Index: palm/trunk/DOC/app/chapter_3.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_3.2.html	(revision 335)
+++ palm/trunk/DOC/app/chapter_3.2.html	(revision 336)
@@ -32,5 +32,5 @@
 <p style="line-height: 100%;">The following configuration
 data
-exclusively applies to model runs on the IBM Regatta hanni of the
+exclusively applies to model runs on the SGI ICE system of the
 HLRN when using several processing elements (i.e. for the parallel
 version of the model). The proper installation of the model is
@@ -38,13 +38,9 @@
 5.0</a>). Furthermore it is supposed that the user is located in
 the
-directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version/SOURCE</font></tt>
-on its local computer. There are the FORTRAN source codes of the
-model (<tt><font style="font-size: 10pt;" size="2">*.f90</font></tt>)
-as
-well as the configuration file (name: <tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>)
-and the make file (name: <tt><font style="font-size: 10pt;" size="2">Makefile</font></tt>).
+directory <tt><font style="font-size: 10pt;" size="2">$HOME/palm/current_version</font></tt>
+&nbsp;on its local computer, where the configuration file (<tt><font style="font-size: 10pt;" size="2">.mrun.config</font></tt>) should reside.
 The configuration file has the following contents (among other things):
 <br>&nbsp;
-</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>
+</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>
 <p style="line-height: 100%;"><font face="Thorndale, serif">The first
 five lines specify values of
@@ -56,15 +52,11 @@
 variable. Again separated by blank t<font face="Thorndale, serif">he
 so-called validity domain</font> can be indicated (later more).
-With the first three variables <b>mrun</b> gets to know in
+With the first four variables <b>mrun</b> gets to know in
 which
 directory the source code lies (</font><tt><i><font face="Thorndale, serif">source_path</font></i></tt><font face="Thorndale, serif">),
-the file name of the main program (</font><tt><i><font face="Thorndale, serif">mainprog</font></i></tt><font face="Thorndale, serif">)
-and that the <font face="Thorndale, serif">make mechanism
-should be
-used </font>for compiling (</font><tt><font face="Thorndale, serif"><i>use_makefile
-=</i> <i>true</i></font></tt><font face="Thorndale, serif">). <b>mrun
+the 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
 </b>needs these information, <font color="#000000">because
 for each
-model run the executable is created by compiling the source files.</font>
+model run the executable is created by compiling the respective source file.</font>
 Normally, only the main program (palm.f90) will be compiled while all
 other object files are just linked. These object files have already
@@ -84,21 +76,12 @@
 interpret these colons as blanks (2 colons written one behind the
 other will be interpreted as a colon). Thus in the example above</font> fopts
-has the value<tt><font face="Thorndale, serif"> </font></tt>&ldquo;<font style="font-size: 10pt; font-family: monospace;" size="2"><i>-O3
--g
--qrealsize=8 -Q -q64 -qmaxmem=-1 -qtune=pwr4 -qarch=pwr4 -qnosave
--qnoescape</i></font><tt><i><font face="Thorndale, serif"><font color="#000000">&rdquo;</font></font></i></tt><font face="Thorndale, serif"><font color="#000000">.
-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">
+has 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">.
+Thus 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">
 For all other options
-see the compiler manual on the IBM (</font><font size="2"><font face="Cumberland, monospace">man</font></font></font><tt><font color="#000000">
-<font size="2"><font face="Cumberland, monospace">f90</font></font></font></tt><font face="Thorndale, serif"><font color="#000000">).
+see 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">).
 Additional libraries
-which the compiler should use are described by
+which the compiler should use may have to be given by
 the environment variable </font></font><tt><font size="2"><font face="Cumberland, monospace"><font color="#000000">lopts</font></font></font></tt><font color="#000000">
-<font face="Thorndale, serif">(loader options).</font></font><font color="#800000">
-</font><font face="Thorndale, serif"><font color="#000000">Here you
-have to indicate a special IBM library (ESSL, </font></font>Engineering
-and Scientific Subroutine Library)<font face="Thorndale, serif"><font color="#000000">.</font><font color="#800000">
-</font>On the
-IBM-Regatta, all compiler options have also to be given to the linker.</font><font color="#000000"><font face="Thorndale, serif"> </font></font>
+<font face="Thorndale, serif">(loader options).</font></font><font color="#000000"><font face="Thorndale, serif"> </font></font>
 </p><p style="line-height: 100%;"><font color="#000000">Compiler and
 loader options usually differ from computer to computer. In the
@@ -111,10 +94,10 @@
 the so-called validity domain which follows in the appropriate
 variable lines after the value of variables.</font></font><font color="#000000">
-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;">
+In 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;">
 </span></font><font color="#000000"><i><font style="font-size: 11pt;" size="2">parallel</font></i></font></tt><font color="#000000">&rdquo;
 stands for </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">fopts</font></font></tt><font color="#000000">
 and </font><tt><font style="font-size: 10pt;" size="2"><font color="#000000">lopts</font></font></tt><font color="#000000">.
 These lines only become active if a run on the parallel computer of
-the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">ibmh</font></i></tt><font color="#000000">)
+the HLRN (</font><tt><i><font style="font-size: 10pt;" size="2">lcsgih</font></i></tt><font color="#000000">)
 on 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">)
 </font>processors is started. The activation takes place when you
@@ -124,5 +107,5 @@
 (see below). This way, the validity domain can be limited also for all
 other environment-variables. If no validity domain
-is indicated then the given values of variables are valid on all
+is indicated then the given values of variables are valid for all
 computers. </font>
 </p><p style="line-height: 100%;">After the value
@@ -208,5 +191,5 @@
 indicated 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>.
 Thus a call of the form </p>
-<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>
+<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>
 <p style="line-height: 100%;">would lead to the fact that
 the input
@@ -217,5 +200,5 @@
 these files are to be copied of <b>mrun</b> then the call
 must be</p>
-<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>
+<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>
 <p style="line-height: 100%;">Instead of the option -r you
 can
@@ -225,5 +208,5 @@
 file all file connection statements are actually executed then
 the call must be: </p>
-<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>
+<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>
 <p style="line-height: 100%;"><font color="#000000">The
 names of the
@@ -258,5 +241,5 @@
 <p style="line-height: 100%;">The example configuration
 file also
-instructs <b>mrun</b> to copy four output files of the
+instructs <b>mrun</b> to copy three output files of the
 model to
 appropriate permanent files of the user at the end of the run.
@@ -266,7 +249,5 @@
 are located, as well as a file with data of horizontally averaged
 vertical profiles
-(<tt><a href="chapter_3.4.html#PLOT1D_DATA">PLOT1D_DATA</a></tt>)
-and an associated parameter file (<tt><a href="chapter_3.4.html#PLOT1D_PAR">PLOT1D_PAR</a></tt>),
-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>.
+(<tt><a href="chapter_3.4.html#DATA_1D_PR_NETCDF">DATA_1D_PR_NETCDF</a></tt>).
 A model run does not presuppose neither the file connection statements
 for
@@ -283,7 +264,7 @@
 execution of a
 model run
-on several processors on the IBM Regatta "hanni" of the HLRN must be
+on several processors on the SGI ICE of the HLRN must be
 supplemented by the following options in each case: </p>
-<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>
+<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>
 <p style="line-height: 100%;">Only the indication of <tt><font style="font-size: 11pt;" size="2">-K
 parallel</font></tt> causes the parallel execution of the
@@ -294,20 +275,17 @@
 option <tt><font style="font-size: 10pt;" size="2">-X</font>
 </tt><font size="2">(</font><font style="font-size: 10pt;" size="2">e.g.
-</font><tt><font style="font-size: 10pt;" size="2">-X
-4</font></tt><font size="2">).</font>
+</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>
 In each case the permitted CPU time in seconds and the required memory
 size in MB must be indicated by the options <tt><font style="font-size: 11pt;" size="2">-t</font></tt>
 and <tt><font style="font-size: 11pt;" size="2">-m</font></tt>,
 respectively<font face="Thorndale, serif">.</font>
-Alternatively, these can be set by the appropriate environment
+Alternatively, memory and cpu-time demands can be set by the appropriate environment
 variables in the configuration file: </p>
-<blockquote style="line-height: 100%;"><tt><font style="font-size: 10pt;" size="2"><font face="Cumberland, monospace">%
-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">%
-cputime <i>1000</i> ibmh parallel</font></font></tt></blockquote>
+<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>
 <p style="line-height: 100%;">The values indicated there
 can be
 overridden with the values of the options <tt><font style="font-size: 10pt;" size="2">-t</font></tt>
 and/or <tt><font style="font-size: 10pt;" size="2">-m</font></tt>,
-respectivly. </p>
+respectivly.</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>
 <hr><p style="line-height: 100%;"><br>
 <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>
Index: palm/trunk/DOC/app/chapter_4.2.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.2.html	(revision 335)
+++ palm/trunk/DOC/app/chapter_4.2.html	(revision 336)
@@ -10663,5 +10663,8 @@
 
 
- <tr>
+ <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
+are given in RGB (red/green/blue) portions. By default, the first
+isosurface has a gray color, the second a red color, the third a blue
+color, etc.</td></tr><tr>
 
 
@@ -10742,5 +10745,5 @@
 cross sections see <a href="#data_output">data_output</a>.
 The theshold value for which the isosurface is
-to be created can be defined with parameter <a href="#threshold">threshold</a>.<br>
+to 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>
 
 
@@ -10782,16 +10785,10 @@
 
 
-The declaration color charts to be
+The declaration of color charts to be
 used 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>
-(file <tt><font style="font-size: 11pt;" size="2">user_interface.f90</font></tt>).&nbsp;
-      <br>
-
-
-A change of particle colors and/or particle diameters (e.g.
-according
-to the local characteristics of the flow field) to be used for the
-visualization, must be carried out by adding respective code extensions
-to <a href="chapter_3.4.html#user_particle_attributes"><tt><font style="font-size: 11pt;" size="2">user_particle_attributes</font></tt></a>
-(in file <tt><font style="font-size: 11pt;" size="2">user_interface.f90</font></tt>).&nbsp;</td>
+(file <tt><font style="font-size: 11pt;" size="2">user_dvrp_coltab.f90</font></tt>).&nbsp;
+
+
+</td>
 
 
@@ -11067,5 +11064,5 @@
 
 
- </tr>
+ </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>
 
 
Index: palm/trunk/DOC/app/chapter_4.5.7.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.5.7.html	(revision 335)
+++ palm/trunk/DOC/app/chapter_4.5.7.html	(revision 336)
@@ -1,26 +1,25 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
 <html><head>
-<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
-chapter 4.5.7</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>
+<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>
 <!--
 @page { size: 21cm 29.7cm }
 -->
 </style></head>
-
 <body style="direction: ltr;" lang="en-US"><h4 style="line-height: 100%;"><font size="4">4.5.7
 Plots of
 isosurfaces, 2d cross sections and particles with dvrp</font></h4>
-<p style="line-height: 100%;">The <span style="font-weight: bold;">dvrp</span>
-software developed by the RRZN
-(Stephan Olbrich, Carsten Chmielewski) allows a creation of plot
-sequences with PALM,
-which can be animated via a special plugin for internet browsers. With
-suitable graphic hardware even stereoscopic views are
-possible. <br>
+<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>
+part of the PALM distribution. Currently (May 2009), this software is
+only available on the the HLRN/IMUK system and partly on RIAM's NEC
+system. 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>
+software was originally developed by the RRZN
+(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,
+which can be displayed via a special plugin for internet browsers. With
+suitable graphic hardware (e.g. NVIDIA quattro FX cards) even stereoscopic views are
+possible.</p><p style="line-height: 100%;">
 In contrast to the other kinds of visualization output realized
-in PALM (<b>profil</b>, <b>iso2d</b> and <b>AVS</b>),
+in PALM (1d-, 2d-, 3d-NetCDF output),
 where the data
-is output in a format suitable for the plot software, the creation of
-plots via <span style="font-weight: bold;">dvrp</span>
+is 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>
 software is
 integrated in PALM, i.e. respective routines are directly called within
@@ -46,18 +45,18 @@
 the main focus of the BMBF project "Application of
 tele-immersion in long-distance networks" (2001-2002),
-which was a joint project of RRZN, ZIB and IMUK. This work is currently
-continued by RRZN in the new DFG-funded project "EVITA - Untersuchung
+which was a joint project of RRZN, ZIB and IMUK. This work was
+continued by RRZN in the DFG-funded project "<a href="http://www.rrzn.uni-hannover.de/evita.html">EVITA</a> - Untersuchung
 effizienter
-<br>Methoden zur visuellen und haptischen tele-immersiven
+Methoden zur visuellen und haptischen tele-immersiven
 Exploration
-<br>komplexer Volumen- und Str&ouml;mungsdaten aus
+komplexer Volumen- und Str&ouml;mungsdaten aus
 parallelisierten,
-<br>dynamischen 3D-Simulationen" (2005-2007). </p>
-<p style="line-height: 100%;">The calls of the <span style="font-weight: bold;">dvrp</span> routines are
+dynamischen 3D-Simulationen" (2005-2007). </p>
+<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
 contained within a
 PALM software package (see chapter <a href="chapter_3.7.html">3.7</a>).
-To use this package, the additional option <tt><font size="2">-p
-&ldquo;dvrp_graphics&rdquo;</font></tt>
-has to be given in the <b>mrun</b> call. This
+To use this package, the additional option<tt style="font-family: monospace;"> </tt><font style="font-family: Courier New,Courier,monospace;" size="2">-p
+<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;">
+</span>has to be given in the <b>mrun</b> call. This
 automatically links the
 required libraries.
@@ -67,22 +66,23 @@
 graphic
 data are not output to local files but directly to a special remote
-computer which is defined via the package parameter <a href="chapter_4.2.html#dvrp_host">dvrp_host</a>.
-The
-default values of the dvrp parameters are cause the output to be
-directed to a so-called streaming server at the
+computer 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
 RRZN. Apart from graphic data an additional html file is created, which
-can be used by an internet browser to view the data (a special <span style="font-weight: bold;">dvrp</span> plugin is
-needed). </p>
-<p style="line-height: 100%;">Since July 2001, the basic
-functionality
-of the <span style="font-weight: bold;">dvrp</span>
-software is
-installed in PALM and steerable via the
-package parameters. However, some code modifications may still need to
-be done by the user (e.g. in
-the subroutine <tt><font style="font-size: 10pt;" size="2">plot_dvrp</font></tt>
-in order to define suitable color tables).
-<br>For further detailed information please ask Siegfried Raasch.
-</p>
+can 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>
+<ol><li>
+Add 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;
+-I/home/h/niksiraa/dvr_mvapich2/lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+&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
+parallel</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;
+&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
+dvrp_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>.
+All streams (and static scenes) are collected to one sequence (one
+static scene), which can be displayed with a browser without using the
+streaming server (the so-called sequence mode). This allows e.g. to
+show animations on a notebook without beeing connected to the internet.
+When the script is called with this option, the sequence is generated
+in subdirectory sequence_data. Copy this subdirectory and the file
+all_streams_sequence.html to a directory on your local computer and
+open the file all_streams_sequence.html with your browser. For this,
+you 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>" !
 <hr><p style="line-height: 100%;"><br>
 <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
Index: palm/trunk/DOC/app/chapter_4.6.html
===================================================================
--- palm/trunk/DOC/app/chapter_4.6.html	(revision 335)
+++ palm/trunk/DOC/app/chapter_4.6.html	(revision 336)
@@ -6379,5 +6379,5 @@
 
 
-    <tr>
+    <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>
 
 
@@ -6634,5 +6634,5 @@
 
 
-    <tr>
+    <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>
 
 
@@ -13789,5 +13789,5 @@
 
 
- <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>
+ <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>
 
 
Index: palm/trunk/DOC/app/chapter_5.0.html
===================================================================
--- palm/trunk/DOC/app/chapter_5.0.html	(revision 335)
+++ palm/trunk/DOC/app/chapter_5.0.html	(revision 336)
@@ -1,6 +1,5 @@
 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
 <html><head>
-<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM
-chapter 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>
+<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>
 <!--
 @page { size: 21cm 29.7cm }
@@ -170,5 +169,7 @@
 identifier&gt;</span>.
 You only have to uncomment lines for those hosts on which you intend to
-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;">
+use PALM.</font></p><p style="line-height: 100%;"><font color="#000000"><span style="font-weight: bold;">Warning:
+When editing the configuration file, please NEVER use the TAB key.
+Otherwise, 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;">
 trunk/SCRIPTS </span>contains additional configuration files
 which are already adjusted for special hosts:<span style="font-family: Courier New,Courier,monospace;">
Index: palm/trunk/SCRIPTS/process_dvr_output
===================================================================
--- palm/trunk/SCRIPTS/process_dvr_output	(revision 335)
+++ palm/trunk/SCRIPTS/process_dvr_output	(revision 336)
@@ -14,4 +14,5 @@
     # Variable declarations + default values
  camera=false
+ create_config_file=false
  create_sequence_output=false
  data_catalog=`pwd`
@@ -19,14 +20,16 @@
  file_identifier=all_streams
  groundplate=false
- palm_run_identifier=""
+ palm_run_identifier="unknown_run"
  topography=false
 
- typeset  -i  i j nstream nscenes
+ typeset  -i  a acceleration=1 k i j nstream nscenes
 
 
     # Read shellscript options
- while  getopts  :d:f:ls option
+ while  getopts  :a:cd:f:ls option
  do
    case  $option  in
+       (a)   acceleration=$OPTARG;;
+       (c)   create_config_file=true;;
        (d)   data_catalog=$OPTARG;;
        (f)   file_identifier=$OPTARG;;
@@ -40,4 +43,23 @@
 
 
+    # Create the config file for the streaming server; do nothing else
+ if [[ $create_config_file = true ]]
+ then
+    cp  ${PALM_BIN}/.dvrserver.config  .
+
+       # Entering the BASEDIR, UID and GID into this file
+    user_id=`id -u`
+    group_id=`id -g`
+
+       # data directory is always the current working directory
+    sed "s/<replace by dvr data directory>/./g" .dvrserver.config > .dvrserver.1
+    sed "s/<replace by user id>/$user_id/g"    .dvrserver.1 > .dvrserver.2
+    sed "s/<replace by group id>/$group_id/g"  .dvrserver.2 > .dvrserver.3
+    mv  .dvrserver.3  .dvrserver.config
+    rm  .dvrserver.1  .dvrserver.2
+    exit
+ fi
+
+
     # Find out the PALM run identifier
  if [[ -f CPU_MEASURES ]]
@@ -45,4 +67,5 @@
     palm_run_identifier=`head -1  CPU_MEASURES`
  fi
+
 
     # Process the streaming server output
@@ -172,14 +195,16 @@
 
        # Change path to the current file identifier
-    sed  "s/DATA_DVR/${file_identifier}_dvr/g"  $dvr_file > tmp_file
+       # Remove path because BASEDIR of streaming server is set to "."
+#    sed  "s/DATA_DVR/${file_identifier}_dvr/g"  $dvr_file > tmp_file
+    sed  "s/DATA_DVR\///g"  $dvr_file > tmp_file
     mv  tmp_file  $dvr_file
 
 
        # If there is a dvr configuration file, set the BASEDIR to the parent
-       # directory of the above given path
+       # directory of the above given path (i.e. ".")
     if [[ -f .dvrserver.config ]]
     then
        old_path=`grep  BASEDIR  .dvrserver.config`
-       sed  "s&${old_path}&BASEDIR=..&g"  .dvrserver.config  >  .dvrserver.config.new
+       sed  "s&${old_path}&BASEDIR=.&g"  .dvrserver.config  >  .dvrserver.config.new
        mv  .dvrserver.config.new  .dvrserver.config
     fi
@@ -326,4 +351,5 @@
  then
 
+    rm -rf  sequence_data
     mkdir  sequence_data
 
@@ -347,15 +373,32 @@
        # Now, merge the data, frame by frame
     (( j = 0 ))
+    (( k = 0 ))
+    (( a = 0 ))
     while (( j < ${frames[1]} ))
     do
 
-       nframe=`printf "%05d" $j`
-
-       (( i = 0 ))
-       while (( i < nstream ))
-       do
-          (( i = i + 1 ))
-          cat  ${streamname[$i]}/$nframe.dvr  >>  sequence_data/$nframe.dvr
-       done
+       rframe=`printf "%05d" $j`
+
+       if (( a == 0 ))
+       then
+
+          wframe=`printf "%05d" $k`
+          (( k = k + 1 ))
+
+          (( i = 0 ))
+          while (( i < nstream ))
+          do
+             (( i = i + 1 ))
+             cat  ${streamname[$i]}/$rframe.dvr  >>  sequence_data/$wframe.dvr
+          done
+
+
+       fi
+
+       (( a = a + 1 ))
+       if (( a == acceleration ))
+       then
+          (( a = 0 ))
+       fi
 
        (( j = j + 1 ))
@@ -368,11 +411,12 @@
     sed  "s/camera.dvr/static_scenes.dvr/g"  tmp1.html  >  tmp2.html
     sed  "s&${streamname[1]}&sequence_data&g"  tmp2.html  >  tmp3.html
+    sed  "s/;0-0/;0-$wframe/g"  tmp3.html  >  tmp4.html
     if [[ "$palm_run_identifier" = "" ]]
     then
-       cp  tmp3.html  ${file_identifier}_sequence.html
+       cp  tmp4.html  ${file_identifier}_sequence.html
     else
-       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
-    fi
-    rm  tmp1.html  tmp2.html  tmp3.html
+       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
+    fi
+    rm  tmp1.html  tmp2.html  tmp3.html  tmp4.html
 
     printf "      data for using sequence mode generated"
Index: palm/trunk/SOURCE/CURRENT_MODIFICATIONS
===================================================================
--- palm/trunk/SOURCE/CURRENT_MODIFICATIONS	(revision 335)
+++ palm/trunk/SOURCE/CURRENT_MODIFICATIONS	(revision 336)
@@ -78,4 +78,7 @@
 skip_particles_for_tail (init_particles)
 
+Value of vertical_particle_advection may differ for each particle group
+(advec_particles, header, modules) 
+
 First constant in array den also defined as type double. (eqn_state_seawater)
 
@@ -115,4 +118,8 @@
 on. (time_integration)
 
+Bugfix: qsws was calculated in case of constant heatflux = .FALSE. (prandtl_fluxes)
+
+Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0) (data_output_2d)
+
 Typographical errors (netcdf)
 
@@ -122,4 +129,7 @@
 Small bugfix concerning 3d 64bit netcdf output format (header)
 
+Bugfix: dt_fixed removed from the restart file, because otherwise, no change
+from a fixed to a variable timestep would be possible in restart runs.
+(read_var_list, write_var_list)
 
-advec_particles, check_parameters, cpu_log, header, init_3d_model, init_particles, modules, netcdf, time_integration
+advec_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
Index: palm/trunk/SOURCE/advec_particles.f90
===================================================================
--- palm/trunk/SOURCE/advec_particles.f90	(revision 335)
+++ palm/trunk/SOURCE/advec_particles.f90	(revision 336)
@@ -5,4 +5,5 @@
 ! -----------------
 ! Particle attributes are set with new routine set_particle_attributes.
+! Vertical particle advection depends on the particle group.
 ! Output of NetCDF messages with aid of message handling routine.
 ! Output of messages replaced by message handling routine
@@ -898,5 +899,5 @@
 !--       Same procedure for interpolation of the w velocity-component (adopt
 !--       index i from v velocity-component)
-          IF ( vertical_particle_advection )  THEN
+          IF ( vertical_particle_advection(particles(n)%group) )  THEN
              j = particles(n)%y * ddy
              k = particles(n)%z / dz + offset_ocean_nzt_m1
Index: palm/trunk/SOURCE/data_output_2d.f90
===================================================================
--- palm/trunk/SOURCE/data_output_2d.f90	(revision 335)
+++ palm/trunk/SOURCE/data_output_2d.f90	(revision 336)
@@ -6,4 +6,5 @@
 ! simulated_time in NetCDF output replaced by time_since_reference_point.
 ! Output of NetCDF messages with aid of message handling routine.
+! Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0)
 ! Output of messages replaced by message handling routine.
 !
@@ -578,5 +579,5 @@
 !
 !--                If required, carry out averaging along z
-                   IF ( section(is,s) == -1 )  THEN
+                   IF ( section(is,s) == -1  .AND.  .NOT. two_d )  THEN
 
                       local_2d = 0.0
Index: palm/trunk/SOURCE/eqn_state_seawater.f90
===================================================================
--- palm/trunk/SOURCE/eqn_state_seawater.f90	(revision 335)
+++ palm/trunk/SOURCE/eqn_state_seawater.f90	(revision 336)
@@ -76,5 +76,7 @@
 !
 !--             Pressure is needed in dbar
-                p1 = hyp(0) * 1E-4
+!                p1 = hyp(0) * 1E-4
+!                p1 = 0.0
+                p1 = hyp(k) * 1E-4
                 p2 = p1 * p1
                 p3 = p2 * p1
@@ -132,5 +134,7 @@
 !
 !--       Pressure is needed in dbar
-          p1 = hyp(0) * 1E-4
+!          p1 = hyp(0) * 1E-4
+!          p1 = 0.0
+          p1 = hyp(k) * 1E-4
           p2 = p1 * p1
           p3 = p2 * p1
Index: palm/trunk/SOURCE/header.f90
===================================================================
--- palm/trunk/SOURCE/header.f90	(revision 335)
+++ palm/trunk/SOURCE/header.f90	(revision 336)
@@ -7,5 +7,5 @@
 ! Coupling with independent precursor runs.
 ! Output of messages replaced by message handling routine.
-! Output of cluster_size
+! Output of several additional dvr parameters
 ! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left,
 ! canyon_wall_south, conserve_volume_flow_mode, dp_external, dp_level_b, 
@@ -108,5 +108,5 @@
 
     INTEGER ::  av, bh, blx, bly, bxl, bxr, byn, bys, ch, cwx, cwy, cxl, cxr, &
-                cyn, cys, i, ihost, io, j, l, ll, mpi_type
+                cyn, cys, i, ihost, io, j, l, ll, m, mpi_type
     REAL    ::  cpuseconds_per_simulated_second
 
@@ -1019,4 +1019,5 @@
        i = 1
        l = 0
+       m = 0
        DO WHILE ( mode_dvrp(i) /= ' ' )
           IF ( mode_dvrp(i)(1:10) == 'isosurface' )  THEN
@@ -1024,17 +1025,37 @@
              l = l + 1
              IF ( do3d(0,j) /= ' ' )  THEN
-                WRITE ( io, 361 )  TRIM( do3d(0,j) ), threshold(l)
+                WRITE ( io, 361 )  TRIM( do3d(0,j) ), threshold(l), &
+                                   isosurface_color(:,l)
              ENDIF
           ELSEIF ( mode_dvrp(i)(1:6) == 'slicer' )  THEN
              READ ( mode_dvrp(i), '(6X,I2)' )  j
-             IF ( do2d(0,j) /= ' ' )  WRITE ( io, 362 )  TRIM( do2d(0,j) )
+             m = m + 1
+             IF ( do2d(0,j) /= ' ' )  THEN
+                WRITE ( io, 362 )  TRIM( do2d(0,j) ), &
+                                   slicer_range_limits_dvrp(:,m)
+             ENDIF
           ELSEIF ( mode_dvrp(i)(1:9) == 'particles' )  THEN
-             WRITE ( io, 363 )
+             WRITE ( io, 363 )  dvrp_psize
+             IF ( particle_dvrpsize /= 'none' )  THEN
+                WRITE ( io, 364 )  'size', TRIM( particle_dvrpsize ), &
+                                   dvrpsize_interval
+             ENDIF
+             IF ( particle_color /= 'none' )  THEN
+                WRITE ( io, 364 )  'color', TRIM( particle_color ), &
+                                   color_interval
+             ENDIF
           ENDIF
           i = i + 1
        ENDDO
 
-       IF ( TRIM( topography ) /= 'flat'  .AND.  cluster_size > 1 )  THEN
-          WRITE ( io, 364 )  cluster_size
+       WRITE ( io, 365 )  groundplate_color, superelevation_x, &
+                          superelevation_y, superelevation, clip_dvrp_l, &
+                          clip_dvrp_r, clip_dvrp_s, clip_dvrp_n
+
+       IF ( TRIM( topography ) /= 'flat' )  THEN
+          WRITE ( io, 366 )  topography_color
+          IF ( cluster_size > 1 )  THEN
+             WRITE ( io, 367 )  cluster_size
+          ENDIF
        ENDIF
 
@@ -1301,5 +1322,4 @@
        IF ( particles_per_point > 1 )  WRITE ( io, 489 )  particles_per_point
        WRITE ( io, 495 )  total_number_of_particles
-       IF ( .NOT. vertical_particle_advection )  WRITE ( io, 482 )
        IF ( maximum_number_of_tailpoints /= 0 )  THEN
           WRITE ( io, 483 )  maximum_number_of_tailpoints
@@ -1343,4 +1363,5 @@
           WRITE ( io, 493 )  psl(i), psr(i), pss(i), psn(i), psb(i), pst(i), &
                              pdx(i), pdy(i), pdz(i)
+          IF ( .NOT. vertical_particle_advection(i) )  WRITE ( io, 482 )
        ENDDO
 
@@ -1602,8 +1623,19 @@
             '       Directory:        ',A// &
             '       The sequence contains:')
-361 FORMAT ('       Isosurface of ',A,'  Threshold value: ', E12.3)
-362 FORMAT ('       Sectional plane ',A)
-363 FORMAT ('       Particles')
-364 FORMAT (/'       Polygon reduction for topography: cluster_size = ', I1)
+361 FORMAT ('       Isosurface of ',A,'  Threshold value: ', E12.3/ &
+            '       Isosurface color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)')
+362 FORMAT ('       Slicer plane ',A/ &
+            '       Slicer limits: [',F6.2,',',F6.2,']')
+363 FORMAT ('       Particles'/ &
+            '          particle size:  ',F7.2,' m')
+364 FORMAT ('          particle ',A,' controlled by "',A,'" with interval [', &
+                       F6.2,',',F6.2,']')
+365 FORMAT (/'       Groundplate color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)'/ &
+            '       Superelevation along (x,y,z): (',F4.1,',',F4.1,',',F4.1, &
+                     ')'/ &
+            '       Clipping limits: from x = ',F9.1,' m to x = ',F9.1,' m'/ &
+            '                        from y = ',F9.1,' m to y = ',F9.1,' m')
+366 FORMAT (/'       Topography color: (',F4.2,',',F4,2,',',F4.2,') (R,G,B)')
+367 FORMAT ('       Polygon reduction for topography: cluster_size = ', I1)
 #endif
 #if defined( __spectra )
@@ -1715,5 +1747,5 @@
             '       Particles are sorted every ',F9.1,' s'/)
 481 FORMAT ('       Particles have random start positions'/)
-482 FORMAT ('       Particles are advected only horizontally'/)
+482 FORMAT ('          Particles are advected only horizontally'/)
 483 FORMAT ('       Particles have tails with a maximum of ',I3,' points')
 484 FORMAT ('            Number of tails of the total domain: ',I10/ &
Index: palm/trunk/SOURCE/init_ocean.f90
===================================================================
--- palm/trunk/SOURCE/init_ocean.f90	(revision 335)
+++ palm/trunk/SOURCE/init_ocean.f90	(revision 336)
@@ -24,4 +24,5 @@
     USE control_parameters
     USE eqn_state_seawater_mod
+    USE pegrid
     USE grid_variables
     USE indices
@@ -29,7 +30,9 @@
     IMPLICIT NONE
 
-    INTEGER ::  k
+    INTEGER ::  k, n
 
     REAL    ::  sa_l, pt_l, rho_l
+
+    REAL, DIMENSION(nzb:nzt+1) ::  rho_init
 
     ALLOCATE( hyp(nzb:nzt+1) )
@@ -45,19 +48,49 @@
 
     hyp(nzt)      = hyp(nzt+1) + rho_surface * g * 0.5 * dzu(nzt+1)
-    rho_reference = rho_surface * 0.5 * dzu(nzt+1)
+    rho_init(nzt) = rho_surface
 
     DO  k = nzt-1, 0, -1
+       hyp(k) = hyp(k+1) + rho_surface * g * dzu(k)
+    ENDDO
 
-       sa_l = 0.5 * ( sa_init(k) + sa_init(k+1) )
-       pt_l = 0.5 * ( pt_init(k) + pt_init(k+1) )
+    IF ( myid == 0 )  THEN
+       print*,'hydro pres using rho_surface'
+       DO  k = nzt+1, 0, -1
+          print*, 'k = ', k, ' hyp = ', hyp(k)
+       ENDDO
+       print*, ' '
+    ENDIF
 
-       rho_l = eqn_state_seawater_func( hyp(k+1), pt_l, sa_l )
+    DO  n = 1, 5
 
-       hyp(k)        = hyp(k+1) + rho_l * g * dzu(k+1)
-       rho_reference = rho_reference + rho_l * dzu(k+1)
+       rho_reference = rho_surface * 0.5 * dzu(nzt+1)
+
+       DO  k = nzt-1, 0, -1
+
+          sa_l = 0.5 * ( sa_init(k) + sa_init(k+1) )
+          pt_l = 0.5 * ( pt_init(k) + pt_init(k+1) )
+
+          rho_init(k) = eqn_state_seawater_func( hyp(k), pt_l, sa_l )
+
+          rho_reference = rho_reference + rho_init(k) * dzu(k+1)
+
+       ENDDO
+
+       rho_reference = rho_reference / ( zw(nzt) - zu(nzb) )
+
+       DO  k = nzt-1, 0, -1
+          hyp(k) = hyp(k+1) + g * 0.5 * ( rho_init(k) + rho_init(k+1 ) ) * &
+                              dzu(k+1)
+       ENDDO
+
+       IF ( myid == 0 )  THEN
+          print*,'hydro pres / rho  n = ', n
+          DO  k = nzt+1, 0, -1
+             print*, 'k = ', k, ' hyp = ', hyp(k), ' rho = ', rho_init(k)
+          ENDDO
+          print*, ' '
+       ENDIF
 
     ENDDO
-
-    rho_reference = rho_reference / ( zw(nzt) - zu(nzb) )
 
 !
@@ -70,5 +103,5 @@
 
        prho_reference = prho_reference + dzu(k+1) * &
-                        eqn_state_seawater_func( hyp(0), pt_l, sa_l )
+                        eqn_state_seawater_func( 0.0, pt_l, sa_l )
 
     ENDDO
Index: palm/trunk/SOURCE/init_particles.f90
===================================================================
--- palm/trunk/SOURCE/init_particles.f90	(revision 335)
+++ palm/trunk/SOURCE/init_particles.f90	(revision 336)
@@ -54,4 +54,5 @@
     USE arrays_3d
     USE control_parameters
+    USE dvrp_variables
     USE grid_variables
     USE indices
@@ -441,4 +442,11 @@
 
 !
+!--    Particles will probably become none-uniform, if their size and color
+!--    will be determined by flow variables
+       IF ( particle_color /= 'none'  .OR.  particle_dvrpsize /= 'none' )  THEN
+          uniform_particles = .FALSE.
+       ENDIF
+
+!
 !--    Set the beginning of the particle tails and their age
        IF ( use_particle_tails )  THEN
Index: palm/trunk/SOURCE/modules.f90
===================================================================
--- palm/trunk/SOURCE/modules.f90	(revision 335)
+++ palm/trunk/SOURCE/modules.f90	(revision 336)
@@ -10,4 +10,5 @@
 ! interval_*_dvrp_prt, isosurface_color, particle_color, particle_dvrpsize,
 ! topography color in dvrp_variables,
+! vertical_particle_advection is a 1d-array,
 ! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left, 
 ! canyon_wall_south, conserve_volume_flow_mode, coupling_start_time,
@@ -971,6 +972,9 @@
                 uniform_particles = .TRUE., use_particle_tails = .FALSE.,      &
                 use_sgs_for_particles = .FALSE.,                               &
-                vertical_particle_advection = .TRUE.,                          &
                 write_particle_statistics = .FALSE.
+
+    LOGICAL, DIMENSION(max_number_of_particle_groups) ::                       &
+                vertical_particle_advection = .TRUE.
+
     LOGICAL, DIMENSION(:), ALLOCATABLE ::  particle_mask, tail_mask
 
Index: palm/trunk/SOURCE/package_parin.f90
===================================================================
--- palm/trunk/SOURCE/package_parin.f90	(revision 335)
+++ palm/trunk/SOURCE/package_parin.f90	(revision 336)
@@ -52,5 +52,5 @@
                                   dt_dvrp, dvrpsize_interval, dvrp_directory,  &
                                   dvrp_file, dvrp_host, dvrp_output,           &
-                                  dvrp_password, dvrp_username,                &
+                                  dvrp_password, dvrp_psize, dvrp_username,    &
                                   groundplate_color, isosurface_color,         &
                                   mode_dvrp, particle_color, particle_dvrpsize,&
@@ -67,5 +67,5 @@
                                   density_ratio, radius, dt_dopts,             &
                                   dt_min_part, dt_prel, dt_sort_particles,     &
-                                  dt_write_particle_data, dvrp_psize,          &
+                                  dt_write_particle_data,                      &
                                   end_time_prel, initial_weighting_factor,     &
                                   maximum_number_of_particles,                 &
Index: palm/trunk/SOURCE/read_var_list.f90
===================================================================
--- palm/trunk/SOURCE/read_var_list.f90	(revision 335)
+++ palm/trunk/SOURCE/read_var_list.f90	(revision 336)
@@ -4,4 +4,5 @@
 ! Current revisions:
 ! -----------------
+! dt_fixed is read into a dummy variable.
 ! Output of messages replaced by message handling routine.
 ! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left, 
@@ -77,4 +78,6 @@
     CHARACTER (LEN=10) ::  binary_version, version_on_file
     CHARACTER (LEN=30) ::  variable_chr
+
+    LOGICAL ::  ldum
 
 
@@ -266,5 +269,9 @@
              READ ( 13 )  drag_coefficient
           CASE ( 'dt_fixed' )
-             READ ( 13 )  dt_fixed
+             READ ( 13 )  ldum   ! restart files created before rev 333
+                                 ! contained dt_fixed by mistake; it is still
+                                 ! read here in order to allow usage of these
+                                 ! older restart files; can be removed in a
+                                 ! later version
           CASE ( 'dt_pr_1d' )
              READ ( 13 )  dt_pr_1d
Index: palm/trunk/SOURCE/write_var_list.f90
===================================================================
--- palm/trunk/SOURCE/write_var_list.f90	(revision 335)
+++ palm/trunk/SOURCE/write_var_list.f90	(revision 336)
@@ -4,4 +4,6 @@
 ! Actual revisions:
 ! -----------------
+! bugfix: -dt_fixed, because otherwise, restart runs cannot change from a
+! fixed to a free timestep.
 ! +canyon_height, canyon_width_x, canyon_width_y, canyon_wall_left, 
 ! canyon_wall_south, conserve_volume_flow_mode, coupling_start_time,
@@ -194,6 +196,4 @@
     WRITE ( 14 )  'drag_coefficient              '
     WRITE ( 14 )  drag_coefficient
-    WRITE ( 14 )  'dt_fixed                      '
-    WRITE ( 14 )  dt_fixed
     WRITE ( 14 )  'dt_pr_1d                      '
     WRITE ( 14 )  dt_pr_1d
