> network editor
     17plots with <b>AVS</b> requires programming a so-called
     18network by
     19using the <span style="font-weight: bold;">AVS</span>
     20network editor
    2621to design the plot
    2722layout. Details are not given here because it is assumed that the user
    2823is familiar with <b>AVS</b>. </p>
    29 <p style="line-height: 100%;"><font color="#000000">Output of 3d volume
     24<p style="line-height: 100%;"><font color="#000000">Output
     25of 3d volume
    3026data requires to set at least two parameters: </font>first, the
    3127temporal
    32 interval of the output time (run parameter <a
    33  href="chapter_4.2.html#dt_do3d"><u>dt_do3d)</u></a><span
    34  style="text-decoration: none;">
     28interval of the output time (run parameter <a href="chapter_4.2.html#dt_do3d"><u>dt_do3d)</u></a><span style="text-decoration: none;">
    3529and second<span style="text-decoration: none;"></span>
    36 the names of the quantities for which volume data output is wanted</span><span
    37  style="text-decoration: none;"><span style="text-decoration: none;"> (<a
    38  href="chapter_4.2.html#data_output">data_output</a></span></span>).<font
    39  color="#000000"> </font><font color="#000000"><span
    40  style="text-decoration: none;"></span></font><font color="#000000"><span
    41  style="text-decoration: none;"></span><span
    42  style="text-decoration: none;"></span></font><font color="#800000"> </font>The
     30the names of the quantities for which volume data output is wanted</span><span style="text-decoration: none;"><span style="text-decoration: none;"> (<a href="chapter_4.2.html#data_output">data_output</a></span></span>).<font color="#000000"> </font><font color="#000000"><span style="text-decoration: none;"></span></font><font color="#000000"><span style="text-decoration: none;"></span><span style="text-decoration: none;"></span></font><font color="#800000"> </font>The
    4331parameter <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>
    4432can be used to limit data output in vertical direction up to a certain
    4533grid
    46 point. If no value has been assigned to <b>data_output</b> or
     34point. If no value has been assigned to <b>data_output</b>
     35or
    4736if the value given for <b>dt_do3d </b>is
    4837larger than the simulated time (see <a href="chapter_4.1.html#end_time">end_time</a>),
    49 <b>then there will be no output!</b> By default, data is output in
     38<b>then there will be no output!</b> By default, data is
     39output in
    504032-bit real format. Alternatively, for parallel runs, data can also be
    5141output in compressed format using 32-bit integers. This yields
    5242a loss of accuracy, but the file size is clearly reduced. The output of
    53 compressed data is described in more detail in <a
    54  href="chapter_4.5.6.html">chapter
     43compressed data is described in more detail in <a href="chapter_4.5.6.html">chapter
    55444.5.6</a>. </p>
    5645<p style="line-height: 100%;">Data, whether compressed or
    57 uncompressed, is output into the local file <a
    58  href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>.
     46uncompressed, is output into the local file <a href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>.
    5947This file must be linked with a permanent file by
    60 using a file connection statement in the <b>mrun</b> configuration
     48using a file connection statement in the <b>mrun</b>
     49configuration
    6150file (see e.g. <a href="chapter_3.2.html">chapter
    62513.2</a>). At the end of the run the local file is copied to this
     
    6453informations about the 3d data, which also has to be copied. The
    6554statements can look like this: </p>
    66 <ul>
    67   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    68  style="font-size: 10pt;" size="2">PLOT3D_DATA out:loc:tr avs ~/PLOT/$fname  _avs<br>PLOT3D_COOR out:loc:tr avs ~/PLOT/$fname  _coor .</font></pre>
    69 </ul>
    70 <p style="line-height: 100%;">If the respective <b>mrun</b> call is
     55<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">PLOT3D_DATA out:loc:tr avs ~/PLOT/$fname _avs<br>PLOT3D_COOR out:loc:tr avs ~/PLOT/$fname _coor .</font></pre></ul>
     56<p style="line-height: 100%;">If the respective <b>mrun</b>
     57call is
    7158like</p>
    72 <ul>
    73   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    74  style="font-size: 10pt;" size="2">mrun -d  test -r “avs”
    75 </font></pre>
    76 </ul>
    77 <p style="line-height: 100%;">then the local file <tt><font
    78  style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt>
    79 is copied to the permanent file <tt><font style="font-size: 10pt;"
    80  size="2">~/PLOT/test/test_avs</font></tt> .
    81 However, the character string “<tt><font style="font-size: 10pt;"
    82  size="2">avs</font></tt>”
     59<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -d test -r &ldquo;avs&rdquo;&hellip;</font></pre></ul>
     60<p style="line-height: 100%;">then the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt>
     61is copied to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_avs</font></tt>
     62.
     63However, the character string &ldquo;<tt><font style="font-size: 10pt;" size="2">avs</font></tt>&rdquo;
    8364activating the file connection staement (see third column of the
    84 statement) must be given in the <b>mrun</b> call as argument of the
    85 option -r (and/or -o). <span style="text-decoration: none;">If t</span>his
     65statement) must be given in the <b>mrun</b> call as
     66argument of the
     67option -r (and/or -o). <span style="text-decoration: none;">If
     68t</span>his
    8669is forgotten by mistake, the model outputs the data to the local
    8770file, but this is not copied to the permanent file and thus the data
    8871are not available for the user after the run has finished.<br>
    89 </p>
    90 <p style="line-height: 100%;">The created data file can be used as
     72</p><p style="line-height: 100%;">The created data
     73file can be used as
    9174input file for the plot software <span style="font-weight: bold;">AVS</span>
    9275although for parallel runs another step is necessary which is
    9376described at the end of this chapter. However, after starting <b>AVS</b>
    94 (by executing the command “avs”), these data file is not read
    95 immediately<font color="#000000">. First, the user has to load a
     77(by executing the command &ldquo;avs&rdquo;), these data file
     78is not read
     79immediately<font color="#000000">. First, the user has to
     80load a
    9681suitable network (created by the
    97 network editor). This module usually contains the module</font> “read
    98 field”, which requires an input
     82network editor). This module usually contains the module</font>
     83&ldquo;read
     84field&rdquo;, which requires an input
    9985file in the so-called "fld-format", which in turn refers to the two
    10086files
     
    10490local files with the names <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>
    10591and <a href="chapter_3.4.html#PLOT3D_FLD_COOR">PLOT3D_FLD_COOR</a>,
    106 which must be combined into one file by a so-called <a
    107  href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.2">output
     92which must be combined into one file by a so-called <a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.2">output
    10893command</a>: </p>
    109 <ul>
    110   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    111  style="font-size: 10pt;" size="2">OC:[[ -f PLOT3D_FLD ]] &amp;&amp; cat PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</font></pre>
    112 </ul>
    113 <p style="line-height: 100%;">The new file PLOT3D_FLD also needs a file
     94<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">OC:[[ -f PLOT3D_FLD ]] &amp;&amp; cat PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</font></pre></ul>
     95<p style="line-height: 100%;">The new file PLOT3D_FLD also
     96needs a file
    11497connection statement: </p>
    115 <ul>
    116   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    117  style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr   avs  ~/PLOT/$fname  _fld fld</font></pre>
    118 </ul>
     98<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr avs ~/PLOT/$fname _fld fld</font></pre></ul>
    11999<p style="line-height: 100%;">The above <b>mrun </b>call
    120100then copies the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_FLD</font></tt>
    121101to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_fld.fld</font>
    122 </tt><font face="Thorndale, serif">.</font> In this case the entry
    123 “<tt><font style="font-size: 10pt;" size="2">fld</font></tt>”
     102</tt><font face="Thorndale, serif">.</font> In
     103this case the entry
     104&ldquo;<tt><font style="font-size: 10pt;" size="2">fld</font></tt>&rdquo;
    124105in the sixth column of the file connection statement is
    125106very important because this ensures that the permanent file name gets
    126 the suffix ” <tt><font style="font-size: 10pt;" size="2">.fld</font></tt>
     107the suffix &rdquo; <tt><font style="font-size: 10pt;" size="2">.fld</font></tt>
    127108".&nbsp; The <span style="font-weight: bold;">AVS</span>
    128 module “read field” expects all files to have this suffix. (Note: With
     109module &ldquo;read field&rdquo; expects all files to have this
     110suffix. (Note: With
    129111this file
    130 connection statements files with cycle numbers receive the names ”<tt><font
    131  style="font-size: 10pt;" size="2">
    132 
    133 _fld.&lt;number of cycle&gt;.fld</font></tt><font
    134  style="font-size: 10pt;" size="2">
     112connection statements files with cycle numbers receive the names
     113&rdquo;<tt><font style="font-size: 10pt;" size="2">&hellip;
     114_fld.&lt;number of cycle&gt;.fld</font></tt><font style="font-size: 10pt;" size="2">
    135115</font>".) </p>
    136 <p style="line-height: 100%;"><font color="#000000">The file
     116<p style="line-height: 100%;"><font color="#000000">The
     117file
    137118connection statements must guarantee that all three permanent files
    138119(volume
     
    140121the volume data file and coordinate file may not be changed after
    141122creation of the files, since they are registered in the fld file and
    142 otherwise cannot be found </font>by the "read field" module. Sometimes
     123otherwise cannot be found </font>by the "read field" module.
     124Sometimes
    143125it may happen<font color="#000000">
    144126that incorrect file names are registered into the fld file. In such
    145127cases the user must edit and correct the fld file accordingly. </font>
    146 </p>
    147 <p style="line-height: 100%;"><font color="#800000"><font
    148  color="#000000">After
     128</p><p style="line-height: 100%;"><font color="#800000"><font color="#000000">After
    149129<font color="#000000">the <span style="font-weight: bold;">AVS</span>
    150 module <font color="#000000">“read
    151 fields” </font>has </font>read in the data, the content of this
     130module <font color="#000000">&ldquo;read
     131fields&rdquo; </font>has </font>read in the data, the
     132content of this
    152133file is listed in a separate <span style="font-weight: bold;">AVS</span>
    153134window where each quantity is represented by its name and output time.</font>
    154 </font></p>
    155 <p style="line-height: 100%;">With parallel runs each PE outputs the
     135</font></p><p style="line-height: 100%;">With
     136parallel runs each PE outputs the
    156137volume data of its subdomain to a separate file with the name
    157138PLOT3D_DATA_&lt;processor-Id&gt;,
     
    159140PLOT3D_DATA_0000). These files are not suitable for&nbsp; <b>AVS</b>,
    160141but after the end of a run they can be combined to one file readable by
    161 <span style="font-weight: bold;">AVS</span>. This is done via a
     142<span style="font-weight: bold;">AVS</span>. This is
     143done via a
    162144further output command in the configuration file: </p>
    163 <ul>
    164   <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
    165  style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] &amp;&amp; combine_plot_fields.x</font></pre>
    166 </ul>
    167 <p style="line-height: 100%;">The program <tt><font
    168  style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt>
     145<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] &amp;&amp; combine_plot_fields.x</font></pre></ul>
     146<p style="line-height: 100%;">The program <tt><font style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt>
    169147collects the data from the individual processor files and outputs it
    170148into the local file <tt><font style="font-size: 10pt;" size="2">PLOT2D_DATA</font></tt>
     
    176154protocol, even if no files were found (i.e. the output command
    177155may remain in the configuration file, even if no appropriate files
    178 are created during the simulation). <span
    179  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span
    180  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span
    181  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span
    182  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span
    183  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span
    184  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span
    185  style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><br>
    186 </p>
    187 <p style="line-height: 100%;">&nbsp;<b>Note:</b> <span
    188  style="font-weight: bold;">AVS</span> can process 64 arrays at maximum
     156are created during the simulation). <span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><br>
     157</p><p style="line-height: 100%;">&nbsp;<b>Note:</b>
     158<span style="font-weight: bold;">AVS</span> can
     159process 64 arrays at maximum
    189160in one file (with vector representations even
    190161only 25). If more arrays should be output, surplus arrays must be
    191162removed from the fld file (see <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>)
    192163manually. &nbsp; </p>
    193 <hr>
    194 <p style="line-height: 100%;"><br>
    195 <font color="#000080"><font color="#000080"><a href="chapter_4.5.4.html"><font
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    199  border="2" height="32" width="32"></font></a><a
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    201  name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p>
    202 <p style="line-height: 100%;">&nbsp;<i>Last change:&nbsp;</i> 20/04/05
    203 (SR)</p>
    204 </body>
    205 </html>
     164<hr><p style="line-height: 100%;"><br>
     165<font color="#000080"><font color="#000080"><a href="chapter_4.5.4.html"><font color="#000080"><img src="left.gif" name="Grafik1" align="bottom" border="2" height="32" width="32"></font></a><a href="index.html"><font color="#000080"><img src="up.gif" name="Grafik2" align="bottom" border="2" height="32" width="32"></font></a><a href="chapter_4.5.6.html"><font color="#000080"><img src="right.gif" name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p><p style="line-height: 100%;">&nbsp;<i>Last
     166change:&nbsp;</i> $Id$</p>
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