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Ignore:
Timestamp:
Sep 1, 2010 2:09:06 PM (14 years ago)
Author:
weinreis
Message:

several parameters for masked output are replaced by arrays

File:
1 edited

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  • palm/trunk/DOC/tec/technical_documentation.html

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    29 <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <meta content="Mozilla/4.73 [en] (X11; U; HP-UX B.10.20 9000/782) [Netscape]" name="GENERATOR"> <meta content="Siegfried Raasch" name="Author"> <meta content="parallel LES model" name="Keywords"><title>PALM technical/numerical documentation</title></head><body><font size="+4">PALM&nbsp;&nbsp;
    30 </font>a
    31 <b>pa</b>rallelized
    32 <b>L</b>ES <b>m</b>odel
    33 <br><hr width="100%">
    34 <br><font size="+2">technical/numerical documentation</font>
    35 <br>&nbsp;
    36 <br>&nbsp;
    37 <br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
    38 </tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
    39 </span></td> </tr>
    40 <tr nosave=""> <td nosave=""><b>Last
    41 change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id$</b></td> </tr>
    42 </tbody>
    43 </table><hr width="100%">
    44 <p><font size="+2">Table of contents</font>
    45 <br>&nbsp;
    46 <br>&nbsp;
    47 </p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
    48 History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
    49 How to change the source
    50 code and how to document modifications<br>
    51  </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
    52 Description of selected model numerics<br>
    53 &nbsp;</p>
    54 </ul><b></b><br>
    55 
    56 <h2><a name="Kapitel1.0"></a>1.0&nbsp;
    57 History of changes</h2>
    58 The following table documents all changes to the PALM repository since 2009. Older changes can be found <a href="tec_doc_1998-2008.html">here</a>.<br>
    59 <br>
    60 Entries in the fifth column specify the type of the change:
    61 change&nbsp;
    62 of existing code (C), new code (N) or bugfix (B). More detailed
    63 information
    64 about the changes may sometimes be found in the header comment lines of the
    65 respective
    66 routines.
    67 <br>&nbsp;
    68 <br>
    69 <table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
    70   <tbody>
    71     <tr>
    72       <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
    73       </td>
    74       <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
    75       </td>
    76       <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
    77       </td>
    78       <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
    79       </td>
    80       <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
    81       </td>
    82       <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
    83       </td>
    84       <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
    85       </td>
    86     </tr>
    87    
    88    
    89    
    90    
    91    
    92    
    93    
    94    
    95    
    96     <tr>
    97       <td style="vertical-align: top;">17/08/10<br>
    98       </td>
    99       <td style="vertical-align: top;">BM<br>
    100       </td>
    101       <td style="vertical-align: top;">544<br>
    102       </td>
    103       <td style="vertical-align: top;">3.7a<br>
    104       </td>
    105       <td style="vertical-align: top;">B/C/N<br>
    106       </td>
    107       <td style="vertical-align: top;">adjustments for lcxt4; bugfix (mbuild): loading of user-defined modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway<br>
    108       </td>
    109       <td style="vertical-align: top;">mrun, mbuild, subjob<br>
    110       </td>
    111     </tr>
    112 
    113     <tr>
    114       <td style="vertical-align: top;">15/06/10<br>
    115       </td>
    116       <td style="vertical-align: top;">RH<br>
    117       </td>
    118       <td style="vertical-align: top;">540<br>
    119       </td>
    120       <td style="vertical-align: top;">3.7a<br>
    121       </td>
    122       <td style="vertical-align: top;">C<br>
    123       </td>
    124       <td style="vertical-align: top;">ssh from compute nodes to login
    125 nodes on hosts lcsgih/lcsgib is done using the names
    126 hicegate0/bicegate0 instead of the IP addresses<br>
    127       </td>
    128       <td style="vertical-align: top;">mrun<br>
    129       </td>
    130     </tr>
    131 <tr>
    132       <td style="vertical-align: top;">21/04/10<br>
    133       </td>
    134       <td style="vertical-align: top;">RH<br>
    135       </td>
    136       <td style="vertical-align: top;">532<br>
    137       </td>
    138       <td style="vertical-align: top;">3.7a<br>
    139       </td>
    140       <td style="vertical-align: top;">C<br>
    141       </td>
    142       <td style="vertical-align: top;">
    143 Large scale vertical motion (subsidence/ascent) can be added as
    144 additional source to the prognostic equation for humidity/passive scalar<br>
    145 &nbsp;<br>
    146 character length for dopr_unit enlarged<br>
    147       <br>
    148 Adjustment of the NCL scripts<span style="font-family: Courier New,Courier,monospace;"> </span>to allow for output of png files <br>
    149  </td>
    150       <td style="vertical-align: top;">modules, prognostic_equations<br>
    151       <br>
    152 .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
    153       </td>
    154     </tr>
    155     <tr>
    156       <td style="vertical-align: top;"><br>
    157       </td>
    158       <td style="vertical-align: top;"><br>
    159       </td>
    160       <td style="vertical-align: top;"><br>
    161       </td>
    162       <td style="vertical-align: top;"><br>
    163       </td>
    164       <td style="vertical-align: top;">B<br>
    165       </td>
    166       <td style="vertical-align: top;">Bugfix: unit of hyp changed to dbar<br>
    167       </td>
    168       <td style="vertical-align: top;">check_parameters<br>
    169       </td>
    170     </tr>
    171 <tr>
    172       <td style="vertical-align: top;">01/04/10<br>
    173       </td>
    174       <td style="vertical-align: top;">RH<br>
    175       </td>
    176       <td style="vertical-align: top;">530<br>
    177       </td>
    178       <td style="vertical-align: top;">3.7a<br>
    179       </td>
    180       <td style="vertical-align: top;">B<br>
    181       </td>
    182       <td style="vertical-align: top;">Bugfix: treatment of special character * in NCL variables containing lists corrected<br>
    183       </td>
    184       <td style="vertical-align: top;">palmplot<br>
    185       </td>
    186     </tr>
    187 <tr>
    188       <td style="vertical-align: top;">31/03/10<br>
    189       </td>
    190       <td style="vertical-align: top;">RH<br>
    191       </td>
    192       <td style="vertical-align: top;">529<br>
    193       </td>
    194       <td style="vertical-align: top;">3.7a<br>
    195       </td>
    196       <td style="vertical-align: top;">C<br>
    197       </td>
    198       <td style="vertical-align: top;">List of variable names have to specified using blank separated lists and single quotes<br>
    199       </td>
    200       <td style="vertical-align: top;">palmplot<br>
    201       </td>
    202     </tr>
    203 <tr>
    204       <td style="vertical-align: top;">30/03/10<br>
    205       </td>
    206       <td style="vertical-align: top;">RH<br>
    207       </td>
    208       <td style="vertical-align: top;">526<br>
    209       </td>
    210       <td style="vertical-align: top;">3.7a<br>
    211       </td>
    212       <td style="vertical-align: top;">C<br>
    213       </td>
    214       <td style="vertical-align: top;">Adjustment of the NCL scripts and <span style="font-family: Courier New,Courier,monospace;">palmplot </span>to allow for special characters in NetCDF variable names <br>
    215       </td>
    216       <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
    217       </td>
    218     </tr>
    219 <tr>
    220       <td style="vertical-align: top;">30/03/10<br>
    221       </td>
    222       <td style="vertical-align: top;">SR<br>
    223       </td>
    224       <td style="vertical-align: top;">525<br>
    225       </td>
    226       <td style="vertical-align: top;">3.7a<br>
    227       </td>
    228       <td style="vertical-align: top;">B<br>
    229       </td>
    230       <td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br>
    231       </td>
    232       <td style="vertical-align: top;">check_parameters<br>
    233       </td>
    234     </tr>
    235 <tr>
    236       <td style="vertical-align: top;">19/03/10<br>
    237       </td>
    238       <td style="vertical-align: top;">SR<br>
    239       </td>
    240       <td style="vertical-align: top;">520<br>
    241       </td>
    242       <td style="vertical-align: top;">3.7a<br>
    243       </td>
    244       <td style="vertical-align: top;">N<br>
    245       </td>
    246       <td style="vertical-align: top;">NetCDF4 support for particle
    247 data. Total number of particles is allowed to increase during the run,
    248 when netcdf_data_format &gt; <span style="font-style: italic;">2</span> is used.<br>
    249       </td>
    250       <td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
    251       </td>
    252     </tr>
    253     <tr>
    254       <td style="vertical-align: top;"><br>
    255       </td>
    256       <td style="vertical-align: top;"><br>
    257       </td>
    258       <td style="vertical-align: top;"><br>
    259       </td>
    260       <td style="vertical-align: top;"><br>
    261       </td>
    262       <td style="vertical-align: top;">C<br>
    263       </td>
    264       <td style="vertical-align: top;">Special characters like * and "
    265 are now allowed for NetCDF variable names. Replacement of these
    266 characters has been removed (routine clean_netcdf_varname removed)<br>
    267       </td>
    268       <td style="vertical-align: top;"><br>
    269       </td>
    270     </tr>
    271 <tr>
    272       <td style="vertical-align: top;">18/03/10<br>
    273       </td>
    274       <td style="vertical-align: top;">SR<br>
    275       </td>
    276       <td style="vertical-align: top;">516<br>
    277       </td>
    278       <td style="vertical-align: top;">3.7a<br>
    279       </td>
    280       <td style="vertical-align: top;">N<br>
    281       </td>
    282       <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
    283       </td>
    284       <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
    285       </td>
    286     </tr>
    287     <tr>
    288       <td style="vertical-align: top;"><br>
    289       </td>
    290       <td style="vertical-align: top;"><br>
    291       </td>
    292       <td style="vertical-align: top;"><br>
    293       </td>
    294       <td style="vertical-align: top;"><br>
    295       </td>
    296       <td style="vertical-align: top;">B<br>
    297       </td>
    298       <td style="vertical-align: top;">opt=1 is forced for PGI-compiler in routine<span style="font-family: Courier New,Courier,monospace;"> buoyancy </span>by compiler-directive. Otherwise, program aborts with SIGFPE.<br>
    299       </td>
    300       <td style="vertical-align: top;">buoyancy<br>
    301       </td>
    302     </tr>
    303 <tr>
    304       <td style="vertical-align: top;">16/03/10<br>
    305       </td>
    306       <td style="vertical-align: top;">RH<br>
    307       </td>
    308       <td style="vertical-align: top;">513<br>
    309       </td>
    310       <td style="vertical-align: top;">3.7a<br>
    311       </td>
    312       <td style="vertical-align: top;">N<br>
    313       </td>
    314       <td style="vertical-align: top;">NCL scripts can be run with the shell script <span style="font-family: Courier New,Courier,monospace;">palmplot.</span><br>
    315       </td>
    316       <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl<br>
    317       </td>
    318     </tr>
    319 <tr>
    320       <td style="vertical-align: top;">12/03/10<br>
    321       </td>
    322       <td style="vertical-align: top;">SR<br>
    323       </td>
    324       <td style="vertical-align: top;">509<br>
    325       </td>
    326       <td style="vertical-align: top;">3.7a<br>
    327       </td>
    328       <td style="vertical-align: top;">B<br>
    329       </td>
    330       <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
    331       </td>
    332       <td style="vertical-align: top;">mbuild<br>
    333       </td>
    334     </tr>
    335 <tr>
    336       <td style="vertical-align: top;">08/03/10<br>
    337       </td>
    338       <td style="vertical-align: top;">SR<br>
    339       </td>
    340       <td style="vertical-align: top;">506<br>
    341       </td>
    342       <td style="vertical-align: top;">3.7a<br>
    343       </td>
    344       <td style="vertical-align: top;">C<br>
    345       </td>
    346       <td style="vertical-align: top;">hack for better usage of <span style="font-weight: bold;">mrun</span> on Kyoto computing center machine (<span style="font-family: Courier New,Courier,monospace;">lckyoto</span>)<br>
    347       </td>
    348       <td style="vertical-align: top;">mrun<br>
    349       </td>
    350     </tr>
    351 <tr>
    352       <td style="vertical-align: top;">03/03/10<br>
    353       </td>
    354       <td style="vertical-align: top;">SR<br>
    355       </td>
    356       <td style="vertical-align: top;">504<br>
    357       </td>
    358       <td style="vertical-align: top;">3.7a<br>
    359       </td>
    360       <td style="vertical-align: top;">C<br>
    361       </td>
    362       <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> is now directly called within <span style="font-weight: bold;">mrun</span> and must not be given by an output command in the configuration file any more. Please remove the respective output command (<span style="font-family: Courier New,Courier,monospace;">OC:combine_plot_fields.x</span>) from your configuration file!<br>
    363       <br>
    364 Utility programs (<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>, <span style="font-family: Courier New,Courier,monospace;">interpret_config</span>) are created by <span style="font-weight: bold;">mbuild</span> separately for each block in the configuration file. Depending on option <span style="font-family: Courier New,Courier,monospace;">-K</span>, <span style="font-weight: bold;">mrun</span> is using the utility programs for the respective block.<br>
    365       <br>
    366 Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
    367       <br>
    368 Default configuration files updated.<br>
    369       </td>
    370       <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
    371       </td>
    372     </tr>
    373 <tr>
    374       <td style="vertical-align: top;">02/03/10<br>
    375       </td>
    376       <td style="vertical-align: top;">SR<br>
    377       </td>
    378       <td style="vertical-align: top;">496<br>
    379       </td>
    380       <td style="vertical-align: top;">3.7a<br>
    381       </td>
    382       <td style="vertical-align: top;">C<br>
    383       </td>
    384       <td style="vertical-align: top;">Particle data for restart runs are only written if environment variable <span style="font-family: Courier New,Courier,monospace;">write_binary</span> = <span style="font-style: italic;">.T.</span>, i.e. particle data are now handled in the same way as the other restart data.<br>
    385       </td>
    386       <td style="vertical-align: top;">palm<br>
    387       </td>
    388     </tr>
    389 <tr>
    390       <td style="vertical-align: top;">01/03/10<br>
    391       </td>
    392       <td style="vertical-align: top;">SR<br>
    393       </td>
    394       <td style="vertical-align: top;">494<br>
    395       </td>
    396       <td style="vertical-align: top;">3.7a<br>
    397       </td>
    398       <td style="vertical-align: top;">N<br>
    399       </td>
    400       <td style="vertical-align: top;">Output in NetCDF4-format.<br>
    401       <br>
    402 NetCDF4 allows for parallel I/O. Also, variables are not limited in
    403 size any more (i.e. arrays can be larger than 2GB). The new
    404 d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>.can be used to select among the different NetCDF file formats (<span style="font-style: italic;">1</span>: classic format, <span style="font-style: italic;">2</span>: 64-bit-offset format (this is now the default), <span style="font-style: italic;">3</span>: NetCDF4/HDF5 format, <span style="font-style: italic;">4</span>: NetCDF4 format with NF90_CLASSIC_MODEL bit set). Setting <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> &gt; <span style="font-style: italic;">2</span>
    405 only affects 2d- and 3d-output, i.e. there is no parallel output for
    406 profiles, time series, spectra, and particles. Parallel output of
    407 particle data may realized in the future.<br>
    408       <br>
    409 In case of parallel output, all PEs write into one file, which means that postprocessing the data with <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>
    410 (merging data from single files - one per PE - into one file) is not
    411 neccessary. In this case, flag files are automatically set, telling <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> that nothing is to be done.<br>
    412       <br>
    413 Using NetCDF4 format requires a NetCDF4/HDF library. Respective
    414 settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
    415 HLRN can be found in the new example configuration file <span style="font-family: Courier New,Courier,monospace;">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</span><br>
    416       <br>
    417       <span style="font-weight: bold;">Attention:</span><br>
    418 So far, NetCDF parallel I/O has only been tested a little. Further
    419 performance optimizations may be required, especially in case of large
    420 data sets (e.g. data chunking, or lustre file system settings with <span style="font-family: Courier New,Courier,monospace;">lfs setstripe</span>). <span style="font-weight: bold;">Please report bugs and performance problems immediately!</span><br>
    421       <br>
    422       <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
    423       <br>
    424 Modules to be loaded for compilation (mbuild) or job execution (mrun) can/should now be given in the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) using variable <span style="font-family: Courier New,Courier,monospace;">modules</span>. Example:<br>
    425       <br>
    426       <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %modules&nbsp;&nbsp;&nbsp;&nbsp; ifort/11.0.069:netcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; lcsgih parallel</span><br>
    427       <br>
    428 This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
    429       <br>
    430       <span style="font-weight: bold;">WARNING:</span><br>
    431       <span style="font-weight: bold;">All fixed settings of modules in the scripts mbuild, mrun, and subjob have been removed! Please set the <span style="font-family: Courier New,Courier,monospace;">modules</span> variable appropriately and remove the mpilib variable in your configuration file.<br>
    432       <br>
    433 </span>Compilation time can be reduced be using parallel make. The
    434 number of allowed simultaneous compiler calls (threads) is set in the
    435 configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
    436       <br>
    437       <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
    438       <br>
    439 allows a maximum of 4 routines to be compiled simultaneously (provided
    440 that the makefile does not show any dependencies between these
    441 routines).<span style="font-weight: bold;"><br>
    442       </span>
    443       </td>
    444       <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
    445       <br>
    446 combine_plot_fields<br>
    447       <br>
    448 mbuild, mrun, subjob<br>
    449       </td>
    450     </tr>
    451     <tr>
    452       <td style="vertical-align: top;"><br>
    453       </td>
    454       <td style="vertical-align: top;"><br>
    455       </td>
    456       <td style="vertical-align: top;"><br>
    457       </td>
    458       <td style="vertical-align: top;"><br>
    459       </td>
    460       <td style="vertical-align: top;">C<br>
    461       </td>
    462       <td style="vertical-align: top;">d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit</span> and <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span> have been removed. Use the new d3par-variable <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> = <span style="font-style: italic;">2</span>
    463 for choosing the NetCDF 64bit-offset format (this is the default from
    464 now on). The offset-format can not be set independently for the
    465 3d-output-data any more.<br>
    466       <br>
    467 d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask_av</span>, and variables <span style="font-family: Courier New,Courier,monospace;">nc_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">format_parallel_io</span> removed. They are replaced by the new parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>. This change concerns the masked data output, which is still not documented.<br>
    468       </td>
    469       <td style="vertical-align: top;">check_open, close_file,<br>
    470 data_output_mask, header, init_masks, modules, parin<br>
    471       <br>
    472       </td>
    473     </tr>
    474     <tr>
    475       <td style="vertical-align: top;"><br>
    476       </td>
    477       <td style="vertical-align: top;"><br>
    478       </td>
    479       <td style="vertical-align: top;"><br>
    480       </td>
    481       <td style="vertical-align: top;"><br>
    482       </td>
    483       <td style="vertical-align: top;">B<br>
    484       </td>
    485       <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
    486       <br>
    487 Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
    488       </td>
    489       <td style="vertical-align: top;">user_statistics<br>
    490       <br>
    491 trunk/UTIL/Makefile<br>
    492       </td>
    493     </tr>
    494 <tr>
    495       <td style="vertical-align: top;">05/02/10<br>
    496       </td>
    497       <td style="vertical-align: top;">SR<br>
    498       </td>
    499       <td style="vertical-align: top;">485<br>
    500       </td>
    501       <td style="vertical-align: top;">3.7a<br>
    502       </td>
    503       <td style="vertical-align: top;">B<br>
    504       </td>
    505       <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">ngp_3d</span>, <span style="font-family: Courier New,Courier,monospace;">ngp_3d_inner</span>
    506 changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
    507 some global statistics (e.g. total kinetic energy) have wrong values.<br>
    508       </td>
    509       <td style="vertical-align: top;">init_3d_model, modules<br>
    510       </td>
    511     </tr>
    512     <tr>
    513       <td style="vertical-align: top;">05/02/10<br>
    514       </td>
    515       <td style="vertical-align: top;">SR<br>
    516       </td>
    517       <td style="vertical-align: top;">484<br>
    518       </td>
    519       <td style="vertical-align: top;">3.7a<br>
    520       </td>
    521       <td style="vertical-align: top;">B<br>
    522       </td>
    523       <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
    524       </td>
    525       <td style="vertical-align: top;">many<br>
    526       </td>
    527     </tr>
    528 <tr>
    529       <td style="vertical-align: top; width: 27px;">05/02/10<br>
    530       </td>
    531       <td style="vertical-align: top; width: 38px;">SR<br>
    532       </td>
    533       <td style="vertical-align: top; width: 42px;">483<br>
    534       </td>
    535       <td style="vertical-align: top; width: 40px;">3.7a<br>
    536       </td>
    537       <td style="vertical-align: top; width: 27px;">N<br>
    538       </td>
    539       <td style="vertical-align: top; width: 497px;"><span style="font-family: Courier New,Courier,monospace;">compare_palm_logs </span>is additionally compiled with <span style="font-weight: bold;">mbuild</span> <span style="font-family: Courier New,Courier,monospace;">-u</span> . (<span style="font-family: Courier New,Courier,monospace;">Makefile</span> in <span style="font-family: Courier New,Courier,monospace;">trunk/UTIL</span>)<br>
    540       <br>
    541 make options (<span style="font-family: Courier New,Courier,monospace;">mopts</span>) to be set by configuration file implemented. (<span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>)<br>
    542       <br>
    543       <span style="font-family: Courier New,Courier,monospace;">humidity</span> = <span style="font-style: italic;">.T.</span> can be used for runs with topography. <span style="font-family: Courier New,Courier,monospace;">wall_humidityflux</span> and<br><span style="font-family: Courier New,Courier,monospace;">
    544 wall_scalarflux</span> are the corresponding new inipar parameters.<br>
    545 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>)<br>
    546       <br>
    547 Large scale vertical motion (subsidence/ascent) can be added as
    548 additional source to the prognostic equation for potential temperature.
    549 See new parameters <span style="font-family: Courier New,Courier,monospace;">large_scale_subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient</span>, and <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient_level</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">Makefile</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    550       <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
    551       <br>
    552 A simple method for installing and running palm (with limited features) has been added. (<span style="font-family: Courier New,Courier,monospace;">Makefile</span>, new scripts <span style="font-weight: bold;">palm_simple_install</span>, <span style="font-weight: bold;">palm_simple_run</span>)<br>
    553       <br>
    554 Masked data output has been implemented but it is not documented in the
    555 user manual so far. This feature can already use NetCDF4 file format.
    556 (check_open, check_parameters, close_file, modules, netcdf, parin,
    557 time_integration, user_parin, new: data_output_mask, init_masks,
    558 user_data_output_mask)<br>
    559       </td>
    560       <td style="vertical-align: top; width: 189px;">check_open, check
    561 parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
    562 netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
    563       <br><span style="font-weight: bold;">
    564 new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
    565 <br>
    566       </td>
    567     </tr>
    568     <tr>
    569       <td style="vertical-align: top; width: 27px;"><br>
    570       </td>
    571       <td style="vertical-align: top; width: 38px;"><br>
    572       </td>
    573       <td style="vertical-align: top; width: 42px;"><br>
    574       </td>
    575       <td style="vertical-align: top; width: 40px;"><br>
    576       </td>
    577       <td style="vertical-align: top; width: 27px;">C<br>
    578       </td>
    579       <td style="vertical-align: top; width: 497px;">2d-decomposition is default for Cray-XT machines. (<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>)<br>
    580       <br><span style="font-family: Courier New,Courier,monospace;">
    581 var_ts</span> is replaced by <span style="font-family: Courier New,Courier,monospace;">dots_max</span>. (<span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
    582       <br>
    583 Every cloud droplet has now an own weighting factor and can be deleted
    584 due to collisions. Condensation and collision of cloud droplets are
    585 adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
    586       <br>
    587 Collision efficiency for large cloud droplets has changed according to table of Rogers and Yau. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<br>
    588       </td>
    589       <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
    590       </td>
    591     </tr>
    592     <tr>
    593       <td style="vertical-align: top; width: 27px;"><br>
    594       </td>
    595       <td style="vertical-align: top; width: 38px;"><br>
    596       </td>
    597       <td style="vertical-align: top; width: 42px;"><br>
    598       </td>
    599       <td style="vertical-align: top; width: 40px;"><br>
    600       </td>
    601       <td style="vertical-align: top; width: 27px;">B<br>
    602       </td>
    603       <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
    604       <br>
    605 Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
    606       <br>
    607 Dimension of array <span style="font-family: Courier New,Courier,monospace;">stat</span> in cascade change to prevent type problems with mpi2 libraries. (<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>)<br>
    608       <br>
    609 Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
    610       <br>
    611 Bugfix: exchange of ghost points for <span style="font-family: Courier New,Courier,monospace;">prho</span> included. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
    612       <br>
    613 Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
    614       <br>
    615 Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
    616       <br>
    617 Bugfix: initial data assignments to some dvrp arrays changed due to error messages from gfortran compiler. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
    618       <br>
    619 Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
    620       <br>
    621 Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
    622       <br>
    623 Bugfix in calculation of collision efficiency. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><br>
    624       </td>
    625       <td style="vertical-align: top; width: 189px;">advec_particles,
    626 calc_precipitation, collision_efficiency, disturb_field, header,
    627 modules, poisfft_hybrid, subjob, sum_up_3d_data,
    628 time_integration<br>
    629 <br>
    630       </td>
    631     </tr>
    632     <tr>
    633       <td style="vertical-align: top; width: 27px;">23/09/09<br>
    634       </td>
    635       <td style="vertical-align: top; width: 38px;">SR<br>
    636       </td>
    637       <td style="vertical-align: top; width: 42px;">392<br>
    638       </td>
    639       <td style="vertical-align: top; width: 40px;">3.7<br>
    640       </td>
    641       <td style="vertical-align: top; width: 27px;">N<br>
    642       </td>
    643       <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
    644 important changes:</span>
    645 atmosphere-ocean coupling has been improved and steering of
    646 dvr-software is more user-friendly now. Beside that, the release
    647 contains a lot of optimizations, changes, and bugfixes which have
    648 accumulated over the last months.<br>
    649 
    650       <br>
    651 
    652 The atmosphere-ocean coupling allows to use independent precursor runs
    653 in order to account for different spin-up times. The time when coupling
    654 has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
    655 The precursor ocean run has to be started using new <span style="font-weight: bold;">mrun</span> option "<span style="font-family: Courier New,Courier,monospace;">-y</span>" in
    656 order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
    657 output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
    658       <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    659       <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    660       <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
    661       <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
    662       <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
    663       <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
    664       <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
    665       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    666       <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
    667       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    668       <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
    669       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    670       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    671       <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
    672       <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
    673       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    674 
    675       <br>
    676 
    677 Clipping of dvrp output implemented. Default colourtable for particles
    678 implemented, particle attributes (color, dvrp_size) can be set with new
    679 parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
    680       <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
    681       <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
    682       <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
    683 Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
    684 and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
    685 (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
    686       <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
    687       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    688       <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
    689       <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
    690 
    691       <br>
    692 
    693 Polygon reduction for topography and ground plate isosurface. Reduction
    694 level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
    695 
    696       <br>
    697 
    698 Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
    699 / <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
    700 in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
    701 
    702       <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
    703 for speed optimization. This gives a significant speedup of more than
    704 10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    705       <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
    706       <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
    707       <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
    708       <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
    709 
    710       <br>
    711 
    712 Scripts have been adapted for machine lck (Yonsei Univ.). (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)<br>
    713 
    714       <br>
    715 
    716 Additional timestep criterion in case of simulations with plant canopy.
    717 (<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
    718 
    719       <br>
    720 
    721 Check for illegal entries in <span style="font-family: Courier New,Courier,monospace;">section_xy</span>|<span style="font-family: Courier New,Courier,monospace;">xz</span>|<span style="font-family: Courier New,Courier,monospace;">yz</span> that
    722 exceed <span style="font-family: Courier New,Courier,monospace;">nz+1</span>|<span style="font-family: Courier New,Courier,monospace;">ny+1</span>|<span style="font-family: Courier New,Courier,monospace;">nx+1</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
    723 
    724       <br>
    725 
    726 External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    727       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    728       <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
    729       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    730       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    731       <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
    732       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    733       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    734 
    735       <br>
    736 
    737 New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
    738 (<span style="font-family: Courier New,Courier,monospace;">header</span>,
    739       <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
    740       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    741       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    742       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    743       <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
    744       <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
    745       <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
    746       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    747 
    748       <br>
    749 
    750 Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
    751 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    752       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    753       <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
    754       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    755       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    756       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    757       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    758 
    759       <br>
    760 
    761 Option for user defined 2D data output in xy cross sections at z=<span style="font-family: Courier New,Courier,monospace;">nzb</span>+1. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    762       <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
    763 
    764       <br>
    765 
    766 xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
    767       <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    768       <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    769       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    770       <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
    771       <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
    772       <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
    773       <td style="vertical-align: top; width: 189px;">average_3d_data,
    774 check_for_restart, check_parameters, data_output_2d, data_output_3d,
    775 data_output_dvrp, data_output_profiles, data_output_ptseries,
    776 data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
    777 diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
    778 header, mbuild, modules, mrun, package_parin, parin,
    779 prognostic_equations, read_3d_binary, read_var_list, subjob,
    780 sum_up_3d_data, surface_coupler, timestep, time_integration,
    781 user_check_parameters, user_data_output_2d, user_data_output_dvrp,
    782 user_header, user_init_grid, write_3d_binary, write_var_list<br>
    783 
    784       <br>
    785 
    786       <span style="font-weight: bold;">new:</span>
    787 set_particle_attributes, set_slicer_attributes_dvrp</td>
    788     </tr>
    789     <tr>
    790       <td style="vertical-align: top; width: 27px;"><br>
    791       </td>
    792       <td style="vertical-align: top; width: 38px;"><br>
    793       </td>
    794       <td style="vertical-align: top; width: 42px;"><br>
    795       </td>
    796       <td style="vertical-align: top; width: 40px;"><br>
    797       </td>
    798       <td style="vertical-align: top; width: 27px;">C<br>
    799       </td>
    800       <td style="vertical-align: top; width: 497px;">Output of messages replaced by
    801 message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
    802       <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
    803       <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
    804       <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
    805       <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
    806       <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
    807       <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
    808       <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
    809       <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    810       <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
    811       <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
    812       <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
    813       <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
    814       <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
    815       <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
    816       <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
    817       <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
    818       <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
    819       <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
    820       <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
    821       <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
    822       <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
    823       <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
    824       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    825       <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
    826       <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
    827       <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
    828       <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
    829       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    830       <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
    831       <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
    832       <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
    833       <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
    834       <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
    835       <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
    836       <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
    837       <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
    838       <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
    839       <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
    840       <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
    841 
    842       <br>
    843 
    844 Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
    845       <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
    846       <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    847       <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
    848       <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
    849       <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
    850       <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
    851       <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
    852       <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
    853 
    854       <br>
    855 
    856 __lcmuk changed to __lc to avoid problems with Intel compiler on
    857 sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
    858 
    859       <br>
    860 
    861 For extended NetCDF files, the updated title attribute includes an
    862 update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
    863 
    864       <br>
    865 
    866 In case of restart runs without extension, initial profiles are not
    867 written to NetCDF-file anymore. So far, time axis always started at
    868 t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
    869       <span style="font-family: Courier New,Courier,monospace;">modules</span>,
    870       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    871       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    872 
    873       <br>
    874 
    875       <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
    876 '<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
    877 can now <br>
    878 
    879 be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
    880 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    881       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    882       <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
    883 
    884       <br>
    885 
    886 2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
    887 
    888       <br>
    889 
    890 A link to the webspage appendix_a.html is printed for further
    891 information about possible reasons of the error that appeared. (message)<br>
    892 
    893       <br>
    894 
    895 Temperature gradient criterion for estimating the boundary layer height
    896 replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
    897 
    898       <br>
    899 
    900 NetCDF unit attribute in timeseries output in case of statistic regions
    901 added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
    902 
    903       <br>
    904 
    905 Maximum number of tails is calculated from maximum number of particles
    906 and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
    907 (<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
    908 
    909       <br>
    910 
    911 Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
    912 is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
    913       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    914       <span style="font-family: Courier New,Courier,monospace;">modules</span>)
    915       <br>
    916 
    917       <br>
    918 
    919 First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
    920 defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
    921 
    922       <br>
    923 
    924 Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
    925 moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
    926 to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
    927 (<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
    928 
    929       <br>
    930 
    931       <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
    932 moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
    933 to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
    934 (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
    935       <span style="font-family: Courier New,Courier,monospace;">header</span>,
    936       <span style="font-family: Courier New,Courier,monospace;">parin</span>,
    937       <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    938       <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
    939       <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
    940       <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
    941       <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
    942       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    943 
    944       <br>
    945 
    946 Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
    947 changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
    948 
    949       <br>
    950 
    951 Adjustments for runs on lcxt4 (necessary due to a software update on
    952 CRAY) and for coupled runs on ibmy. (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)</td>
    953       <td style="vertical-align: top; width: 189px;">advec_particles,
    954 advec_s_bc,
    955 buoyancy, calc_spectra, check_for_restart, check_open,
    956 check_parameters, close_file, coriolis, cpu_log, data_output_2d,
    957 data_output_3d, data_output_dvrp, data_output_profiles,
    958 data_output_ptseries, data_output_spectra, data_output_tseries,
    959 eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
    960 init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
    961 message, mrun, netcdf, package_parin, parin, plant_canopy_model,
    962 poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
    963 surface_coupler, temperton_fft, timestep,
    964 user_actions,user_check_parameters, user_data_output_dvrp,
    965 user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
    966 user_parin, user_read_restart_data, user_spectra, write_var_list </td>
    967     </tr>
    968     <tr>
    969       <td style="vertical-align: top; width: 27px;"><br>
    970       </td>
    971       <td style="vertical-align: top; width: 38px;"><br>
    972       </td>
    973       <td style="vertical-align: top; width: 42px;"><br>
    974       </td>
    975       <td style="vertical-align: top; width: 40px;"><br>
    976       </td>
    977       <td style="vertical-align: top; width: 27px;">B<br>
    978       </td>
    979       <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
    980 pressure profile in case of ocean runs is now calculated in 5 iteration
    981 steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
    982 
    983       <br>
    984 
    985 Bugfix: wrong sign in buoyancy production of ocean part in case of not
    986 using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
    987 (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
    988 
    989       <br>
    990 
    991 Bugfix: output of averaged 2d/3d quantities requires that an avaraging
    992 interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
    993 
    994       <br>
    995 
    996 Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
    997 (<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
    998 
    999       <br>
    1000 
    1001 Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
    1002 (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
    1003 
    1004       <br>
    1005 
    1006 Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
    1007 if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
    1008 is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
    1009 and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
    1010 calls. This implies a possible performance loss; an alternative
    1011 strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
    1012 
    1013       <br>
    1014 
    1015 Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
    1016 
    1017       <br>
    1018 
    1019 Bugfix: zero initialization of arrays within buildings for '<span style="font-style: italic;">cyclic_fill</span>'. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
    1020 
    1021       <br>
    1022 
    1023 Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
    1024 =&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
    1025 for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
    1026       <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
    1027 
    1028       <br>
    1029 
    1030 Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
    1031 becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
    1032 
    1033       <br>
    1034 
    1035 Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
    1036 
    1037       <br>
    1038 
    1039 Bugfix: error in check, if particles moved further than one subdomain
    1040 length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
    1041 
    1042       <br>
    1043 
    1044 Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
    1045 is only written to file if its third index is &gt; 0, arrays for tails
    1046 are allocated with a minimum size of 10 tails if there is no tail
    1047 initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
    1048       <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
    1049 
    1050       <br>
    1051 
    1052 Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
    1053 
    1054       <br>
    1055 
    1056 Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
    1057 changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
    1058 NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
    1059 
    1060       <br>
    1061 
    1062 Bugfix: output of particle time series only if particle advection is
    1063 switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
    1064 
    1065       <br>
    1066 
    1067 Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
    1068 = <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
    1069 (<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
    1070 
    1071       <br>
    1072 
    1073 Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
    1074 z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
    1075 
    1076       <br>
    1077 
    1078 Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
    1079 
    1080       <br>
    1081 
    1082 If the inversion height calculated by the prerun is zero,
    1083 inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
    1084 
    1085       <br>
    1086 
    1087 Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
    1088 
    1089       <br>
    1090 
    1091 Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
    1092 removed from the restart file, because otherwise, no change from a
    1093 fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
    1094       <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
    1095 
    1096       <br>
    1097 
    1098 Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
    1099 in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
    1100       <td style="vertical-align: top; width: 189px;">advec_particles,
    1101 check_parameters, cpu_log, data_output_2d, data_output_3d, header,
    1102 init_3d_model, init_particles, init_ocean, modules, netcdf,
    1103 prandtl_fluxes, production_e, read_var_list, time_integration,
    1104 user_last_actions, write_var_list<br>
    1105 
    1106       </td>
    1107     </tr>
    1108     <tr>
    1109       <td style="vertical-align: top; width: 27px;">02/02/09<br>
    1110       </td>
    1111       <td style="vertical-align: top; width: 38px;">SR<br>
    1112       </td>
    1113       <td style="vertical-align: top; width: 42px;">228<br>
    1114       </td>
    1115       <td style="vertical-align: top; width: 40px;">3.6<br>
    1116       </td>
    1117       <td style="vertical-align: top; width: 27px;">N<br>
    1118       </td>
    1119       <td style="vertical-align: top; width: 497px;">This
    1120 release contains further additions, changes, and bugfixes for the
    1121 SGI-ICE system, as well as important changes like the splitting of the
    1122 user-interface into single files, a complete revision of the
    1123 pre-compiling mechanism allowing to use different make-depositories
    1124 simultaneously, and a revision of the reading-mechanism from restart
    1125 files, which has no more restrictions in case that the previous and
    1126 current run have different domain/subdomain sizes. A new handling of
    1127 all kind of output messages is introduced with this release and will be
    1128 applied to all existing messages within the next releases.<br>
    1129 
    1130       <br>
    1131 
    1132       <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
    1133 
    1134       <br>
    1135 
    1136 Restart runs on SGI-ICE are working. (mrun)<br>
    1137 
    1138 2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
    1139 
    1140       <br>
    1141 
    1142 Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
    1143 case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
    1144 "<span style="font-style: italic;">-K parallel</span>" for coupling.
    1145 Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
    1146       <span style="font-family: Courier New,Courier,monospace;">subjob</span>
    1147 for lcxt4.<br>
    1148 
    1149       <br>
    1150 
    1151 DVRP arguments changed to single precision, mode pathlines added.<br>
    1152 
    1153       <br>
    1154 
    1155 User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
    1156 
    1157       <br>
    1158 
    1159 User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
    1160       <td style="vertical-align: top; width: 189px;">check_for_restart,
    1161 check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
    1162 modules, package_parin, palm, surface_coupler, timestep<br>
    1163 
    1164       <br>
    1165 
    1166 Makefile,&nbsp;mbuild, mrun, subjob<br>
    1167 
    1168       <br>
    1169 
    1170       <span style="font-weight: bold;">new:</span><br>
    1171 
    1172 init_coupling, user_additional_routines, user_check_parameters</td>
    1173     </tr>
    1174     <tr>
    1175       <td style="vertical-align: top; width: 27px;"><br>
    1176       </td>
    1177       <td style="vertical-align: top; width: 38px;"><br>
    1178       </td>
    1179       <td style="vertical-align: top; width: 42px;"><br>
    1180       </td>
    1181       <td style="vertical-align: top; width: 40px;"><br>
    1182       </td>
    1183       <td style="vertical-align: top; width: 27px;">C<br>
    1184       </td>
    1185       <td style="vertical-align: top; width: 497px;">User interface has been
    1186 split into single files.<br>
    1187 
    1188       <br>
    1189 
    1190 Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
    1191 changed to INTEGER(8) in order to avoid "out of range" problems, which
    1192 result in measured negative time intervals. (cpu_log, local_tremain,
    1193 local_tremain_ini)<br>
    1194 
    1195       <br>
    1196 
    1197 Reading mechanism from restart files
    1198 completely revised. The subdomain/total domain size is now allowed to
    1199 vary arbitrarily between the current and previous run. (read_var_list,
    1200 read_3d_binary, user_read_restart_data)<br>
    1201 
    1202       <br>
    1203 
    1204 Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
    1205 completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
    1206 One depository per block (given in the config-file) is created. Always
    1207 all files from the source directory are copied to the respective
    1208 depository. No additional file checks are done any more (mrun version
    1209 2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
    1210 "<span style="font-family: Courier New,Courier,monospace;">-K</span>".
    1211 (mbuild, mrun)<br>
    1212 
    1213       <br>
    1214 
    1215 Output messages (including required stop of execution) can now be
    1216 handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
    1217 All output messages will be replaced by this routine step by step
    1218 within the next revisions.<br>
    1219 
    1220       <br>
    1221 
    1222 Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
    1223 explicitly set for better reading, although this has been already done
    1224 in boundary_conds. (advec_s_bc)<br>
    1225 
    1226       <br>
    1227 
    1228 Origin of the xy-coordinate system shifted from the center of the first
    1229 grid cell (indices <span style="font-family: Courier New,Courier,monospace;">i=0</span>, <span style="font-family: Courier New,Courier,monospace;">j=0</span>) to the
    1230 south-left corner of this cell. (netcdf) Topography definition
    1231 according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
    1232 (init_grid, modules, user_header, user_init_grid, user_parin)</td>
    1233       <td style="vertical-align: top; width: 189px;">advec_s_bc,
    1234 check_parameters, cpu_log, init_grid, local_stop, local_tremain,
    1235 local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
    1236 user_read_restart_data<br>
    1237 
    1238       <br>
    1239 
    1240 Makefile, mbuild, mrun<br>
    1241 
    1242       <br>
    1243 
    1244       <span style="font-weight: bold;">removed:</span><br>
    1245 
    1246 user_interface<br>
    1247 
    1248       <br>
    1249 
    1250       <span style="font-weight: bold;">new:</span><br>
    1251 
    1252 message,
    1253 user_3d_data_averaging, user_actions, user_advec_particles,
    1254 user_check_data_output, user_check_data_output_pr, user_data_output_2d,
    1255 user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
    1256 user_dvrp_coltab, user_header, user_init_3d_model, user_init,
    1257 user_init_grid, user_init_particles, user_init_plant_canopy,
    1258 user_last_actions, user_parin, user_parin, user_particle_attributes,
    1259 user_read_restart_data, user_spectra, user_statistics</td>
    1260     </tr>
    1261     <tr>
    1262       <td style="vertical-align: top; width: 27px;"><br>
    1263       </td>
    1264       <td style="vertical-align: top; width: 38px;"><br>
    1265       </td>
    1266       <td style="vertical-align: top; width: 42px;"><br>
    1267       </td>
    1268       <td style="vertical-align: top; width: 40px;"><br>
    1269       </td>
    1270       <td style="vertical-align: top; width: 27px;">B<br>
    1271       </td>
    1272       <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
    1273 reallocated in case that multigrid is used. (calc_spectra)<br>
    1274 
    1275       <br>
    1276 
    1277 Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
    1278 inflow_turbulence,&nbsp;timestep)<br>
    1279 
    1280       <br>
    1281 
    1282 Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
    1283       </span>adjusted to the required output size (1 gridpoint less,
    1284 along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
    1285 in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
    1286 compiler. (combine_plot_fields)<br>
    1287 
    1288       <br>
    1289 
    1290 Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
    1291 case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
    1292 (header)<br>
    1293 
    1294       <br>
    1295 
    1296 Inconsistency
    1297 removed: as the thermal stratification is not taken into account for
    1298 the evaluation of the wall fluxes at vertical walls, the eddy viscosity
    1299       <span style="font-family: Courier New,Courier,monospace;">km</span>
    1300 must not be used for the evaluation of the velocity gradients <span style="font-family: Courier New,Courier,monospace;">dudy</span>, <span style="font-family: Courier New,Courier,monospace;">dwdy</span>, <span style="font-family: Courier New,Courier,monospace;">dvdx</span> and <span style="font-family: Courier New,Courier,monospace;">dwdx</span>.
    1301 (production_e)<br>
    1302 
    1303       <br>
    1304 
    1305 Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
    1306 case of oceans runs. (sort_particles)<br>
    1307 
    1308       <br>
    1309 
    1310 Bugfix: no output of particle concentration and radius unless particles
    1311 have been started. (data_output_2d)<br>
    1312 
    1313       <br>
    1314 
    1315 Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
    1316 from restart files ignored if total numbers of grid points do not
    1317 match. (read_3d_binary)<br>
    1318 
    1319       <br>
    1320 
    1321 Bugfix: abort in case that absolute temperature is below zero.
    1322 (init_cloud_physics)</td>
    1323       <td style="vertical-align: top; width: 189px;">advec_particles,
    1324 calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
    1325 header, inflow_turbulence, init_cloud_physics, production_e,
    1326 read_3d_binary, timestep<br>
    1327 
    1328       <br>
    1329 
    1330 combine_plot_fields</td>
    1331     </tr>
    1332   </tbody>
    1333 </table>
    1334 <b><blink></blink></b><br>&nbsp;
    1335 <br>&nbsp;
    1336 <h2><a name="Kapitel2.0"></a>2.0&nbsp; How
    1337 to change the source
    1338 code and how to document modifications<br>
    1339 </h2>Currently
    1340 (Sep 23rd, 2009), only selected users are allowed to commit changes to
    1341 the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
    1342 <br>
    1343 <ol>
    1344   <li>Change source code in your current working copy. Document changes in the respective file headers unter "<span style="font-family: Courier New,Courier,monospace;">Current revisions:</span>".
    1345 Additionally, document all changes in a local file (e.g.
    1346 ~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
    1347 have been changed. Classify changes in three cases, new (N), changed
    1348 (C), and bugfix (B). <span style="font-weight: bold;">Try to be as short and as precise as possible in describing the changes!</span><br>
    1349     <br>
    1350   </li>
    1351   <li>Test the changed version, unless it works sufficiently.<br>
    1352     <br>
    1353   </li>
    1354  
    1355   <li>Commit the changes to the repository<br>
    1356     <br>
    1357     <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
    1358     </span><br>
    1359 where "<span style="font-family: Courier New,Courier,monospace;">message string</span>" is a short, <span style="font-weight: bold;">meaningful</span> summary of the changes.<br>
    1360     <br>
    1361 Alternatively, in case that you have made quite a lot of changes, you
    1362 can also give the contents of your file CURRENT_MODIFICATIONS as the
    1363 log message:<br>
    1364     <br>
    1365     <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
    1366     <br>
    1367   </li>
    1368 
    1369   <li>Enter the changes into the technical documentation (under <span style="font-family: Courier New,Courier,monospace;">.../trunk/DOC/tec/technical_documentation.html</span>).<br>
    1370     <br>
    1371   </li>
    1372   <li>Move the change comments in the file headers from "Current
    1373 revisions:" to "Former revisions:". Set the current svn id in front of
    1374 that.<br>
    1375     <br>
    1376     <span style="font-weight: bold;">Example:</span><br>
    1377     <br>
    1378     <span style="font-weight: bold;">before move:</span><br>
    1379     <br>
    1380     <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
    1381     <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
    1382     <span style="font-family: Courier New,Courier,monospace;">! <span style="font-weight: bold;">new dummy argument abcd</span></span><span style="font-family: Courier New,Courier,monospace;"></span><br style="font-family: Courier New,Courier,monospace;">
    1383     <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
    1384     <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
    1385     <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
    1386     <span style="font-family: Courier New,Courier,monospace;">! ï¿œId: init_3d_model.f90 <span style="color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span> ï¿œ</span><br style="font-family: Courier New,Courier,monospace;">
    1387     <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
    1388     <span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
    1389     <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
    1390     <br>
    1391     <span style="font-weight: bold;">after move:</span><br>
    1392     <br>
    1393     <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
    1394 
    1395     <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
    1396 
    1397     <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
    1398 
    1399     <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
    1400 
    1401     <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
    1402 
    1403     <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
    1404 
    1405     <span style="font-family: Courier New,Courier,monospace;">! ï¿œId: </span><span style="font-family: Courier New,Courier,monospace;">init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"> ï¿œ<br>
    1406 !</span><br style="font-family: Courier New,Courier,monospace;">
    1407     <span style="font-family: Courier New,Courier,monospace;">! </span><span style="font-family: Courier New,Courier,monospace; color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold; color: rgb(51, 51, 255);"></span><br>
    1408 ! </span><span style="font-family: Courier New,Courier,monospace; font-weight: bold;">new dummy argument abcd</span><br style="font-family: Courier New,Courier,monospace;">
    1409 
    1410     <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
    1411 
    1412     <span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
    1413 
    1414     <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
    1415     <br>
    1416     <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">ï¿œ</span>"
    1417 in this example should read "$", but "$" cannot be used here, because
    1418 otherwise svn would replace these entries after every change to this
    1419 technical documentation.</span><br>
    1420  </span><br>
    1421   </li>
    1422   <li>Commit the changes in the technical documentation and the file headers:<br>
    1423     <br>
    1424     <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
    1425     <br>
    1426  <br>
    1427   </li>
    1428 </ol>
    1429 
    1430 <h2>
    1431 <a name="Kapitel3.0"></a>3.0&nbsp; Description
    1432 of selected parts of the
    1433 model source code</h2>
    1434 <b></b>
    1435 <p>This section gives links to existing descriptions about special
     1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
     2<HTML>
     3<HEAD>
     4        <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
     5        <TITLE>PALM technical/numerical documentation</TITLE>
     6        <META NAME="GENERATOR" CONTENT="OpenOffice.org 3.0  (Unix)">
     7        <META NAME="AUTHOR" CONTENT="Siegfried Raasch">
     8        <META NAME="CREATED" CONTENT="0;0">
     9        <META NAME="CHANGED" CONTENT="20100901;15562900">
     10        <META NAME="KEYWORDS" CONTENT="parallel LES model">
     11</HEAD>
     12<BODY LANG="en-US" DIR="LTR">
     13<P STYLE="margin-bottom: 0in"><FONT SIZE=7>PALM&nbsp;&nbsp; </FONT>a
     14<B>pa</B>rallelized <B>L</B>ES <B>m</B>odel
     15</P>
     16<HR>
     17<P STYLE="margin-bottom: 0in"><BR><FONT SIZE=5>technical/numerical
     18documentation</FONT> <BR>&nbsp; <BR>&nbsp;
     19</P>
     20<P ALIGN=CENTER STYLE="margin-bottom: 0in">&nbsp;
     21</P>
     22<TABLE CELLPADDING=0 CELLSPACING=0>
     23        <TR>
     24                <TD>
     25                        <P><B>Current fixed release:</B></P>
     26                </TD>
     27                <TD>
     28                        <P><B>3.7a</B></P>
     29                </TD>
     30        </TR>
     31        <TR>
     32                <TD>
     33                        <P><B>Last change of this document</B>:&nbsp;</P>
     34                </TD>
     35                <TD>
     36                        <P><B>$Id: technical_documentation.html 544 2010-08-17 10:44:58Z
     37                        maronga $</B></P>
     38                </TD>
     39        </TR>
     40</TABLE>
     41<HR>
     42<P><FONT SIZE=5>Table of contents</FONT> <BR>&nbsp; <BR>&nbsp;
     43</P>
     44<UL>
     45        <P><A HREF="#Kapitel1.0">1.0</A>&nbsp; History of changes
     46        </P>
     47        <P><A HREF="#Kapitel2.0">2.0</A>&nbsp; How to change the source code
     48        and how to document modifications</P>
     49        <P><A HREF="#Kapitel3.0">3.0</A>&nbsp; Description of selected model
     50        numerics<BR>&nbsp;</P>
     51</UL>
     52<P><BR><BR>
     53</P>
     54<H2><A NAME="Kapitel1.0"></A>1.0&nbsp; History of changes</H2>
     55<P STYLE="margin-bottom: 0in">The following table documents all
     56changes to the PALM repository since 2009. Older changes can be found
     57<A HREF="tec_doc_1998-2008.html">here</A>.<BR><BR>Entries in the
     58fifth column specify the type of the change: change&nbsp; of existing
     59code (C), new code (N) or bugfix (B). More detailed information about
     60the changes may sometimes be found in the header comment lines of the
     61respective routines. <BR>&nbsp;
     62</P>
     63<TABLE WIDTH=1223 BORDER=1 CELLPADDING=2 CELLSPACING=3>
     64        <COL WIDTH=37>
     65        <COL WIDTH=56>
     66        <COL WIDTH=68>
     67        <COL WIDTH=62>
     68        <COL WIDTH=36>
     69        <COL WIDTH=518>
     70        <COL WIDTH=393>
     71        <TR>
     72                <TD WIDTH=37>
     73                        <P><FONT SIZE=4><B>date</B></FONT></P>
     74                </TD>
     75                <TD WIDTH=56>
     76                        <P><FONT SIZE=4><B>author</B></FONT></P>
     77                </TD>
     78                <TD WIDTH=68>
     79                        <P><FONT SIZE=4><B>svn revision</B></FONT></P>
     80                </TD>
     81                <TD WIDTH=62>
     82                        <P><FONT SIZE=4><B>last release</B></FONT></P>
     83                </TD>
     84                <TD WIDTH=36>
     85                        <P><FONT SIZE=4><B>type</B></FONT></P>
     86                </TD>
     87                <TD WIDTH=518>
     88                        <P><FONT SIZE=4><B>description</B></FONT></P>
     89                </TD>
     90                <TD WIDTH=393>
     91                        <P><FONT SIZE=4><B>affected routines</B></FONT></P>
     92                </TD>
     93        </TR>
     94        <TR>
     95                <TD WIDTH=37 SDVAL="40187" SDNUM="1033;0;MM/DD/YY">
     96                        <P STYLE="font-weight: normal"><FONT SIZE=3>01/09/10</FONT></P>
     97                </TD>
     98                <TD WIDTH=56>
     99                        <P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P>
     100                </TD>
     101                <TD WIDTH=68 SDVAL="553" SDNUM="1033;">
     102                        <P STYLE="font-weight: normal"><FONT SIZE=3>553</FONT></P>
     103                </TD>
     104                <TD WIDTH=62>
     105                        <P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P>
     106                </TD>
     107                <TD WIDTH=36>
     108                        <P STYLE="font-weight: normal"><FONT SIZE=3>C</FONT></P>
     109                </TD>
     110                <TD WIDTH=518>
     111                        <P STYLE="font-weight: normal"><FONT SIZE=3>d3dpar-parameters for
     112                        masked output <FONT FACE="Courier New, monospace">data_output_mask_*,
     113                        data_output_mask_user_*, mask_*_x, mask_*_y, mask_*_z,
     114                        mask_*_x_loop, mask_*_y_loop </FONT><FONT FACE="Times New Roman, serif">and
     115                        </FONT><FONT FACE="Courier New, monospace">mask_*_z_loop </FONT>have
     116                        been replaced by corresponding arrays <FONT FACE="Courier New, monospace">data_output_masks,
     117                        data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
     118                        mask_y_loop </FONT><FONT FACE="Times New Roman, serif">and</FONT><FONT FACE="Courier New, monospace">
     119                        mask_z_loop</FONT></FONT></P>
     120                        <P STYLE="font-weight: normal"><FONT SIZE=3>inipar-parameter <FONT FACE="Courier New, monospace">masks</FONT>
     121                        has been removed. </FONT>
     122                        </P>
     123                        <P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
     124                        the masked data output, which is still not documented.</FONT></P>
     125                </TD>
     126                <TD WIDTH=393>
     127                        <P STYLE="font-weight: normal"><FONT SIZE=3>check_parameters,
     128                        init_masks, modules, parin, user_parin</FONT></P>
     129                </TD>
     130        </TR>
     131        <TR>
     132                <TD WIDTH=37>
     133                        <P>17/08/10</P>
     134                </TD>
     135                <TD WIDTH=56>
     136                        <P>BM</P>
     137                </TD>
     138                <TD WIDTH=68>
     139                        <P>544</P>
     140                </TD>
     141                <TD WIDTH=62>
     142                        <P>3.7a</P>
     143                </TD>
     144                <TD WIDTH=36>
     145                        <P>B/C/N</P>
     146                </TD>
     147                <TD WIDTH=518>
     148                        <P>adjustments for lcxt4; bugfix (mbuild): loading of user-defined
     149                        modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</P>
     150                </TD>
     151                <TD WIDTH=393>
     152                        <P>mrun, mbuild, subjob</P>
     153                </TD>
     154        </TR>
     155        <TR>
     156                <TD WIDTH=37>
     157                        <P>15/06/10</P>
     158                </TD>
     159                <TD WIDTH=56>
     160                        <P>RH</P>
     161                </TD>
     162                <TD WIDTH=68>
     163                        <P>540</P>
     164                </TD>
     165                <TD WIDTH=62>
     166                        <P>3.7a</P>
     167                </TD>
     168                <TD WIDTH=36>
     169                        <P>C</P>
     170                </TD>
     171                <TD WIDTH=518>
     172                        <P>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is
     173                        done using the names hicegate0/bicegate0 instead of the IP
     174                        addresses</P>
     175                </TD>
     176                <TD WIDTH=393>
     177                        <P>mrun</P>
     178                </TD>
     179        </TR>
     180        <TR>
     181                <TD WIDTH=37>
     182                        <P>21/04/10</P>
     183                </TD>
     184                <TD WIDTH=56>
     185                        <P>RH</P>
     186                </TD>
     187                <TD WIDTH=68>
     188                        <P>532</P>
     189                </TD>
     190                <TD WIDTH=62>
     191                        <P>3.7a</P>
     192                </TD>
     193                <TD WIDTH=36>
     194                        <P>C</P>
     195                </TD>
     196                <TD WIDTH=518>
     197                        <P>Large scale vertical motion (subsidence/ascent) can be added as
     198                        additional source to the prognostic equation for humidity/passive
     199                        scalar<BR>&nbsp;<BR>character length for dopr_unit
     200                        enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
     201                        of png files
     202                        </P>
     203                </TD>
     204                <TD WIDTH=393>
     205                        <P>modules, prognostic_equations<BR><BR>.ncl.config.default,
     206                        cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</P>
     207                </TD>
     208        </TR>
     209        <TR>
     210                <TD WIDTH=37>
     211                        <P><BR>
     212                        </P>
     213                </TD>
     214                <TD WIDTH=56>
     215                        <P><BR>
     216                        </P>
     217                </TD>
     218                <TD WIDTH=68>
     219                        <P><BR>
     220                        </P>
     221                </TD>
     222                <TD WIDTH=62>
     223                        <P><BR>
     224                        </P>
     225                </TD>
     226                <TD WIDTH=36>
     227                        <P>B</P>
     228                </TD>
     229                <TD WIDTH=518>
     230                        <P>Bugfix: unit of hyp changed to dbar</P>
     231                </TD>
     232                <TD WIDTH=393>
     233                        <P>check_parameters</P>
     234                </TD>
     235        </TR>
     236        <TR>
     237                <TD WIDTH=37>
     238                        <P>01/04/10</P>
     239                </TD>
     240                <TD WIDTH=56>
     241                        <P>RH</P>
     242                </TD>
     243                <TD WIDTH=68>
     244                        <P>530</P>
     245                </TD>
     246                <TD WIDTH=62>
     247                        <P>3.7a</P>
     248                </TD>
     249                <TD WIDTH=36>
     250                        <P>B</P>
     251                </TD>
     252                <TD WIDTH=518>
     253                        <P>Bugfix: treatment of special character * in NCL variables
     254                        containing lists corrected</P>
     255                </TD>
     256                <TD WIDTH=393>
     257                        <P>palmplot</P>
     258                </TD>
     259        </TR>
     260        <TR>
     261                <TD WIDTH=37>
     262                        <P>31/03/10</P>
     263                </TD>
     264                <TD WIDTH=56>
     265                        <P>RH</P>
     266                </TD>
     267                <TD WIDTH=68>
     268                        <P>529</P>
     269                </TD>
     270                <TD WIDTH=62>
     271                        <P>3.7a</P>
     272                </TD>
     273                <TD WIDTH=36>
     274                        <P>C</P>
     275                </TD>
     276                <TD WIDTH=518>
     277                        <P>List of variable names have to specified using blank separated
     278                        lists and single quotes</P>
     279                </TD>
     280                <TD WIDTH=393>
     281                        <P>palmplot</P>
     282                </TD>
     283        </TR>
     284        <TR>
     285                <TD WIDTH=37>
     286                        <P>30/03/10</P>
     287                </TD>
     288                <TD WIDTH=56>
     289                        <P>RH</P>
     290                </TD>
     291                <TD WIDTH=68>
     292                        <P>526</P>
     293                </TD>
     294                <TD WIDTH=62>
     295                        <P>3.7a</P>
     296                </TD>
     297                <TD WIDTH=36>
     298                        <P>C</P>
     299                </TD>
     300                <TD WIDTH=518>
     301                        <P>Adjustment of the NCL scripts and <FONT FACE="Courier New, Courier, monospace">palmplot
     302                        </FONT>to allow for special characters in NetCDF variable names
     303                        </P>
     304                </TD>
     305                <TD WIDTH=393>
     306                        <P>palmplot, .ncl.config.default, cross_sections.ncl,
     307                        profiles.ncl, timeseries.ncl, spectra.ncl</P>
     308                </TD>
     309        </TR>
     310        <TR>
     311                <TD WIDTH=37>
     312                        <P>30/03/10</P>
     313                </TD>
     314                <TD WIDTH=56>
     315                        <P>SR</P>
     316                </TD>
     317                <TD WIDTH=68>
     318                        <P>525</P>
     319                </TD>
     320                <TD WIDTH=62>
     321                        <P>3.7a</P>
     322                </TD>
     323                <TD WIDTH=36>
     324                        <P>B</P>
     325                </TD>
     326                <TD WIDTH=518>
     327                        <P>Bugfix: &quot;/&quot; in netcdf profile variable names replaced
     328                        by &quot;:&quot;</P>
     329                </TD>
     330                <TD WIDTH=393>
     331                        <P>check_parameters</P>
     332                </TD>
     333        </TR>
     334        <TR>
     335                <TD WIDTH=37>
     336                        <P>19/03/10</P>
     337                </TD>
     338                <TD WIDTH=56>
     339                        <P>SR</P>
     340                </TD>
     341                <TD WIDTH=68>
     342                        <P>520</P>
     343                </TD>
     344                <TD WIDTH=62>
     345                        <P>3.7a</P>
     346                </TD>
     347                <TD WIDTH=36>
     348                        <P>N</P>
     349                </TD>
     350                <TD WIDTH=518>
     351                        <P>NetCDF4 support for particle data. Total number of particles is
     352                        allowed to increase during the run, when netcdf_data_format &gt; <I>2</I>
     353                        is used.</P>
     354                </TD>
     355                <TD WIDTH=393>
     356                        <P>advec_particles, check_open, netcdf</P>
     357                </TD>
     358        </TR>
     359        <TR>
     360                <TD WIDTH=37>
     361                        <P><BR>
     362                        </P>
     363                </TD>
     364                <TD WIDTH=56>
     365                        <P><BR>
     366                        </P>
     367                </TD>
     368                <TD WIDTH=68>
     369                        <P><BR>
     370                        </P>
     371                </TD>
     372                <TD WIDTH=62>
     373                        <P><BR>
     374                        </P>
     375                </TD>
     376                <TD WIDTH=36>
     377                        <P>C</P>
     378                </TD>
     379                <TD WIDTH=518>
     380                        <P>Special characters like * and &quot; are now allowed for NetCDF
     381                        variable names. Replacement of these characters has been removed
     382                        (routine clean_netcdf_varname removed)</P>
     383                </TD>
     384                <TD WIDTH=393>
     385                        <P><BR>
     386                        </P>
     387                </TD>
     388        </TR>
     389        <TR>
     390                <TD WIDTH=37>
     391                        <P>18/03/10</P>
     392                </TD>
     393                <TD WIDTH=56>
     394                        <P>SR</P>
     395                </TD>
     396                <TD WIDTH=68>
     397                        <P>516</P>
     398                </TD>
     399                <TD WIDTH=62>
     400                        <P>3.7a</P>
     401                </TD>
     402                <TD WIDTH=36>
     403                        <P>N</P>
     404                </TD>
     405                <TD WIDTH=518>
     406                        <P>Simple installation method has been documented (see chapter
     407                        5.0). Respective scripts and configuration files have been
     408                        updated.</P>
     409                </TD>
     410                <TD WIDTH=393>
     411                        <P>palm_simple_install, palm_simple_run</P>
     412                </TD>
     413        </TR>
     414        <TR>
     415                <TD WIDTH=37>
     416                        <P><BR>
     417                        </P>
     418                </TD>
     419                <TD WIDTH=56>
     420                        <P><BR>
     421                        </P>
     422                </TD>
     423                <TD WIDTH=68>
     424                        <P><BR>
     425                        </P>
     426                </TD>
     427                <TD WIDTH=62>
     428                        <P><BR>
     429                        </P>
     430                </TD>
     431                <TD WIDTH=36>
     432                        <P>B</P>
     433                </TD>
     434                <TD WIDTH=518>
     435                        <P>opt=1 is forced for PGI-compiler in routine <FONT FACE="Courier New, Courier, monospace">buoyancy
     436                        </FONT>by compiler-directive. Otherwise, program aborts with
     437                        SIGFPE.</P>
     438                </TD>
     439                <TD WIDTH=393>
     440                        <P>buoyancy</P>
     441                </TD>
     442        </TR>
     443        <TR>
     444                <TD WIDTH=37>
     445                        <P>16/03/10</P>
     446                </TD>
     447                <TD WIDTH=56>
     448                        <P>RH</P>
     449                </TD>
     450                <TD WIDTH=68>
     451                        <P>513</P>
     452                </TD>
     453                <TD WIDTH=62>
     454                        <P>3.7a</P>
     455                </TD>
     456                <TD WIDTH=36>
     457                        <P>N</P>
     458                </TD>
     459                <TD WIDTH=518>
     460                        <P>NCL scripts can be run with the shell script <FONT FACE="Courier New, Courier, monospace">palmplot.</FONT></P>
     461                </TD>
     462                <TD WIDTH=393>
     463                        <P>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</P>
     464                </TD>
     465        </TR>
     466        <TR>
     467                <TD WIDTH=37>
     468                        <P>12/03/10</P>
     469                </TD>
     470                <TD WIDTH=56>
     471                        <P>SR</P>
     472                </TD>
     473                <TD WIDTH=68>
     474                        <P>509</P>
     475                </TD>
     476                <TD WIDTH=62>
     477                        <P>3.7a</P>
     478                </TD>
     479                <TD WIDTH=36>
     480                        <P>B</P>
     481                </TD>
     482                <TD WIDTH=518>
     483                        <P>bugfix for rev 504: remode_md was given a wrong value</P>
     484                </TD>
     485                <TD WIDTH=393>
     486                        <P>mbuild</P>
     487                </TD>
     488        </TR>
     489        <TR>
     490                <TD WIDTH=37>
     491                        <P>08/03/10</P>
     492                </TD>
     493                <TD WIDTH=56>
     494                        <P>SR</P>
     495                </TD>
     496                <TD WIDTH=68>
     497                        <P>506</P>
     498                </TD>
     499                <TD WIDTH=62>
     500                        <P>3.7a</P>
     501                </TD>
     502                <TD WIDTH=36>
     503                        <P>C</P>
     504                </TD>
     505                <TD WIDTH=518>
     506                        <P>hack for better usage of <B>mrun</B> on Kyoto computing center
     507                        machine (<FONT FACE="Courier New, Courier, monospace">lckyoto</FONT>)</P>
     508                </TD>
     509                <TD WIDTH=393>
     510                        <P>mrun</P>
     511                </TD>
     512        </TR>
     513        <TR>
     514                <TD WIDTH=37>
     515                        <P>03/03/10</P>
     516                </TD>
     517                <TD WIDTH=56>
     518                        <P>SR</P>
     519                </TD>
     520                <TD WIDTH=68>
     521                        <P>504</P>
     522                </TD>
     523                <TD WIDTH=62>
     524                        <P>3.7a</P>
     525                </TD>
     526                <TD WIDTH=36>
     527                        <P>C</P>
     528                </TD>
     529                <TD WIDTH=518>
     530                        <P><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
     531                        is now directly called within <B>mrun</B> and must not be given by
     532                        an output command in the configuration file any more. Please
     533                        remove the respective output command (<FONT FACE="Courier New, Courier, monospace">OC:combine_plot_fields.x</FONT>)
     534                        from your configuration file!<BR><BR>Utility programs
     535                        (<FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>,
     536                        <FONT FACE="Courier New, Courier, monospace">interpret_config</FONT>)
     537                        are created by <B>mbuild</B> separately for each block in the
     538                        configuration file. Depending on option <FONT FACE="Courier New, Courier, monospace">-K</FONT>,
     539                        <B>mrun</B> is using the utility programs for the respective
     540                        block.<BR><BR>Utility programs are also compiled in parallel,
     541                        depending on variable <FONT FACE="Courier New, Courier, monospace">%mopts</FONT>
     542                        in the configuration file..<BR><BR>Default configuration files
     543                        updated.</P>
     544                </TD>
     545                <TD WIDTH=393>
     546                        <P>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</P>
     547                </TD>
     548        </TR>
     549        <TR>
     550                <TD WIDTH=37>
     551                        <P>02/03/10</P>
     552                </TD>
     553                <TD WIDTH=56>
     554                        <P>SR</P>
     555                </TD>
     556                <TD WIDTH=68>
     557                        <P>496</P>
     558                </TD>
     559                <TD WIDTH=62>
     560                        <P>3.7a</P>
     561                </TD>
     562                <TD WIDTH=36>
     563                        <P>C</P>
     564                </TD>
     565                <TD WIDTH=518>
     566                        <P>Particle data for restart runs are only written if environment
     567                        variable <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>
     568                        = <I>.T.</I>, i.e. particle data are now handled in the same way
     569                        as the other restart data.</P>
     570                </TD>
     571                <TD WIDTH=393>
     572                        <P>palm</P>
     573                </TD>
     574        </TR>
     575        <TR>
     576                <TD WIDTH=37>
     577                        <P>01/03/10</P>
     578                </TD>
     579                <TD WIDTH=56>
     580                        <P>SR</P>
     581                </TD>
     582                <TD WIDTH=68>
     583                        <P>494</P>
     584                </TD>
     585                <TD WIDTH=62>
     586                        <P>3.7a</P>
     587                </TD>
     588                <TD WIDTH=36>
     589                        <P>N</P>
     590                </TD>
     591                <TD WIDTH=518>
     592                        <P>Output in NetCDF4-format.<BR><BR>NetCDF4 allows for parallel
     593                        I/O. Also, variables are not limited in size any more (i.e. arrays
     594                        can be larger than 2GB). The new d3par-parameter
     595                        <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.can
     596                        be used to select among the different NetCDF file formats (<I>1</I>:
     597                        classic format, <I>2</I>: 64-bit-offset format (this is now the
     598                        default), <I>3</I>: NetCDF4/HDF5 format, <I>4</I>: NetCDF4 format
     599                        with NF90_CLASSIC_MODEL bit set). Setting <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
     600                        &gt; <I>2</I> only affects 2d- and 3d-output, i.e. there is no
     601                        parallel output for profiles, time series, spectra, and particles.
     602                        Parallel output of particle data may realized in the future.<BR><BR>In
     603                        case of parallel output, all PEs write into one file, which means
     604                        that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
     605                        (merging data from single files - one per PE - into one file) is
     606                        not neccessary. In this case, flag files are automatically set,
     607                        telling <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
     608                        that nothing is to be done.<BR><BR>Using NetCDF4 format requires a
     609                        NetCDF4/HDF library. Respective settings for -I, -L, and -l
     610                        compiler/loader options for the SGI-ICE at HLRN can be found in
     611                        the new example configuration file
     612                        <FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
     613                        far, NetCDF parallel I/O has only been tested a little. Further
     614                        performance optimizations may be required, especially in case of
     615                        large data sets (e.g. data chunking, or lustre file system
     616                        settings with <FONT FACE="Courier New, Courier, monospace">lfs
     617                        setstripe</FONT>). <B>Please report bugs and performance problems
     618                        immediately!</B><BR><BR><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
     619                        outputs cpu-time needed for file merging.<BR><BR>Modules to be
     620                        loaded for compilation (mbuild) or job execution (mrun) can/should
     621                        now be given in the configuration file (<FONT FACE="Courier New, Courier, monospace">.mrun.config</FONT>)
     622                        using variable <FONT FACE="Courier New, Courier, monospace">modules</FONT>.
     623                        Example:<BR><BR>&nbsp;&nbsp; <FONT FACE="Courier New, Courier, monospace">%modules&nbsp;&nbsp;&nbsp;&nbsp;
     624                        ifort/11.0.069:netcdf&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; lcsgih
     625                        parallel</FONT><BR><BR>This method replaces the (undocumented)
     626                        <FONT FACE="Courier New, Courier, monospace">mpilib</FONT>-variable.<BR><BR><B>WARNING:</B><BR><B>All
     627                        fixed settings of modules in the scripts mbuild, mrun, and subjob
     628                        have been removed! Please set the </B><FONT FACE="Courier New, Courier, monospace"><B>modules</B></FONT><B>
     629                        variable appropriately and remove the mpilib variable in your
     630                        configuration file.<BR><BR></B>Compilation time can be reduced be
     631                        using parallel make. The number of allowed simultaneous compiler
     632                        calls (threads) is set in the configuration file using variable
     633                        <FONT FACE="Courier New, Courier, monospace">mopt</FONT>, e.g.<BR><BR>&nbsp;&nbsp;
     634                        <FONT FACE="Courier New, Courier, monospace">%mopts&nbsp; -j:4 &nbsp;
     635                        lcsgih parallel</FONT><BR><BR>allows a maximum of 4 routines to be
     636                        compiled simultaneously (provided that the makefile does not show
     637                        any dependencies between these routines).</P>
     638                </TD>
     639                <TD WIDTH=393>
     640                        <P>check_open, check_parameters, close_file, data_output_2d,
     641                        data_output_3d, header, modules, netcdf,
     642                        parin<BR><BR>combine_plot_fields<BR><BR>mbuild, mrun, subjob</P>
     643                </TD>
     644        </TR>
     645        <TR>
     646                <TD WIDTH=37>
     647                        <P><BR>
     648                        </P>
     649                </TD>
     650                <TD WIDTH=56>
     651                        <P><BR>
     652                        </P>
     653                </TD>
     654                <TD WIDTH=68>
     655                        <P><BR>
     656                        </P>
     657                </TD>
     658                <TD WIDTH=62>
     659                        <P><BR>
     660                        </P>
     661                </TD>
     662                <TD WIDTH=36>
     663                        <P>C</P>
     664                </TD>
     665                <TD WIDTH=518>
     666                        <P>d3par-parameters <FONT FACE="Courier New, Courier, monospace">netcdf_64bit</FONT>
     667                        and <FONT FACE="Courier New, Courier, monospace">netcdf_64bit_3d</FONT>
     668                        have been removed. Use the new d3par-variable <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
     669                        = <I>2</I> for choosing the NetCDF 64bit-offset format (this is
     670                        the default from now on). The offset-format can not be set
     671                        independently for the 3d-output-data any more.<BR><BR>d3par-parameters
     672                        <FONT FACE="Courier New, Courier, monospace">netcdf_format_mask</FONT>,
     673                        <FONT FACE="Courier New, Courier, monospace">netcdf_format_mask_av</FONT>,
     674                        and variables <FONT FACE="Courier New, Courier, monospace">nc_format_mask</FONT>,
     675                        <FONT FACE="Courier New, Courier, monospace">format_parallel_io</FONT>
     676                        removed. They are replaced by the new parameter
     677                        <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
     678                        This change concerns the masked data output, which is still not
     679                        documented.</P>
     680                </TD>
     681                <TD WIDTH=393>
     682                        <P>check_open, close_file,<BR>data_output_mask, header,
     683                        init_masks, modules, parin</P>
     684                </TD>
     685        </TR>
     686        <TR>
     687                <TD WIDTH=37>
     688                        <P><BR>
     689                        </P>
     690                </TD>
     691                <TD WIDTH=56>
     692                        <P><BR>
     693                        </P>
     694                </TD>
     695                <TD WIDTH=68>
     696                        <P><BR>
     697                        </P>
     698                </TD>
     699                <TD WIDTH=62>
     700                        <P><BR>
     701                        </P>
     702                </TD>
     703                <TD WIDTH=36>
     704                        <P>B</P>
     705                </TD>
     706                <TD WIDTH=518>
     707                        <P>Bugfix in trunk/UTIL/Makefile: forgot to compile for
     708                        interpret_config.<BR><BR>Bugfix: timeseries data have to be
     709                        collected by PE0 (user_statistics).</P>
     710                </TD>
     711                <TD WIDTH=393>
     712                        <P>user_statistics<BR><BR>trunk/UTIL/Makefile</P>
     713                </TD>
     714        </TR>
     715        <TR>
     716                <TD WIDTH=37>
     717                        <P>05/02/10</P>
     718                </TD>
     719                <TD WIDTH=56>
     720                        <P>SR</P>
     721                </TD>
     722                <TD WIDTH=68>
     723                        <P>485</P>
     724                </TD>
     725                <TD WIDTH=62>
     726                        <P>3.7a</P>
     727                </TD>
     728                <TD WIDTH=36>
     729                        <P>B</P>
     730                </TD>
     731                <TD WIDTH=518>
     732                        <P><FONT FACE="Courier New, Courier, monospace">ngp_3d</FONT>,
     733                        <FONT FACE="Courier New, Courier, monospace">ngp_3d_inner</FONT>
     734                        changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid
     735                        points some global statistics (e.g. total kinetic energy) have
     736                        wrong values.</P>
     737                </TD>
     738                <TD WIDTH=393>
     739                        <P>init_3d_model, modules</P>
     740                </TD>
     741        </TR>
     742        <TR>
     743                <TD WIDTH=37>
     744                        <P>05/02/10</P>
     745                </TD>
     746                <TD WIDTH=56>
     747                        <P>SR</P>
     748                </TD>
     749                <TD WIDTH=68>
     750                        <P>484</P>
     751                </TD>
     752                <TD WIDTH=62>
     753                        <P>3.7a</P>
     754                </TD>
     755                <TD WIDTH=36>
     756                        <P>B</P>
     757                </TD>
     758                <TD WIDTH=518>
     759                        <P>Typo in file headers removed (&quot;current&quot; instead of
     760                        &quot;actual&quot;).</P>
     761                </TD>
     762                <TD WIDTH=393>
     763                        <P>many</P>
     764                </TD>
     765        </TR>
     766        <TR>
     767                <TD WIDTH=37>
     768                        <P>05/02/10</P>
     769                </TD>
     770                <TD WIDTH=56>
     771                        <P>SR</P>
     772                </TD>
     773                <TD WIDTH=68>
     774                        <P>483</P>
     775                </TD>
     776                <TD WIDTH=62>
     777                        <P>3.7a</P>
     778                </TD>
     779                <TD WIDTH=36>
     780                        <P>N</P>
     781                </TD>
     782                <TD WIDTH=518>
     783                        <P><FONT FACE="Courier New, Courier, monospace">compare_palm_logs
     784                        </FONT>is additionally compiled with <B>mbuild</B> <FONT FACE="Courier New, Courier, monospace">-u</FONT>
     785                        . (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT> in
     786                        <FONT FACE="Courier New, Courier, monospace">trunk/UTIL</FONT>)<BR><BR>make
     787                        options (<FONT FACE="Courier New, Courier, monospace">mopts</FONT>)
     788                        to be set by configuration file implemented. (<B>mrun</B>,
     789                        <B>mbuild</B>)<BR><BR><FONT FACE="Courier New, Courier, monospace">humidity</FONT>
     790                        = <I>.T.</I> can be used for runs with topography.
     791                        <FONT FACE="Courier New, Courier, monospace">wall_humidityflux</FONT>
     792                        and<BR><FONT FACE="Courier New, Courier, monospace">wall_scalarflux</FONT>
     793                        are the corresponding new inipar parameters.<BR>(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     794                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
     795                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>)<BR><BR>Large
     796                        scale vertical motion (subsidence/ascent) can be added as
     797                        additional source to the prognostic equation for potential
     798                        temperature. See new parameters <FONT FACE="Courier New, Courier, monospace">large_scale_subsidence</FONT>,
     799                        <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient</FONT>,
     800                        and <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient_level</FONT>.
     801                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     802                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     803                        <FONT FACE="Courier New, Courier, monospace">Makefile</FONT>,
     804                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     805                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     806                        <FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
     807                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     808                        <FONT FACE="Courier New, Courier, monospace">subsidence</FONT>,
     809                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Scripts
     810                        have been updated for Cray-XT5 machine (lcxt5m) and
     811                        Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
     812                        and running palm (with limited features) has been added.
     813                        (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, new
     814                        scripts <B>palm_simple_install</B>, <B>palm_simple_run</B>)<BR><BR>Masked
     815                        data output has been implemented but it is not documented in the
     816                        user manual so far. This feature can already use NetCDF4 file
     817                        format. (check_open, check_parameters, close_file, modules,
     818                        netcdf, parin, time_integration, user_parin, new:
     819                        data_output_mask, init_masks, user_data_output_mask)</P>
     820                </TD>
     821                <TD WIDTH=393>
     822                        <P>check_open, check parameters, close_file, header,
     823                        init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
     824                        prognostic_equations, read_var_list, time_integration, user_parin,
     825                        write_var_list<BR><BR><B>new:</B> data_output_mask,&nbsp;
     826                        init_masks, palm_simple_install, palm_simple_run, subsidence,
     827                        user_data_output_mask</P>
     828                </TD>
     829        </TR>
     830        <TR>
     831                <TD WIDTH=37>
     832                        <P><BR>
     833                        </P>
     834                </TD>
     835                <TD WIDTH=56>
     836                        <P><BR>
     837                        </P>
     838                </TD>
     839                <TD WIDTH=68>
     840                        <P><BR>
     841                        </P>
     842                </TD>
     843                <TD WIDTH=62>
     844                        <P><BR>
     845                        </P>
     846                </TD>
     847                <TD WIDTH=36>
     848                        <P>C</P>
     849                </TD>
     850                <TD WIDTH=518>
     851                        <P>2d-decomposition is default for Cray-XT machines.
     852                        (<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">var_ts</FONT>
     853                        is replaced by <FONT FACE="Courier New, Courier, monospace">dots_max</FONT>.
     854                        (<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     855                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Every
     856                        cloud droplet has now an own weighting factor and can be deleted
     857                        due to collisions. Condensation and collision of cloud droplets
     858                        are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
     859                        efficiency for large cloud droplets has changed according to table
     860                        of Rogers and Yau. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
     861                </TD>
     862                <TD WIDTH=393>
     863                        <P>advec_particles, collision_efficiency, init_3d_model,
     864                        init_pegrid, modules</P>
     865                </TD>
     866        </TR>
     867        <TR>
     868                <TD WIDTH=37>
     869                        <P><BR>
     870                        </P>
     871                </TD>
     872                <TD WIDTH=56>
     873                        <P><BR>
     874                        </P>
     875                </TD>
     876                <TD WIDTH=68>
     877                        <P><BR>
     878                        </P>
     879                </TD>
     880                <TD WIDTH=62>
     881                        <P><BR>
     882                        </P>
     883                </TD>
     884                <TD WIDTH=36>
     885                        <P>B</P>
     886                </TD>
     887                <TD WIDTH=518>
     888                        <P>Bugfix for generating serial jobs. (<B>subjob</B>)<BR><BR>Bugfix:
     889                        index problem concerning gradient_level indices removed.
     890                        (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
     891                        of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
     892                        in cascade change to prevent type problems with mpi2 libraries.
     893                        (<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
     894                        was split to make runs reproducible when using ifort compiler.
     895                        (<FONT FACE="Courier New, Courier, monospace">disturb_field</FONT>)<BR><BR>Bugfix:
     896                        exchange of ghost points for <FONT FACE="Courier New, Courier, monospace">prho</FONT>
     897                        included. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix
     898                        in calculation of time-averaged surface heatfluxes.
     899                        (<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
     900                        in calculation of precipitation_rate.
     901                        (<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
     902                        initial data assignments to some dvrp arrays changed due to error
     903                        messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
     904                        in calculation of cloud droplet velocity.
     905                        (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
     906                        in transfer of particles at south/left edge.
     907                        (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
     908                        in calculation of collision efficiency. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
     909                </TD>
     910                <TD WIDTH=393>
     911                        <P>advec_particles, calc_precipitation, collision_efficiency,
     912                        disturb_field, header, modules, poisfft_hybrid, subjob,
     913                        sum_up_3d_data, time_integration</P>
     914                </TD>
     915        </TR>
     916        <TR>
     917                <TD WIDTH=37>
     918                        <P>23/09/09</P>
     919                </TD>
     920                <TD WIDTH=56>
     921                        <P>SR</P>
     922                </TD>
     923                <TD WIDTH=68>
     924                        <P>392</P>
     925                </TD>
     926                <TD WIDTH=62>
     927                        <P>3.7</P>
     928                </TD>
     929                <TD WIDTH=36>
     930                        <P>N</P>
     931                </TD>
     932                <TD WIDTH=518>
     933                        <P><B>Most important changes:</B> atmosphere-ocean coupling has
     934                        been improved and steering of dvr-software is more user-friendly
     935                        now. Beside that, the release contains a lot of optimizations,
     936                        changes, and bugfixes which have accumulated over the last
     937                        months.<BR><BR>The atmosphere-ocean coupling allows to use
     938                        independent precursor runs in order to account for different
     939                        spin-up times. The time when coupling has to be started is given
     940                        by new inipar parameter <FONT FACE="Courier New, Courier, monospace">coupling_start_time</FONT>.
     941                        The precursor ocean run has to be started using new <B>mrun</B>
     942                        option &quot;<FONT FACE="Courier New, Courier, monospace">-y</FONT>&quot;
     943                        in order to add the appendix &quot;<FONT FACE="Courier New, Courier, monospace">_O</FONT>&quot;
     944                        to all output files. (<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
     945                        <FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     946                        <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     947                        <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
     948                        <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
     949                        <FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
     950                        <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
     951                        <FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
     952                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     953                        <FONT FACE="Courier New, Courier, monospace">init_coupling</FONT>,
     954                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>, <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
     955                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     956                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     957                        <FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
     958                        <FONT FACE="Courier New, Courier, monospace">time_integration</FONT>,
     959                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Clipping
     960                        of dvrp output implemented. Default colourtable for particles
     961                        implemented, particle attributes (color, dvrp_size) can be set
     962                        with new parameters <FONT FACE="Courier New, Courier, monospace">particle_color</FONT>,
     963                        <FONT FACE="Courier New, Courier, monospace">particle_dvrpsize</FONT>,
     964                        <FONT FACE="Courier New, Courier, monospace">color_interval</FONT>,
     965                        <FONT FACE="Courier New, Courier, monospace">dvrpsize_interval</FONT>.
     966                        Slicer attributes (dvrp) are set with new routine
     967                        <FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>
     968                        and are controlled with existing parameters <FONT FACE="Courier New, Courier, monospace">slicer_range_limits</FONT>.
     969                        (<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
     970                        <FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
     971                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     972                        <FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>,&nbsp;
     973                        <FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>)<BR><BR>Polygon
     974                        reduction for topography and ground plate isosurface. Reduction
     975                        level for buildings can be chosen with parameter cluster_size.
     976                        (<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>)<BR><BR>Variables
     977                        <FONT FACE="Courier New, Courier, monospace">bc_lr</FONT> / <FONT FACE="Courier New, Courier, monospace">bc_ns</FONT>&nbsp;
     978                        in most subroutines replaced by LOGICAL variables
     979                        <FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
     980                        for speed optimization. This gives a significant speedup of more
     981                        than 10%. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     982                        <FONT FACE="Courier New, Courier, monospace">diffusion_u</FONT>,
     983                        <FONT FACE="Courier New, Courier, monospace">diffusion_v</FONT>,
     984                        <FONT FACE="Courier New, Courier, monospace">diffusion_w</FONT>,
     985                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Scripts
     986                        have been adapted for machine lck (Yonsei Univ.). (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
     987                        <FONT FACE="Courier New, Courier, monospace">mbuild</FONT>,
     988                        <FONT FACE="Courier New, Courier, monospace">subjob</FONT>)<BR><BR>Additional
     989                        timestep criterion in case of simulations with plant canopy.
     990                        (<FONT FACE="Courier New, Courier, monospace">timestep</FONT>)<BR><BR>Check
     991                        for illegal entries in <FONT FACE="Courier New, Courier, monospace">section_xy</FONT>|<FONT FACE="Courier New, Courier, monospace">xz</FONT>|<FONT FACE="Courier New, Courier, monospace">yz</FONT>
     992                        that exceed <FONT FACE="Courier New, Courier, monospace">nz+1</FONT>|<FONT FACE="Courier New, Courier, monospace">ny+1</FONT>|<FONT FACE="Courier New, Courier, monospace">nx+1</FONT>.
     993                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>External
     994                        pressure gradient can be used as driving force. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     995                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     996                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
     997                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     998                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     999                        <FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
     1000                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1001                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>New
     1002                        topography case '<I>single_street_canyon</I>'. (<FONT FACE="Courier New, Courier, monospace">header</FONT>,
     1003                        <FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
     1004                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     1005                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     1006                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1007                        <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
     1008                        <FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
     1009                        <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
     1010                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
     1011                        to predefine a target bulk velocity for <FONT FACE="Courier New, Courier, monospace">conserve_volume_flow</FONT>.
     1012                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     1013                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     1014                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
     1015                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     1016                        <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     1017                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1018                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
     1019                        for user defined 2D data output in xy cross sections at z=<FONT FACE="Courier New, Courier, monospace">nzb</FONT>+1.
     1020                        (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     1021                        <FONT FACE="Courier New, Courier, monospace">user_data_output_2d</FONT>)<BR><BR>xy
     1022                        cross section output of surface heatfluxes (sensible and latent).
     1023                        (<FONT FACE="Courier New, Courier, monospace">average_3d_data</FONT>,
     1024                        <FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     1025                        <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     1026                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     1027                        <FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
     1028                        <FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>,
     1029                        <FONT FACE="Courier New, Courier, monospace">write_3d_binary</FONT>)</P>
     1030                </TD>
     1031                <TD WIDTH=393>
     1032                        <P>average_3d_data, check_for_restart, check_parameters,
     1033                        data_output_2d, data_output_3d, data_output_dvrp,
     1034                        data_output_profiles, data_output_ptseries, data_output_spectra,
     1035                        data_output_tseries, diffusion_u, diffusion_v, diffusion_w,
     1036                        init_coupling, init_dvrp, init_grid, init_3d_model, header,
     1037                        mbuild, modules, mrun, package_parin, parin, prognostic_equations,
     1038                        read_3d_binary, read_var_list, subjob, sum_up_3d_data,
     1039                        surface_coupler, timestep, time_integration,
     1040                        user_check_parameters, user_data_output_2d, user_data_output_dvrp,
     1041                        user_header, user_init_grid, write_3d_binary, write_var_list<BR><BR><B>new:</B>
     1042                        set_particle_attributes, set_slicer_attributes_dvrp</P>
     1043                </TD>
     1044        </TR>
     1045        <TR>
     1046                <TD WIDTH=37>
     1047                        <P><BR>
     1048                        </P>
     1049                </TD>
     1050                <TD WIDTH=56>
     1051                        <P><BR>
     1052                        </P>
     1053                </TD>
     1054                <TD WIDTH=68>
     1055                        <P><BR>
     1056                        </P>
     1057                </TD>
     1058                <TD WIDTH=62>
     1059                        <P><BR>
     1060                        </P>
     1061                </TD>
     1062                <TD WIDTH=36>
     1063                        <P>C</P>
     1064                </TD>
     1065                <TD WIDTH=518>
     1066                        <P>Output of messages replaced by message handling routine.
     1067                        (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
     1068                        <FONT FACE="Courier New, Courier, monospace">advec_s_bc</FONT>,
     1069                        <FONT FACE="Courier New, Courier, monospace">buoyancy</FONT>,
     1070                        <FONT FACE="Courier New, Courier, monospace">calc_spectra</FONT>,
     1071                        <FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
     1072                        <FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
     1073                        <FONT FACE="Courier New, Courier, monospace">coriolis</FONT>,
     1074                        <FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>,
     1075                        <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     1076                        <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
     1077                        <FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
     1078                        <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
     1079                        <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
     1080                        <FONT FACE="Courier New, Courier, monospace">fft_xy</FONT>,
     1081                        <FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>,
     1082                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,&nbsp;
     1083                        <FONT FACE="Courier New, Courier, monospace">init_1d_model</FONT>,
     1084                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
     1085                        <FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
     1086                        <FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
     1087                        <FONT FACE="Courier New, Courier, monospace">init_particles</FONT>,
     1088                        <FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>,
     1089                        <FONT FACE="Courier New, Courier, monospace">netcdf</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     1090                        <FONT FACE="Courier New, Courier, monospace">plant_canopy_model</FONT>,
     1091                        <FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>,
     1092                        <FONT FACE="Courier New, Courier, monospace">poismg</FONT>,
     1093                        <FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
     1094                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1095                        <FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
     1096                        <FONT FACE="Courier New, Courier, monospace">temperton_fft</FONT>,
     1097                        <FONT FACE="Courier New, Courier, monospace">timestep</FONT>,
     1098                        <FONT FACE="Courier New, Courier, monospace">user_actions</FONT>,
     1099                        <FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>,
     1100                        <FONT FACE="Courier New, Courier, monospace">user_dvrp_coltab</FONT>,
     1101                        <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
     1102                        <FONT FACE="Courier New, Courier, monospace">user_init_plant_canopy</FONT>,
     1103                        <FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
     1104                        <FONT FACE="Courier New, Courier, monospace">user_read_restart_data</FONT>,
     1105                        <FONT FACE="Courier New, Courier, monospace">user_spectra</FONT>)<BR><BR>Output
     1106                        of NetCDF messages with aid of message handling routine.
     1107                        (<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
     1108                        <FONT FACE="Courier New, Courier, monospace">close_file</FONT>,
     1109                        <FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     1110                        <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
     1111                        <FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
     1112                        <FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
     1113                        <FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,&nbsp;
     1114                        <FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
     1115                        <FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>__lcmuk
     1116                        changed to __lc to avoid problems with Intel compiler on sgi-ice.
     1117                        (<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
     1118                        extended NetCDF files, the updated title attribute includes an
     1119                        update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
     1120                        case of restart runs without extension, initial profiles are not
     1121                        written to NetCDF-file anymore. So far, time axis always started
     1122                        at t=0. (<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
     1123                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>,
     1124                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1125                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">initializing_actions</FONT>='<I>read_data_for_recycling</I>'
     1126                        renamed to '<I>cyclic_fill</I>'. A cyclic fill can now <BR>be used
     1127                        independent of <FONT FACE="Courier New, Courier, monospace">turbulent_inflow</FONT>.
     1128                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     1129                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     1130                        <FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>2
     1131                        NetCDF error numbers changed. (<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>A
     1132                        link to the webspage appendix_a.html is printed for further
     1133                        information about possible reasons of the error that appeared.
     1134                        (message)<BR><BR>Temperature gradient criterion for estimating the
     1135                        boundary layer height replaced by the gradient criterion of
     1136                        Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
     1137                        unit attribute in timeseries output in case of statistic regions
     1138                        added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
     1139                        number of tails is calculated from maximum number of particles and
     1140                        <FONT FACE="Courier New, Courier, monospace">skip_particles_for_tail</FONT>.
     1141                        (<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Value
     1142                        of <FONT FACE="Courier New, Courier, monospace">vertical_particle_advection</FONT>
     1143                        is allowed to differ for each particle group. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
     1144                        <FONT FACE="Courier New, Courier, monospace">header</FONT>,
     1145                        <FONT FACE="Courier New, Courier, monospace">modules</FONT>)
     1146                        <BR><BR>First constant in array <FONT FACE="Courier New, Courier, monospace">den</FONT>
     1147                        also defined as type double. (<FONT FACE="Courier New, Courier, monospace">eqn_state_seawater</FONT>)<BR><BR>Parameter
     1148                        <FONT FACE="Courier New, Courier, monospace">dvrp_psize</FONT>
     1149                        moved from <FONT FACE="Courier New, Courier, monospace">particles_par</FONT>
     1150                        to <FONT FACE="Courier New, Courier, monospace">dvrp_graphics_par</FONT>.
     1151                        (<FONT FACE="Courier New, Courier, monospace">package_parin</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>
     1152                        moved from <FONT FACE="Courier New, Courier, monospace">userpar</FONT>
     1153                        to <FONT FACE="Courier New, Courier, monospace">inipar</FONT>
     1154                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
     1155                        <FONT FACE="Courier New, Courier, monospace">header</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
     1156                        <FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1157                        <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
     1158                        <FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
     1159                        <FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
     1160                        <FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
     1161                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Default
     1162                        value of <FONT FACE="Courier New, Courier, monospace">grid_matching</FONT>
     1163                        changed to '<I>strict</I>'. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Adjustments
     1164                        for runs on lcxt4 (necessary due to a software update on CRAY) and
     1165                        for coupled runs on ibmy. (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
     1166                        <FONT FACE="Courier New, Courier, monospace">subjob</FONT>)</P>
     1167                </TD>
     1168                <TD WIDTH=393>
     1169                        <P>advec_particles, advec_s_bc, buoyancy, calc_spectra,
     1170                        check_for_restart, check_open, check_parameters, close_file,
     1171                        coriolis, cpu_log, data_output_2d, data_output_3d,
     1172                        data_output_dvrp, data_output_profiles, data_output_ptseries,
     1173                        data_output_spectra, data_output_tseries, eqn_state_seawater,
     1174                        fft_xy, flow_statistics, header, init_1d_model, init_3d_model,
     1175                        init_dvrp, init_grid, init_particles, init_pegrid, message, mrun,
     1176                        netcdf, package_parin, parin, plant_canopy_model, poisfft,
     1177                        poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
     1178                        surface_coupler, temperton_fft, timestep,
     1179                        user_actions,user_check_parameters, user_data_output_dvrp,
     1180                        user_dvrp_coltab, user_header, user_init_grid,
     1181                        user_init_plant_canopy, user_parin, user_read_restart_data,
     1182                        user_spectra, write_var_list
     1183                        </P>
     1184                </TD>
     1185        </TR>
     1186        <TR>
     1187                <TD WIDTH=37>
     1188                        <P><BR>
     1189                        </P>
     1190                </TD>
     1191                <TD WIDTH=56>
     1192                        <P><BR>
     1193                        </P>
     1194                </TD>
     1195                <TD WIDTH=68>
     1196                        <P><BR>
     1197                        </P>
     1198                </TD>
     1199                <TD WIDTH=62>
     1200                        <P><BR>
     1201                        </P>
     1202                </TD>
     1203                <TD WIDTH=36>
     1204                        <P>B</P>
     1205                </TD>
     1206                <TD WIDTH=518>
     1207                        <P>Bugfix: Initial hydrostatic pressure profile in case of ocean
     1208                        runs is now calculated in 5 iteration steps. (<FONT FACE="Courier New, Courier, monospace">init_ocean</FONT>)<BR><BR>Bugfix:
     1209                        wrong sign in buoyancy production of ocean part in case of not
     1210                        using the reference density (only in 3D routine <FONT FACE="Courier New, Courier, monospace">production_e</FONT>).
     1211                        (<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix:
     1212                        output of averaged 2d/3d quantities requires that an avaraging
     1213                        interval has been set, respective error message is included.
     1214                        (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
     1215                        Output on unit 14 only if requested by <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>.
     1216                        (<FONT FACE="Courier New, Courier, monospace">user_last_actions</FONT>)<BR><BR>Bugfix
     1217                        to avoid zero division by <FONT FACE="Courier New, Courier, monospace">km_neutral</FONT>.
     1218                        (<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix
     1219                        for extended NetCDF files: In order to avoid 'data mode' errors if
     1220                        updated attributes are larger than their original size,
     1221                        <FONT FACE="Courier New, Courier, monospace">NF90_PUT_ATT</FONT>
     1222                        is called in 'define mode' enclosed by <FONT FACE="Courier New, Courier, monospace">NF90_REDEF</FONT>
     1223                        and <FONT FACE="Courier New, Courier, monospace">NF90_ENDDEF</FONT>
     1224                        calls. This implies a possible performance loss; an alternative
     1225                        strategy would be to ensure equal attribute size in a job chain.
     1226                        (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
     1227                        correction of initial volume flow for non-flat topography.
     1228                        (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
     1229                        zero initialization of arrays within buildings for '<I>cyclic_fill</I>'.
     1230                        (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
     1231                        <FONT FACE="Courier New, Courier, monospace">to_be_resorted</FONT>
     1232                        =&gt; <FONT FACE="Courier New, Courier, monospace">s_av</FONT> for
     1233                        time-averaged scalars. (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
     1234                        <FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>Bugfix:
     1235                        avoid that <FONT FACE="Courier New, Courier, monospace">ngp_2dh_s_inner</FONT>
     1236                        becomes zero. (<FONT FACE="Courier New, Courier, monospace">init_3_model</FONT>)<BR><BR>Typographical
     1237                        error: unit of wpt in dots_unit. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix:
     1238                        error in check, if particles moved further than one subdomain
     1239                        length. This check must not be applied for newly released
     1240                        particles. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix:
     1241                        several tail counters are initialized, <FONT FACE="Courier New, Courier, monospace">particle_tail_coordinates</FONT>
     1242                        is only written to file if its third index is &gt; 0, arrays for
     1243                        tails are allocated with a minimum size of 10 tails if there is no
     1244                        tail initially. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
     1245                        <FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Bugfix:
     1246                        pressure included for profile output. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
     1247                        Type of <FONT FACE="Courier New, Courier, monospace">count</FONT>
     1248                        and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
     1249                        changed to default <FONT FACE="Courier New, Courier, monospace">INTEGER</FONT>
     1250                        on NEC machines. (<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>)<BR><BR>Bugfix:
     1251                        output of particle time series only if particle advection is
     1252                        switched on. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix:
     1253                        qsws was calculated in case of <FONT FACE="Courier New, Courier, monospace">constant
     1254                        heatflux</FONT> = <FONT FACE="Courier New, Courier, monospace">.FALSE.</FONT>.
     1255                        (<FONT FACE="Courier New, Courier, monospace">prandtl_fluxes</FONT>)<BR><BR>Bugfix:
     1256                        averaging along z is not allowed for 2d quantities (e.g. u* and
     1257                        z0). (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>)<BR><BR>Typographical
     1258                        errors. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>If
     1259                        the inversion height calculated by the prerun is zero,
     1260                        inflow_damping_height must be explicitly specified.
     1261                        (<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Small
     1262                        bugfix concerning 3d 64bit netcdf output format. (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Bugfix:
     1263                        <FONT FACE="Courier New, Courier, monospace">dt_fixed</FONT>
     1264                        removed from the restart file, because otherwise, no change from a
     1265                        fixed to a variable timestep would be possible in restart runs.
     1266                        (<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
     1267                        <FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Bugfix:
     1268                        initial setting of <FONT FACE="Courier New, Courier, monospace">time_coupling</FONT>
     1269                        in coupled restart runs. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)</P>
     1270                </TD>
     1271                <TD WIDTH=393>
     1272                        <P>advec_particles, check_parameters, cpu_log, data_output_2d,
     1273                        data_output_3d, header, init_3d_model, init_particles, init_ocean,
     1274                        modules, netcdf, prandtl_fluxes, production_e, read_var_list,
     1275                        time_integration, user_last_actions, write_var_list</P>
     1276                </TD>
     1277        </TR>
     1278        <TR>
     1279                <TD WIDTH=37>
     1280                        <P>02/02/09</P>
     1281                </TD>
     1282                <TD WIDTH=56>
     1283                        <P>SR</P>
     1284                </TD>
     1285                <TD WIDTH=68>
     1286                        <P>228</P>
     1287                </TD>
     1288                <TD WIDTH=62>
     1289                        <P>3.6</P>
     1290                </TD>
     1291                <TD WIDTH=36>
     1292                        <P>N</P>
     1293                </TD>
     1294                <TD WIDTH=518>
     1295                        <P>This release contains further additions, changes, and bugfixes
     1296                        for the SGI-ICE system, as well as important changes like the
     1297                        splitting of the user-interface into single files, a complete
     1298                        revision of the pre-compiling mechanism allowing to use different
     1299                        make-depositories simultaneously, and a revision of the
     1300                        reading-mechanism from restart files, which has no more
     1301                        restrictions in case that the previous and current run have
     1302                        different domain/subdomain sizes. A new handling of all kind of
     1303                        output messages is introduced with this release and will be
     1304                        applied to all existing messages within the next releases.<BR><BR><B>New
     1305                        features are:</B><BR><BR>Restart runs on SGI-ICE are working.
     1306                        (mrun)<BR>2d-decomposition is default on SGI-ICE systems.
     1307                        (init_pegrid)<BR><BR>Ocean-atmosphere coupling realized with
     1308                        MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
     1309                        called with <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
     1310                        &quot;<I>-K parallel</I>&quot; for coupling. Adjustments in <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
     1311                        <FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, and
     1312                        <FONT FACE="Courier New, Courier, monospace">subjob</FONT> for
     1313                        lcxt4.<BR><BR>DVRP arguments changed to single precision, mode
     1314                        pathlines added.<BR><BR>User can add additional routines in files
     1315                        <FONT FACE="Courier New, Courier, monospace">user_additional_routines</FONT>.<BR><BR>User
     1316                        can check user parameters and deduce further quantities in
     1317                        <FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT></P>
     1318                </TD>
     1319                <TD WIDTH=393>
     1320                        <P>check_for_restart, check_parameters, data_output_dvrp,
     1321                        init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
     1322                        surface_coupler, timestep<BR><BR>Makefile,&nbsp;mbuild, mrun,
     1323                        subjob<BR><BR><B>new:</B><BR>init_coupling,
     1324                        user_additional_routines, user_check_parameters</P>
     1325                </TD>
     1326        </TR>
     1327        <TR>
     1328                <TD WIDTH=37>
     1329                        <P><BR>
     1330                        </P>
     1331                </TD>
     1332                <TD WIDTH=56>
     1333                        <P><BR>
     1334                        </P>
     1335                </TD>
     1336                <TD WIDTH=68>
     1337                        <P><BR>
     1338                        </P>
     1339                </TD>
     1340                <TD WIDTH=62>
     1341                        <P><BR>
     1342                        </P>
     1343                </TD>
     1344                <TD WIDTH=36>
     1345                        <P>C</P>
     1346                </TD>
     1347                <TD WIDTH=518>
     1348                        <P>User interface has been split into single files.<BR><BR>Type of
     1349                        variables <FONT FACE="Courier New, Courier, monospace">count</FONT>
     1350                        and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
     1351                        changed to INTEGER(8) in order to avoid &quot;out of range&quot;
     1352                        problems, which result in measured negative time intervals.
     1353                        (cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
     1354                        mechanism from restart files completely revised. The
     1355                        subdomain/total domain size is now allowed to vary arbitrarily
     1356                        between the current and previous run. (read_var_list,
     1357                        read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
     1358                        mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
     1359                        completely revised: the source-tarfile remains in the source
     1360                        directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
     1361                        One depository per block (given in the config-file) is created.
     1362                        Always all files from the source directory are copied to the
     1363                        respective depository. No additional file checks are done any more
     1364                        (mrun version 2.1). The depository name used contains the
     1365                        conditions given by <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
     1366                        &quot;<FONT FACE="Courier New, Courier, monospace">-K</FONT>&quot;.
     1367                        (mbuild, mrun)<BR><BR>Output messages (including required stop of
     1368                        execution) can now be handled with the new subroutine&nbsp;<FONT FACE="Courier New, Courier, monospace">message</FONT>.
     1369                        All output messages will be replaced by this routine step by step
     1370                        within the next revisions.<BR><BR>Neumann boundary condition at
     1371                        <FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
     1372                        explicitly set for better reading, although this has been already
     1373                        done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
     1374                        xy-coordinate system shifted from the center of the first grid
     1375                        cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
     1376                        <FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
     1377                        south-left corner of this cell. (netcdf) Topography definition
     1378                        according to new user parameter <FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>.
     1379                        (init_grid, modules, user_header, user_init_grid, user_parin)</P>
     1380                </TD>
     1381                <TD WIDTH=393>
     1382                        <P>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop,
     1383                        local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
     1384                        read_var_list, user_read_restart_data<BR><BR>Makefile, mbuild,
     1385                        mrun<BR><BR><B>removed:</B><BR>user_interface<BR><BR><B>new:</B><BR>message,
     1386                        user_3d_data_averaging, user_actions, user_advec_particles,
     1387                        user_check_data_output, user_check_data_output_pr,
     1388                        user_data_output_2d, user_data_output_3d, user_data_output_dvrp,
     1389                        user_define_netcdf_grid, user_dvrp_coltab, user_header,
     1390                        user_init_3d_model, user_init, user_init_grid,
     1391                        user_init_particles, user_init_plant_canopy, user_last_actions,
     1392                        user_parin, user_parin, user_particle_attributes,
     1393                        user_read_restart_data, user_spectra, user_statistics</P>
     1394                </TD>
     1395        </TR>
     1396        <TR>
     1397                <TD WIDTH=37>
     1398                        <P><BR>
     1399                        </P>
     1400                </TD>
     1401                <TD WIDTH=56>
     1402                        <P><BR>
     1403                        </P>
     1404                </TD>
     1405                <TD WIDTH=68>
     1406                        <P><BR>
     1407                        </P>
     1408                </TD>
     1409                <TD WIDTH=62>
     1410                        <P><BR>
     1411                        </P>
     1412                </TD>
     1413                <TD WIDTH=36>
     1414                        <P>B</P>
     1415                </TD>
     1416                <TD WIDTH=518>
     1417                        <P>Bugfix: array <FONT FACE="Courier New, Courier, monospace">d</FONT>
     1418                        is reallocated in case that multigrid is used.
     1419                        (calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
     1420                        (check_for_restart, cpu_statistics,
     1421                        inflow_turbulence,&nbsp;timestep)<BR><BR>Size of <FONT FACE="Courier New, Courier, monospace">pf3d
     1422                        </FONT>adjusted to the required output size (1 gridpoint less,
     1423                        along all three dimensions), because output of a subset of the
     1424                        data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
     1425                        in the NF90_PUT_VAR statement caused segmentation fault with the
     1426                        INTEL compiler. (combine_plot_fields)<BR><BR>Bugfix: error in <FONT FACE="Courier New, Courier, monospace">zu</FONT>
     1427                        index in case of <FONT FACE="Courier New, Courier, monospace">section_xy=-1</FONT>.
     1428                        (header)<BR><BR>Inconsistency removed: as the thermal
     1429                        stratification is not taken into account for the evaluation of the
     1430                        wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
     1431                        must not be used for the evaluation of the velocity gradients
     1432                        <FONT FACE="Courier New, Courier, monospace">dudy</FONT>, <FONT FACE="Courier New, Courier, monospace">dwdy</FONT>,
     1433                        <FONT FACE="Courier New, Courier, monospace">dvdx</FONT> and <FONT FACE="Courier New, Courier, monospace">dwdx</FONT>.
     1434                        (production_e)<BR><BR>Bugfix in calculating <FONT FACE="Courier New, Courier, monospace">k</FONT>
     1435                        index in case of oceans runs. (sort_particles)<BR><BR>Bugfix: no
     1436                        output of particle concentration and radius unless particles have
     1437                        been started. (data_output_2d)<BR><BR>Bugfix: reading of
     1438                        <FONT FACE="Courier New, Courier, monospace">spectrum_x|y</FONT>
     1439                        from restart files ignored if total numbers of grid points do not
     1440                        match. (read_3d_binary)<BR><BR>Bugfix: abort in case that absolute
     1441                        temperature is below zero. (init_cloud_physics)</P>
     1442                </TD>
     1443                <TD WIDTH=393>
     1444                        <P>advec_particles, calc_spectra, check_for_restart,
     1445                        cpu_statistics, data_output_2d, header, inflow_turbulence,
     1446                        init_cloud_physics, production_e, read_3d_binary,
     1447                        timestep<BR><BR>combine_plot_fields</P>
     1448                </TD>
     1449        </TR>
     1450</TABLE>
     1451<P><BR>&nbsp; <BR>&nbsp;
     1452</P>
     1453<H2><A NAME="Kapitel2.0"></A>2.0&nbsp; How to change the source code
     1454and how to document modifications</H2>
     1455<P>Currently (Sep 23rd, 2009), only selected users are allowed to
     1456commit changes to the repository. Rules given below are preliminary,
     1457until we have switched to the &quot;trac&quot;-System.</P>
     1458<OL>
     1459        <LI><P>Change source code in your current working copy. Document
     1460        changes in the respective file headers unter &quot;<FONT FACE="Courier New, Courier, monospace">Current
     1461        revisions:</FONT>&quot;. Additionally, document all changes in a
     1462        local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
     1463        including the files that have been changed. Classify changes in
     1464        three cases, new (N), changed (C), and bugfix (B). <B>Try to be as
     1465        short and as precise as possible in describing the changes!</B></P>
     1466        <LI><P>Test the changed version, unless it works sufficiently.</P>
     1467        <LI><P>Commit the changes to the repository<BR><BR>&nbsp;&nbsp; <FONT FACE="Courier New, Courier, monospace">svn
     1468        commit -m &quot;message string&quot; trunk<BR></FONT><BR>where
     1469        &quot;<FONT FACE="Courier New, Courier, monospace">message string</FONT>&quot;
     1470        is a short, <B>meaningful</B> summary of the
     1471        changes.<BR><BR>Alternatively, in case that you have made quite a
     1472        lot of changes, you can also give the contents of your file
     1473        CURRENT_MODIFICATIONS as the log message:<BR><BR>&nbsp;&nbsp; <FONT FACE="Courier New, Courier, monospace">svn
     1474        commit -F CURRENT_MODIFICATIONS trunk</FONT></P>
     1475        <LI><P>Enter the changes into the technical documentation (under
     1476        <FONT FACE="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</FONT>).</P>
     1477        <LI><P>Move the change comments in the file headers from &quot;Current
     1478        revisions:&quot; to &quot;Former revisions:&quot;. Set the current
     1479        svn id in front of that.<BR><BR><B>Example:</B><BR><BR><B>before
     1480        move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
     1481        Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1482        -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1483        </FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
     1484        argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1485        Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1486        -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1487        ￜId: init_3d_model.f90 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
     1488        2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace">
     1489        ￜ</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1490        407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1491        var_ts is replaced by dots_max </FONT><BR><BR><B>after move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
     1492        Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1493        -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1494        </FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1495        Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1496        -----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1497        ￜId: init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</FONT>
     1498        <FONT FACE="Courier New, Courier, monospace">ￜ<BR>!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1499        </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
     1500        2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"><BR>!
     1501        </FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
     1502        argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1503        407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
     1504        var_ts is replaced by dots_max<BR><BR></FONT><FONT FACE="Times New Roman, Times, serif">Note
     1505        that the &quot;</FONT><FONT FACE="Courier New, Courier, monospace">ￜ</FONT><FONT FACE="Times New Roman, Times, serif">&quot;
     1506        in this example should read &quot;$&quot;, but &quot;$&quot; cannot
     1507        be used here, because otherwise svn would replace these entries
     1508        after every change to this technical documentation.</FONT></P>
     1509        <LI><P>Commit the changes in the technical documentation and the
     1510        file headers:<BR><BR>&nbsp;&nbsp; <FONT FACE="Courier New, Courier, monospace">svn
     1511        commit -m &quot;last commit documented&quot; trunk</FONT><BR><BR><BR>
     1512        </P>
     1513</OL>
     1514<H2><A NAME="Kapitel3.0"></A>3.0&nbsp; Description of selected parts
     1515of the model source code</H2>
     1516<P>This section gives links to existing descriptions about special
    14361517parts of the PALM code, e.g. special numerical methods that are used
    14371518(including mathematical background). Documents are stored in single
    14381519files with different formats. Some are in German (sorry for the
    1439 inconvenience).
    1440 <br>&nbsp;
    1441 </p><ul> <li> <a name="UPS"></a>upstream-spline
    1442 advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
    1443 , only in German)</li> <li> <a name="Cloud_physics"></a>cloud
    1444 physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
    1445 )</li>
    1446   <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
    1447   </li>
    1448   <li>Runge-Kutta
    1449 time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
    1450 , only in German)</li>
    1451 
    1452 </ul><br>
    1453 &nbsp;
    1454 <br>&nbsp;
    1455 <br>&nbsp;
    1456 <br>&nbsp;
    1457 <br>&nbsp;
    1458 <br>&nbsp;
    1459 <br>&nbsp;
    1460 <br>&nbsp;
    1461 </body></html>
     1520inconvenience). <BR>&nbsp;
     1521</P>
     1522<UL>
     1523        <LI><P STYLE="margin-bottom: 0in"><A NAME="UPS"></A>upstream-spline
     1524        advection scheme ( <A HREF="methods/upstream_spline/ups.pdf">.pdf</A>
     1525        , only in German)
     1526        </P>
     1527        <LI><P STYLE="margin-bottom: 0in"><A NAME="Cloud_physics"></A>cloud
     1528        physics module ( <A HREF="methods/cloud_physics/cloud_physics.pdf">.pdf</A>
     1529        )
     1530        </P>
     1531        <LI><P STYLE="margin-bottom: 0in"><A NAME="Bitkompression"></A>data
     1532        compression with <A HREF="methods/bit_compression/bit_compression.html">bit
     1533        shifting method</A> (only in German)</P>
     1534        <LI><P>Runge-Kutta time integration scheme ( <A HREF="methods/runge_kutta/runge_kutta.pdf">.pdf</A>
     1535        , only in German)
     1536        </P>
     1537</UL>
     1538<P><BR>&nbsp; <BR>&nbsp; <BR>&nbsp; <BR>&nbsp; <BR>&nbsp; <BR>&nbsp;
     1539<BR>&nbsp; <BR>&nbsp;
     1540</P>
     1541</BODY>
     1542</HTML>
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