Changeset 336


Ignore:
Timestamp:
Jun 10, 2009 11:19:35 AM (12 years ago)
Author:
raasch
Message:

several small bugfixes; some more dvrp changes

Location:
palm/trunk
Files:
1 added
17 edited

Legend:

Unmodified
Added
Removed
  • palm/trunk/DOC/app/chapter_3.2.html

    r97 r336  
    3232<p style="line-height: 100%;">The following configuration
    3333data
    34 exclusively applies to model runs on the IBM Regatta hanni of the
     34exclusively applies to model runs on the SGI ICE system of the
    3535HLRN when using several processing elements (i.e. for the parallel
    3636version of the model). The proper installation of the model is
     
    38385.0</a>). Furthermore it is supposed that the user is located in
    3939the
    40 directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version/SOURCE</font></tt>
    41 on its local computer. There are the FORTRAN source codes of the
    42 model (<tt><font style="font-size: 10pt;" size="2">*.f90</font></tt>)
    43 as
    44 well as the configuration file (name: <tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>)
    45 and the make file (name: <tt><font style="font-size: 10pt;" size="2">Makefile</font></tt>).
     40directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version</font></tt>
     41&nbsp;on its local computer, where the configuration file (<tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>) should reside.
    4642The configuration file has the following contents (among other things):
    4743<br>&nbsp;
    48 </p><pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">% source_path <i>$HOME/palm/current_version/SOURCE</i></font><br><font style="font-size: 10pt;" size="2">% mainprog <i>palm.f90</i></font><br><font style="font-size: 10pt;" size="2">% use_makefile <i>true</i></font><br><font style="font-size: 10pt;" size="2">% fopts <i>-O3:-g:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:-qarch=pwr4:-qnosave:-qnoescape ibmh parallel<span style="background: transparent none repeat scroll 0% 50%; -moz-background-clip: initial; -moz-background-origin: initial; -moz-background-inline-policy: initial;"></span></i></font><br><font style="font-size: 10pt;" size="2">% lopts <span style="font-style: italic;">-O3:-g:-qrealsize=8:-Q:-q64:-qmaxmem=-1:-qtune=pwr4:-qarch=pwr4:-qnosave:-qnoescape:-lesslsmp ibmh parallel</span></font><br><font style="font-size: 10pt;" size="2">#</font><br><font style="font-size: 10pt;" size="2">EC:[[ \$locat = execution]] &amp; &amp; <i>cat </i>RUN_CONTROL </font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font style="font-size: 10pt;" size="2"> in:job:npe d3# ~/palm/current_version/JOBS/$fname/INPUT _p3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#RUN_CONTROL"><font style="font-size: 10pt;" size="2">RUN_CONTROL</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _rc</font><br><a href="chapter_3.4.html#HEADER"><font style="font-size: 10pt;" size="2">HEADER</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3# ~/palm/current_version/JOBS/$fname/MONITORING _header</font><br><a href="chapter_3.4.html#PLOT1D_PAR"><font style="font-size: 10pt;" size="2">PLOT1D_PAR</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr_par</font><br><a href="chapter_3.4.html#PLOT1D_DATA"><font style="font-size: 10pt;" size="2">PLOT1D_DATA</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr_in</font></pre>
     44</p><pre style="line-height: 100%;"><font style="font-size: 10pt;" size="2">%mainprog          palm.f90<br>%base_directory    $HOME/palm/current_version<br>%base_data         ~/palm/current_version/JOBS<br>%source_path       $base_directory/trunk/SOURCE<br>#<br></font><font style="font-size: 10pt;" size="2">%fopts      -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-convert:little_endian  lcsgih parallel<br></font><font style="font-size: 10pt;" size="2">%lopts      -g:-w:-xT:-O3:-cpp:-r8:-ftz:-fno-alias:-no-prec-div:-no-prec-sqrt:-ip:-nbs:-Vaxlib                 lcsgih parallel</font><font style="font-size: 10pt;" size="2"><br>#</font><br><font style="font-size: 10pt;" size="2">EC:[[ \$locat = execution]] &amp; &amp; <i>cat </i>RUN_CONTROL </font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#PARIN"><font style="font-size: 10pt;" size="2">PARIN</font></a><font style="font-size: 10pt;" size="2"> in:job  d3#  $base_data/$fname/INPUT _p3d</font><br><font style="font-size: 10pt;" size="2">#</font><br><a href="chapter_3.4.html#RUN_CONTROL"><font style="font-size: 10pt;" size="2">RUN_CONTROL</font></a><font style="font-size: 10pt;" size="2"> out:loc:tr d3#   $base_data/$fname/MONITORING _rc</font><br><a href="chapter_3.4.html#HEADER"><font style="font-size: 10pt;" size="2">HEADER</font></a><font style="font-size: 10pt;" size="2">      out:loc:tr d3#   $base_data/$fname/MONITORING _header</font><span style="font-family: mon;"><span style="text-decoration: underline;"><br></span><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></span><font style="font-size: 10pt;" size="2">   out:loc:tr pr# ~/palm/current_version/JOBS/$fname/OUTPUT _pr  nc</font></pre>
    4945<p style="line-height: 100%;"><font face="Thorndale, serif">The first
    5046five lines specify values of
     
    5652variable. Again separated by blank t<font face="Thorndale, serif">he
    5753so-called validity domain</font> can be indicated (later more).
    58 With the first three variables <b>mrun</b> gets to know in
     54With the first four variables <b>mrun</b> gets to know in
    5955which
    6056directory the source code lies (</font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">),
    61 the file name of the main program (</font><tt><i><font face="Thorndale, serif">mainprog</font></i></tt><font face="Thorndale, serif">)
    62 and that the <font face="Thorndale, serif">make mechanism
    63 should be
    64 used </font>for compiling (</font><tt><font face="Thorndale, serif"><i>use_makefile
    65 =</i> <i>true</i></font></tt><font face="Thorndale, serif">). <b>mrun
     57the file name of the main program (</font><tt><i><font face="Thorndale, serif">mainprog</font></i></tt><font face="Thorndale, serif">)</font><font face="Thorndale, serif">. Also, two variables are defined which contain path informations used later in the file (<span style="font-style: italic;">base_directory</span>, <span style="font-style: italic;">base_data</span>).&nbsp; <b>mrun
    6658</b>needs these information, <font color="#000000">because
    6759for each
    68 model run the executable is created by compiling the source files.</font>
     60model run the executable is created by compiling the respective source file.</font>
    6961Normally, only the main program (palm.f90) will be compiled while all
    7062other object files are just linked. These object files have already
     
    8476interpret these colons as blanks (2 colons written one behind the
    8577other will be interpreted as a colon). Thus in the example above</font> fopts
    86 has the value<tt><font face="Thorndale, serif"> </font></tt>&ldquo;<font style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3
    87 -g
    88 -qrealsize=8 -Q -q64 -qmaxmem=-1 -qtune=pwr4 -qarch=pwr4 -qnosave
    89 -qnoescape</i></font><tt><i><font face="Thorndale, serif"><font color="#000000">&rdquo;</font></font></i></tt><font face="Thorndale, serif"><font color="#000000">.
    90 Thus a PALM executable is generated using high level optimization (</font></font><font color="#000000"><span style="font-style: italic; font-family: monospace;">-O3</span></font><font face="Thorndale, serif"><font color="#000000">).</font></font><font color="#000000"><font face="Thorndale, serif">
     78has the value<tt><font face="Thorndale, serif"> </font></tt>&ldquo;<tt>-g -w -xT -O3 -cpp -r8 -ftz -fno-alias -no-prec-div -no-prec-sqrt -ip -nbs -convert little_endian<i><font face="Thorndale, serif"><font color="#000000">&rdquo;</font></font></i></tt><font face="Thorndale, serif"><font color="#000000">.
     79Thus a PALM executable is generated using high level optimization (</font></font><font color="#000000"><span style="font-family: monospace;">-O3</span></font><font face="Thorndale, serif"><font color="#000000">).</font></font><font color="#000000"><font face="Thorndale, serif">
    9180For all other options
    92 see the compiler manual on the IBM (</font><font size="2"><font face="Cumberland, monospace">man</font></font></font><tt><font color="#000000">
    93 <font size="2"><font face="Cumberland, monospace">f90</font></font></font></tt><font face="Thorndale, serif"><font color="#000000">).
     81see the compiler manual on the SGI (</font><font size="2"><font face="Cumberland, monospace">man</font></font></font><tt><font color="#000000"> <span style="font-family: Cumberland,monospace;">ifort</span></font></tt><font face="Thorndale, serif"><font color="#000000">).
    9482Additional libraries
    95 which the compiler should use are described by
     83which the compiler should use may have to be given by
    9684the environment variable </font></font><tt><font size="2"><font face="Cumberland, monospace"><font color="#000000">lopts</font></font></font></tt><font color="#000000">
    97 <font face="Thorndale, serif">(loader options).</font></font><font color="#800000">
    98 </font><font face="Thorndale, serif"><font color="#000000">Here you
    99 have to indicate a special IBM library (ESSL, </font></font>Engineering
    100 and Scientific Subroutine Library)<font face="Thorndale, serif"><font color="#000000">.</font><font color="#800000">
    101 </font>On the
    102 IBM-Regatta, all compiler options have also to be given to the linker.</font><font color="#000000"><font face="Thorndale, serif"> </font></font>
     85<font face="Thorndale, serif">(loader options).</font></font><font color="#000000"><font face="Thorndale, serif"> </font></font>
    10386</p><p style="line-height: 100%;"><font color="#000000">Compiler and
    10487loader options usually differ from computer to computer. In the
     
    11194the so-called validity domain which follows in the appropriate
    11295variable lines after the value of variables.</font></font><font color="#000000">
    113 In the example above the entry &ldquo;</font><font color="#000000"><font style="font-size: 11pt; font-style: italic; font-family: monospace;" size="2">ibmh</font></font><tt><font color="#000000"><span style="font-style: italic; font-family: monospace;">
     96In the example above the entry &ldquo;</font><font color="#000000"><font style="font-size: 11pt; font-style: italic; font-family: monospace;" size="2">lcsgih</font></font><tt><font color="#000000"><span style="font-style: italic; font-family: monospace;">
    11497</span></font><font color="#000000"><i><font style="font-size: 11pt;" size="2">parallel</font></i></font></tt><font color="#000000">&rdquo;
    11598stands for </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000">
    11699and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000">.
    117100These lines only become active if a run on the parallel computer of
    118 the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">ibmh</font></i></tt><font color="#000000">)
     101the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">lcsgih</font></i></tt><font color="#000000">)
    119102on several <font color="#000000">(</font><tt><i><font style="font-size: 10pt;" size="2"><font color="#000000">parallel</font></font></i></tt><font color="#000000">)
    120103</font>processors is started. The activation takes place when you
     
    124107(see below). This way, the validity domain can be limited also for all
    125108other environment-variables. If no validity domain
    126 is indicated then the given values of variables are valid on all
     109is indicated then the given values of variables are valid for all
    127110computers. </font>
    128111</p><p style="line-height: 100%;">After the value
     
    208191indicated within the mrun <b>call</b> by the option <a href="http://www.muk.uni-hannover.de/institut/software/mrun_beschreibung.html#Opt-r">-r</a>.
    209192Thus a call of the form </p>
    210 <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - h ibmh -d abcde -r d3</font></pre></ul>
     193<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - h lcsgih -d abcde -r "d3#"</font></pre></ul>
    211194<p style="line-height: 100%;">would lead to the fact that
    212195the input
     
    217200these files are to be copied of <b>mrun</b> then the call
    218201must be</p>
    219 <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -r "d3 pr"</font></pre></ul>
     202<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h lcsgih -d abcde -r "d3# pr#"</font></pre></ul>
    220203<p style="line-height: 100%;">Instead of the option -r you
    221204can
     
    225208file all file connection statements are actually executed then
    226209the call must be: </p>
    227 <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h ibmh -d abcde -i d3 -o "d3 pr"</font></pre></ul>
     210<ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun -h lcsgih -d abcde -i "d3#" -o "d3# pr#"</font></pre></ul>
    228211<p style="line-height: 100%;"><font color="#000000">The
    229212names of the
     
    258241<p style="line-height: 100%;">The example configuration
    259242file also
    260 instructs <b>mrun</b> to copy four output files of the
     243instructs <b>mrun</b> to copy three output files of the
    261244model to
    262245appropriate permanent files of the user at the end of the run.
     
    266249are located, as well as a file with data of horizontally averaged
    267250vertical profiles
    268 (<tt><a href="chapter_3.4.html#PLOT1D_DATA">PLOT1D_DATA</a></tt>)
    269 and an associated parameter file (<tt><a href="chapter_3.4.html#PLOT1D_PAR">PLOT1D_PAR</a></tt>),
    270 which can be used as input files for the plot program <a href="http://www.muk.uni-hannover.de/institut/software/profil_beschreibung.html">profil</a>.
     251(<tt><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></tt>).
    271252A model run does not presuppose neither the file connection statements
    272253for
     
    283264execution of a
    284265model run
    285 on several processors on the IBM Regatta "hanni" of the HLRN must be
     266on several processors on the SGI ICE of the HLRN must be
    286267supplemented by the following options in each case: </p>
    287 <ul> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - K parallel -X &hellip; -t &hellip; -m &hellip;</font></pre></ul>
     268<ul style="font-family: monospace;"> <pre style="margin-bottom: 0.5cm; line-height: 100%;"><font style="font-size: 10pt;" size="2">mrun - K parallel -X ... -T ... -t ... -m ---</font></pre></ul>
    288269<p style="line-height: 100%;">Only the indication of <tt><font style="font-size: 11pt;" size="2">-K
    289270parallel</font></tt> causes the parallel execution of the
     
    294275option <tt><font style="font-size: 10pt;" size="2">-X</font>
    295276</tt><font size="2">(</font><font style="font-size: 10pt;" size="2">e.g.
    296 </font><tt><font style="font-size: 10pt;" size="2">-X
    297 4</font></tt><font size="2">).</font>
     277</font><tt><font style="font-size: 10pt;" size="2">-X 32</font></tt><font size="2">) and the number of tasks (processors) on onde node have to be given by option -T.</font>
    298278In each case the permitted CPU time in seconds and the required memory
    299279size in MB must be indicated by the options <tt><font style="font-size: 11pt;" size="2">-t</font></tt>
    300280and <tt><font style="font-size: 11pt;" size="2">-m</font></tt>,
    301281respectively<font face="Thorndale, serif">.</font>
    302 Alternatively, these can be set by the appropriate environment
     282Alternatively, memory and cpu-time demands can be set by the appropriate environment
    303283variables in the configuration file: </p>
    304 <blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%
    305 memory&nbsp; <i>1630</i> ibmh parallel</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><br> </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%
    306 cputime <i>1000</i> ibmh parallel</font></font></tt></blockquote>
     284<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%memory&nbsp; <i>1500</i> lcsgih parallel</font></font></tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace"><br> </font></font><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%cputime <i>1000</i> lcsgih parallel</font></font></tt></blockquote>
    307285<p style="line-height: 100%;">The values indicated there
    308286can be
    309287overridden with the values of the options <tt><font style="font-size: 10pt;" size="2">-t</font></tt>
    310288and/or <tt><font style="font-size: 10pt;" size="2">-m</font></tt>,
    311 respectivly. </p>
     289respectivly.</p><p style="line-height: 100%;"><span style="font-weight: bold;">Warning: When changing the coniguration file, please never use the TAB key!</span> </p>
    312290<hr><p style="line-height: 100%;"><br>
    313291<font color="#000080"><font color="#000080"><a href="chapter_3.1.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_3.3.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%;"><i>Last change:&nbsp;</i>
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    r291 r336  
    1066310663
    1066410664
    10665  <tr>
     10665 <tr><td style="vertical-align: top;"><a name="groundplate_color"></a><span style="font-weight: bold;">groundplate_color</span></td><td style="vertical-align: top;">R(3)</td><td style="vertical-align: top;"><span style="font-style: italic;">0.0, 0.6, 0.0</span></td><td style="vertical-align: top;">Color of the ground plate.<br><br>The color is given in RGB (red/green/blue) portions. The default color of the ground plate is green.</td></tr><tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="isosurface_color"></a>isosurface_color</span></td><td style="vertical-align: top;">R(3,10)</td><td style="vertical-align: top;"><span style="font-style: italic;">0.9, 0.9, 0.9</span><br style="font-style: italic;"><span style="font-style: italic;">0.8, 0.1, 0.1</span><br style="font-style: italic;"><span style="font-style: italic;">0.1, 0.1, 0.8<br>0.1, 0.8, 0.1<br>0.6, 0.1, 0.1<br>0.1, 0.1, 0.6<br>0.1, 0.6, 0.1<br>0.4, 0.1, 0.1<br>0.1, 0.1, 0.4<br>0.1, 0.4, 0.1</span></td><td style="vertical-align: top;">Color of the isosurface(s).<br><br>Colors
     10666are given in RGB (red/green/blue) portions. By default, the first
     10667isosurface has a gray color, the second a red color, the third a blue
     10668color, etc.</td></tr><tr>
    1066610669
    1066710670
     
    1074210745cross sections see <a href="#data_output">data_output</a>.
    1074310746The theshold value for which the isosurface is
    10744 to be created can be defined with parameter <a href="#threshold">threshold</a>.<br>
     10747to be created can be defined with parameter <a href="#threshold">threshold</a>. The isosurface color is controlled by parameter <a href="#isosurface_color">isosurface_color</a>.<br>
    1074510748
    1074610749
     
    1078210785
    1078310786
    10784 The declaration color charts to be
     10787The declaration of color charts to be
    1078510788used still have to be given "manually" in subroutine <a href="chapter_3.4.html#user_dvrp_coltab"><span style="font-family: monospace;">user_dvrp_coltab</span></a>
    10786 (file <tt><font style="font-size: 11pt;" size="2">user_interface.f90</font></tt>).&nbsp;
    10787       <br>
    10788 
    10789 
    10790 A change of particle colors and/or particle diameters (e.g.
    10791 according
    10792 to the local characteristics of the flow field) to be used for the
    10793 visualization, must be carried out by adding respective code extensions
    10794 to <a href="chapter_3.4.html#user_particle_attributes"><tt><font style="font-size: 11pt;" size="2">user_particle_attributes</font></tt></a>
    10795 (in file <tt><font style="font-size: 11pt;" size="2">user_interface.f90</font></tt>).&nbsp;</td>
     10789(file <tt><font style="font-size: 11pt;" size="2">user_dvrp_coltab.f90</font></tt>).&nbsp;
     10790
     10791
     10792</td>
    1079610793
    1079710794
     
    1106711064
    1106811065
    11069  </tr>
     11066 </tr><tr><td style="vertical-align: top;"><span style="font-weight: bold;"><a name="topography_color"></a>topography_color</span></td><td style="vertical-align: top;">R(3)</td><td style="vertical-align: top;"><span style="font-style: italic;">0.8, 0.7, 0.6</span></td><td style="vertical-align: top;">Color of the topography.<br><br>The color is given in RGB (red/green/blue) portions. If topograpy is switched on (see <a href="chapter_4.1.html#topography">topography</a>), its default color is a kind of gray.</td></tr>
    1107011067
    1107111068
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    r62 r336  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
    3 <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
    4 chapter 4.5.7</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041029;14344622"> <meta name="CHANGED" content="20050119;9531085"> <meta name="KEYWORDS" content="parallel LES model"> <style>
     3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 4.5.7</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041029;14344622"> <meta name="CHANGED" content="20050119;9531085"> <meta name="KEYWORDS" content="parallel LES model"> <style>
    54<!--
    65@page { size: 21cm 29.7cm }
    76-->
    87</style></head>
    9 
    108<body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.7
    119Plots of
    1210isosurfaces, 2d cross sections and particles with dvrp</font></h4>
    13 <p style="line-height: 100%;">The <span style="font-weight: bold;">dvrp</span>
    14 software developed by the RRZN
    15 (Stephan Olbrich, Carsten Chmielewski) allows a creation of plot
    16 sequences with PALM,
    17 which can be animated via a special plugin for internet browsers. With
    18 suitable graphic hardware even stereoscopic views are
    19 possible. <br>
     11<p style="line-height: 100%;"><span style="font-weight: bold;">Preliminary note:</span></p><p style="line-height: 100%;">Usage of the <span style="font-weight: bold;">dvrp</span>-software requires installation of additional software components (dvrp-library, streaming-server, browser-plugin) which are <span style="font-weight: bold;">not</span>
     12part of the PALM distribution. Currently (May 2009), this software is
     13only available on the the HLRN/IMUK system and partly on RIAM's NEC
     14system. If you are interested in using <span style="font-weight: bold;">dvrp</span> on your system, please contact the PALM developers.</p><br><span style="font-weight: bold;">General remarks:</span><p style="line-height: 100%;">The <span style="font-weight: bold;">dvrp</span>
     15software was originally developed by the RRZN
     16(Stephan Olbrich, Carsten Chmielewski) and is meanwhile continuosly developed and improved under the name <span style="font-weight: bold;">dsvr</span> by the University of D&uuml;sseldorf (Prof. Stephan Olbrich, see webpage of the <a href="http://www.dsvr-software.de/">dsvr-software</a>). It allows to create 3d-animations with PALM,
     17which can be displayed via a special plugin for internet browsers. With
     18suitable graphic hardware (e.g. NVIDIA quattro FX cards) even stereoscopic views are
     19possible.</p><p style="line-height: 100%;">
    2020In contrast to the other kinds of visualization output realized
    21 in PALM (<b>profil</b>, <b>iso2d</b> and <b>AVS</b>),
     21in PALM (1d-, 2d-, 3d-NetCDF output),
    2222where the data
    23 is output in a format suitable for the plot software, the creation of
    24 plots via <span style="font-weight: bold;">dvrp</span>
     23is output in a format suitable for many kinds of post-processing graphic software, the creation of animations via <span style="font-weight: bold;">dvrp</span>
    2524software is
    2625integrated in PALM, i.e. respective routines are directly called within
     
    4645the main focus of the BMBF project "Application of
    4746tele-immersion in long-distance networks" (2001-2002),
    48 which was a joint project of RRZN, ZIB and IMUK. This work is currently
    49 continued by RRZN in the new DFG-funded project "EVITA - Untersuchung
     47which was a joint project of RRZN, ZIB and IMUK. This work was
     48continued by RRZN in the DFG-funded project "<a href="http://www.rrzn.uni-hannover.de/evita.html">EVITA</a> - Untersuchung
    5049effizienter
    51 <br>Methoden zur visuellen und haptischen tele-immersiven
     50Methoden zur visuellen und haptischen tele-immersiven
    5251Exploration
    53 <br>komplexer Volumen- und Str&ouml;mungsdaten aus
     52komplexer Volumen- und Str&ouml;mungsdaten aus
    5453parallelisierten,
    55 <br>dynamischen 3D-Simulationen" (2005-2007). </p>
    56 <p style="line-height: 100%;">The calls of the <span style="font-weight: bold;">dvrp</span> routines are
     54dynamischen 3D-Simulationen" (2005-2007). </p>
     55<p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold;">Using dvrp with PALM:</span></p><p style="line-height: 100%;">The calls of the <span style="font-weight: bold;">dvrp</span> routines are
    5756contained within a
    5857PALM software package (see chapter <a href="chapter_3.7.html">3.7</a>).
    59 To use this package, the additional option <tt><font size="2">-p
    60 &ldquo;dvrp_graphics&rdquo;</font></tt>
    61 has to be given in the <b>mrun</b> call. This
     58To use this package, the additional option<tt style="font-family: monospace;"> </tt><font style="font-family: Courier New,Courier,monospace;" size="2">-p
     59<span style="font-family: Helvetica,Arial,sans-serif;">&ldquo;</span>dvrp_graphics<span style="font-family: Helvetica,Arial,sans-serif;">&rdquo;</span></font><span style="font-family: monospace;">
     60</span>has to be given in the <b>mrun</b> call. This
    6261automatically links the
    6362required libraries.
     
    6766graphic
    6867data are not output to local files but directly to a special remote
    69 computer which is defined via the package parameter <a href="chapter_4.2.html#dvrp_host">dvrp_host</a>.
    70 The
    71 default values of the dvrp parameters are cause the output to be
    72 directed to a so-called streaming server at the
     68computer which is defined via the package parameter <a href="chapter_4.2.html#dvrp_host">dvrp_host</a>. If the default values of the dvrp parameters are used, data are send to a so-called <span style="font-style: italic;">streaming server</span> at the
    7369RRZN. Apart from graphic data an additional html file is created, which
    74 can be used by an internet browser to view the data (a special <span style="font-weight: bold;">dvrp</span> plugin is
    75 needed). </p>
    76 <p style="line-height: 100%;">Since July 2001, the basic
    77 functionality
    78 of the <span style="font-weight: bold;">dvrp</span>
    79 software is
    80 installed in PALM and steerable via the
    81 package parameters. However, some code modifications may still need to
    82 be done by the user (e.g. in
    83 the subroutine <tt><font style="font-size: 10pt;" size="2">plot_dvrp</font></tt>
    84 in order to define suitable color tables).
    85 <br>For further detailed information please ask Siegfried Raasch.
    86 </p>
     70can be opened by an internet browser to view the data (a special <span style="font-weight: bold;">dvrp</span> plugin is required for this).</p><p style="line-height: 100%;"></p><p style="line-height: 100%;"><span style="font-weight: bold;">Quickstart guide for using dvrp on the HLRN/IMUK-System (May 2009):</span> </p>
     71<ol><li>
     72Add the following define statements for environment variables to the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>):<br><br><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"> &nbsp; &nbsp;%dvr_inc&nbsp;&nbsp;
     73-I/home/h/niksiraa/dvr_mvapich2/lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
     74&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; lcsgih parallel</span><br style="font-family: Courier New,Courier,monospace;"><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;%dvr_lib&nbsp;&nbsp;&nbsp;-L/home/h/niksiraa/dvr_mvapich2/lib:-lDVRP2:-lftp&nbsp; &nbsp; lcsgih
     75parallel</span><br><br><br></li><li>Add the dvrp-steering parameters to your NAMELIST-parameter file, e.g.<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp;&amp;d3par &nbsp;end_time = 3600.0,<br>&nbsp; ... &nbsp; &nbsp; /<br><br>&nbsp;&amp;dvrp_graphics_par &nbsp; dvrp_username = '&lt;replace by your IMUK username&gt;',<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; dvrp_host = '130.75.105.2',<br>&nbsp;
     76&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
     77dvrp_directory = '&lt;replace by a name of your choice&gt;', ... /<br></span><br>For other dvrp-parameters see <a href="chapter_4.2.html#Paketparameter">chapter 4.2</a>. An example parameter file can be found in directory <span style="font-family: Courier New,Courier,monospace;">..../trunk/EXAMPLES/dvr_building</span>.<span style="font-family: Courier New,Courier,monospace;"><br><br></span></li><li>Submit the job&nbsp; with <span style="font-weight: bold;">mrun</span>-command<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mrun .... -p dvrp_graphics ....</span><br><br></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">After the job has finished, the dvrp-output can be found on the IMUK-cluster in a subdirectory under <span style="font-family: Courier New,Courier,monospace;">/data/raasch/Dvrp_daten</span>. The name of the subdirectory is determined by the dvrp-parameter <a href="chapter_4.2.html#dvrp_directory">dvrp_directory</a> (see above), i.e. if the user has set <span style="font-family: Courier New,Courier,monospace;">dvrp_directory</span> = <span style="font-style: italic;">'movie_1'</span>, the dvrp-data are stored under&nbsp;<span style="font-family: Courier New,Courier,monospace;">/data/raasch/Dvrp_daten/movie_1</span>.<br><br></span></span></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">Change to this subdirectory (e.g. </span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"><span style="font-family: Courier New,Courier,monospace;">/data/raasch/Dvrp_daten/movie_1</span></span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">) and enter the command<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;process_dvr_output</span><br><br>It will create a file with name <span style="font-family: Courier New,Courier,monospace;">all_streams_streaming.html</span>.<br><br></span></span></li><li><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;">Call the opera-browser (i.e. enter the command <span style="font-family: Courier New,Courier,monospace;">opera</span>) and open the file </span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"><span style="font-family: Courier New,Courier,monospace;">all_streams_streaming.html</span>.</span></span><span style="font-family: Courier New,Courier,monospace;"><span style="font-family: Times New Roman,Times,serif;"></span><br><br></span>A complete example parameter file for ... can be found under &nbsp;.../trunk/.....<br></li></ol><span style="font-weight: bold;">Further features:<br></span>The script<span style="font-family: Courier New,Courier,monospace;"> process_dvr_output </span>has additional options:<br><br><span style="font-weight: bold; font-family: Courier New,Courier,monospace;">-s</span> &nbsp; &nbsp; : <span style="font-weight: bold;">create sequence output</span>.
     78All streams (and static scenes) are collected to one sequence (one
     79static scene), which can be displayed with a browser without using the
     80streaming server (the so-called sequence mode). This allows e.g. to
     81show animations on a notebook without beeing connected to the internet.
     82When the script is called with this option, the sequence is generated
     83in subdirectory sequence_data. Copy this subdirectory and the file
     84all_streams_sequence.html to a directory on your local computer and
     85open the file all_streams_sequence.html with your browser. For this,
     86you will need to install the the dvr-plugin (see webpage of the <a href="http://www.dsvr-software.de/">dsvr-software</a>) on your local computer, which is also available for Windows.<br><br><span style="font-weight: bold;">-a</span> &nbsp; &nbsp; &nbsp;: <span style="font-weight: bold;">acceleration factor</span>. If, in case of sequence mode, the performance of the animation is to slow, you can accelerate it. E.g., by using <span style="font-family: Courier New,Courier,monospace;">"-a 2</span>", only every second frame of the original streams will be used for the sequence.<br><br><br><br><br><span style="font-weight: bold;">Current limitations (May 09):</span><br>Only a special opera-version on host "bora" can be used. Log-in on "bora" and call &nbsp;<span style="font-family: Courier New,Courier,monospace;">/usr/local/bin/opera</span>. <span style="font-weight: bold;">Before that(!!!)</span>, enter the command "<span style="font-family: Courier New,Courier,monospace;">export LD_PRELOAD=libXm.so</span>" !
    8787<hr><p style="line-height: 100%;"><br>
    8888<font color="#000080"><font color="#000080"><a href="chapter_4.5.6.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_4.6.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
  • palm/trunk/DOC/app/chapter_4.6.html

    r305 r336  
    63796379
    63806380
    6381     <tr>
     6381    <tr><td align="undefined" valign="undefined"><a href="chapter_4.2.html#groundplate_color"><span style="font-weight: bold;">groundplate_color</span></a></td><td align="undefined" valign="undefined">P</td><td align="undefined" valign="undefined">R(3)</td><td align="undefined" valign="undefined"><span style="font-style: italic;">0.0, 0.6, 0.0</span></td><td align="undefined" valign="undefined">Color of the ground plate</td></tr><tr>
    63826382
    63836383
     
    66346634
    66356635
    6636     <tr>
     6636    <tr><td align="undefined" valign="undefined"><a href="chapter_4.2.html#isosurface_color"><span style="font-weight: bold;">isosurface_color</span></a></td><td align="undefined" valign="undefined">P</td><td align="undefined" valign="undefined">R(3,10)</td><td align="undefined" valign="undefined"><span style="font-style: italic;">0.9, 0.9, 0.9</span><br style="font-style: italic;"><span style="font-style: italic;">0.8, 0.1, 0.1</span><br style="font-style: italic;"><span style="font-style: italic;">......</span></td><td align="undefined" valign="undefined">Color of the isosurface(s).</td></tr><tr>
    66376637
    66386638
     
    1378913789
    1379013790
    13791  <tr><td style="vertical-align: top;"><a style="font-weight: bold;" href="chapter_4.1.html#topography_grid_convention">topography_grid_convention</a></td><td style="vertical-align: top;">I</td><td style="vertical-align: top;">C * 11</td><td><span style="font-style: italic;">default depends on value of <a href="chapter_4.1.html#topography">topography</a>; see text for details</span><span style="font-style: italic;"></span></td><td style="vertical-align: top;">Convention for defining the&nbsp;topography grid.</td></tr><tr>
     13791 <tr><td align="undefined" valign="undefined"><a href="chapter_4.2.html#topography_color"><span style="font-weight: bold;">topography_color</span></a></td><td align="undefined" valign="undefined">P</td><td align="undefined" valign="undefined">R(3)</td><td align="undefined" valign="undefined"><span style="font-style: italic;">0.8, 0.7, 0.6</span></td><td align="undefined" valign="undefined">Color of the topography.</td></tr><tr><td style="vertical-align: top;"><a style="font-weight: bold;" href="chapter_4.1.html#topography_grid_convention">topography_grid_convention</a></td><td style="vertical-align: top;">I</td><td style="vertical-align: top;">C * 11</td><td><span style="font-style: italic;">default depends on value of <a href="chapter_4.1.html#topography">topography</a>; see text for details</span><span style="font-style: italic;"></span></td><td style="vertical-align: top;">Convention for defining the&nbsp;topography grid.</td></tr><tr>
    1379213792
    1379313793
  • palm/trunk/DOC/app/chapter_5.0.html

    r290 r336  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
    3 <meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
    4 chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
     3<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 5.0</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20041103;12380720"> <meta name="CHANGED" content="20041123;15532356"> <meta name="KEYWORDS" content="parallel LES model"> <style>
    54<!--
    65@page { size: 21cm 29.7cm }
     
    170169identifier&gt;</span>.
    171170You only have to uncomment lines for those hosts on which you intend to
    172 use PALM.</font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
     171use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
     172When editing the configuration file, please NEVER use the TAB key.
     173Otherwise, very confusing errors in mrun execution may occur.</span></font></p><p style="line-height: 100%;"><font color="#000000">Beside the default configuration file</font><font style="font-family: Courier New,Courier,monospace;" color="#000000"> .mrun.config.default</font><font color="#000000">, the directory<span style="font-family: Courier New,Courier,monospace;">
    173174trunk/SCRIPTS </span>contains additional configuration files
    174175which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
  • palm/trunk/SCRIPTS/process_dvr_output

    r262 r336  
    1414    # Variable declarations + default values
    1515 camera=false
     16 create_config_file=false
    1617 create_sequence_output=false
    1718 data_catalog=`pwd`
     
    1920 file_identifier=all_streams
    2021 groundplate=false
    21  palm_run_identifier=""
     22 palm_run_identifier="unknown_run"
    2223 topography=false
    2324
    24  typeset  -i  i j nstream nscenes
     25 typeset  -i  a acceleration=1 k i j nstream nscenes
    2526
    2627
    2728    # Read shellscript options
    28  while  getopts  :d:f:ls option
     29 while  getopts  :a:cd:f:ls option
    2930 do
    3031   case  $option  in
     32       (a)   acceleration=$OPTARG;;
     33       (c)   create_config_file=true;;
    3134       (d)   data_catalog=$OPTARG;;
    3235       (f)   file_identifier=$OPTARG;;
     
    4043
    4144
     45    # Create the config file for the streaming server; do nothing else
     46 if [[ $create_config_file = true ]]
     47 then
     48    cp  ${PALM_BIN}/.dvrserver.config  .
     49
     50       # Entering the BASEDIR, UID and GID into this file
     51    user_id=`id -u`
     52    group_id=`id -g`
     53
     54       # data directory is always the current working directory
     55    sed "s/<replace by dvr data directory>/./g" .dvrserver.config > .dvrserver.1
     56    sed "s/<replace by user id>/$user_id/g"    .dvrserver.1 > .dvrserver.2
     57    sed "s/<replace by group id>/$group_id/g"  .dvrserver.2 > .dvrserver.3
     58    mv  .dvrserver.3  .dvrserver.config
     59    rm  .dvrserver.1  .dvrserver.2
     60    exit
     61 fi
     62
     63
    4264    # Find out the PALM run identifier
    4365 if [[ -f CPU_MEASURES ]]
     
    4567    palm_run_identifier=`head -1  CPU_MEASURES`
    4668 fi
     69
    4770
    4871    # Process the streaming server output
     
    172195
    173196       # Change path to the current file identifier
    174     sed  "s/DATA_DVR/${file_identifier}_dvr/g"  $dvr_file > tmp_file
     197       # Remove path because BASEDIR of streaming server is set to "."
     198#    sed  "s/DATA_DVR/${file_identifier}_dvr/g"  $dvr_file > tmp_file
     199    sed  "s/DATA_DVR\///g"  $dvr_file > tmp_file
    175200    mv  tmp_file  $dvr_file
    176201
    177202
    178203       # If there is a dvr configuration file, set the BASEDIR to the parent
    179        # directory of the above given path
     204       # directory of the above given path (i.e. ".")
    180205    if [[ -f .dvrserver.config ]]
    181206    then
    182207       old_path=`grep  BASEDIR  .dvrserver.config`
    183        sed  "s&${old_path}&BASEDIR=..&g"  .dvrserver.config  >  .dvrserver.config.new
     208       sed  "s&${old_path}&BASEDIR=.&g"  .dvrserver.config  >  .dvrserver.config.new
    184209       mv  .dvrserver.config.new  .dvrserver.config
    185210    fi
     
    326351 then
    327352
     353    rm -rf  sequence_data
    328354    mkdir  sequence_data
    329355
     
    347373       # Now, merge the data, frame by frame
    348374    (( j = 0 ))
     375    (( k = 0 ))
     376    (( a = 0 ))
    349377    while (( j < ${frames[1]} ))
    350378    do
    351379
    352        nframe=`printf "%05d" $j`
    353 
    354        (( i = 0 ))
    355        while (( i < nstream ))
    356        do
    357           (( i = i + 1 ))
    358           cat  ${streamname[$i]}/$nframe.dvr  >>  sequence_data/$nframe.dvr
    359        done
     380       rframe=`printf "%05d" $j`
     381
     382       if (( a == 0 ))
     383       then
     384
     385          wframe=`printf "%05d" $k`
     386          (( k = k + 1 ))
     387
     388          (( i = 0 ))
     389          while (( i < nstream ))
     390          do
     391             (( i = i + 1 ))
     392             cat  ${streamname[$i]}/$rframe.dvr  >>  sequence_data/$wframe.dvr
     393          done
     394
     395
     396       fi
     397
     398       (( a = a + 1 ))
     399       if (( a == acceleration ))
     400       then
     401          (( a = 0 ))
     402       fi
    360403
    361404       (( j = j + 1 ))
     
    368411    sed  "s/camera.dvr/static_scenes.dvr/g"  tmp1.html  >  tmp2.html
    369412    sed  "s&${streamname[1]}&sequence_data&g"  tmp2.html  >  tmp3.html
     413    sed  "s/;0-0/;0-$wframe/g"  tmp3.html  >  tmp4.html
    370414    if [[ "$palm_run_identifier" = "" ]]
    371415    then
    372        cp  tmp3.html  ${file_identifier}_sequence.html
     416       cp  tmp4.html  ${file_identifier}_sequence.html
    373417    else
    374        sed "s&DATA_DVR/sequence_data/\*\*\*\*\*.dvr (DVR 3D Sequence)&DVR 3D sequence generated by $palm_run_identifier&g"  tmp3.html  >  ${file_identifier}_sequence.html
    375     fi
    376     rm  tmp1.html  tmp2.html  tmp3.html
     418       sed "s&DATA_DVR/sequence_data/\*\*\*\*\*.dvr (DVR 3D Sequence)&DVR 3D sequence generated by $palm_run_identifier&g"  tmp4.html  >  ${file_identifier}_sequence.html
     419    fi
     420    rm  tmp1.html  tmp2.html  tmp3.html  tmp4.html
    377421
    378422    printf "      data for using sequence mode generated"
  • palm/trunk/SOURCE/CURRENT_MODIFICATIONS

    r335 r336  
    7878skip_particles_for_tail (init_particles)
    7979
     80Value of vertical_particle_advection may differ for each particle group
     81(advec_particles, header, modules)
     82
    8083First constant in array den also defined as type double. (eqn_state_seawater)
    8184
     
    115118on. (time_integration)
    116119
     120Bugfix: qsws was calculated in case of constant heatflux = .FALSE. (prandtl_fluxes)
     121
     122Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0) (data_output_2d)
     123
    117124Typographical errors (netcdf)
    118125
     
    122129Small bugfix concerning 3d 64bit netcdf output format (header)
    123130
     131Bugfix: dt_fixed removed from the restart file, because otherwise, no change
     132from a fixed to a variable timestep would be possible in restart runs.
     133(read_var_list, write_var_list)
    124134
    125 advec_particles, check_parameters, cpu_log, header, init_3d_model, init_particles, modules, netcdf, time_integration
     135advec_particles, check_parameters, cpu_log, data_output_2d, header, init_3d_model, init_particles, modules, netcdf, prandtl_fluxes, read_var_list, time_integration, write_var_list
  • palm/trunk/SOURCE/advec_particles.f90

    r276 r336  
    55! -----------------
    66! Particle attributes are set with new routine set_particle_attributes.
     7! Vertical particle advection depends on the particle group.
    78! Output of NetCDF messages with aid of message handling routine.
    89! Output of messages replaced by message handling routine
     
    898899!--       Same procedure for interpolation of the w velocity-component (adopt
    899900!--       index i from v velocity-component)
    900           IF ( vertical_particle_advection )  THEN
     901          IF ( vertical_particle_advection(particles(n)%group) )  THEN
    901902             j = particles(n)%y * ddy
    902903             k = particles(n)%z / dz + offset_ocean_nzt_m1
  • palm/trunk/SOURCE/data_output_2d.f90

    r291 r336  
    66! simulated_time in NetCDF output replaced by time_since_reference_point.
    77! Output of NetCDF messages with aid of message handling routine.
     8! Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0)
    89! Output of messages replaced by message handling routine.
    910!
     
    578579!
    579580!--                If required, carry out averaging along z
    580                    IF ( section(is,s) == -1 )  THEN
     581                   IF ( section(is,s) == -1  .AND.  .NOT. two_d )  THEN
    581582
    582583                      local_2d = 0.0
  • palm/trunk/SOURCE/eqn_state_seawater.f90

    r231 r336  
    7676!
    7777!--             Pressure is needed in dbar
    78                 p1 = hyp(0) * 1E-4
     78!                p1 = hyp(0) * 1E-4
     79!                p1 = 0.0
     80                p1 = hyp(k) * 1E-4
    7981                p2 = p1 * p1
    8082                p3 = p2 * p1
     
    132134!
    133135!--       Pressure is needed in dbar
    134           p1 = hyp(0) * 1E-4
     136!          p1 = hyp(0) * 1E-4
     137!          p1 = 0.0
     138          p1 = hyp(k) * 1E-4
    135139          p2 = p1 * p1
    136140          p3 = p2 * p1
  • palm/trunk/SOURCE/header.f90

    r328 r336  
    77! Coupling with independent precursor runs.
    88! Output of messages replaced by message handling routine.
    9 ! Output of cluster_size
     9! Output of several additional dvr parameters
    1010! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left,
    1111! canyon_wall_south, conserve_volume_flow_mode, dp_external, dp_level_b,
     
    108108
    109109    INTEGER ::  av, bh, blx, bly, bxl, bxr, byn, bys, ch, cwx, cwy, cxl, cxr, &
    110                 cyn, cys, i, ihost, io, j, l, ll, mpi_type
     110                cyn, cys, i, ihost, io, j, l, ll, m, mpi_type
    111111    REAL    ::  cpuseconds_per_simulated_second
    112112
     
    10191019       i = 1
    10201020       l = 0
     1021       m = 0
    10211022       DO WHILE ( mode_dvrp(i) /= ' ' )
    10221023          IF ( mode_dvrp(i)(1:10) == 'isosurface' )  THEN
     
    10241025             l = l + 1
    10251026             IF ( do3d(0,j) /= ' ' )  THEN
    1026                 WRITE ( io, 361 )  TRIM( do3d(0,j) ), threshold(l)
     1027                WRITE ( io, 361 )  TRIM( do3d(0,j) ), threshold(l), &
     1028                                   isosurface_color(:,l)
    10271029             ENDIF
    10281030          ELSEIF ( mode_dvrp(i)(1:6) == 'slicer' )  THEN
    10291031             READ ( mode_dvrp(i), '(6X,I2)' )  j
    1030              IF ( do2d(0,j) /= ' ' )  WRITE ( io, 362 )  TRIM( do2d(0,j) )
     1032             m = m + 1
     1033             IF ( do2d(0,j) /= ' ' )  THEN
     1034                WRITE ( io, 362 )  TRIM( do2d(0,j) ), &
     1035                                   slicer_range_limits_dvrp(:,m)
     1036             ENDIF
    10311037          ELSEIF ( mode_dvrp(i)(1:9) == 'particles' )  THEN
    1032              WRITE ( io, 363 )
     1038             WRITE ( io, 363 )  dvrp_psize
     1039             IF ( particle_dvrpsize /= 'none' )  THEN
     1040                WRITE ( io, 364 )  'size', TRIM( particle_dvrpsize ), &
     1041                                   dvrpsize_interval
     1042             ENDIF
     1043             IF ( particle_color /= 'none' )  THEN
     1044                WRITE ( io, 364 )  'color', TRIM( particle_color ), &
     1045                                   color_interval
     1046             ENDIF
    10331047          ENDIF
    10341048          i = i + 1
    10351049       ENDDO
    10361050
    1037        IF ( TRIM( topography ) /= 'flat'  .AND.  cluster_size > 1 )  THEN
    1038           WRITE ( io, 364 )  cluster_size
     1051       WRITE ( io, 365 )  groundplate_color, superelevation_x, &
     1052                          superelevation_y, superelevation, clip_dvrp_l, &
     1053                          clip_dvrp_r, clip_dvrp_s, clip_dvrp_n
     1054
     1055       IF ( TRIM( topography ) /= 'flat' )  THEN
     1056          WRITE ( io, 366 )  topography_color
     1057          IF ( cluster_size > 1 )  THEN
     1058             WRITE ( io, 367 )  cluster_size
     1059          ENDIF
    10391060       ENDIF
    10401061
     
    13011322       IF ( particles_per_point > 1 )  WRITE ( io, 489 )  particles_per_point
    13021323       WRITE ( io, 495 )  total_number_of_particles
    1303        IF ( .NOT. vertical_particle_advection )  WRITE ( io, 482 )
    13041324       IF ( maximum_number_of_tailpoints /= 0 )  THEN
    13051325          WRITE ( io, 483 )  maximum_number_of_tailpoints
     
    13431363          WRITE ( io, 493 )  psl(i), psr(i), pss(i), psn(i), psb(i), pst(i), &
    13441364                             pdx(i), pdy(i), pdz(i)
     1365          IF ( .NOT. vertical_particle_advection(i) )  WRITE ( io, 482 )
    13451366       ENDDO
    13461367
     
    16021623            '       Directory:        ',A// &
    16031624            '       The sequence contains:')
    1604 361 FORMAT ('       Isosurface of ',A,'  Threshold value: ', E12.3)
    1605 362 FORMAT ('       Sectional plane ',A)
    1606 363 FORMAT ('       Particles')
    1607 364 FORMAT (/'       Polygon reduction for topography: cluster_size = ', I1)
     1625361 FORMAT ('       Isosurface of ',A,'  Threshold value: ', E12.3/ &
     1626            '       Isosurface color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)')
     1627362 FORMAT ('       Slicer plane ',A/ &
     1628            '       Slicer limits: [',F6.2,',',F6.2,']')
     1629363 FORMAT ('       Particles'/ &
     1630            '          particle size:  ',F7.2,' m')
     1631364 FORMAT ('          particle ',A,' controlled by "',A,'" with interval [', &
     1632                       F6.2,',',F6.2,']')
     1633365 FORMAT (/'       Groundplate color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)'/ &
     1634            '       Superelevation along (x,y,z): (',F4.1,',',F4.1,',',F4.1, &
     1635                     ')'/ &
     1636            '       Clipping limits: from x = ',F9.1,' m to x = ',F9.1,' m'/ &
     1637            '                        from y = ',F9.1,' m to y = ',F9.1,' m')
     1638366 FORMAT (/'       Topography color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)')
     1639367 FORMAT ('       Polygon reduction for topography: cluster_size = ', I1)
    16081640#endif
    16091641#if defined( __spectra )
     
    17151747            '       Particles are sorted every ',F9.1,' s'/)
    17161748481 FORMAT ('       Particles have random start positions'/)
    1717 482 FORMAT ('       Particles are advected only horizontally'/)
     1749482 FORMAT ('          Particles are advected only horizontally'/)
    17181750483 FORMAT ('       Particles have tails with a maximum of ',I3,' points')
    17191751484 FORMAT ('            Number of tails of the total domain: ',I10/ &
  • palm/trunk/SOURCE/init_ocean.f90

    r139 r336  
    2424    USE control_parameters
    2525    USE eqn_state_seawater_mod
     26    USE pegrid
    2627    USE grid_variables
    2728    USE indices
     
    2930    IMPLICIT NONE
    3031
    31     INTEGER ::  k
     32    INTEGER ::  k, n
    3233
    3334    REAL    ::  sa_l, pt_l, rho_l
     35
     36    REAL, DIMENSION(nzb:nzt+1) ::  rho_init
    3437
    3538    ALLOCATE( hyp(nzb:nzt+1) )
     
    4548
    4649    hyp(nzt)      = hyp(nzt+1) + rho_surface * g * 0.5 * dzu(nzt+1)
    47     rho_reference = rho_surface * 0.5 * dzu(nzt+1)
     50    rho_init(nzt) = rho_surface
    4851
    4952    DO  k = nzt-1, 0, -1
     53       hyp(k) = hyp(k+1) + rho_surface * g * dzu(k)
     54    ENDDO
    5055
    51        sa_l = 0.5 * ( sa_init(k) + sa_init(k+1) )
    52        pt_l = 0.5 * ( pt_init(k) + pt_init(k+1) )
     56    IF ( myid == 0 )  THEN
     57       print*,'hydro pres using rho_surface'
     58       DO  k = nzt+1, 0, -1
     59          print*, 'k = ', k, ' hyp = ', hyp(k)
     60       ENDDO
     61       print*, ' '
     62    ENDIF
    5363
    54        rho_l = eqn_state_seawater_func( hyp(k+1), pt_l, sa_l )
     64    DO  n = 1, 5
    5565
    56        hyp(k)        = hyp(k+1) + rho_l * g * dzu(k+1)
    57        rho_reference = rho_reference + rho_l * dzu(k+1)
     66       rho_reference = rho_surface * 0.5 * dzu(nzt+1)
     67
     68       DO  k = nzt-1, 0, -1
     69
     70          sa_l = 0.5 * ( sa_init(k) + sa_init(k+1) )
     71          pt_l = 0.5 * ( pt_init(k) + pt_init(k+1) )
     72
     73          rho_init(k) = eqn_state_seawater_func( hyp(k), pt_l, sa_l )
     74
     75          rho_reference = rho_reference + rho_init(k) * dzu(k+1)
     76
     77       ENDDO
     78
     79       rho_reference = rho_reference / ( zw(nzt) - zu(nzb) )
     80
     81       DO  k = nzt-1, 0, -1
     82          hyp(k) = hyp(k+1) + g * 0.5 * ( rho_init(k) + rho_init(k+1 ) ) * &
     83                              dzu(k+1)
     84       ENDDO
     85
     86       IF ( myid == 0 )  THEN
     87          print*,'hydro pres / rho  n = ', n
     88          DO  k = nzt+1, 0, -1
     89             print*, 'k = ', k, ' hyp = ', hyp(k), ' rho = ', rho_init(k)
     90          ENDDO
     91          print*, ' '
     92       ENDIF
    5893
    5994    ENDDO
    60 
    61     rho_reference = rho_reference / ( zw(nzt) - zu(nzb) )
    6295
    6396!
     
    70103
    71104       prho_reference = prho_reference + dzu(k+1) * &
    72                         eqn_state_seawater_func( hyp(0), pt_l, sa_l )
     105                        eqn_state_seawater_func( 0.0, pt_l, sa_l )
    73106
    74107    ENDDO
  • palm/trunk/SOURCE/init_particles.f90

    r277 r336  
    5454    USE arrays_3d
    5555    USE control_parameters
     56    USE dvrp_variables
    5657    USE grid_variables
    5758    USE indices
     
    441442
    442443!
     444!--    Particles will probably become none-uniform, if their size and color
     445!--    will be determined by flow variables
     446       IF ( particle_color /= 'none'  .OR.  particle_dvrpsize /= 'none' )  THEN
     447          uniform_particles = .FALSE.
     448       ENDIF
     449
     450!
    443451!--    Set the beginning of the particle tails and their age
    444452       IF ( use_particle_tails )  THEN
  • palm/trunk/SOURCE/modules.f90

    r318 r336  
    1010! interval_*_dvrp_prt, isosurface_color, particle_color, particle_dvrpsize,
    1111! topography color in dvrp_variables,
     12! vertical_particle_advection is a 1d-array,
    1213! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left,
    1314! canyon_wall_south, conserve_volume_flow_mode, coupling_start_time,
     
    971972                uniform_particles = .TRUE., use_particle_tails = .FALSE.,      &
    972973                use_sgs_for_particles = .FALSE.,                               &
    973                 vertical_particle_advection = .TRUE.,                          &
    974974                write_particle_statistics = .FALSE.
     975
     976    LOGICAL, DIMENSION(max_number_of_particle_groups) ::                       &
     977                vertical_particle_advection = .TRUE.
     978
    975979    LOGICAL, DIMENSION(:), ALLOCATABLE ::  particle_mask, tail_mask
    976980
  • palm/trunk/SOURCE/package_parin.f90

    r284 r336  
    5252                                  dt_dvrp, dvrpsize_interval, dvrp_directory,  &
    5353                                  dvrp_file, dvrp_host, dvrp_output,           &
    54                                   dvrp_password, dvrp_username,                &
     54                                  dvrp_password, dvrp_psize, dvrp_username,    &
    5555                                  groundplate_color, isosurface_color,         &
    5656                                  mode_dvrp, particle_color, particle_dvrpsize,&
     
    6767                                  density_ratio, radius, dt_dopts,             &
    6868                                  dt_min_part, dt_prel, dt_sort_particles,     &
    69                                   dt_write_particle_data, dvrp_psize,          &
     69                                  dt_write_particle_data,                      &
    7070                                  end_time_prel, initial_weighting_factor,     &
    7171                                  maximum_number_of_particles,                 &
  • palm/trunk/SOURCE/read_var_list.f90

    r328 r336  
    44! Current revisions:
    55! -----------------
     6! dt_fixed is read into a dummy variable.
    67! Output of messages replaced by message handling routine.
    78! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left,
     
    7778    CHARACTER (LEN=10) ::  binary_version, version_on_file
    7879    CHARACTER (LEN=30) ::  variable_chr
     80
     81    LOGICAL ::  ldum
    7982
    8083
     
    266269             READ ( 13 )  drag_coefficient
    267270          CASE ( 'dt_fixed' )
    268              READ ( 13 )  dt_fixed
     271             READ ( 13 )  ldum   ! restart files created before rev 333
     272                                 ! contained dt_fixed by mistake; it is still
     273                                 ! read here in order to allow usage of these
     274                                 ! older restart files; can be removed in a
     275                                 ! later version
    269276          CASE ( 'dt_pr_1d' )
    270277             READ ( 13 )  dt_pr_1d
  • palm/trunk/SOURCE/write_var_list.f90

    r291 r336  
    44! Actual revisions:
    55! -----------------
     6! bugfix: -dt_fixed, because otherwise, restart runs cannot change from a
     7! fixed to a free timestep.
    68! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left,
    79! canyon_wall_south, conserve_volume_flow_mode, coupling_start_time,
     
    194196    WRITE ( 14 )  'drag_coefficient              '
    195197    WRITE ( 14 )  drag_coefficient
    196     WRITE ( 14 )  'dt_fixed                      '
    197     WRITE ( 14 )  dt_fixed
    198198    WRITE ( 14 )  'dt_pr_1d                      '
    199199    WRITE ( 14 )  dt_pr_1d
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