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19<h4 style="line-height: 100%;"><font size="4">4.5.5 Plots of 3d volume
20data with AVS</font></h4>
21<p style="line-height: 100%;">In contrast to the plot output described
22so far, which can be handled more or less automatically, the creation
24plots with <b>AVS</b> requires programming a so-called network by
25using the <span style="font-weight: bold;">AVS</span> network editor
26to design the plot
27layout. Details are not given here because it is assumed that the user
28is familiar with <b>AVS</b>. </p>
29<p style="line-height: 100%;"><font color="#000000">Output of 3d volume
30data requires to set at least two parameters: </font>first, the
32interval 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;">
35and second<span style="text-decoration: none;"></span>
36the 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
43parameter <a href="chapter_4.2.html#nz_do3d">nz_do3d</a>
44can be used to limit data output in vertical direction up to a certain
46point. If no value has been assigned to <b>data_output</b> or
47if the value given for <b>dt_do3d </b>is
48larger 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
5032-bit real format. Alternatively, for parallel runs, data can also be
51output in compressed format using 32-bit integers. This yields
52a loss of accuracy, but the file size is clearly reduced. The output of
53compressed data is described in more detail in <a
54 href="chapter_4.5.6.html">chapter
554.5.6</a>. </p>
56<p style="line-height: 100%;">Data, whether compressed or
57uncompressed, is output into the local file <a
58 href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>.
59This file must be linked with a permanent file by
60using a file connection statement in the <b>mrun</b> configuration
61file (see e.g. <a href="chapter_3.2.html">chapter
623.2</a>). At the end of the run the local file is copied to this
63file. Additionally, mrun creates a file containing some coordinate
64informations about the 3d data, which also has to be copied. The
65statements can look like this: </p>
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>
70<p style="line-height: 100%;">If the respective <b>mrun</b> call is
73  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
74 style="font-size: 10pt;" size="2">mrun -d  test -r “avs”…</font></pre>
76<p style="line-height: 100%;">then the local file <tt><font
77 style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt>
78is copied to the permanent file <tt><font style="font-size: 10pt;"
79 size="2">~/PLOT/test/test_avs</font></tt> .
80However, the character string “<tt><font style="font-size: 10pt;"
81 size="2">avs</font></tt>”
82activating the file connection staement (see third column of the
83statement) must be given in the <b>mrun</b> call as argument of the
84option -r (and/or -o). <span style="text-decoration: none;">If t</span>his
85is forgotten by mistake, the model outputs the data to the local
86file, but this is not copied to the permanent file and thus the data
87are not available for the user after the run has finished.<br>
89<p style="line-height: 100%;">The created data file can be used as
90input file for the plot software <span style="font-weight: bold;">AVS</span>
91although for parallel runs another step is necessary which is
92described at the end of this chapter. However, after starting <b>AVS</b>
93(by executing the command “avs”), these data file is not read
94immediately<font color="#000000">. First, the user has to load a
95suitable network (created by the
96network editor). This module usually contains the module</font> “read
97field”, which requires an input
98file in the so-called "fld-format", which in turn refers to the two
100specified above (containing the volume data and coordinate
101informations) and describes their exact structure. This fld file is
102also generated by PALM by creating two different
103local files with the names <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>
104and <a href="chapter_3.4.html#PLOT3D_FLD_COOR">PLOT3D_FLD_COOR</a>,
105which must be combined into one file by a so-called <a
106 href="">output
107command</a>: </p>
109  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
110 style="font-size: 10pt;" size="2">OC:[[ -f PLOT3D_FLD ]] &amp;&amp; cat PLOT3D_FLD_COOR &gt;&gt; PLOT3D_FLD</font></pre>
112<p style="line-height: 100%;">The new file PLOT3D_FLD also needs a file
113connection statement: </p>
115  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
116 style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr   avs  ~/PLOT/$fname  _fld fld</font></pre>
118<p style="line-height: 100%;">The above <b>mrun </b>call
119then copies the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_FLD</font></tt>
120to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_fld.fld</font>
121</tt><font face="Thorndale, serif">.</font> In this case the entry
122“<tt><font style="font-size: 10pt;" size="2">fld</font></tt>”
123in the sixth column of the file connection statement is
124very important because this ensures that the permanent file name gets
125the suffix ” <tt><font style="font-size: 10pt;" size="2">.fld</font></tt>
126".&nbsp; The <span style="font-weight: bold;">AVS</span>
127module “read field” expects all files to have this suffix. (Note: With
128this file
129connection statements files with cycle numbers receive the names ”<tt><font
130 style="font-size: 10pt;" size="2">…
131_fld.&lt;number of cycle&gt;.fld</font></tt><font
132 style="font-size: 10pt;" size="2">
133</font>".) </p>
134<p style="line-height: 100%;"><font color="#000000">The file
135connection statements must guarantee that all three permanent files
137data, coordinates, fld file) lie in the same directory. The names of
138the volume data file and coordinate file may not be changed after
139creation of the files, since they are registered in the fld file and
140otherwise cannot be found </font>by the "read field" module. Sometimes
141it may happen<font color="#000000">
142that incorrect file names are registered into the fld file. In such
143cases the user must edit and correct the fld file accordingly. </font>
145<p style="line-height: 100%;"><font color="#800000"><font
146 color="#000000">After
147<font color="#000000">the <span style="font-weight: bold;">AVS</span>
148module <font color="#000000">“read
149fields” </font>has </font>read in the data, the content of this
150file is listed in a separate <span style="font-weight: bold;">AVS</span>
151window where each quantity is represented by its name and output time.</font>
153<p style="line-height: 100%;">With parallel runs each PE outputs the
154volume data of its subdomain to a separate file with the name
156whereby &lt;processor-Id&gt; is a four digit number (e.g.
157PLOT3D_DATA_0000). These files are not suitable for&nbsp; <b>AVS</b>,
158but after the end of a run they can be combined to one file readable by
159<span style="font-weight: bold;">AVS</span>. This is done via a
160further output command in the configuration file: </p>
162  <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font
163 style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] &amp;&amp; combine_plot_fields.x</font></pre>
165<p style="line-height: 100%;">The program <tt><font
166 style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt>
167collects the data from the individual processor files and outputs it
168into the local file <tt><font style="font-size: 10pt;" size="2">PLOT2D_DATA</font></tt>
169which can be processed by <span style="font-weight: bold;">AVS</span>.
170Using this call, possibly existing
171files of 2d cross sections (xy, xz, yz) are
172also combined.&nbsp;The tool writes
173informative messages about the actions accomplished into the job
174protocol, even if no files were found (i.e. the output command
175may remain in the configuration file, even if no appropriate files
176are created during the simulation). <span
177 style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><tt><span
178 style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></tt><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><br>
185<p style="line-height: 100%;">&nbsp;<b>Note:</b> <span
186 style="font-weight: bold;">AVS</span> can process 64 arrays at maximum
187in one file (with vector representations even
188only 25). If more arrays should be output, surplus arrays must be
189removed from the fld file (see <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>)
190manually. &nbsp; </p>
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200<p style="line-height: 100%;">&nbsp;<i>Last change:&nbsp;</i> 20/04/05
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