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| 6 | <title>PALM chapter 4.5.5</title> |
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| 8 | <meta name="AUTHOR" content="Siegfried Raasch"> |
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| 19 | <h4 style="line-height: 100%;"><font size="4">4.5.5 Plots of 3d volume |
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| 20 | data with AVS</font></h4> |
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| 21 | <p style="line-height: 100%;">In contrast to the plot output described |
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| 22 | so far, which can be handled more or less automatically, the creation |
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| 23 | of |
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| 24 | plots with <b>AVS</b> requires programming a so-called network by |
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| 25 | using the <span style="font-weight: bold;">AVS</span> network editor |
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| 26 | to design the plot |
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| 27 | layout. Details are not given here because it is assumed that the user |
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| 28 | is familiar with <b>AVS</b>. </p> |
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| 29 | <p style="line-height: 100%;"><font color="#000000">Output of 3d volume |
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| 30 | data requires to set at least two parameters: </font>first, the |
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| 31 | temporal |
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| 32 | interval of the output time (run parameter <a |
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| 33 | href="chapter_4.2.html#dt_do3d"><u>dt_do3d)</u></a><span |
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| 34 | style="text-decoration: none;"> |
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| 35 | and second<span style="text-decoration: none;"></span> |
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| 36 | the names of the quantities for which volume data output is wanted</span><span |
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| 37 | style="text-decoration: none;"><span style="text-decoration: none;"> (<a |
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| 38 | href="chapter_4.2.html#data_output">data_output</a></span></span>).<font |
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| 39 | color="#000000"> </font><font color="#000000"><span |
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| 40 | style="text-decoration: none;"></span></font><font color="#000000"><span |
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| 41 | style="text-decoration: none;"></span><span |
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| 42 | style="text-decoration: none;"></span></font><font color="#800000"> </font>The |
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| 43 | parameter <a href="chapter_4.2.html#nz_do3d">nz_do3d</a> |
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| 44 | can be used to limit data output in vertical direction up to a certain |
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| 45 | grid |
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| 46 | point. If no value has been assigned to <b>data_output</b> or |
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| 47 | if the value given for <b>dt_do3d </b>is |
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| 48 | larger than the simulated time (see <a href="chapter_4.1.html#end_time">end_time</a>), |
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| 49 | <b>then there will be no output!</b> By default, data is output in |
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| 50 | 32-bit real format. Alternatively, for parallel runs, data can also be |
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| 51 | output in compressed format using 32-bit integers. This yields |
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| 52 | a loss of accuracy, but the file size is clearly reduced. The output of |
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| 53 | compressed data is described in more detail in <a |
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| 54 | href="chapter_4.5.6.html">chapter |
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| 55 | 4.5.6</a>. </p> |
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| 56 | <p style="line-height: 100%;">Data, whether compressed or |
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| 57 | uncompressed, is output into the local file <a |
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| 58 | href="chapter_3.4.html#PLOT3D_DATA">PLOT3D_DATA</a>. |
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| 59 | This file must be linked with a permanent file by |
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| 60 | using a file connection statement in the <b>mrun</b> configuration |
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| 61 | file (see e.g. <a href="chapter_3.2.html">chapter |
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| 62 | 3.2</a>). At the end of the run the local file is copied to this |
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| 63 | file. Additionally, mrun creates a file containing some coordinate |
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| 64 | informations about the 3d data, which also has to be copied. The |
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| 65 | statements can look like this: </p> |
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| 66 | <ul> |
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| 67 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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| 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> |
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| 69 | </ul> |
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| 70 | <p style="line-height: 100%;">If the respective <b>mrun</b> call is |
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| 71 | like</p> |
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| 72 | <ul> |
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| 73 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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| 74 | style="font-size: 10pt;" size="2">mrun -d test -r avs
</font></pre> |
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| 75 | </ul> |
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| 76 | <p style="line-height: 100%;">then the local file <tt><font |
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| 77 | style="font-size: 10pt;" size="2">PLOT3D_DATA</font></tt> |
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| 78 | is copied to the permanent file <tt><font style="font-size: 10pt;" |
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| 79 | size="2">~/PLOT/test/test_avs</font></tt> . |
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| 80 | However, the character string <tt><font style="font-size: 10pt;" |
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| 81 | size="2">avs</font></tt> |
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| 82 | activating the file connection staement (see third column of the |
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| 83 | statement) must be given in the <b>mrun</b> call as argument of the |
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| 84 | option -r (and/or -o). <span style="text-decoration: none;">If t</span>his |
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| 85 | is forgotten by mistake, the model outputs the data to the local |
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| 86 | file, but this is not copied to the permanent file and thus the data |
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| 87 | are not available for the user after the run has finished.<br> |
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| 88 | </p> |
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| 89 | <p style="line-height: 100%;">The created data file can be used as |
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| 90 | input file for the plot software <span style="font-weight: bold;">AVS</span> |
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| 91 | although for parallel runs another step is necessary which is |
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| 92 | described at the end of this chapter. However, after starting <b>AVS</b> |
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| 93 | (by executing the command avs), these data file is not read |
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| 94 | immediately<font color="#000000">. First, the user has to load a |
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| 95 | suitable network (created by the |
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| 96 | network editor). This module usually contains the module</font> read |
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| 97 | field, which requires an input |
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| 98 | file in the so-called "fld-format", which in turn refers to the two |
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| 99 | files |
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| 100 | specified above (containing the volume data and coordinate |
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| 101 | informations) and describes their exact structure. This fld file is |
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| 102 | also generated by PALM by creating two different |
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| 103 | local files with the names <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a> |
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| 104 | and <a href="chapter_3.4.html#PLOT3D_FLD_COOR">PLOT3D_FLD_COOR</a>, |
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| 105 | which must be combined into one file by a so-called <a |
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| 106 | href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#chapter6.2">output |
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| 107 | command</a>: </p> |
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| 108 | <ul> |
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| 109 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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| 110 | style="font-size: 10pt;" size="2">OC:[[ -f PLOT3D_FLD ]] && cat PLOT3D_FLD_COOR >> PLOT3D_FLD</font></pre> |
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| 111 | </ul> |
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| 112 | <p style="line-height: 100%;">The new file PLOT3D_FLD also needs a file |
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| 113 | connection statement: </p> |
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| 114 | <ul> |
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| 115 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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| 116 | style="font-size: 10pt;" size="2">PLOT3D_FLD out:loc:tr avs ~/PLOT/$fname _fld fld</font></pre> |
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| 117 | </ul> |
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| 118 | <p style="line-height: 100%;">The above <b>mrun </b>call |
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| 119 | then copies the local file <tt><font style="font-size: 10pt;" size="2">PLOT3D_FLD</font></tt> |
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| 120 | to the permanent file <tt><font style="font-size: 10pt;" size="2">~/PLOT/test/test_fld.fld</font> |
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| 121 | </tt><font face="Thorndale, serif">.</font> In this case the entry |
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| 122 | <tt><font style="font-size: 10pt;" size="2">fld</font></tt> |
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| 123 | in the sixth column of the file connection statement is |
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| 124 | very important because this ensures that the permanent file name gets |
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| 125 | the suffix <tt><font style="font-size: 10pt;" size="2">.fld</font></tt> |
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| 126 | ". The <span style="font-weight: bold;">AVS</span> |
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| 127 | module read field expects all files to have this suffix. (Note: With |
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| 128 | this file |
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| 129 | connection statements files with cycle numbers receive the names <tt><font |
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| 130 | style="font-size: 10pt;" size="2">
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| 131 | _fld.<number of cycle>.fld</font></tt><font |
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| 132 | style="font-size: 10pt;" size="2"> |
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| 133 | </font>".) </p> |
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| 134 | <p style="line-height: 100%;"><font color="#000000">The file |
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| 135 | connection statements must guarantee that all three permanent files |
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| 136 | (volume |
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| 137 | data, coordinates, fld file) lie in the same directory. The names of |
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| 138 | the volume data file and coordinate file may not be changed after |
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| 139 | creation of the files, since they are registered in the fld file and |
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| 140 | otherwise cannot be found </font>by the "read field" module. Sometimes |
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| 141 | it may happen<font color="#000000"> |
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| 142 | that incorrect file names are registered into the fld file. In such |
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| 143 | cases the user must edit and correct the fld file accordingly. </font> |
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| 144 | </p> |
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| 145 | <p style="line-height: 100%;"><font color="#800000"><font |
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| 146 | color="#000000">After |
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| 147 | <font color="#000000">the <span style="font-weight: bold;">AVS</span> |
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| 148 | module <font color="#000000">read |
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| 149 | fields </font>has </font>read in the data, the content of this |
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| 150 | file is listed in a separate <span style="font-weight: bold;">AVS</span> |
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| 151 | window where each quantity is represented by its name and output time.</font> |
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| 152 | </font></p> |
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| 153 | <p style="line-height: 100%;">With parallel runs each PE outputs the |
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| 154 | volume data of its subdomain to a separate file with the name |
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| 155 | PLOT3D_DATA_<processor-Id>, |
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| 156 | whereby <processor-Id> is a four digit number (e.g. |
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| 157 | PLOT3D_DATA_0000). These files are not suitable for <b>AVS</b>, |
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| 158 | but after the end of a run they can be combined to one file readable by |
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| 159 | <span style="font-weight: bold;">AVS</span>. This is done via a |
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| 160 | further output command in the configuration file: </p> |
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| 161 | <ul> |
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| 162 | <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font |
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| 163 | style="font-size: 10pt;" size="2">OC:[[$ ( echo $localhost | cut -c1-3 ) = ibmh ]] && combine_plot_fields.x</font></pre> |
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| 164 | </ul> |
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| 165 | <p style="line-height: 100%;">The program <tt><font |
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| 166 | style="font-size: 10pt;" size="2">combine_plot_fields.x</font></tt> |
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| 167 | collects the data from the individual processor files and outputs it |
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| 168 | into the local file <tt><font style="font-size: 10pt;" size="2">PLOT2D_DATA</font></tt> |
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| 169 | which can be processed by <span style="font-weight: bold;">AVS</span>. |
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| 170 | Using this call, possibly existing |
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| 171 | files of 2d cross sections (xy, xz, yz) are |
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| 172 | also combined. The tool writes |
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| 173 | informative messages about the actions accomplished into the job |
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| 174 | protocol, even if no files were found (i.e. the output command |
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| 175 | may remain in the configuration file, even if no appropriate files |
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| 176 | are created during the simulation). <span |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 183 | style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span><br> |
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| 184 | </p> |
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| 185 | <p style="line-height: 100%;"> <b>Note:</b> <span |
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| 186 | style="font-weight: bold;">AVS</span> can process 64 arrays at maximum |
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| 187 | in one file (with vector representations even |
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| 188 | only 25). If more arrays should be output, surplus arrays must be |
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| 189 | removed from the fld file (see <a href="chapter_3.4.html#PLOT3D_FLD">PLOT3D_FLD</a>) |
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| 190 | manually. </p> |
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| 191 | <hr> |
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| 192 | <p style="line-height: 100%;"><br> |
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| 193 | <font color="#000080"><font color="#000080"><a href="chapter_4.5.4.html"><font |
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| 194 | color="#000080"><img src="left.gif" name="Grafik1" align="bottom" |
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| 195 | border="2" height="32" width="32"></font></a><a href="index.html"><font |
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| 196 | color="#000080"><img src="up.gif" name="Grafik2" align="bottom" |
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| 197 | border="2" height="32" width="32"></font></a><a |
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| 198 | href="chapter_4.5.6.html"><font color="#000080"><img src="right.gif" |
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| 199 | name="Grafik3" align="bottom" border="2" height="32" width="32"></font></a></font></font></p> |
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| 200 | <p style="line-height: 100%;"> <i>Last change: </i> 20/04/05 |
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| 201 | (SR)</p> |
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| 202 | </body> |
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| 203 | </html> |
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