Changeset 555 for palm/trunk/DOC/app


Ignore:
Timestamp:
Sep 7, 2010 7:32:53 AM (11 years ago)
Author:
raasch
Message:

New:
---

Changed:


Documentation for surface_heatflux in case of prandtl_layer = .F. improved.

bugfix for wrong netcdf/3.6.3 module on lcsgi (mbuild, mrun)

Errors:


Bugfix in if statement (disturb_heatflux)

Bugfix: in 2201 statement: closing " was missing (interpret_config)

Bugfix: default setting of nzb_local for flat topography (init_grid)

Bugfix: wrong dimension used for ts_value_l (user_statistics)

disturb_heatflux, init_grid, interpret_config, user_statistics

Location:
palm/trunk/DOC/app
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • palm/trunk/DOC/app/chapter_3.5.3.html

    r132 r555  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
     3
    34<meta http-equiv="CONTENT-TYPE" content="text/html; charset=windows-1252"><title>PALM chapter 3.5.3</title> <meta name="GENERATOR" content="StarOffice 7 (Win32)"> <meta name="AUTHOR" content="Siegfried Raasch"> <meta name="CREATED" content="20040802;14001660"> <meta name="CHANGED" content="20041112;14483720"> <meta name="KEYWORDS" content="parallel LES model"> <style>
    45<!--
    56@page { size: 21cm 29.7cm }
    67-->
    7 </style></head>
    8 <body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.5.3 Definition of user-defined
     8</style></head><body style="direction: ltr;" lang="en-US"><h3 style="line-height: 100%;">3.5.3 Definition of user-defined
    99subdomains</h3>
    1010<p style="line-height: 100%;">By default, the values of
     
    2020<p style="line-height: 100%;">The exact definition of
    2121these subdomains
    22 has to be made by the user within the user-defined subroutine
    23 <tt><font style="font-size: 10pt;" size="2">init_user</font></tt>.
     22has to be made by the user within the user-defined subroutine <tt><font style="font-size: 10pt;" size="2">user_init</font></tt>.
    2423The
    2524subdomains are defined with a mask array named <tt><font style="font-size: 10pt;" size="2">rmask</font></tt>,
     
    9392if
    9493the user sets <a href="chapter_4.1.html#statistic_regions">statistic_regions</a>
    95 &ge; <i>1</i>. Beyond that, names for the user-defined
     94&#8805; <i>1</i>. Beyond that, names for the user-defined
    9695subdomains can be
    9796assigned
  • palm/trunk/DOC/app/chapter_4.1.html

    r531 r555  
    11<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
    22<html><head>
     3
    34
    45
     
    98479848the pressure
    98489849boundary condition <a href="#bc_p_b">bc_p_b</a>
    9849 = <i>'neumann+inhomo'</i>&nbsp; is not allowed. </p>
     9850= <i>'neumann+inhomo'</i>&nbsp; is not allowed.<br>
     9851</p>
     9852      <p>If the Prandtl-layer is switched off and fluxes shall be prescribed at the surface (by setting <a href="#surface_heatflux">surface_heatflux</a>), it is required to set the parameter <a href="#use_surface_fluxes">use_surface_fluxes</a> = <span style="font-style: italic;">.T.</span>.<br>
     9853 </p>
     9854
    98509855
    98519856
     
    1277412779can be used to impose random perturbations on the (homogeneous) surface
    1277512780heat
    12776 flux field <span style="font-style: italic;">shf</span>.&nbsp;</p>
     12781flux field <span style="font-style: italic;">shf</span>.<br>
     12782</p>
     12783      <p><span style="font-weight: bold;">Attention:</span><br>
     12784Setting of <span style="font-weight: bold;">surface_heatflux</span> requires setting of <a href="#use_surface_fluxes">use_surface_fluxes</a>=<span style="font-style: italic;">.T.</span>, if the Prandtl-layer is switched off (<a href="#prandtl_layer">prandtl_layer</a>=<span style="font-style: italic;">.F.</span>).&nbsp;</p>
     12785
    1277712786
    1277812787
  • palm/trunk/DOC/app/chapter_4.2.html

    r531 r555  
    68966896
    68976897
    6898  <td style="vertical-align: top;">Total
     6898 <td style="vertical-align: top;">Total (resolved and subgrid-scale)
    68996899kinetic energy of
    69006900the flow (in m<sup>2</sup>/s<sup>2</sup>)
     
    69266926
    69276927
    6928  <td style="vertical-align: top;">Perturbation
    6929 kinetic
     6928 <td style="vertical-align: top;">Resolved-scale kinetic
    69306929energy of the flow (in m<sup>2</sup>/s<sup>2</sup>)<sup>
    69316930            </sup>(normalized
     
    1189011889
    1189111890
    11892       <td style="vertical-align: top;"><i>ŽreflectŽ</i></td>
     11891      <td style="vertical-align: top;"><i>ï¿œreflectï¿œ</i></td>
    1189311892
    1189411893
     
    1191511914default, particles are reflected at the bottom boundary.
    1191611915Alternatively, a particle absorption can set by <b>bc_par_b</b>
    11917 = <i>ŽabsorbŽ</i>.</p>
     11916= <i>ï¿œabsorbï¿œ</i>.</p>
    1191811917
    1191911918
     
    1195811957
    1195911958
    11960       <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
     11959      <td style="vertical-align: top;"><i>ï¿œcyclicï¿œ</i></td>
    1196111960
    1196211961
     
    1198411983are used along x.
    1198511984Alternatively, reflection (<b>bc_par_lr</b>
    11986 = <i>ŽreflectŽ</i>) or absorption (<b>bc_par_lr</b>
    11987 = <i>ŽabsorbŽ</i>)
     11985= <i>ï¿œreflectï¿œ</i>) or absorption (<b>bc_par_lr</b>
     11986= <i>ï¿œabsorbï¿œ</i>)
    1198811987can be set. <br>
    1198911988
     
    1204612045
    1204712046
    12048       <td style="vertical-align: top;"><i>ŽcyclicŽ</i></td>
     12047      <td style="vertical-align: top;"><i>ï¿œcyclicï¿œ</i></td>
    1204912048
    1205012049
     
    1207212071are used along y.
    1207312072Alternatively, reflection (<b>bc_par_ns</b>
    12074 = <i>ŽreflectŽ</i>) or absorption (<b>bc_par_ns</b>
    12075 = <i>ŽabsorbŽ</i>)
     12073= <i>ï¿œreflectï¿œ</i>) or absorption (<b>bc_par_ns</b>
     12074= <i>ï¿œabsorbï¿œ</i>)
    1207612075can be set.<br>
    1207712076
     
    1212412123
    1212512124
    12126       <td style="vertical-align: top;"><i>ŽabsorbŽ</i></td>
     12125      <td style="vertical-align: top;"><i>ï¿œabsorbï¿œ</i></td>
    1212712126
    1212812127
     
    1214912148particles are absorbed at the top boundary.
    1215012149Alternatively, a reflection condition can be set by <b>bc_par_t</b>
    12151 = <i>ŽreflectŽ</i>.</p>
     12150= <i>ï¿œreflectï¿œ</i>.</p>
    1215212151
    1215312152
  • palm/trunk/DOC/app/chapter_4.5.7.html

    r388 r555  
    11<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
    22<html><head>
     3
    34
    45<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>
     
    6869computer 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
    6970RRZN. Apart from graphic data an additional html file is created, which
    70 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><p style="line-height: 100%;">In the following, please replace the string<span style="font-family: Courier New,Courier,monospace; font-weight: bold;"> &lt;UNAME&gt; </span>with your IMUK username, wherever it appears. Please also replace the string<span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold;"> &lt;UDIR&gt;</span> </span>with a subdirectory name of your choice. <span style="font-weight: bold;"></span> </p>
     71can 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 (June 2010):</span></p><p style="line-height: 100%;">In the following, please replace the string<span style="font-family: Courier New,Courier,monospace; font-weight: bold;"> &lt;UNAME&gt; </span>with your IMUK username, wherever it appears. Please also replace the string<span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold;"> &lt;UDIR&gt;</span> </span>with a subdirectory name of your choice. <span style="font-weight: bold;"></span> </p>
    7172<ol><li>
    7273Add 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;
    7374-I/home/h/niksiraa/dvr_mvapich2/lib&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
    7475&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
    75 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 = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>',<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; dvrp_host = '130.75.105.2',<br>&nbsp;
     76parallel</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 = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>',<br>&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; dvrp_host = '130.75.105.6',<br>&nbsp;
    7677&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp;
    77 dvrp_directory = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>/<span style="font-weight: bold;">&lt;UDIR&gt;</span>', ... /<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 &nbsp;</span>.<span style="font-family: Courier New,Courier,monospace;"><br><br></span></li><li>On the IMUK-system, create a subdirectory in which the dvrp-data are stored and give it access permit for group <span style="font-style: italic;">palm</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mkdir /data/raasch/Dvrp_daten/<span style="font-weight: bold;">&lt;UNAME&gt;<br>
    78 </span>&nbsp;&nbsp; chmod g+rwx</span><span style="font-family: Courier New,Courier,monospace;"> /data/raasch/Dvrp_daten/<span style="font-weight: bold;">&lt;UNAME&gt;</span></span><br><br>This directory has to be created only once, before dvrp is used for the first time.<br>
    79 <br></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;">'<span style="font-weight: bold;">&lt;UNAME&gt;</span>/movie_1'</span>, the dvrp-data are stored under&nbsp;<span style="font-family: Courier New,Courier,monospace;">/data/raasch/Dvrp_daten/<span style="font-weight: bold;">&lt;UNAME&gt;</span>/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/&lt;UNAME&gt;/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></span><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>.
     78dvrp_directory = '<span style="font-weight: bold;">&lt;UNAME&gt;</span>/<span style="font-weight: bold;">&lt;UDIR&gt;</span>', ... /<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 &nbsp;</span>.<span style="font-family: Courier New,Courier,monospace;"><br><br></span></li><li>Ask the IMUK system operator (Notker Fechner) to mount the filesystem<span style="font-family: Courier New,Courier,monospace;"> /dvrdata </span>on your local computer.<br>
     79    <br>
     80</li>
     81  <li>On the IMUK-system (your local computer), create a subdirectory
     82in which the dvrp-data are stored and give it access permit for group <span style="font-style: italic;">palm</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">&nbsp; &nbsp;mkdir /dvrdata/<span style="font-weight: bold;">&lt;UNAME&gt;<br>
     83</span>&nbsp;&nbsp; chmod g+rwx /dvrdata</span><span style="font-family: Courier New,Courier,monospace;">/<span style="font-weight: bold;">&lt;UNAME&gt;</span></span><br><br><span style="font-weight: bold;">Steps 3. and 4. have to be done only once, before dvrp is used for the first time.</span><br>
     84<br></li>
     85<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;">/dvrdata</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;">'<span style="font-weight: bold;">&lt;UNAME&gt;</span>/movie_1'</span>, the dvrp-data are stored under&nbsp;<span style="font-family: Courier New,Courier,monospace;">/dvrdata/<span style="font-weight: bold;">&lt;UNAME&gt;</span>/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;">/dvrdata/&lt;UNAME&gt;/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></span><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>.
    8086All streams (and static scenes) are collected to one sequence (one
    8187static scene), which can be displayed with a browser without using the
     
    8389show animations on a notebook without beeing connected to the internet.
    8490When the script is called with this option, the sequence is generated
    85 in subdirectory sequence_data. Copy this subdirectory and the file
    86 all_streams_sequence.html to a directory on your local computer and
    87 open the file all_streams_sequence.html with your browser. For this,
     91in subdirectory sequence_data. Copy this subdirectory and the file<span style="font-family: Courier New,Courier,monospace;">
     92all_streams_sequence.html </span>to a directory on your local computer and
     93open the file<span style="font-family: Courier New,Courier,monospace;"> all_streams_sequence.html </span>with your browser. For this,
    8894you 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/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>" !
    8995<hr><p style="line-height: 100%;"><br>
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