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25<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;
26</font>a
27<b>pa</b>rallelized
28<b>L</b>ES <b>m</b>odel
29<br><hr width="100%">
30<br><font size="+2">technical/numerical documentation</font>
31<br>&nbsp;
32<br>&nbsp;
33<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
34</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
35</span></td> </tr>
36<tr nosave=""> <td nosave=""><b>Last
37change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 529 2010-03-31 10:36:23Z heinze $</b></td> </tr>
38</tbody>
39</table><hr width="100%">
40<p><font size="+2">Table of contents</font>
41<br>&nbsp;
42<br>&nbsp;
43</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
44History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
45How to change the source
46code and how to document modifications<br>
47 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
48Description of selected model numerics<br>
49&nbsp;</p>
50</ul><b></b><br>
51
52<h2><a name="Kapitel1.0"></a>1.0&nbsp;
53History of changes</h2>
54The 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>
55<br>
56Entries in the fifth column specify the type of the change:
57change&nbsp;
58of existing code (C), new code (N) or bugfix (B). More detailed
59information
60about the changes may sometimes be found in the header comment lines of the
61respective
62routines.
63<br>&nbsp;
64<br>
65<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
66  <tbody>
67    <tr>
68      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
69      </td>
70      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
71      </td>
72      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
73      </td>
74      <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
75      </td>
76      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
77      </td>
78      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
79      </td>
80      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
81      </td>
82    </tr>
83   
84   
85   
86   
87   
88   
89   
90   
91   
92   
93    <tr>
94      <td style="vertical-align: top;">31/03/10<br>
95      </td>
96      <td style="vertical-align: top;">RH<br>
97      </td>
98      <td style="vertical-align: top;">529<br>
99      </td>
100      <td style="vertical-align: top;">3.7a<br>
101      </td>
102      <td style="vertical-align: top;">C<br>
103      </td>
104      <td style="vertical-align: top;">List of variable names have to specified using blank separated lists and single quotes<br>
105      </td>
106      <td style="vertical-align: top;">palmplot<br>
107      </td>
108    </tr>
109<tr>
110      <td style="vertical-align: top;">30/03/10<br>
111      </td>
112      <td style="vertical-align: top;">RH<br>
113      </td>
114      <td style="vertical-align: top;">526<br>
115      </td>
116      <td style="vertical-align: top;">3.7a<br>
117      </td>
118      <td style="vertical-align: top;">C<br>
119      </td>
120      <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>
121      </td>
122      <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
123      </td>
124    </tr>
125<tr>
126      <td style="vertical-align: top;">30/03/10<br>
127      </td>
128      <td style="vertical-align: top;">SR<br>
129      </td>
130      <td style="vertical-align: top;">525<br>
131      </td>
132      <td style="vertical-align: top;">3.7a<br>
133      </td>
134      <td style="vertical-align: top;">B<br>
135      </td>
136      <td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br>
137      </td>
138      <td style="vertical-align: top;">check_parameters<br>
139      </td>
140    </tr>
141<tr>
142      <td style="vertical-align: top;">19/03/10<br>
143      </td>
144      <td style="vertical-align: top;">SR<br>
145      </td>
146      <td style="vertical-align: top;">520<br>
147      </td>
148      <td style="vertical-align: top;">3.7a<br>
149      </td>
150      <td style="vertical-align: top;">N<br>
151      </td>
152      <td style="vertical-align: top;">NetCDF4 support for particle
153data. Total number of particles is allowed to increase during the run,
154when netcdf_data_format &gt; <span style="font-style: italic;">2</span> is used.<br>
155      </td>
156      <td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
157      </td>
158    </tr>
159    <tr>
160      <td style="vertical-align: top;"><br>
161      </td>
162      <td style="vertical-align: top;"><br>
163      </td>
164      <td style="vertical-align: top;"><br>
165      </td>
166      <td style="vertical-align: top;"><br>
167      </td>
168      <td style="vertical-align: top;">C<br>
169      </td>
170      <td style="vertical-align: top;">Special characters like * and "
171are now allowed for NetCDF variable names. Replacement of these
172characters has been removed (routine clean_netcdf_varname removed)<br>
173      </td>
174      <td style="vertical-align: top;"><br>
175      </td>
176    </tr>
177<tr>
178      <td style="vertical-align: top;">18/03/10<br>
179      </td>
180      <td style="vertical-align: top;">SR<br>
181      </td>
182      <td style="vertical-align: top;">516<br>
183      </td>
184      <td style="vertical-align: top;">3.7a<br>
185      </td>
186      <td style="vertical-align: top;">N<br>
187      </td>
188      <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
189      </td>
190      <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
191      </td>
192    </tr>
193    <tr>
194      <td style="vertical-align: top;"><br>
195      </td>
196      <td style="vertical-align: top;"><br>
197      </td>
198      <td style="vertical-align: top;"><br>
199      </td>
200      <td style="vertical-align: top;"><br>
201      </td>
202      <td style="vertical-align: top;">B<br>
203      </td>
204      <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>
205      </td>
206      <td style="vertical-align: top;">buoyancy<br>
207      </td>
208    </tr>
209<tr>
210      <td style="vertical-align: top;">16/03/10<br>
211      </td>
212      <td style="vertical-align: top;">RH<br>
213      </td>
214      <td style="vertical-align: top;">513<br>
215      </td>
216      <td style="vertical-align: top;">3.7a<br>
217      </td>
218      <td style="vertical-align: top;">N<br>
219      </td>
220      <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>
221      </td>
222      <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl<br>
223      </td>
224    </tr>
225<tr>
226      <td style="vertical-align: top;">12/03/10<br>
227      </td>
228      <td style="vertical-align: top;">SR<br>
229      </td>
230      <td style="vertical-align: top;">509<br>
231      </td>
232      <td style="vertical-align: top;">3.7a<br>
233      </td>
234      <td style="vertical-align: top;">E<br>
235      </td>
236      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
237      </td>
238      <td style="vertical-align: top;">mbuild<br>
239      </td>
240    </tr>
241<tr>
242      <td style="vertical-align: top;">08/03/10<br>
243      </td>
244      <td style="vertical-align: top;">SR<br>
245      </td>
246      <td style="vertical-align: top;">506<br>
247      </td>
248      <td style="vertical-align: top;">3.7a<br>
249      </td>
250      <td style="vertical-align: top;">C<br>
251      </td>
252      <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>
253      </td>
254      <td style="vertical-align: top;">mrun<br>
255      </td>
256    </tr>
257<tr>
258      <td style="vertical-align: top;">03/03/10<br>
259      </td>
260      <td style="vertical-align: top;">SR<br>
261      </td>
262      <td style="vertical-align: top;">504<br>
263      </td>
264      <td style="vertical-align: top;">3.7a<br>
265      </td>
266      <td style="vertical-align: top;">C<br>
267      </td>
268      <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>
269      <br>
270Utility 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>
271      <br>
272Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
273      <br>
274Default configuration files updated.<br>
275      </td>
276      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
277      </td>
278    </tr>
279<tr>
280      <td style="vertical-align: top;">02/03/10<br>
281      </td>
282      <td style="vertical-align: top;">SR<br>
283      </td>
284      <td style="vertical-align: top;">496<br>
285      </td>
286      <td style="vertical-align: top;">3.7a<br>
287      </td>
288      <td style="vertical-align: top;">C<br>
289      </td>
290      <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>
291      </td>
292      <td style="vertical-align: top;">palm<br>
293      </td>
294    </tr>
295<tr>
296      <td style="vertical-align: top;">01/03/10<br>
297      </td>
298      <td style="vertical-align: top;">SR<br>
299      </td>
300      <td style="vertical-align: top;">494<br>
301      </td>
302      <td style="vertical-align: top;">3.7a<br>
303      </td>
304      <td style="vertical-align: top;">N<br>
305      </td>
306      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
307      <br>
308NetCDF4 allows for parallel I/O. Also, variables are not limited in
309size any more (i.e. arrays can be larger than 2GB). The new
310d3par-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>
311only affects 2d- and 3d-output, i.e. there is no parallel output for
312profiles, time series, spectra, and particles. Parallel output of
313particle data may realized in the future.<br>
314      <br>
315In 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>
316(merging data from single files - one per PE - into one file) is not
317neccessary. 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>
318      <br>
319Using NetCDF4 format requires a NetCDF4/HDF library. Respective
320settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
321HLRN 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>
322      <br>
323      <span style="font-weight: bold;">Attention:</span><br>
324So far, NetCDF parallel I/O has only been tested a little. Further
325performance optimizations may be required, especially in case of large
326data 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>
327      <br>
328      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
329      <br>
330Modules 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>
331      <br>
332      <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>
333      <br>
334This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
335      <br>
336      <span style="font-weight: bold;">WARNING:</span><br>
337      <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>
338      <br>
339</span>Compilation time can be reduced be using parallel make. The
340number of allowed simultaneous compiler calls (threads) is set in the
341configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
342      <br>
343      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
344      <br>
345allows a maximum of 4 routines to be compiled simultaneously (provided
346that the makefile does not show any dependencies between these
347routines).<span style="font-weight: bold;"><br>
348      </span>
349      </td>
350      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
351      <br>
352combine_plot_fields<br>
353      <br>
354mbuild, mrun, subjob<br>
355      </td>
356    </tr>
357    <tr>
358      <td style="vertical-align: top;"><br>
359      </td>
360      <td style="vertical-align: top;"><br>
361      </td>
362      <td style="vertical-align: top;"><br>
363      </td>
364      <td style="vertical-align: top;"><br>
365      </td>
366      <td style="vertical-align: top;">C<br>
367      </td>
368      <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>
369for choosing the NetCDF 64bit-offset format (this is the default from
370now on). The offset-format can not be set independently for the
3713d-output-data any more.<br>
372      <br>
373d3par-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>
374      </td>
375      <td style="vertical-align: top;">check_open, close_file,<br>
376data_output_mask, header, init_masks, modules, parin<br>
377      <br>
378      </td>
379    </tr>
380    <tr>
381      <td style="vertical-align: top;"><br>
382      </td>
383      <td style="vertical-align: top;"><br>
384      </td>
385      <td style="vertical-align: top;"><br>
386      </td>
387      <td style="vertical-align: top;"><br>
388      </td>
389      <td style="vertical-align: top;">B<br>
390      </td>
391      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
392      <br>
393Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
394      </td>
395      <td style="vertical-align: top;">user_statistics<br>
396      <br>
397trunk/UTIL/Makefile<br>
398      </td>
399    </tr>
400<tr>
401      <td style="vertical-align: top;">05/02/10<br>
402      </td>
403      <td style="vertical-align: top;">SR<br>
404      </td>
405      <td style="vertical-align: top;">485<br>
406      </td>
407      <td style="vertical-align: top;">3.7a<br>
408      </td>
409      <td style="vertical-align: top;">B<br>
410      </td>
411      <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>
412changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
413some global statistics (e.g. total kinetic energy) have wrong values.<br>
414      </td>
415      <td style="vertical-align: top;">init_3d_model, modules<br>
416      </td>
417    </tr>
418    <tr>
419      <td style="vertical-align: top;">05/02/10<br>
420      </td>
421      <td style="vertical-align: top;">SR<br>
422      </td>
423      <td style="vertical-align: top;">484<br>
424      </td>
425      <td style="vertical-align: top;">3.7a<br>
426      </td>
427      <td style="vertical-align: top;">B<br>
428      </td>
429      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
430      </td>
431      <td style="vertical-align: top;">many<br>
432      </td>
433    </tr>
434<tr>
435      <td style="vertical-align: top; width: 27px;">05/02/10<br>
436      </td>
437      <td style="vertical-align: top; width: 38px;">SR<br>
438      </td>
439      <td style="vertical-align: top; width: 42px;">483<br>
440      </td>
441      <td style="vertical-align: top; width: 40px;">3.7a<br>
442      </td>
443      <td style="vertical-align: top; width: 27px;">N<br>
444      </td>
445      <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>
446      <br>
447make 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>
448      <br>
449      <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;">
450wall_scalarflux</span> are the corresponding new inipar parameters.<br>
451(<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>
452      <br>
453Large scale vertical motion (subsidence/ascent) can be added as
454additional source to the prognostic equation for potential temperature.
455See 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>
456      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
457      <br>
458A 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>
459      <br>
460Masked data output has been implemented but it is not documented in the
461user manual so far. This feature can already use NetCDF4 file format.
462(check_open, check_parameters, close_file, modules, netcdf, parin,
463time_integration, user_parin, new: data_output_mask, init_masks,
464user_data_output_mask)<br>
465      </td>
466      <td style="vertical-align: top; width: 189px;">check_open, check
467parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
468netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
469      <br><span style="font-weight: bold;">
470new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
471<br>
472      </td>
473    </tr>
474    <tr>
475      <td style="vertical-align: top; width: 27px;"><br>
476      </td>
477      <td style="vertical-align: top; width: 38px;"><br>
478      </td>
479      <td style="vertical-align: top; width: 42px;"><br>
480      </td>
481      <td style="vertical-align: top; width: 40px;"><br>
482      </td>
483      <td style="vertical-align: top; width: 27px;">C<br>
484      </td>
485      <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>
486      <br><span style="font-family: Courier New,Courier,monospace;">
487var_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>
488      <br>
489Every cloud droplet has now an own weighting factor and can be deleted
490due to collisions. Condensation and collision of cloud droplets are
491adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
492      <br>
493Collision 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>
494      </td>
495      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
496      </td>
497    </tr>
498    <tr>
499      <td style="vertical-align: top; width: 27px;"><br>
500      </td>
501      <td style="vertical-align: top; width: 38px;"><br>
502      </td>
503      <td style="vertical-align: top; width: 42px;"><br>
504      </td>
505      <td style="vertical-align: top; width: 40px;"><br>
506      </td>
507      <td style="vertical-align: top; width: 27px;">B<br>
508      </td>
509      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
510      <br>
511Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
512      <br>
513Dimension 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>
514      <br>
515Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
516      <br>
517Bugfix: 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>
518      <br>
519Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
520      <br>
521Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
522      <br>
523Bugfix: 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>
524      <br>
525Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
526      <br>
527Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
528      <br>
529Bugfix 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>
530      </td>
531      <td style="vertical-align: top; width: 189px;">advec_particles,
532calc_precipitation, collision_efficiency, disturb_field, header,
533modules, poisfft_hybrid, subjob, sum_up_3d_data,
534time_integration<br>
535<br>
536      </td>
537    </tr>
538    <tr>
539      <td style="vertical-align: top; width: 27px;">23/09/09<br>
540      </td>
541      <td style="vertical-align: top; width: 38px;">SR<br>
542      </td>
543      <td style="vertical-align: top; width: 42px;">392<br>
544      </td>
545      <td style="vertical-align: top; width: 40px;">3.7<br>
546      </td>
547      <td style="vertical-align: top; width: 27px;">N<br>
548      </td>
549      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
550important changes:</span>
551atmosphere-ocean coupling has been improved and steering of
552dvr-software is more user-friendly now. Beside that, the release
553contains a lot of optimizations, changes, and bugfixes which have
554accumulated over the last months.<br>
555
556      <br>
557
558The atmosphere-ocean coupling allows to use independent precursor runs
559in order to account for different spin-up times. The time when coupling
560has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
561The 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
562order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
563output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
564      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
565      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
566      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
567      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
568      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
569      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
570      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
571      <span style="font-family: Courier New,Courier,monospace;">header</span>,
572      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
573      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
574      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
575      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
576      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
577      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
578      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
579      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
580
581      <br>
582
583Clipping of dvrp output implemented. Default colourtable for particles
584implemented, particle attributes (color, dvrp_size) can be set with new
585parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
586      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
587      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
588      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
589Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
590and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
591(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
592      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
593      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
594      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
595      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
596
597      <br>
598
599Polygon reduction for topography and ground plate isosurface. Reduction
600level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
601
602      <br>
603
604Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
605/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
606in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
607
608      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
609for speed optimization. This gives a significant speedup of more than
61010%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
611      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
612      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
613      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
614      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
615
616      <br>
617
618Scripts 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>
619
620      <br>
621
622Additional timestep criterion in case of simulations with plant canopy.
623(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
624
625      <br>
626
627Check 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
628exceed <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>
629
630      <br>
631
632External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
633      <span style="font-family: Courier New,Courier,monospace;">header</span>,
634      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
635      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
636      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
637      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
638      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
639      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
640
641      <br>
642
643New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
644(<span style="font-family: Courier New,Courier,monospace;">header</span>,
645      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
646      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
647      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
648      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
649      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
650      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
651      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
652      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
653
654      <br>
655
656Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
657(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
658      <span style="font-family: Courier New,Courier,monospace;">header</span>,
659      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
660      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
661      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
662      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
663      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
664
665      <br>
666
667Option 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>,
668      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
669
670      <br>
671
672xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
673      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
674      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
675      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
676      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
677      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
678      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
679      <td style="vertical-align: top; width: 189px;">average_3d_data,
680check_for_restart, check_parameters, data_output_2d, data_output_3d,
681data_output_dvrp, data_output_profiles, data_output_ptseries,
682data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
683diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
684header, mbuild, modules, mrun, package_parin, parin,
685prognostic_equations, read_3d_binary, read_var_list, subjob,
686sum_up_3d_data, surface_coupler, timestep, time_integration,
687user_check_parameters, user_data_output_2d, user_data_output_dvrp,
688user_header, user_init_grid, write_3d_binary, write_var_list<br>
689
690      <br>
691
692      <span style="font-weight: bold;">new:</span>
693set_particle_attributes, set_slicer_attributes_dvrp</td>
694    </tr>
695    <tr>
696      <td style="vertical-align: top; width: 27px;"><br>
697      </td>
698      <td style="vertical-align: top; width: 38px;"><br>
699      </td>
700      <td style="vertical-align: top; width: 42px;"><br>
701      </td>
702      <td style="vertical-align: top; width: 40px;"><br>
703      </td>
704      <td style="vertical-align: top; width: 27px;">C<br>
705      </td>
706      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
707message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
708      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
709      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
710      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
711      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
712      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
713      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
714      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
715      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
716      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
717      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
718      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
719      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
720      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
721      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
722      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
723      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
724      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
725      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
726      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
727      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
728      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
729      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
730      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
731      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
732      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
733      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
734      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
735      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
736      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
737      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
738      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
739      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
740      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
741      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
742      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
743      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
744      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
745      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
746      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
747
748      <br>
749
750Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
751      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
752      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
753      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
754      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
755      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
756      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
757      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
758      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
759
760      <br>
761
762__lcmuk changed to __lc to avoid problems with Intel compiler on
763sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
764
765      <br>
766
767For extended NetCDF files, the updated title attribute includes an
768update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
769
770      <br>
771
772In case of restart runs without extension, initial profiles are not
773written to NetCDF-file anymore. So far, time axis always started at
774t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
775      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
776      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
777      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
778
779      <br>
780
781      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
782'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
783can now <br>
784
785be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
786(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
787      <span style="font-family: Courier New,Courier,monospace;">header</span>,
788      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
789
790      <br>
791
7922 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
793
794      <br>
795
796A link to the webspage appendix_a.html is printed for further
797information about possible reasons of the error that appeared. (message)<br>
798
799      <br>
800
801Temperature gradient criterion for estimating the boundary layer height
802replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
803
804      <br>
805
806NetCDF unit attribute in timeseries output in case of statistic regions
807added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
808
809      <br>
810
811Maximum number of tails is calculated from maximum number of particles
812and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
813(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
814
815      <br>
816
817Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
818is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
819      <span style="font-family: Courier New,Courier,monospace;">header</span>,
820      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
821      <br>
822
823      <br>
824
825First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
826defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
827
828      <br>
829
830Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
831moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
832to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
833(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
834
835      <br>
836
837      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
838moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
839to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
840(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
841      <span style="font-family: Courier New,Courier,monospace;">header</span>,
842      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
843      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
844      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
845      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
846      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
847      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
848      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
849
850      <br>
851
852Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
853changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
854
855      <br>
856
857Adjustments for runs on lcxt4 (necessary due to a software update on
858CRAY) 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>
859      <td style="vertical-align: top; width: 189px;">advec_particles,
860advec_s_bc,
861buoyancy, calc_spectra, check_for_restart, check_open,
862check_parameters, close_file, coriolis, cpu_log, data_output_2d,
863data_output_3d, data_output_dvrp, data_output_profiles,
864data_output_ptseries, data_output_spectra, data_output_tseries,
865eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
866init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
867message, mrun, netcdf, package_parin, parin, plant_canopy_model,
868poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
869surface_coupler, temperton_fft, timestep,
870user_actions,user_check_parameters, user_data_output_dvrp,
871user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
872user_parin, user_read_restart_data, user_spectra, write_var_list </td>
873    </tr>
874    <tr>
875      <td style="vertical-align: top; width: 27px;"><br>
876      </td>
877      <td style="vertical-align: top; width: 38px;"><br>
878      </td>
879      <td style="vertical-align: top; width: 42px;"><br>
880      </td>
881      <td style="vertical-align: top; width: 40px;"><br>
882      </td>
883      <td style="vertical-align: top; width: 27px;">B<br>
884      </td>
885      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
886pressure profile in case of ocean runs is now calculated in 5 iteration
887steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
888
889      <br>
890
891Bugfix: wrong sign in buoyancy production of ocean part in case of not
892using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
893(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
894
895      <br>
896
897Bugfix: output of averaged 2d/3d quantities requires that an avaraging
898interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
899
900      <br>
901
902Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
903(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
904
905      <br>
906
907Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
908(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
909
910      <br>
911
912Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
913if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
914is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
915and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
916calls. This implies a possible performance loss; an alternative
917strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
918
919      <br>
920
921Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
922
923      <br>
924
925Bugfix: 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>
926
927      <br>
928
929Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
930=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
931for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
932      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
933
934      <br>
935
936Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
937becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
938
939      <br>
940
941Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
942
943      <br>
944
945Bugfix: error in check, if particles moved further than one subdomain
946length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
947
948      <br>
949
950Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
951is only written to file if its third index is &gt; 0, arrays for tails
952are allocated with a minimum size of 10 tails if there is no tail
953initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
954      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
955
956      <br>
957
958Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
959
960      <br>
961
962Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
963changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
964NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
965
966      <br>
967
968Bugfix: output of particle time series only if particle advection is
969switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
970
971      <br>
972
973Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
974= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
975(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
976
977      <br>
978
979Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
980z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
981
982      <br>
983
984Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
985
986      <br>
987
988If the inversion height calculated by the prerun is zero,
989inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
990
991      <br>
992
993Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
994
995      <br>
996
997Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
998removed from the restart file, because otherwise, no change from a
999fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
1000      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
1001
1002      <br>
1003
1004Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
1005in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
1006      <td style="vertical-align: top; width: 189px;">advec_particles,
1007check_parameters, cpu_log, data_output_2d, data_output_3d, header,
1008init_3d_model, init_particles, init_ocean, modules, netcdf,
1009prandtl_fluxes, production_e, read_var_list, time_integration,
1010user_last_actions, write_var_list<br>
1011
1012      </td>
1013    </tr>
1014    <tr>
1015      <td style="vertical-align: top; width: 27px;">02/02/09<br>
1016      </td>
1017      <td style="vertical-align: top; width: 38px;">SR<br>
1018      </td>
1019      <td style="vertical-align: top; width: 42px;">228<br>
1020      </td>
1021      <td style="vertical-align: top; width: 40px;">3.6<br>
1022      </td>
1023      <td style="vertical-align: top; width: 27px;">N<br>
1024      </td>
1025      <td style="vertical-align: top; width: 497px;">This
1026release contains further additions, changes, and bugfixes for the
1027SGI-ICE system, as well as important changes like the splitting of the
1028user-interface into single files, a complete revision of the
1029pre-compiling mechanism allowing to use different make-depositories
1030simultaneously, and a revision of the reading-mechanism from restart
1031files, which has no more restrictions in case that the previous and
1032current run have different domain/subdomain sizes. A new handling of
1033all kind of output messages is introduced with this release and will be
1034applied to all existing messages within the next releases.<br>
1035
1036      <br>
1037
1038      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
1039
1040      <br>
1041
1042Restart runs on SGI-ICE are working. (mrun)<br>
1043
10442d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
1045
1046      <br>
1047
1048Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
1049case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1050"<span style="font-style: italic;">-K parallel</span>" for coupling.
1051Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
1052      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
1053for lcxt4.<br>
1054
1055      <br>
1056
1057DVRP arguments changed to single precision, mode pathlines added.<br>
1058
1059      <br>
1060
1061User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
1062
1063      <br>
1064
1065User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
1066      <td style="vertical-align: top; width: 189px;">check_for_restart,
1067check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
1068modules, package_parin, palm, surface_coupler, timestep<br>
1069
1070      <br>
1071
1072Makefile,&nbsp;mbuild, mrun, subjob<br>
1073
1074      <br>
1075
1076      <span style="font-weight: bold;">new:</span><br>
1077
1078init_coupling, user_additional_routines, user_check_parameters</td>
1079    </tr>
1080    <tr>
1081      <td style="vertical-align: top; width: 27px;"><br>
1082      </td>
1083      <td style="vertical-align: top; width: 38px;"><br>
1084      </td>
1085      <td style="vertical-align: top; width: 42px;"><br>
1086      </td>
1087      <td style="vertical-align: top; width: 40px;"><br>
1088      </td>
1089      <td style="vertical-align: top; width: 27px;">C<br>
1090      </td>
1091      <td style="vertical-align: top; width: 497px;">User interface has been
1092split into single files.<br>
1093
1094      <br>
1095
1096Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
1097changed to INTEGER(8) in order to avoid "out of range" problems, which
1098result in measured negative time intervals. (cpu_log, local_tremain,
1099local_tremain_ini)<br>
1100
1101      <br>
1102
1103Reading mechanism from restart files
1104completely revised. The subdomain/total domain size is now allowed to
1105vary arbitrarily between the current and previous run. (read_var_list,
1106read_3d_binary, user_read_restart_data)<br>
1107
1108      <br>
1109
1110Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
1111completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
1112One depository per block (given in the config-file) is created. Always
1113all files from the source directory are copied to the respective
1114depository. No additional file checks are done any more (mrun version
11152.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1116"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
1117(mbuild, mrun)<br>
1118
1119      <br>
1120
1121Output messages (including required stop of execution) can now be
1122handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
1123All output messages will be replaced by this routine step by step
1124within the next revisions.<br>
1125
1126      <br>
1127
1128Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
1129explicitly set for better reading, although this has been already done
1130in boundary_conds. (advec_s_bc)<br>
1131
1132      <br>
1133
1134Origin of the xy-coordinate system shifted from the center of the first
1135grid 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
1136south-left corner of this cell. (netcdf) Topography definition
1137according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
1138(init_grid, modules, user_header, user_init_grid, user_parin)</td>
1139      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1140check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1141local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1142user_read_restart_data<br>
1143
1144      <br>
1145
1146Makefile, mbuild, mrun<br>
1147
1148      <br>
1149
1150      <span style="font-weight: bold;">removed:</span><br>
1151
1152user_interface<br>
1153
1154      <br>
1155
1156      <span style="font-weight: bold;">new:</span><br>
1157
1158message,
1159user_3d_data_averaging, user_actions, user_advec_particles,
1160user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1161user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1162user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1163user_init_grid, user_init_particles, user_init_plant_canopy,
1164user_last_actions, user_parin, user_parin, user_particle_attributes,
1165user_read_restart_data, user_spectra, user_statistics</td>
1166    </tr>
1167    <tr>
1168      <td style="vertical-align: top; width: 27px;"><br>
1169      </td>
1170      <td style="vertical-align: top; width: 38px;"><br>
1171      </td>
1172      <td style="vertical-align: top; width: 42px;"><br>
1173      </td>
1174      <td style="vertical-align: top; width: 40px;"><br>
1175      </td>
1176      <td style="vertical-align: top; width: 27px;">B<br>
1177      </td>
1178      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1179reallocated in case that multigrid is used. (calc_spectra)<br>
1180
1181      <br>
1182
1183Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1184inflow_turbulence,&nbsp;timestep)<br>
1185
1186      <br>
1187
1188Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1189      </span>adjusted to the required output size (1 gridpoint less,
1190along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1191in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1192compiler. (combine_plot_fields)<br>
1193
1194      <br>
1195
1196Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1197case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1198(header)<br>
1199
1200      <br>
1201
1202Inconsistency
1203removed: as the thermal stratification is not taken into account for
1204the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1205      <span style="font-family: Courier New,Courier,monospace;">km</span>
1206must 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>.
1207(production_e)<br>
1208
1209      <br>
1210
1211Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1212case of oceans runs. (sort_particles)<br>
1213
1214      <br>
1215
1216Bugfix: no output of particle concentration and radius unless particles
1217have been started. (data_output_2d)<br>
1218
1219      <br>
1220
1221Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1222from restart files ignored if total numbers of grid points do not
1223match. (read_3d_binary)<br>
1224
1225      <br>
1226
1227Bugfix: abort in case that absolute temperature is below zero.
1228(init_cloud_physics)</td>
1229      <td style="vertical-align: top; width: 189px;">advec_particles,
1230calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1231header, inflow_turbulence, init_cloud_physics, production_e,
1232read_3d_binary, timestep<br>
1233
1234      <br>
1235
1236combine_plot_fields</td>
1237    </tr>
1238  </tbody>
1239</table>
1240<b><blink></blink></b><br>&nbsp;
1241<br>&nbsp;
1242<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1243to change the source
1244code and how to document modifications<br>
1245</h2>Currently
1246(Sep 23rd, 2009), only selected users are allowed to commit changes to
1247the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1248<br>
1249<ol>
1250  <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>".
1251Additionally, document all changes in a local file (e.g.
1252~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1253have been changed. Classify changes in three cases, new (N), changed
1254(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>
1255    <br>
1256  </li>
1257  <li>Test the changed version, unless it works sufficiently.<br>
1258    <br>
1259  </li>
1260 
1261  <li>Commit the changes to the repository<br>
1262    <br>
1263    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1264    </span><br>
1265where "<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>
1266    <br>
1267Alternatively, in case that you have made quite a lot of changes, you
1268can also give the contents of your file CURRENT_MODIFICATIONS as the
1269log message:<br>
1270    <br>
1271    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1272    <br>
1273  </li>
1274
1275  <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>
1276    <br>
1277  </li>
1278  <li>Move the change comments in the file headers from "Current
1279revisions:" to "Former revisions:". Set the current svn id in front of
1280that.<br>
1281    <br>
1282    <span style="font-weight: bold;">Example:</span><br>
1283    <br>
1284    <span style="font-weight: bold;">before move:</span><br>
1285    <br>
1286    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1287    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1288    <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;">
1289    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1290    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1291    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1292    <span style="font-family: Courier New,Courier,monospace;">! §Id: init_3d_model.f90 <span style="color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span> §</span><br style="font-family: Courier New,Courier,monospace;">
1293    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1294    <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;">
1295    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1296    <br>
1297    <span style="font-weight: bold;">after move:</span><br>
1298    <br>
1299    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1300
1301    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1302
1303    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1304
1305    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1306
1307    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1308
1309    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1310
1311    <span style="font-family: Courier New,Courier,monospace;">! §Id: </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;"> §<br>
1312!</span><br style="font-family: Courier New,Courier,monospace;">
1313    <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>
1314! </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;">
1315
1316    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1317
1318    <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;">
1319
1320    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1321    <br>
1322    <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">§</span>"
1323in this example should read "$", but "$" cannot be used here, because
1324otherwise svn would replace these entries after every change to this
1325technical documentation.</span><br>
1326 </span><br>
1327  </li>
1328  <li>Commit the changes in the technical documentation and the file headers:<br>
1329    <br>
1330    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1331    <br>
1332 <br>
1333  </li>
1334</ol>
1335
1336<h2>
1337<a name="Kapitel3.0"></a>3.0&nbsp; Description
1338of selected parts of the
1339model source code</h2>
1340<b></b>
1341<p>This section gives links to existing descriptions about special
1342parts of the PALM code, e.g. special numerical methods that are used
1343(including mathematical background). Documents are stored in single
1344files with different formats. Some are in German (sorry for the
1345inconvenience).
1346<br>&nbsp;
1347</p><ul> <li> <a name="UPS"></a>upstream-spline
1348advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1349, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1350physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1351)</li> 
1352  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1353  </li>
1354  <li>Runge-Kutta
1355time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1356, only in German)</li>
1357
1358</ul><br>
1359&nbsp;
1360<br>&nbsp;
1361<br>&nbsp;
1362<br>&nbsp;
1363<br>&nbsp;
1364<br>&nbsp;
1365<br>&nbsp;
1366<br>&nbsp;
1367</body></html>
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