source: palm/trunk/DOC/tec/technical_documentation.html @ 526

Last change on this file since 526 was 526, checked in by heinze, 15 years ago

Adjustment of the NCL scripts and palmplot to allow for the use of special characters in NetCDF variable names

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23<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;
24</font>a
25<b>pa</b>rallelized
26<b>L</b>ES <b>m</b>odel
27<br><hr width="100%">
28<br><font size="+2">technical/numerical documentation</font>
29<br>&nbsp;
30<br>&nbsp;
31<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
32</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
33</span></td> </tr>
34<tr nosave=""> <td nosave=""><b>Last
35change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 526 2010-03-30 14:04:38Z heinze $</b></td> </tr>
36</tbody>
37</table><hr width="100%">
38<p><font size="+2">Table of contents</font>
39<br>&nbsp;
40<br>&nbsp;
41</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
42History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
43How to change the source
44code and how to document modifications<br>
45 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
46Description of selected model numerics<br>
47&nbsp;</p>
48</ul><b></b><br>
49
50<h2><a name="Kapitel1.0"></a>1.0&nbsp;
51History of changes</h2>
52The 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>
53<br>
54Entries in the fifth column specify the type of the change:
55change&nbsp;
56of existing code (C), new code (N) or bugfix (B). More detailed
57information
58about the changes may sometimes be found in the header comment lines of the
59respective
60routines.
61<br>&nbsp;
62<br>
63<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
64  <tbody>
65    <tr>
66      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
67      </td>
68      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
69      </td>
70      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
71      </td>
72      <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
73      </td>
74      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
75      </td>
76      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
77      </td>
78      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
79      </td>
80    </tr>
81   
82   
83   
84   
85   
86   
87   
88   
89   
90   
91    <tr>
92      <td style="vertical-align: top;">30/03/10<br>
93      </td>
94      <td style="vertical-align: top;">RH<br>
95      </td>
96      <td style="vertical-align: top;">526<br>
97      </td>
98      <td style="vertical-align: top;">3.7a<br>
99      </td>
100      <td style="vertical-align: top;">C<br>
101      </td>
102      <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>
103      </td>
104      <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
105      </td>
106    </tr>
107<tr>
108      <td style="vertical-align: top;">30/03/10<br>
109      </td>
110      <td style="vertical-align: top;">SR<br>
111      </td>
112      <td style="vertical-align: top;">525<br>
113      </td>
114      <td style="vertical-align: top;">3.7a<br>
115      </td>
116      <td style="vertical-align: top;">B<br>
117      </td>
118      <td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br>
119      </td>
120      <td style="vertical-align: top;">check_parameters<br>
121      </td>
122    </tr>
123<tr>
124      <td style="vertical-align: top;">19/03/10<br>
125      </td>
126      <td style="vertical-align: top;">SR<br>
127      </td>
128      <td style="vertical-align: top;">520<br>
129      </td>
130      <td style="vertical-align: top;">3.7a<br>
131      </td>
132      <td style="vertical-align: top;">N<br>
133      </td>
134      <td style="vertical-align: top;">NetCDF4 support for particle
135data. Total number of particles is allowed to increase during the run,
136when netcdf_data_format &gt; <span style="font-style: italic;">2</span> is used.<br>
137      </td>
138      <td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
139      </td>
140    </tr>
141    <tr>
142      <td style="vertical-align: top;"><br>
143      </td>
144      <td style="vertical-align: top;"><br>
145      </td>
146      <td style="vertical-align: top;"><br>
147      </td>
148      <td style="vertical-align: top;"><br>
149      </td>
150      <td style="vertical-align: top;">C<br>
151      </td>
152      <td style="vertical-align: top;">Special characters like * and "
153are now allowed for NetCDF variable names. Replacement of these
154characters has been removed (routine clean_netcdf_varname removed)<br>
155      </td>
156      <td style="vertical-align: top;"><br>
157      </td>
158    </tr>
159<tr>
160      <td style="vertical-align: top;">18/03/10<br>
161      </td>
162      <td style="vertical-align: top;">SR<br>
163      </td>
164      <td style="vertical-align: top;">516<br>
165      </td>
166      <td style="vertical-align: top;">3.7a<br>
167      </td>
168      <td style="vertical-align: top;">N<br>
169      </td>
170      <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
171      </td>
172      <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
173      </td>
174    </tr>
175    <tr>
176      <td style="vertical-align: top;"><br>
177      </td>
178      <td style="vertical-align: top;"><br>
179      </td>
180      <td style="vertical-align: top;"><br>
181      </td>
182      <td style="vertical-align: top;"><br>
183      </td>
184      <td style="vertical-align: top;">B<br>
185      </td>
186      <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>
187      </td>
188      <td style="vertical-align: top;">buoyancy<br>
189      </td>
190    </tr>
191<tr>
192      <td style="vertical-align: top;">16/03/10<br>
193      </td>
194      <td style="vertical-align: top;">RH<br>
195      </td>
196      <td style="vertical-align: top;">513<br>
197      </td>
198      <td style="vertical-align: top;">3.7a<br>
199      </td>
200      <td style="vertical-align: top;">N<br>
201      </td>
202      <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>
203      </td>
204      <td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl<br>
205      </td>
206    </tr>
207<tr>
208      <td style="vertical-align: top;">12/03/10<br>
209      </td>
210      <td style="vertical-align: top;">SR<br>
211      </td>
212      <td style="vertical-align: top;">509<br>
213      </td>
214      <td style="vertical-align: top;">3.7a<br>
215      </td>
216      <td style="vertical-align: top;">E<br>
217      </td>
218      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
219      </td>
220      <td style="vertical-align: top;">mbuild<br>
221      </td>
222    </tr>
223<tr>
224      <td style="vertical-align: top;">08/03/10<br>
225      </td>
226      <td style="vertical-align: top;">SR<br>
227      </td>
228      <td style="vertical-align: top;">506<br>
229      </td>
230      <td style="vertical-align: top;">3.7a<br>
231      </td>
232      <td style="vertical-align: top;">C<br>
233      </td>
234      <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>
235      </td>
236      <td style="vertical-align: top;">mrun<br>
237      </td>
238    </tr>
239<tr>
240      <td style="vertical-align: top;">03/03/10<br>
241      </td>
242      <td style="vertical-align: top;">SR<br>
243      </td>
244      <td style="vertical-align: top;">504<br>
245      </td>
246      <td style="vertical-align: top;">3.7a<br>
247      </td>
248      <td style="vertical-align: top;">C<br>
249      </td>
250      <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>
251      <br>
252Utility 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>
253      <br>
254Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
255      <br>
256Default configuration files updated.<br>
257      </td>
258      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
259      </td>
260    </tr>
261<tr>
262      <td style="vertical-align: top;">02/03/10<br>
263      </td>
264      <td style="vertical-align: top;">SR<br>
265      </td>
266      <td style="vertical-align: top;">496<br>
267      </td>
268      <td style="vertical-align: top;">3.7a<br>
269      </td>
270      <td style="vertical-align: top;">C<br>
271      </td>
272      <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>
273      </td>
274      <td style="vertical-align: top;">palm<br>
275      </td>
276    </tr>
277<tr>
278      <td style="vertical-align: top;">01/03/10<br>
279      </td>
280      <td style="vertical-align: top;">SR<br>
281      </td>
282      <td style="vertical-align: top;">494<br>
283      </td>
284      <td style="vertical-align: top;">3.7a<br>
285      </td>
286      <td style="vertical-align: top;">N<br>
287      </td>
288      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
289      <br>
290NetCDF4 allows for parallel I/O. Also, variables are not limited in
291size any more (i.e. arrays can be larger than 2GB). The new
292d3par-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>
293only affects 2d- and 3d-output, i.e. there is no parallel output for
294profiles, time series, spectra, and particles. Parallel output of
295particle data may realized in the future.<br>
296      <br>
297In 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>
298(merging data from single files - one per PE - into one file) is not
299neccessary. 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>
300      <br>
301Using NetCDF4 format requires a NetCDF4/HDF library. Respective
302settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
303HLRN 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>
304      <br>
305      <span style="font-weight: bold;">Attention:</span><br>
306So far, NetCDF parallel I/O has only been tested a little. Further
307performance optimizations may be required, especially in case of large
308data 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>
309      <br>
310      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
311      <br>
312Modules 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>
313      <br>
314      <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>
315      <br>
316This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
317      <br>
318      <span style="font-weight: bold;">WARNING:</span><br>
319      <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>
320      <br>
321</span>Compilation time can be reduced be using parallel make. The
322number of allowed simultaneous compiler calls (threads) is set in the
323configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
324      <br>
325      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
326      <br>
327allows a maximum of 4 routines to be compiled simultaneously (provided
328that the makefile does not show any dependencies between these
329routines).<span style="font-weight: bold;"><br>
330      </span>
331      </td>
332      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
333      <br>
334combine_plot_fields<br>
335      <br>
336mbuild, mrun, subjob<br>
337      </td>
338    </tr>
339    <tr>
340      <td style="vertical-align: top;"><br>
341      </td>
342      <td style="vertical-align: top;"><br>
343      </td>
344      <td style="vertical-align: top;"><br>
345      </td>
346      <td style="vertical-align: top;"><br>
347      </td>
348      <td style="vertical-align: top;">C<br>
349      </td>
350      <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>
351for choosing the NetCDF 64bit-offset format (this is the default from
352now on). The offset-format can not be set independently for the
3533d-output-data any more.<br>
354      <br>
355d3par-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>
356      </td>
357      <td style="vertical-align: top;">check_open, close_file,<br>
358data_output_mask, header, init_masks, modules, parin<br>
359      <br>
360      </td>
361    </tr>
362    <tr>
363      <td style="vertical-align: top;"><br>
364      </td>
365      <td style="vertical-align: top;"><br>
366      </td>
367      <td style="vertical-align: top;"><br>
368      </td>
369      <td style="vertical-align: top;"><br>
370      </td>
371      <td style="vertical-align: top;">B<br>
372      </td>
373      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
374      <br>
375Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
376      </td>
377      <td style="vertical-align: top;">user_statistics<br>
378      <br>
379trunk/UTIL/Makefile<br>
380      </td>
381    </tr>
382<tr>
383      <td style="vertical-align: top;">05/02/10<br>
384      </td>
385      <td style="vertical-align: top;">SR<br>
386      </td>
387      <td style="vertical-align: top;">485<br>
388      </td>
389      <td style="vertical-align: top;">3.7a<br>
390      </td>
391      <td style="vertical-align: top;">B<br>
392      </td>
393      <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>
394changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
395some global statistics (e.g. total kinetic energy) have wrong values.<br>
396      </td>
397      <td style="vertical-align: top;">init_3d_model, modules<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;">484<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;">Typo in file headers removed ("current" instead of "actual").<br>
412      </td>
413      <td style="vertical-align: top;">many<br>
414      </td>
415    </tr>
416<tr>
417      <td style="vertical-align: top; width: 27px;">05/02/10<br>
418      </td>
419      <td style="vertical-align: top; width: 38px;">SR<br>
420      </td>
421      <td style="vertical-align: top; width: 42px;">483<br>
422      </td>
423      <td style="vertical-align: top; width: 40px;">3.7a<br>
424      </td>
425      <td style="vertical-align: top; width: 27px;">N<br>
426      </td>
427      <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>
428      <br>
429make 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>
430      <br>
431      <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;">
432wall_scalarflux</span> are the corresponding new inipar parameters.<br>
433(<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>
434      <br>
435Large scale vertical motion (subsidence/ascent) can be added as
436additional source to the prognostic equation for potential temperature.
437See 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>
438      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
439      <br>
440A 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>
441      <br>
442Masked data output has been implemented but it is not documented in the
443user manual so far. This feature can already use NetCDF4 file format.
444(check_open, check_parameters, close_file, modules, netcdf, parin,
445time_integration, user_parin, new: data_output_mask, init_masks,
446user_data_output_mask)<br>
447      </td>
448      <td style="vertical-align: top; width: 189px;">check_open, check
449parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
450netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
451      <br><span style="font-weight: bold;">
452new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
453<br>
454      </td>
455    </tr>
456    <tr>
457      <td style="vertical-align: top; width: 27px;"><br>
458      </td>
459      <td style="vertical-align: top; width: 38px;"><br>
460      </td>
461      <td style="vertical-align: top; width: 42px;"><br>
462      </td>
463      <td style="vertical-align: top; width: 40px;"><br>
464      </td>
465      <td style="vertical-align: top; width: 27px;">C<br>
466      </td>
467      <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>
468      <br><span style="font-family: Courier New,Courier,monospace;">
469var_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>
470      <br>
471Every cloud droplet has now an own weighting factor and can be deleted
472due to collisions. Condensation and collision of cloud droplets are
473adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
474      <br>
475Collision 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>
476      </td>
477      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
478      </td>
479    </tr>
480    <tr>
481      <td style="vertical-align: top; width: 27px;"><br>
482      </td>
483      <td style="vertical-align: top; width: 38px;"><br>
484      </td>
485      <td style="vertical-align: top; width: 42px;"><br>
486      </td>
487      <td style="vertical-align: top; width: 40px;"><br>
488      </td>
489      <td style="vertical-align: top; width: 27px;">B<br>
490      </td>
491      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
492      <br>
493Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
494      <br>
495Dimension 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>
496      <br>
497Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
498      <br>
499Bugfix: 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>
500      <br>
501Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
502      <br>
503Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
504      <br>
505Bugfix: 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>
506      <br>
507Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
508      <br>
509Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
510      <br>
511Bugfix 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>
512      </td>
513      <td style="vertical-align: top; width: 189px;">advec_particles,
514calc_precipitation, collision_efficiency, disturb_field, header,
515modules, poisfft_hybrid, subjob, sum_up_3d_data,
516time_integration<br>
517<br>
518      </td>
519    </tr>
520    <tr>
521      <td style="vertical-align: top; width: 27px;">23/09/09<br>
522      </td>
523      <td style="vertical-align: top; width: 38px;">SR<br>
524      </td>
525      <td style="vertical-align: top; width: 42px;">392<br>
526      </td>
527      <td style="vertical-align: top; width: 40px;">3.7<br>
528      </td>
529      <td style="vertical-align: top; width: 27px;">N<br>
530      </td>
531      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
532important changes:</span>
533atmosphere-ocean coupling has been improved and steering of
534dvr-software is more user-friendly now. Beside that, the release
535contains a lot of optimizations, changes, and bugfixes which have
536accumulated over the last months.<br>
537
538      <br>
539
540The atmosphere-ocean coupling allows to use independent precursor runs
541in order to account for different spin-up times. The time when coupling
542has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
543The 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
544order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
545output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
546      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
547      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
548      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
549      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
550      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
551      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
552      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
553      <span style="font-family: Courier New,Courier,monospace;">header</span>,
554      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
555      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
556      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
557      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
558      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
559      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
560      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
561      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
562
563      <br>
564
565Clipping of dvrp output implemented. Default colourtable for particles
566implemented, particle attributes (color, dvrp_size) can be set with new
567parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
568      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
569      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
570      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
571Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
572and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
573(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
574      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
575      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
576      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
577      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
578
579      <br>
580
581Polygon reduction for topography and ground plate isosurface. Reduction
582level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
583
584      <br>
585
586Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
587/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
588in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
589
590      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
591for speed optimization. This gives a significant speedup of more than
59210%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
593      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
594      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
595      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
596      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
597
598      <br>
599
600Scripts 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>
601
602      <br>
603
604Additional timestep criterion in case of simulations with plant canopy.
605(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
606
607      <br>
608
609Check 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
610exceed <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>
611
612      <br>
613
614External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
615      <span style="font-family: Courier New,Courier,monospace;">header</span>,
616      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
617      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
618      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
619      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
620      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
621      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
622
623      <br>
624
625New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
626(<span style="font-family: Courier New,Courier,monospace;">header</span>,
627      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
628      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
629      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
630      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
631      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
632      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
633      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
634      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
635
636      <br>
637
638Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
639(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
640      <span style="font-family: Courier New,Courier,monospace;">header</span>,
641      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
642      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
643      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
644      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
645      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
646
647      <br>
648
649Option 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>,
650      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
651
652      <br>
653
654xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
655      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
656      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
657      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
658      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
659      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
660      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
661      <td style="vertical-align: top; width: 189px;">average_3d_data,
662check_for_restart, check_parameters, data_output_2d, data_output_3d,
663data_output_dvrp, data_output_profiles, data_output_ptseries,
664data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
665diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
666header, mbuild, modules, mrun, package_parin, parin,
667prognostic_equations, read_3d_binary, read_var_list, subjob,
668sum_up_3d_data, surface_coupler, timestep, time_integration,
669user_check_parameters, user_data_output_2d, user_data_output_dvrp,
670user_header, user_init_grid, write_3d_binary, write_var_list<br>
671
672      <br>
673
674      <span style="font-weight: bold;">new:</span>
675set_particle_attributes, set_slicer_attributes_dvrp</td>
676    </tr>
677    <tr>
678      <td style="vertical-align: top; width: 27px;"><br>
679      </td>
680      <td style="vertical-align: top; width: 38px;"><br>
681      </td>
682      <td style="vertical-align: top; width: 42px;"><br>
683      </td>
684      <td style="vertical-align: top; width: 40px;"><br>
685      </td>
686      <td style="vertical-align: top; width: 27px;">C<br>
687      </td>
688      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
689message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
690      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
691      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
692      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
693      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
694      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
695      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
696      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
697      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
698      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
699      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
700      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
701      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
702      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
703      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
704      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
705      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
706      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
707      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
708      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
709      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
710      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
711      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
712      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
713      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
714      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
715      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
716      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
717      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
718      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
719      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
720      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
721      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
722      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
723      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
724      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
725      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
726      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
727      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
728      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
729
730      <br>
731
732Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
733      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
734      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
735      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
736      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
737      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
738      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
739      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
740      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
741
742      <br>
743
744__lcmuk changed to __lc to avoid problems with Intel compiler on
745sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
746
747      <br>
748
749For extended NetCDF files, the updated title attribute includes an
750update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
751
752      <br>
753
754In case of restart runs without extension, initial profiles are not
755written to NetCDF-file anymore. So far, time axis always started at
756t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
757      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
758      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
759      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
760
761      <br>
762
763      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
764'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
765can now <br>
766
767be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
768(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
769      <span style="font-family: Courier New,Courier,monospace;">header</span>,
770      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
771
772      <br>
773
7742 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
775
776      <br>
777
778A link to the webspage appendix_a.html is printed for further
779information about possible reasons of the error that appeared. (message)<br>
780
781      <br>
782
783Temperature gradient criterion for estimating the boundary layer height
784replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
785
786      <br>
787
788NetCDF unit attribute in timeseries output in case of statistic regions
789added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
790
791      <br>
792
793Maximum number of tails is calculated from maximum number of particles
794and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
795(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
796
797      <br>
798
799Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
800is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
801      <span style="font-family: Courier New,Courier,monospace;">header</span>,
802      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
803      <br>
804
805      <br>
806
807First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
808defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
809
810      <br>
811
812Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
813moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
814to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
815(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
816
817      <br>
818
819      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
820moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
821to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
822(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
823      <span style="font-family: Courier New,Courier,monospace;">header</span>,
824      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
825      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
826      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
827      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
828      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
829      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
830      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
831
832      <br>
833
834Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
835changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
836
837      <br>
838
839Adjustments for runs on lcxt4 (necessary due to a software update on
840CRAY) 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>
841      <td style="vertical-align: top; width: 189px;">advec_particles,
842advec_s_bc,
843buoyancy, calc_spectra, check_for_restart, check_open,
844check_parameters, close_file, coriolis, cpu_log, data_output_2d,
845data_output_3d, data_output_dvrp, data_output_profiles,
846data_output_ptseries, data_output_spectra, data_output_tseries,
847eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
848init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
849message, mrun, netcdf, package_parin, parin, plant_canopy_model,
850poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
851surface_coupler, temperton_fft, timestep,
852user_actions,user_check_parameters, user_data_output_dvrp,
853user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
854user_parin, user_read_restart_data, user_spectra, write_var_list </td>
855    </tr>
856    <tr>
857      <td style="vertical-align: top; width: 27px;"><br>
858      </td>
859      <td style="vertical-align: top; width: 38px;"><br>
860      </td>
861      <td style="vertical-align: top; width: 42px;"><br>
862      </td>
863      <td style="vertical-align: top; width: 40px;"><br>
864      </td>
865      <td style="vertical-align: top; width: 27px;">B<br>
866      </td>
867      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
868pressure profile in case of ocean runs is now calculated in 5 iteration
869steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
870
871      <br>
872
873Bugfix: wrong sign in buoyancy production of ocean part in case of not
874using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
875(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
876
877      <br>
878
879Bugfix: output of averaged 2d/3d quantities requires that an avaraging
880interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
881
882      <br>
883
884Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
885(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
886
887      <br>
888
889Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
890(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
891
892      <br>
893
894Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
895if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
896is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
897and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
898calls. This implies a possible performance loss; an alternative
899strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
900
901      <br>
902
903Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
904
905      <br>
906
907Bugfix: 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>
908
909      <br>
910
911Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
912=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
913for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
914      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
915
916      <br>
917
918Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
919becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
920
921      <br>
922
923Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
924
925      <br>
926
927Bugfix: error in check, if particles moved further than one subdomain
928length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
929
930      <br>
931
932Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
933is only written to file if its third index is &gt; 0, arrays for tails
934are allocated with a minimum size of 10 tails if there is no tail
935initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
936      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
937
938      <br>
939
940Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
941
942      <br>
943
944Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
945changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
946NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
947
948      <br>
949
950Bugfix: output of particle time series only if particle advection is
951switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
952
953      <br>
954
955Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
956= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
957(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
958
959      <br>
960
961Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
962z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
963
964      <br>
965
966Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
967
968      <br>
969
970If the inversion height calculated by the prerun is zero,
971inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
972
973      <br>
974
975Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
976
977      <br>
978
979Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
980removed from the restart file, because otherwise, no change from a
981fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
982      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
983
984      <br>
985
986Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
987in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
988      <td style="vertical-align: top; width: 189px;">advec_particles,
989check_parameters, cpu_log, data_output_2d, data_output_3d, header,
990init_3d_model, init_particles, init_ocean, modules, netcdf,
991prandtl_fluxes, production_e, read_var_list, time_integration,
992user_last_actions, write_var_list<br>
993
994      </td>
995    </tr>
996    <tr>
997      <td style="vertical-align: top; width: 27px;">02/02/09<br>
998      </td>
999      <td style="vertical-align: top; width: 38px;">SR<br>
1000      </td>
1001      <td style="vertical-align: top; width: 42px;">228<br>
1002      </td>
1003      <td style="vertical-align: top; width: 40px;">3.6<br>
1004      </td>
1005      <td style="vertical-align: top; width: 27px;">N<br>
1006      </td>
1007      <td style="vertical-align: top; width: 497px;">This
1008release contains further additions, changes, and bugfixes for the
1009SGI-ICE system, as well as important changes like the splitting of the
1010user-interface into single files, a complete revision of the
1011pre-compiling mechanism allowing to use different make-depositories
1012simultaneously, and a revision of the reading-mechanism from restart
1013files, which has no more restrictions in case that the previous and
1014current run have different domain/subdomain sizes. A new handling of
1015all kind of output messages is introduced with this release and will be
1016applied to all existing messages within the next releases.<br>
1017
1018      <br>
1019
1020      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
1021
1022      <br>
1023
1024Restart runs on SGI-ICE are working. (mrun)<br>
1025
10262d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
1027
1028      <br>
1029
1030Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
1031case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1032"<span style="font-style: italic;">-K parallel</span>" for coupling.
1033Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
1034      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
1035for lcxt4.<br>
1036
1037      <br>
1038
1039DVRP arguments changed to single precision, mode pathlines added.<br>
1040
1041      <br>
1042
1043User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
1044
1045      <br>
1046
1047User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
1048      <td style="vertical-align: top; width: 189px;">check_for_restart,
1049check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
1050modules, package_parin, palm, surface_coupler, timestep<br>
1051
1052      <br>
1053
1054Makefile,&nbsp;mbuild, mrun, subjob<br>
1055
1056      <br>
1057
1058      <span style="font-weight: bold;">new:</span><br>
1059
1060init_coupling, user_additional_routines, user_check_parameters</td>
1061    </tr>
1062    <tr>
1063      <td style="vertical-align: top; width: 27px;"><br>
1064      </td>
1065      <td style="vertical-align: top; width: 38px;"><br>
1066      </td>
1067      <td style="vertical-align: top; width: 42px;"><br>
1068      </td>
1069      <td style="vertical-align: top; width: 40px;"><br>
1070      </td>
1071      <td style="vertical-align: top; width: 27px;">C<br>
1072      </td>
1073      <td style="vertical-align: top; width: 497px;">User interface has been
1074split into single files.<br>
1075
1076      <br>
1077
1078Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
1079changed to INTEGER(8) in order to avoid "out of range" problems, which
1080result in measured negative time intervals. (cpu_log, local_tremain,
1081local_tremain_ini)<br>
1082
1083      <br>
1084
1085Reading mechanism from restart files
1086completely revised. The subdomain/total domain size is now allowed to
1087vary arbitrarily between the current and previous run. (read_var_list,
1088read_3d_binary, user_read_restart_data)<br>
1089
1090      <br>
1091
1092Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
1093completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
1094One depository per block (given in the config-file) is created. Always
1095all files from the source directory are copied to the respective
1096depository. No additional file checks are done any more (mrun version
10972.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1098"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
1099(mbuild, mrun)<br>
1100
1101      <br>
1102
1103Output messages (including required stop of execution) can now be
1104handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
1105All output messages will be replaced by this routine step by step
1106within the next revisions.<br>
1107
1108      <br>
1109
1110Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
1111explicitly set for better reading, although this has been already done
1112in boundary_conds. (advec_s_bc)<br>
1113
1114      <br>
1115
1116Origin of the xy-coordinate system shifted from the center of the first
1117grid 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
1118south-left corner of this cell. (netcdf) Topography definition
1119according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
1120(init_grid, modules, user_header, user_init_grid, user_parin)</td>
1121      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1122check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1123local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1124user_read_restart_data<br>
1125
1126      <br>
1127
1128Makefile, mbuild, mrun<br>
1129
1130      <br>
1131
1132      <span style="font-weight: bold;">removed:</span><br>
1133
1134user_interface<br>
1135
1136      <br>
1137
1138      <span style="font-weight: bold;">new:</span><br>
1139
1140message,
1141user_3d_data_averaging, user_actions, user_advec_particles,
1142user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1143user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1144user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1145user_init_grid, user_init_particles, user_init_plant_canopy,
1146user_last_actions, user_parin, user_parin, user_particle_attributes,
1147user_read_restart_data, user_spectra, user_statistics</td>
1148    </tr>
1149    <tr>
1150      <td style="vertical-align: top; width: 27px;"><br>
1151      </td>
1152      <td style="vertical-align: top; width: 38px;"><br>
1153      </td>
1154      <td style="vertical-align: top; width: 42px;"><br>
1155      </td>
1156      <td style="vertical-align: top; width: 40px;"><br>
1157      </td>
1158      <td style="vertical-align: top; width: 27px;">B<br>
1159      </td>
1160      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1161reallocated in case that multigrid is used. (calc_spectra)<br>
1162
1163      <br>
1164
1165Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1166inflow_turbulence,&nbsp;timestep)<br>
1167
1168      <br>
1169
1170Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1171      </span>adjusted to the required output size (1 gridpoint less,
1172along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1173in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1174compiler. (combine_plot_fields)<br>
1175
1176      <br>
1177
1178Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1179case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1180(header)<br>
1181
1182      <br>
1183
1184Inconsistency
1185removed: as the thermal stratification is not taken into account for
1186the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1187      <span style="font-family: Courier New,Courier,monospace;">km</span>
1188must 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>.
1189(production_e)<br>
1190
1191      <br>
1192
1193Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1194case of oceans runs. (sort_particles)<br>
1195
1196      <br>
1197
1198Bugfix: no output of particle concentration and radius unless particles
1199have been started. (data_output_2d)<br>
1200
1201      <br>
1202
1203Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1204from restart files ignored if total numbers of grid points do not
1205match. (read_3d_binary)<br>
1206
1207      <br>
1208
1209Bugfix: abort in case that absolute temperature is below zero.
1210(init_cloud_physics)</td>
1211      <td style="vertical-align: top; width: 189px;">advec_particles,
1212calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1213header, inflow_turbulence, init_cloud_physics, production_e,
1214read_3d_binary, timestep<br>
1215
1216      <br>
1217
1218combine_plot_fields</td>
1219    </tr>
1220  </tbody>
1221</table>
1222<b><blink></blink></b><br>&nbsp;
1223<br>&nbsp;
1224<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1225to change the source
1226code and how to document modifications<br>
1227</h2>Currently
1228(Sep 23rd, 2009), only selected users are allowed to commit changes to
1229the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1230<br>
1231<ol>
1232  <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>".
1233Additionally, document all changes in a local file (e.g.
1234~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1235have been changed. Classify changes in three cases, new (N), changed
1236(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>
1237    <br>
1238  </li>
1239  <li>Test the changed version, unless it works sufficiently.<br>
1240    <br>
1241  </li>
1242 
1243  <li>Commit the changes to the repository<br>
1244    <br>
1245    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1246    </span><br>
1247where "<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>
1248    <br>
1249Alternatively, in case that you have made quite a lot of changes, you
1250can also give the contents of your file CURRENT_MODIFICATIONS as the
1251log message:<br>
1252    <br>
1253    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1254    <br>
1255  </li>
1256
1257  <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>
1258    <br>
1259  </li>
1260  <li>Move the change comments in the file headers from "Current
1261revisions:" to "Former revisions:". Set the current svn id in front of
1262that.<br>
1263    <br>
1264    <span style="font-weight: bold;">Example:</span><br>
1265    <br>
1266    <span style="font-weight: bold;">before move:</span><br>
1267    <br>
1268    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1269    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1270    <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;">
1271    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1272    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1273    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1274    <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;">
1275    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1276    <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;">
1277    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1278    <br>
1279    <span style="font-weight: bold;">after move:</span><br>
1280    <br>
1281    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1282
1283    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1284
1285    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1286
1287    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1288
1289    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1290
1291    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1292
1293    <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>
1294!</span><br style="font-family: Courier New,Courier,monospace;">
1295    <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>
1296! </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;">
1297
1298    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1299
1300    <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;">
1301
1302    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1303    <br>
1304    <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">§</span>"
1305in this example should read "$", but "$" cannot be used here, because
1306otherwise svn would replace these entries after every change to this
1307technical documentation.</span><br>
1308 </span><br>
1309  </li>
1310  <li>Commit the changes in the technical documentation and the file headers:<br>
1311    <br>
1312    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1313    <br>
1314 <br>
1315  </li>
1316</ol>
1317
1318<h2>
1319<a name="Kapitel3.0"></a>3.0&nbsp; Description
1320of selected parts of the
1321model source code</h2>
1322<b></b>
1323<p>This section gives links to existing descriptions about special
1324parts of the PALM code, e.g. special numerical methods that are used
1325(including mathematical background). Documents are stored in single
1326files with different formats. Some are in German (sorry for the
1327inconvenience).
1328<br>&nbsp;
1329</p><ul> <li> <a name="UPS"></a>upstream-spline
1330advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1331, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1332physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1333)</li> 
1334  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1335  </li>
1336  <li>Runge-Kutta
1337time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1338, only in German)</li>
1339
1340</ul><br>
1341&nbsp;
1342<br>&nbsp;
1343<br>&nbsp;
1344<br>&nbsp;
1345<br>&nbsp;
1346<br>&nbsp;
1347<br>&nbsp;
1348<br>&nbsp;
1349</body></html>
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