Index: palm/trunk/DOC/app/chapter_4.5.5.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.5.html	(revision 54)
+++ palm/trunk/DOC/app/chapter_4.5.5.html	(revision 388)
@@ -1,62 +1,51 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="CONTENT-TYPE"
- content="text/html; charset=windows-1252">
-  <title>PALM chapter 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>
-	<!--
-		@page { size: 21cm 29.7cm }
-	-->
-	</style>
-</head>
-<body dir="ltr" lang="en-US">
-<h4 style="line-height: 100%;"><font size="4">4.5.5 Plots of 3d volume
+<html><head>
+<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
+chapter 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>
+<!--
+@page { size: 21cm 29.7cm }
+-->
+</style></head>
+
+<body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.5
+Plots of 3d volume
 data with AVS</font></h4>
-<p style="line-height: 100%;">In contrast to the plot output described
+<p style="line-height: 100%;">In contrast to the plot
+output described
 so far, which can be handled more or less automatically, the creation
 of
-plots with <b>AVS</b> requires programming a so-called network by
-using the <span style="font-weight: bold;">AVS</span> network editor
+plots with <b>AVS</b> requires programming a so-called
+network by
+using the <span style="font-weight: bold;">AVS</span>
+network editor
 to design the plot
 layout. Details are not given here because it is assumed that the user
 is familiar with <b>AVS</b>. </p>
-<p style="line-height: 100%;"><font color="#000000">Output of 3d volume
+<p style="line-height: 100%;"><font color="#000000">Output
+of 3d volume
 data requires to set at least two parameters: </font>first, the
 temporal
-interval of the output time (run parameter <a
- href="chapter_4.2.html#dt_do3d"><u>dt_do3d)</u></a><span
- style="text-decoration: none;">
+interval of the output time (run parameter <a href="chapter_4.2.html#dt_do3d"><u>dt_do3d)</u></a><span style="text-decoration: none;">
 and second<span style="text-decoration: none;"></span>
-the 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
+the 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
 parameter <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>
 can be used to limit data output in vertical direction up to a certain
 grid
-point. If no value has been assigned to <b>data_output</b> or
+point. If no value has been assigned to <b>data_output</b>
+or
 if the value given for <b>dt_do3d </b>is
 larger than the simulated time (see <a href="chapter_4.1.html#end_time">end_time</a>),
-<b>then there will be no output!</b> By default, data is output in
+<b>then there will be no output!</b> By default, data is
+output in
 32-bit real format. Alternatively, for parallel runs, data can also be
 output in compressed format using 32-bit integers. This yields
 a loss of accuracy, but the file size is clearly reduced. The output of
-compressed data is described in more detail in <a
- href="chapter_4.5.6.html">chapter
+compressed data is described in more detail in <a href="chapter_4.5.6.html">chapter
 4.5.6</a>. </p>
 <p style="line-height: 100%;">Data, whether compressed or
-uncompressed, is output into the local file <a
- href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>.
+uncompressed, is output into the local file <a href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>.
 This file must be linked with a permanent file by
-using a file connection statement in the <b>mrun</b> configuration
+using a file connection statement in the <b>mrun</b>
+configuration
 file (see e.g. <a href="chapter_3.2.html">chapter
 3.2</a>). At the end of the run the local file is copied to this
@@ -64,37 +53,34 @@
 informations about the 3d data, which also has to be copied. The
 statements can look like this: </p>
-<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>
-<p style="line-height: 100%;">If the respective <b>mrun</b> call is
+<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>
+<p style="line-height: 100%;">If the respective <b>mrun</b>
+call is
 like</p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">mrun -d  test -r avs
-</font></pre>
-</ul>
-<p style="line-height: 100%;">then the local file <tt><font
- style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt>
-is copied to the permanent file <tt><font style="font-size: 10pt;"
- size="2">~/PLOT/test/test_avs</font></tt> .
-However, the character string <tt><font style="font-size: 10pt;"
- size="2">avs</font></tt>
+<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>
+<p style="line-height: 100%;">then the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt>
+is copied to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_avs</font></tt>
+.
+However, the character string &ldquo;<tt><font style="font-size: 10pt;" size="2">avs</font></tt>&rdquo;
 activating the file connection staement (see third column of the
-statement) must be given in the <b>mrun</b> call as argument of the
-option -r (and/or -o). <span style="text-decoration: none;">If t</span>his
+statement) must be given in the <b>mrun</b> call as
+argument of the
+option -r (and/or -o). <span style="text-decoration: none;">If
+t</span>his
 is forgotten by mistake, the model outputs the data to the local
 file, but this is not copied to the permanent file and thus the data
 are not available for the user after the run has finished.<br>
-</p>
-<p style="line-height: 100%;">The created data file can be used as
+</p><p style="line-height: 100%;">The created data
+file can be used as
 input file for the plot software <span style="font-weight: bold;">AVS</span>
 although for parallel runs another step is necessary which is
 described at the end of this chapter. However, after starting <b>AVS</b>
-(by executing the command avs), these data file is not read
-immediately<font color="#000000">. First, the user has to load a
+(by executing the command &ldquo;avs&rdquo;), these data file
+is not read
+immediately<font color="#000000">. First, the user has to
+load a
 suitable network (created by the
-network editor). This module usually contains the module</font> read
-field, which requires an input
+network editor). This module usually contains the module</font>
+&ldquo;read
+field&rdquo;, which requires an input
 file in the so-called "fld-format", which in turn refers to the two
 files
@@ -104,35 +90,30 @@
 local files with the names <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>
 and <a href="chapter_3.4.html#PLOT3D_FLD_COOR">PLOT3D_FLD_COOR</a>,
-which 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
+which 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
 command</a>: </p>
-<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>
-<p style="line-height: 100%;">The new file PLOT3D_FLD also needs a file
+<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>
+<p style="line-height: 100%;">The new file PLOT3D_FLD also
+needs a file
 connection statement: </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr   avs  ~/PLOT/$fname  _fld fld</font></pre>
-</ul>
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr avs ~/PLOT/$fname _fld fld</font></pre></ul>
 <p style="line-height: 100%;">The above <b>mrun </b>call
 then copies the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_FLD</font></tt>
 to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_fld.fld</font>
-</tt><font face="Thorndale, serif">.</font> In this case the entry
-<tt><font style="font-size: 10pt;" size="2">fld</font></tt>
+</tt><font face="Thorndale, serif">.</font> In
+this case the entry
+&ldquo;<tt><font style="font-size: 10pt;" size="2">fld</font></tt>&rdquo;
 in the sixth column of the file connection statement is
 very important because this ensures that the permanent file name gets
-the suffix  <tt><font style="font-size: 10pt;" size="2">.fld</font></tt>
+the suffix &rdquo; <tt><font style="font-size: 10pt;" size="2">.fld</font></tt>
 ".&nbsp; The <span style="font-weight: bold;">AVS</span>
-module read field expects all files to have this suffix. (Note: With
+module &ldquo;read field&rdquo; expects all files to have this
+suffix. (Note: With
 this file
-connection statements files with cycle numbers receive the names <tt><font
- style="font-size: 10pt;" size="2">
-
-_fld.&lt;number of cycle&gt;.fld</font></tt><font
- style="font-size: 10pt;" size="2">
+connection statements files with cycle numbers receive the names
+&rdquo;<tt><font style="font-size: 10pt;" size="2">&hellip;
+_fld.&lt;number of cycle&gt;.fld</font></tt><font style="font-size: 10pt;" size="2">
 </font>".) </p>
-<p style="line-height: 100%;"><font color="#000000">The file
+<p style="line-height: 100%;"><font color="#000000">The
+file
 connection statements must guarantee that all three permanent files
 (volume
@@ -140,18 +121,18 @@
 the volume data file and coordinate file may not be changed after
 creation of the files, since they are registered in the fld file and
-otherwise cannot be found </font>by the "read field" module. Sometimes
+otherwise cannot be found </font>by the "read field" module.
+Sometimes
 it may happen<font color="#000000">
 that incorrect file names are registered into the fld file. In such
 cases the user must edit and correct the fld file accordingly. </font>
-</p>
-<p style="line-height: 100%;"><font color="#800000"><font
- color="#000000">After
+</p><p style="line-height: 100%;"><font color="#800000"><font color="#000000">After
 <font color="#000000">the <span style="font-weight: bold;">AVS</span>
-module <font color="#000000">read
-fields </font>has </font>read in the data, the content of this
+module <font color="#000000">&ldquo;read
+fields&rdquo; </font>has </font>read in the data, the
+content of this
 file is listed in a separate <span style="font-weight: bold;">AVS</span>
 window where each quantity is represented by its name and output time.</font>
-</font></p>
-<p style="line-height: 100%;">With parallel runs each PE outputs the
+</font></p><p style="line-height: 100%;">With
+parallel runs each PE outputs the
 volume data of its subdomain to a separate file with the name
 PLOT3D_DATA_&lt;processor-Id&gt;,
@@ -159,12 +140,9 @@
 PLOT3D_DATA_0000). These files are not suitable for&nbsp; <b>AVS</b>,
 but after the end of a run they can be combined to one file readable by
-<span style="font-weight: bold;">AVS</span>. This is done via a
+<span style="font-weight: bold;">AVS</span>. This is
+done via a
 further output command in the configuration file: </p>
-<ul>
-  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
- style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] &amp;&amp; combine_plot_fields.x</font></pre>
-</ul>
-<p style="line-height: 100%;">The program <tt><font
- style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt>
+<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] &amp;&amp; combine_plot_fields.x</font></pre></ul>
+<p style="line-height: 100%;">The program <tt><font style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt>
 collects the data from the individual processor files and outputs it
 into the local file <tt><font style="font-size: 10pt;" size="2">PLOT2D_DATA</font></tt>
@@ -176,30 +154,14 @@
 protocol, even if no files were found (i.e. the output command
 may remain in the configuration file, even if no appropriate files
-are 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>
-</p>
-<p style="line-height: 100%;">&nbsp;<b>Note:</b> <span
- style="font-weight: bold;">AVS</span> can process 64 arrays at maximum
+are 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>
+</p><p style="line-height: 100%;">&nbsp;<b>Note:</b>
+<span style="font-weight: bold;">AVS</span> can
+process 64 arrays at maximum
 in one file (with vector representations even
 only 25). If more arrays should be output, surplus arrays must be
 removed from the fld file (see <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>)
 manually. &nbsp; </p>
-<hr>
-<p style="line-height: 100%;"><br>
-<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 change:&nbsp;</i> 20/04/05
-(SR)</p>
-</body>
-</html>
+<hr><p style="line-height: 100%;"><br>
+<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
+change:&nbsp;</i> $Id$</p>
+</body></html>
