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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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22<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;
23</font>a
24<b>pa</b>rallelized
25<b>L</b>ES <b>m</b>odel
26<br><hr width="100%">
27<br><font size="+2">technical/numerical documentation</font>
28<br>&nbsp;
29<br>&nbsp;
30<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
31</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
32</span></td> </tr>
33<tr nosave=""> <td nosave=""><b>Last
34change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 525 2010-03-30 02:08:09Z raasch $</b></td> </tr>
35</tbody>
36</table><hr width="100%">
37<p><font size="+2">Table of contents</font>
38<br>&nbsp;
39<br>&nbsp;
40</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
41History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
42How to change the source
43code and how to document modifications<br>
44 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
45Description of selected model numerics<br>
46&nbsp;</p>
47</ul><b></b><br>
48
49<h2><a name="Kapitel1.0"></a>1.0&nbsp;
50History of changes</h2>
51The 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>
52<br>
53Entries in the fifth column specify the type of the change:
54change&nbsp;
55of existing code (C), new code (N) or bugfix (B). More detailed
56information
57about the changes may sometimes be found in the header comment lines of the
58respective
59routines.
60<br>&nbsp;
61<br>
62<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
63  <tbody>
64    <tr>
65      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
66      </td>
67      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
68      </td>
69      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
70      </td>
71      <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
72      </td>
73      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
74      </td>
75      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
76      </td>
77      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
78      </td>
79    </tr>
80   
81   
82   
83   
84   
85   
86   
87   
88   
89   
90    <tr>
91      <td style="vertical-align: top;">30/03/10<br>
92      </td>
93      <td style="vertical-align: top;">SR<br>
94      </td>
95      <td style="vertical-align: top;">525<br>
96      </td>
97      <td style="vertical-align: top;">3.7a<br>
98      </td>
99      <td style="vertical-align: top;">B<br>
100      </td>
101      <td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br>
102      </td>
103      <td style="vertical-align: top;">check_parameters<br>
104      </td>
105    </tr>
106<tr>
107      <td style="vertical-align: top;">19/03/10<br>
108      </td>
109      <td style="vertical-align: top;">SR<br>
110      </td>
111      <td style="vertical-align: top;">520<br>
112      </td>
113      <td style="vertical-align: top;">3.7a<br>
114      </td>
115      <td style="vertical-align: top;">N<br>
116      </td>
117      <td style="vertical-align: top;">NetCDF4 support for particle
118data. Total number of particles is allowed to increase during the run,
119when netcdf_data_format &gt; <span style="font-style: italic;">2</span> is used.<br>
120      </td>
121      <td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
122      </td>
123    </tr>
124    <tr>
125      <td style="vertical-align: top;"><br>
126      </td>
127      <td style="vertical-align: top;"><br>
128      </td>
129      <td style="vertical-align: top;"><br>
130      </td>
131      <td style="vertical-align: top;"><br>
132      </td>
133      <td style="vertical-align: top;">C<br>
134      </td>
135      <td style="vertical-align: top;">Special characters like * and "
136are now allowed for NetCDF variable names. Replacement of these
137characters has been removed (routine clean_netcdf_varname removed)<br>
138      </td>
139      <td style="vertical-align: top;"><br>
140      </td>
141    </tr>
142<tr>
143      <td style="vertical-align: top;">18/03/10<br>
144      </td>
145      <td style="vertical-align: top;">SR<br>
146      </td>
147      <td style="vertical-align: top;">516<br>
148      </td>
149      <td style="vertical-align: top;">3.7a<br>
150      </td>
151      <td style="vertical-align: top;">N<br>
152      </td>
153      <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
154      </td>
155      <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
156      </td>
157    </tr>
158    <tr>
159      <td style="vertical-align: top;"><br>
160      </td>
161      <td style="vertical-align: top;"><br>
162      </td>
163      <td style="vertical-align: top;"><br>
164      </td>
165      <td style="vertical-align: top;"><br>
166      </td>
167      <td style="vertical-align: top;">B<br>
168      </td>
169      <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>
170      </td>
171      <td style="vertical-align: top;">buoyancy<br>
172      </td>
173    </tr>
174<tr>
175      <td style="vertical-align: top;">16/03/10<br>
176      </td>
177      <td style="vertical-align: top;">RH<br>
178      </td>
179      <td style="vertical-align: top;">513<br>
180      </td>
181      <td style="vertical-align: top;">3.7a<br>
182      </td>
183      <td style="vertical-align: top;">N<br>
184      </td>
185      <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>
186      </td>
187      <td style="vertical-align: top;">palmplot .ncl.config.default cross_sections.ncl profiles.ncl<br>
188      </td>
189    </tr>
190<tr>
191      <td style="vertical-align: top;">12/03/10<br>
192      </td>
193      <td style="vertical-align: top;">SR<br>
194      </td>
195      <td style="vertical-align: top;">509<br>
196      </td>
197      <td style="vertical-align: top;">3.7a<br>
198      </td>
199      <td style="vertical-align: top;">E<br>
200      </td>
201      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
202      </td>
203      <td style="vertical-align: top;">mbuild<br>
204      </td>
205    </tr>
206<tr>
207      <td style="vertical-align: top;">08/03/10<br>
208      </td>
209      <td style="vertical-align: top;">SR<br>
210      </td>
211      <td style="vertical-align: top;">506<br>
212      </td>
213      <td style="vertical-align: top;">3.7a<br>
214      </td>
215      <td style="vertical-align: top;">C<br>
216      </td>
217      <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>
218      </td>
219      <td style="vertical-align: top;">mrun<br>
220      </td>
221    </tr>
222<tr>
223      <td style="vertical-align: top;">03/03/10<br>
224      </td>
225      <td style="vertical-align: top;">SR<br>
226      </td>
227      <td style="vertical-align: top;">504<br>
228      </td>
229      <td style="vertical-align: top;">3.7a<br>
230      </td>
231      <td style="vertical-align: top;">C<br>
232      </td>
233      <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>
234      <br>
235Utility 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>
236      <br>
237Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
238      <br>
239Default configuration files updated.<br>
240      </td>
241      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
242      </td>
243    </tr>
244<tr>
245      <td style="vertical-align: top;">02/03/10<br>
246      </td>
247      <td style="vertical-align: top;">SR<br>
248      </td>
249      <td style="vertical-align: top;">496<br>
250      </td>
251      <td style="vertical-align: top;">3.7a<br>
252      </td>
253      <td style="vertical-align: top;">C<br>
254      </td>
255      <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>
256      </td>
257      <td style="vertical-align: top;">palm<br>
258      </td>
259    </tr>
260<tr>
261      <td style="vertical-align: top;">01/03/10<br>
262      </td>
263      <td style="vertical-align: top;">SR<br>
264      </td>
265      <td style="vertical-align: top;">494<br>
266      </td>
267      <td style="vertical-align: top;">3.7a<br>
268      </td>
269      <td style="vertical-align: top;">N<br>
270      </td>
271      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
272      <br>
273NetCDF4 allows for parallel I/O. Also, variables are not limited in
274size any more (i.e. arrays can be larger than 2GB). The new
275d3par-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>
276only affects 2d- and 3d-output, i.e. there is no parallel output for
277profiles, time series, spectra, and particles. Parallel output of
278particle data may realized in the future.<br>
279      <br>
280In 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>
281(merging data from single files - one per PE - into one file) is not
282neccessary. 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>
283      <br>
284Using NetCDF4 format requires a NetCDF4/HDF library. Respective
285settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
286HLRN 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>
287      <br>
288      <span style="font-weight: bold;">Attention:</span><br>
289So far, NetCDF parallel I/O has only been tested a little. Further
290performance optimizations may be required, especially in case of large
291data 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>
292      <br>
293      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
294      <br>
295Modules 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>
296      <br>
297      <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>
298      <br>
299This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
300      <br>
301      <span style="font-weight: bold;">WARNING:</span><br>
302      <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>
303      <br>
304</span>Compilation time can be reduced be using parallel make. The
305number of allowed simultaneous compiler calls (threads) is set in the
306configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
307      <br>
308      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
309      <br>
310allows a maximum of 4 routines to be compiled simultaneously (provided
311that the makefile does not show any dependencies between these
312routines).<span style="font-weight: bold;"><br>
313      </span>
314      </td>
315      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
316      <br>
317combine_plot_fields<br>
318      <br>
319mbuild, mrun, subjob<br>
320      </td>
321    </tr>
322    <tr>
323      <td style="vertical-align: top;"><br>
324      </td>
325      <td style="vertical-align: top;"><br>
326      </td>
327      <td style="vertical-align: top;"><br>
328      </td>
329      <td style="vertical-align: top;"><br>
330      </td>
331      <td style="vertical-align: top;">C<br>
332      </td>
333      <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>
334for choosing the NetCDF 64bit-offset format (this is the default from
335now on). The offset-format can not be set independently for the
3363d-output-data any more.<br>
337      <br>
338d3par-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>
339      </td>
340      <td style="vertical-align: top;">check_open, close_file,<br>
341data_output_mask, header, init_masks, modules, parin<br>
342      <br>
343      </td>
344    </tr>
345    <tr>
346      <td style="vertical-align: top;"><br>
347      </td>
348      <td style="vertical-align: top;"><br>
349      </td>
350      <td style="vertical-align: top;"><br>
351      </td>
352      <td style="vertical-align: top;"><br>
353      </td>
354      <td style="vertical-align: top;">B<br>
355      </td>
356      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
357      <br>
358Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
359      </td>
360      <td style="vertical-align: top;">user_statistics<br>
361      <br>
362trunk/UTIL/Makefile<br>
363      </td>
364    </tr>
365<tr>
366      <td style="vertical-align: top;">05/02/10<br>
367      </td>
368      <td style="vertical-align: top;">SR<br>
369      </td>
370      <td style="vertical-align: top;">485<br>
371      </td>
372      <td style="vertical-align: top;">3.7a<br>
373      </td>
374      <td style="vertical-align: top;">B<br>
375      </td>
376      <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>
377changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
378some global statistics (e.g. total kinetic energy) have wrong values.<br>
379      </td>
380      <td style="vertical-align: top;">init_3d_model, modules<br>
381      </td>
382    </tr>
383    <tr>
384      <td style="vertical-align: top;">05/02/10<br>
385      </td>
386      <td style="vertical-align: top;">SR<br>
387      </td>
388      <td style="vertical-align: top;">484<br>
389      </td>
390      <td style="vertical-align: top;">3.7a<br>
391      </td>
392      <td style="vertical-align: top;">B<br>
393      </td>
394      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
395      </td>
396      <td style="vertical-align: top;">many<br>
397      </td>
398    </tr>
399<tr>
400      <td style="vertical-align: top; width: 27px;">05/02/10<br>
401      </td>
402      <td style="vertical-align: top; width: 38px;">SR<br>
403      </td>
404      <td style="vertical-align: top; width: 42px;">483<br>
405      </td>
406      <td style="vertical-align: top; width: 40px;">3.7a<br>
407      </td>
408      <td style="vertical-align: top; width: 27px;">N<br>
409      </td>
410      <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>
411      <br>
412make 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>
413      <br>
414      <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;">
415wall_scalarflux</span> are the corresponding new inipar parameters.<br>
416(<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>
417      <br>
418Large scale vertical motion (subsidence/ascent) can be added as
419additional source to the prognostic equation for potential temperature.
420See 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>
421      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
422      <br>
423A 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>
424      <br>
425Masked data output has been implemented but it is not documented in the
426user manual so far. This feature can already use NetCDF4 file format.
427(check_open, check_parameters, close_file, modules, netcdf, parin,
428time_integration, user_parin, new: data_output_mask, init_masks,
429user_data_output_mask)<br>
430      </td>
431      <td style="vertical-align: top; width: 189px;">check_open, check
432parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
433netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
434      <br><span style="font-weight: bold;">
435new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
436<br>
437      </td>
438    </tr>
439    <tr>
440      <td style="vertical-align: top; width: 27px;"><br>
441      </td>
442      <td style="vertical-align: top; width: 38px;"><br>
443      </td>
444      <td style="vertical-align: top; width: 42px;"><br>
445      </td>
446      <td style="vertical-align: top; width: 40px;"><br>
447      </td>
448      <td style="vertical-align: top; width: 27px;">C<br>
449      </td>
450      <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>
451      <br><span style="font-family: Courier New,Courier,monospace;">
452var_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>
453      <br>
454Every cloud droplet has now an own weighting factor and can be deleted
455due to collisions. Condensation and collision of cloud droplets are
456adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
457      <br>
458Collision 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>
459      </td>
460      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
461      </td>
462    </tr>
463    <tr>
464      <td style="vertical-align: top; width: 27px;"><br>
465      </td>
466      <td style="vertical-align: top; width: 38px;"><br>
467      </td>
468      <td style="vertical-align: top; width: 42px;"><br>
469      </td>
470      <td style="vertical-align: top; width: 40px;"><br>
471      </td>
472      <td style="vertical-align: top; width: 27px;">B<br>
473      </td>
474      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
475      <br>
476Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
477      <br>
478Dimension 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>
479      <br>
480Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
481      <br>
482Bugfix: 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>
483      <br>
484Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
485      <br>
486Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
487      <br>
488Bugfix: 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>
489      <br>
490Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
491      <br>
492Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
493      <br>
494Bugfix 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>
495      </td>
496      <td style="vertical-align: top; width: 189px;">advec_particles,
497calc_precipitation, collision_efficiency, disturb_field, header,
498modules, poisfft_hybrid, subjob, sum_up_3d_data,
499time_integration<br>
500<br>
501      </td>
502    </tr>
503    <tr>
504      <td style="vertical-align: top; width: 27px;">23/09/09<br>
505      </td>
506      <td style="vertical-align: top; width: 38px;">SR<br>
507      </td>
508      <td style="vertical-align: top; width: 42px;">392<br>
509      </td>
510      <td style="vertical-align: top; width: 40px;">3.7<br>
511      </td>
512      <td style="vertical-align: top; width: 27px;">N<br>
513      </td>
514      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
515important changes:</span>
516atmosphere-ocean coupling has been improved and steering of
517dvr-software is more user-friendly now. Beside that, the release
518contains a lot of optimizations, changes, and bugfixes which have
519accumulated over the last months.<br>
520
521      <br>
522
523The atmosphere-ocean coupling allows to use independent precursor runs
524in order to account for different spin-up times. The time when coupling
525has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
526The 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
527order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
528output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
529      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
530      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
531      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
532      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
533      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
534      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
535      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
536      <span style="font-family: Courier New,Courier,monospace;">header</span>,
537      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
538      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
539      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
540      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
541      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
542      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
543      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
544      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
545
546      <br>
547
548Clipping of dvrp output implemented. Default colourtable for particles
549implemented, particle attributes (color, dvrp_size) can be set with new
550parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
551      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
552      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
553      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
554Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
555and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
556(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
557      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
558      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
559      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
560      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
561
562      <br>
563
564Polygon reduction for topography and ground plate isosurface. Reduction
565level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
566
567      <br>
568
569Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
570/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
571in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
572
573      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
574for speed optimization. This gives a significant speedup of more than
57510%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
576      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
577      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
578      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
579      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
580
581      <br>
582
583Scripts 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>
584
585      <br>
586
587Additional timestep criterion in case of simulations with plant canopy.
588(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
589
590      <br>
591
592Check 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
593exceed <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>
594
595      <br>
596
597External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
598      <span style="font-family: Courier New,Courier,monospace;">header</span>,
599      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
600      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
601      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
602      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
603      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
604      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
605
606      <br>
607
608New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
609(<span style="font-family: Courier New,Courier,monospace;">header</span>,
610      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
611      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
612      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
613      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
614      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
615      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
616      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
617      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
618
619      <br>
620
621Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
622(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
623      <span style="font-family: Courier New,Courier,monospace;">header</span>,
624      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
625      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
626      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
627      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
628      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
629
630      <br>
631
632Option 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>,
633      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
634
635      <br>
636
637xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
638      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
639      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
640      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
641      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
642      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
643      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
644      <td style="vertical-align: top; width: 189px;">average_3d_data,
645check_for_restart, check_parameters, data_output_2d, data_output_3d,
646data_output_dvrp, data_output_profiles, data_output_ptseries,
647data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
648diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
649header, mbuild, modules, mrun, package_parin, parin,
650prognostic_equations, read_3d_binary, read_var_list, subjob,
651sum_up_3d_data, surface_coupler, timestep, time_integration,
652user_check_parameters, user_data_output_2d, user_data_output_dvrp,
653user_header, user_init_grid, write_3d_binary, write_var_list<br>
654
655      <br>
656
657      <span style="font-weight: bold;">new:</span>
658set_particle_attributes, set_slicer_attributes_dvrp</td>
659    </tr>
660    <tr>
661      <td style="vertical-align: top; width: 27px;"><br>
662      </td>
663      <td style="vertical-align: top; width: 38px;"><br>
664      </td>
665      <td style="vertical-align: top; width: 42px;"><br>
666      </td>
667      <td style="vertical-align: top; width: 40px;"><br>
668      </td>
669      <td style="vertical-align: top; width: 27px;">C<br>
670      </td>
671      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
672message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
673      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
674      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
675      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
676      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
677      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
678      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
679      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
680      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
681      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
682      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
683      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
684      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
685      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
686      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
687      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
688      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
689      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
690      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
691      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
692      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
693      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
694      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
695      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
696      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
697      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
698      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
699      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
700      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
701      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
702      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
703      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
704      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
705      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
706      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
707      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
708      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
709      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
710      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
711      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
712
713      <br>
714
715Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
716      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
717      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
718      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
719      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
720      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
721      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
722      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
723      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
724
725      <br>
726
727__lcmuk changed to __lc to avoid problems with Intel compiler on
728sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
729
730      <br>
731
732For extended NetCDF files, the updated title attribute includes an
733update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
734
735      <br>
736
737In case of restart runs without extension, initial profiles are not
738written to NetCDF-file anymore. So far, time axis always started at
739t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
740      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
741      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
742      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
743
744      <br>
745
746      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
747'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
748can now <br>
749
750be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
751(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
752      <span style="font-family: Courier New,Courier,monospace;">header</span>,
753      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
754
755      <br>
756
7572 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
758
759      <br>
760
761A link to the webspage appendix_a.html is printed for further
762information about possible reasons of the error that appeared. (message)<br>
763
764      <br>
765
766Temperature gradient criterion for estimating the boundary layer height
767replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
768
769      <br>
770
771NetCDF unit attribute in timeseries output in case of statistic regions
772added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
773
774      <br>
775
776Maximum number of tails is calculated from maximum number of particles
777and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
778(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
779
780      <br>
781
782Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
783is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
784      <span style="font-family: Courier New,Courier,monospace;">header</span>,
785      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
786      <br>
787
788      <br>
789
790First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
791defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
792
793      <br>
794
795Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
796moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
797to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
798(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
799
800      <br>
801
802      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
803moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
804to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
805(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
806      <span style="font-family: Courier New,Courier,monospace;">header</span>,
807      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
808      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
809      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
810      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
811      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
812      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
813      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
814
815      <br>
816
817Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
818changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
819
820      <br>
821
822Adjustments for runs on lcxt4 (necessary due to a software update on
823CRAY) 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>
824      <td style="vertical-align: top; width: 189px;">advec_particles,
825advec_s_bc,
826buoyancy, calc_spectra, check_for_restart, check_open,
827check_parameters, close_file, coriolis, cpu_log, data_output_2d,
828data_output_3d, data_output_dvrp, data_output_profiles,
829data_output_ptseries, data_output_spectra, data_output_tseries,
830eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
831init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
832message, mrun, netcdf, package_parin, parin, plant_canopy_model,
833poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
834surface_coupler, temperton_fft, timestep,
835user_actions,user_check_parameters, user_data_output_dvrp,
836user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
837user_parin, user_read_restart_data, user_spectra, write_var_list </td>
838    </tr>
839    <tr>
840      <td style="vertical-align: top; width: 27px;"><br>
841      </td>
842      <td style="vertical-align: top; width: 38px;"><br>
843      </td>
844      <td style="vertical-align: top; width: 42px;"><br>
845      </td>
846      <td style="vertical-align: top; width: 40px;"><br>
847      </td>
848      <td style="vertical-align: top; width: 27px;">B<br>
849      </td>
850      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
851pressure profile in case of ocean runs is now calculated in 5 iteration
852steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
853
854      <br>
855
856Bugfix: wrong sign in buoyancy production of ocean part in case of not
857using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
858(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
859
860      <br>
861
862Bugfix: output of averaged 2d/3d quantities requires that an avaraging
863interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
864
865      <br>
866
867Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
868(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
869
870      <br>
871
872Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
873(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
874
875      <br>
876
877Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
878if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
879is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
880and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
881calls. This implies a possible performance loss; an alternative
882strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
883
884      <br>
885
886Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
887
888      <br>
889
890Bugfix: 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>
891
892      <br>
893
894Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
895=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
896for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
897      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
898
899      <br>
900
901Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
902becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
903
904      <br>
905
906Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
907
908      <br>
909
910Bugfix: error in check, if particles moved further than one subdomain
911length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
912
913      <br>
914
915Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
916is only written to file if its third index is &gt; 0, arrays for tails
917are allocated with a minimum size of 10 tails if there is no tail
918initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
919      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
920
921      <br>
922
923Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
924
925      <br>
926
927Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
928changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
929NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
930
931      <br>
932
933Bugfix: output of particle time series only if particle advection is
934switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
935
936      <br>
937
938Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
939= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
940(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
941
942      <br>
943
944Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
945z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
946
947      <br>
948
949Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
950
951      <br>
952
953If the inversion height calculated by the prerun is zero,
954inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
955
956      <br>
957
958Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
959
960      <br>
961
962Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
963removed from the restart file, because otherwise, no change from a
964fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
965      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
966
967      <br>
968
969Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
970in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
971      <td style="vertical-align: top; width: 189px;">advec_particles,
972check_parameters, cpu_log, data_output_2d, data_output_3d, header,
973init_3d_model, init_particles, init_ocean, modules, netcdf,
974prandtl_fluxes, production_e, read_var_list, time_integration,
975user_last_actions, write_var_list<br>
976
977      </td>
978    </tr>
979    <tr>
980      <td style="vertical-align: top; width: 27px;">02/02/09<br>
981      </td>
982      <td style="vertical-align: top; width: 38px;">SR<br>
983      </td>
984      <td style="vertical-align: top; width: 42px;">228<br>
985      </td>
986      <td style="vertical-align: top; width: 40px;">3.6<br>
987      </td>
988      <td style="vertical-align: top; width: 27px;">N<br>
989      </td>
990      <td style="vertical-align: top; width: 497px;">This
991release contains further additions, changes, and bugfixes for the
992SGI-ICE system, as well as important changes like the splitting of the
993user-interface into single files, a complete revision of the
994pre-compiling mechanism allowing to use different make-depositories
995simultaneously, and a revision of the reading-mechanism from restart
996files, which has no more restrictions in case that the previous and
997current run have different domain/subdomain sizes. A new handling of
998all kind of output messages is introduced with this release and will be
999applied to all existing messages within the next releases.<br>
1000
1001      <br>
1002
1003      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
1004
1005      <br>
1006
1007Restart runs on SGI-ICE are working. (mrun)<br>
1008
10092d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
1010
1011      <br>
1012
1013Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
1014case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1015"<span style="font-style: italic;">-K parallel</span>" for coupling.
1016Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
1017      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
1018for lcxt4.<br>
1019
1020      <br>
1021
1022DVRP arguments changed to single precision, mode pathlines added.<br>
1023
1024      <br>
1025
1026User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
1027
1028      <br>
1029
1030User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
1031      <td style="vertical-align: top; width: 189px;">check_for_restart,
1032check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
1033modules, package_parin, palm, surface_coupler, timestep<br>
1034
1035      <br>
1036
1037Makefile,&nbsp;mbuild, mrun, subjob<br>
1038
1039      <br>
1040
1041      <span style="font-weight: bold;">new:</span><br>
1042
1043init_coupling, user_additional_routines, user_check_parameters</td>
1044    </tr>
1045    <tr>
1046      <td style="vertical-align: top; width: 27px;"><br>
1047      </td>
1048      <td style="vertical-align: top; width: 38px;"><br>
1049      </td>
1050      <td style="vertical-align: top; width: 42px;"><br>
1051      </td>
1052      <td style="vertical-align: top; width: 40px;"><br>
1053      </td>
1054      <td style="vertical-align: top; width: 27px;">C<br>
1055      </td>
1056      <td style="vertical-align: top; width: 497px;">User interface has been
1057split into single files.<br>
1058
1059      <br>
1060
1061Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
1062changed to INTEGER(8) in order to avoid "out of range" problems, which
1063result in measured negative time intervals. (cpu_log, local_tremain,
1064local_tremain_ini)<br>
1065
1066      <br>
1067
1068Reading mechanism from restart files
1069completely revised. The subdomain/total domain size is now allowed to
1070vary arbitrarily between the current and previous run. (read_var_list,
1071read_3d_binary, user_read_restart_data)<br>
1072
1073      <br>
1074
1075Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
1076completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
1077One depository per block (given in the config-file) is created. Always
1078all files from the source directory are copied to the respective
1079depository. No additional file checks are done any more (mrun version
10802.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1081"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
1082(mbuild, mrun)<br>
1083
1084      <br>
1085
1086Output messages (including required stop of execution) can now be
1087handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
1088All output messages will be replaced by this routine step by step
1089within the next revisions.<br>
1090
1091      <br>
1092
1093Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
1094explicitly set for better reading, although this has been already done
1095in boundary_conds. (advec_s_bc)<br>
1096
1097      <br>
1098
1099Origin of the xy-coordinate system shifted from the center of the first
1100grid 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
1101south-left corner of this cell. (netcdf) Topography definition
1102according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
1103(init_grid, modules, user_header, user_init_grid, user_parin)</td>
1104      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1105check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1106local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1107user_read_restart_data<br>
1108
1109      <br>
1110
1111Makefile, mbuild, mrun<br>
1112
1113      <br>
1114
1115      <span style="font-weight: bold;">removed:</span><br>
1116
1117user_interface<br>
1118
1119      <br>
1120
1121      <span style="font-weight: bold;">new:</span><br>
1122
1123message,
1124user_3d_data_averaging, user_actions, user_advec_particles,
1125user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1126user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1127user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1128user_init_grid, user_init_particles, user_init_plant_canopy,
1129user_last_actions, user_parin, user_parin, user_particle_attributes,
1130user_read_restart_data, user_spectra, user_statistics</td>
1131    </tr>
1132    <tr>
1133      <td style="vertical-align: top; width: 27px;"><br>
1134      </td>
1135      <td style="vertical-align: top; width: 38px;"><br>
1136      </td>
1137      <td style="vertical-align: top; width: 42px;"><br>
1138      </td>
1139      <td style="vertical-align: top; width: 40px;"><br>
1140      </td>
1141      <td style="vertical-align: top; width: 27px;">B<br>
1142      </td>
1143      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1144reallocated in case that multigrid is used. (calc_spectra)<br>
1145
1146      <br>
1147
1148Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1149inflow_turbulence,&nbsp;timestep)<br>
1150
1151      <br>
1152
1153Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1154      </span>adjusted to the required output size (1 gridpoint less,
1155along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1156in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1157compiler. (combine_plot_fields)<br>
1158
1159      <br>
1160
1161Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1162case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1163(header)<br>
1164
1165      <br>
1166
1167Inconsistency
1168removed: as the thermal stratification is not taken into account for
1169the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1170      <span style="font-family: Courier New,Courier,monospace;">km</span>
1171must 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>.
1172(production_e)<br>
1173
1174      <br>
1175
1176Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1177case of oceans runs. (sort_particles)<br>
1178
1179      <br>
1180
1181Bugfix: no output of particle concentration and radius unless particles
1182have been started. (data_output_2d)<br>
1183
1184      <br>
1185
1186Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1187from restart files ignored if total numbers of grid points do not
1188match. (read_3d_binary)<br>
1189
1190      <br>
1191
1192Bugfix: abort in case that absolute temperature is below zero.
1193(init_cloud_physics)</td>
1194      <td style="vertical-align: top; width: 189px;">advec_particles,
1195calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1196header, inflow_turbulence, init_cloud_physics, production_e,
1197read_3d_binary, timestep<br>
1198
1199      <br>
1200
1201combine_plot_fields</td>
1202    </tr>
1203  </tbody>
1204</table>
1205<b><blink></blink></b><br>&nbsp;
1206<br>&nbsp;
1207<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1208to change the source
1209code and how to document modifications<br>
1210</h2>Currently
1211(Sep 23rd, 2009), only selected users are allowed to commit changes to
1212the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1213<br>
1214<ol>
1215  <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>".
1216Additionally, document all changes in a local file (e.g.
1217~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1218have been changed. Classify changes in three cases, new (N), changed
1219(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>
1220    <br>
1221  </li>
1222  <li>Test the changed version, unless it works sufficiently.<br>
1223    <br>
1224  </li>
1225 
1226  <li>Commit the changes to the repository<br>
1227    <br>
1228    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1229    </span><br>
1230where "<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>
1231    <br>
1232Alternatively, in case that you have made quite a lot of changes, you
1233can also give the contents of your file CURRENT_MODIFICATIONS as the
1234log message:<br>
1235    <br>
1236    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1237    <br>
1238  </li>
1239
1240  <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>
1241    <br>
1242  </li>
1243  <li>Move the change comments in the file headers from "Current
1244revisions:" to "Former revisions:". Set the current svn id in front of
1245that.<br>
1246    <br>
1247    <span style="font-weight: bold;">Example:</span><br>
1248    <br>
1249    <span style="font-weight: bold;">before move:</span><br>
1250    <br>
1251    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1252    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1253    <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;">
1254    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1255    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1256    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1257    <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;">
1258    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1259    <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;">
1260    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1261    <br>
1262    <span style="font-weight: bold;">after move:</span><br>
1263    <br>
1264    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1265
1266    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1267
1268    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1269
1270    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1271
1272    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1273
1274    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1275
1276    <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>
1277!</span><br style="font-family: Courier New,Courier,monospace;">
1278    <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>
1279! </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;">
1280
1281    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1282
1283    <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;">
1284
1285    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1286    <br>
1287    <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">§</span>"
1288in this example should read "$", but "$" cannot be used here, because
1289otherwise svn would replace these entries after every change to this
1290technical documentation.</span><br>
1291 </span><br>
1292  </li>
1293  <li>Commit the changes in the technical documentation and the file headers:<br>
1294    <br>
1295    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1296    <br>
1297 <br>
1298  </li>
1299</ol>
1300
1301<h2>
1302<a name="Kapitel3.0"></a>3.0&nbsp; Description
1303of selected parts of the
1304model source code</h2>
1305<b></b>
1306<p>This section gives links to existing descriptions about special
1307parts of the PALM code, e.g. special numerical methods that are used
1308(including mathematical background). Documents are stored in single
1309files with different formats. Some are in German (sorry for the
1310inconvenience).
1311<br>&nbsp;
1312</p><ul> <li> <a name="UPS"></a>upstream-spline
1313advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1314, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1315physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1316)</li> 
1317  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1318  </li>
1319  <li>Runge-Kutta
1320time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1321, only in German)</li>
1322
1323</ul><br>
1324&nbsp;
1325<br>&nbsp;
1326<br>&nbsp;
1327<br>&nbsp;
1328<br>&nbsp;
1329<br>&nbsp;
1330<br>&nbsp;
1331<br>&nbsp;
1332</body></html>
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