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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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21<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;
22</font>a
23<b>pa</b>rallelized
24<b>L</b>ES <b>m</b>odel
25<br><hr width="100%">
26<br><font size="+2">technical/numerical documentation</font>
27<br>&nbsp;
28<br>&nbsp;
29<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
30</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
31</span></td> </tr>
32<tr nosave=""> <td nosave=""><b>Last
33change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 520 2010-03-19 05:39:46Z raasch $</b></td> </tr>
34</tbody>
35</table><hr width="100%">
36<p><font size="+2">Table of contents</font>
37<br>&nbsp;
38<br>&nbsp;
39</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
40History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
41How to change the source
42code and how to document modifications<br>
43 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
44Description of selected model numerics<br>
45&nbsp;</p>
46</ul><b></b><br>
47
48<h2><a name="Kapitel1.0"></a>1.0&nbsp;
49History of changes</h2>
50The 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>
51<br>
52Entries in the fifth column specify the type of the change:
53change&nbsp;
54of existing code (C), new code (N) or bugfix (B). More detailed
55information
56about the changes may sometimes be found in the header comment lines of the
57respective
58routines.
59<br>&nbsp;
60<br>
61<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
62  <tbody>
63    <tr>
64      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
65      </td>
66      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
67      </td>
68      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
69      </td>
70      <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
71      </td>
72      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
73      </td>
74      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
75      </td>
76      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
77      </td>
78    </tr>
79   
80   
81   
82   
83   
84   
85   
86   
87   
88   
89    <tr>
90      <td style="vertical-align: top;">19/03/10<br>
91      </td>
92      <td style="vertical-align: top;">SR<br>
93      </td>
94      <td style="vertical-align: top;">520<br>
95      </td>
96      <td style="vertical-align: top;">3.7a<br>
97      </td>
98      <td style="vertical-align: top;">N<br>
99      </td>
100      <td style="vertical-align: top;">NetCDF4 support for particle
101data. Total number of particles is allowed to increase during the run,
102when netcdf_data_format &gt; <span style="font-style: italic;">2</span> is used.<br>
103      </td>
104      <td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
105      </td>
106    </tr>
107    <tr>
108      <td style="vertical-align: top;"><br>
109      </td>
110      <td style="vertical-align: top;"><br>
111      </td>
112      <td style="vertical-align: top;"><br>
113      </td>
114      <td style="vertical-align: top;"><br>
115      </td>
116      <td style="vertical-align: top;">C<br>
117      </td>
118      <td style="vertical-align: top;">Special characters like * and "
119are now allowed for NetCDF variable names. Replacement of these
120characters has been removed (routine clean_netcdf_varname removed)<br>
121      </td>
122      <td style="vertical-align: top;"><br>
123      </td>
124    </tr>
125<tr>
126      <td style="vertical-align: top;">18/03/10<br>
127      </td>
128      <td style="vertical-align: top;">SR<br>
129      </td>
130      <td style="vertical-align: top;">516<br>
131      </td>
132      <td style="vertical-align: top;">3.7a<br>
133      </td>
134      <td style="vertical-align: top;">N<br>
135      </td>
136      <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
137      </td>
138      <td style="vertical-align: top;">palm_simple_install, palm_simple_run<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;">B<br>
151      </td>
152      <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>
153      </td>
154      <td style="vertical-align: top;">buoyancy<br>
155      </td>
156    </tr>
157<tr>
158      <td style="vertical-align: top;">16/03/10<br>
159      </td>
160      <td style="vertical-align: top;">RH<br>
161      </td>
162      <td style="vertical-align: top;">513<br>
163      </td>
164      <td style="vertical-align: top;">3.7a<br>
165      </td>
166      <td style="vertical-align: top;">N<br>
167      </td>
168      <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>
169      </td>
170      <td style="vertical-align: top;">palmplot .ncl.config.default cross_sections.ncl profiles.ncl<br>
171      </td>
172    </tr>
173<tr>
174      <td style="vertical-align: top;">12/03/10<br>
175      </td>
176      <td style="vertical-align: top;">SR<br>
177      </td>
178      <td style="vertical-align: top;">509<br>
179      </td>
180      <td style="vertical-align: top;">3.7a<br>
181      </td>
182      <td style="vertical-align: top;">E<br>
183      </td>
184      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
185      </td>
186      <td style="vertical-align: top;">mbuild<br>
187      </td>
188    </tr>
189<tr>
190      <td style="vertical-align: top;">08/03/10<br>
191      </td>
192      <td style="vertical-align: top;">SR<br>
193      </td>
194      <td style="vertical-align: top;">506<br>
195      </td>
196      <td style="vertical-align: top;">3.7a<br>
197      </td>
198      <td style="vertical-align: top;">C<br>
199      </td>
200      <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>
201      </td>
202      <td style="vertical-align: top;">mrun<br>
203      </td>
204    </tr>
205<tr>
206      <td style="vertical-align: top;">03/03/10<br>
207      </td>
208      <td style="vertical-align: top;">SR<br>
209      </td>
210      <td style="vertical-align: top;">504<br>
211      </td>
212      <td style="vertical-align: top;">3.7a<br>
213      </td>
214      <td style="vertical-align: top;">C<br>
215      </td>
216      <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>
217      <br>
218Utility 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>
219      <br>
220Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
221      <br>
222Default configuration files updated.<br>
223      </td>
224      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
225      </td>
226    </tr>
227<tr>
228      <td style="vertical-align: top;">02/03/10<br>
229      </td>
230      <td style="vertical-align: top;">SR<br>
231      </td>
232      <td style="vertical-align: top;">496<br>
233      </td>
234      <td style="vertical-align: top;">3.7a<br>
235      </td>
236      <td style="vertical-align: top;">C<br>
237      </td>
238      <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>
239      </td>
240      <td style="vertical-align: top;">palm<br>
241      </td>
242    </tr>
243<tr>
244      <td style="vertical-align: top;">01/03/10<br>
245      </td>
246      <td style="vertical-align: top;">SR<br>
247      </td>
248      <td style="vertical-align: top;">494<br>
249      </td>
250      <td style="vertical-align: top;">3.7a<br>
251      </td>
252      <td style="vertical-align: top;">N<br>
253      </td>
254      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
255      <br>
256NetCDF4 allows for parallel I/O. Also, variables are not limited in
257size any more (i.e. arrays can be larger than 2GB). The new
258d3par-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>
259only affects 2d- and 3d-output, i.e. there is no parallel output for
260profiles, time series, spectra, and particles. Parallel output of
261particle data may realized in the future.<br>
262      <br>
263In 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>
264(merging data from single files - one per PE - into one file) is not
265neccessary. 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>
266      <br>
267Using NetCDF4 format requires a NetCDF4/HDF library. Respective
268settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
269HLRN 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>
270      <br>
271      <span style="font-weight: bold;">Attention:</span><br>
272So far, NetCDF parallel I/O has only been tested a little. Further
273performance optimizations may be required, especially in case of large
274data 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>
275      <br>
276      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
277      <br>
278Modules 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>
279      <br>
280      <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>
281      <br>
282This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
283      <br>
284      <span style="font-weight: bold;">WARNING:</span><br>
285      <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>
286      <br>
287</span>Compilation time can be reduced be using parallel make. The
288number of allowed simultaneous compiler calls (threads) is set in the
289configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
290      <br>
291      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
292      <br>
293allows a maximum of 4 routines to be compiled simultaneously (provided
294that the makefile does not show any dependencies between these
295routines).<span style="font-weight: bold;"><br>
296      </span>
297      </td>
298      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
299      <br>
300combine_plot_fields<br>
301      <br>
302mbuild, mrun, subjob<br>
303      </td>
304    </tr>
305    <tr>
306      <td style="vertical-align: top;"><br>
307      </td>
308      <td style="vertical-align: top;"><br>
309      </td>
310      <td style="vertical-align: top;"><br>
311      </td>
312      <td style="vertical-align: top;"><br>
313      </td>
314      <td style="vertical-align: top;">C<br>
315      </td>
316      <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>
317for choosing the NetCDF 64bit-offset format (this is the default from
318now on). The offset-format can not be set independently for the
3193d-output-data any more.<br>
320      <br>
321d3par-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>
322      </td>
323      <td style="vertical-align: top;">check_open, close_file,<br>
324data_output_mask, header, init_masks, modules, parin<br>
325      <br>
326      </td>
327    </tr>
328    <tr>
329      <td style="vertical-align: top;"><br>
330      </td>
331      <td style="vertical-align: top;"><br>
332      </td>
333      <td style="vertical-align: top;"><br>
334      </td>
335      <td style="vertical-align: top;"><br>
336      </td>
337      <td style="vertical-align: top;">B<br>
338      </td>
339      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
340      <br>
341Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
342      </td>
343      <td style="vertical-align: top;">user_statistics<br>
344      <br>
345trunk/UTIL/Makefile<br>
346      </td>
347    </tr>
348<tr>
349      <td style="vertical-align: top;">05/02/10<br>
350      </td>
351      <td style="vertical-align: top;">SR<br>
352      </td>
353      <td style="vertical-align: top;">485<br>
354      </td>
355      <td style="vertical-align: top;">3.7a<br>
356      </td>
357      <td style="vertical-align: top;">B<br>
358      </td>
359      <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>
360changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
361some global statistics (e.g. total kinetic energy) have wrong values.<br>
362      </td>
363      <td style="vertical-align: top;">init_3d_model, modules<br>
364      </td>
365    </tr>
366    <tr>
367      <td style="vertical-align: top;">05/02/10<br>
368      </td>
369      <td style="vertical-align: top;">SR<br>
370      </td>
371      <td style="vertical-align: top;">484<br>
372      </td>
373      <td style="vertical-align: top;">3.7a<br>
374      </td>
375      <td style="vertical-align: top;">B<br>
376      </td>
377      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
378      </td>
379      <td style="vertical-align: top;">many<br>
380      </td>
381    </tr>
382<tr>
383      <td style="vertical-align: top; width: 27px;">05/02/10<br>
384      </td>
385      <td style="vertical-align: top; width: 38px;">SR<br>
386      </td>
387      <td style="vertical-align: top; width: 42px;">483<br>
388      </td>
389      <td style="vertical-align: top; width: 40px;">3.7a<br>
390      </td>
391      <td style="vertical-align: top; width: 27px;">N<br>
392      </td>
393      <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>
394      <br>
395make 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>
396      <br>
397      <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;">
398wall_scalarflux</span> are the corresponding new inipar parameters.<br>
399(<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>
400      <br>
401Large scale vertical motion (subsidence/ascent) can be added as
402additional source to the prognostic equation for potential temperature.
403See 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>
404      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
405      <br>
406A 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>
407      <br>
408Masked data output has been implemented but it is not documented in the
409user manual so far. This feature can already use NetCDF4 file format.
410(check_open, check_parameters, close_file, modules, netcdf, parin,
411time_integration, user_parin, new: data_output_mask, init_masks,
412user_data_output_mask)<br>
413      </td>
414      <td style="vertical-align: top; width: 189px;">check_open, check
415parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
416netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
417      <br><span style="font-weight: bold;">
418new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
419<br>
420      </td>
421    </tr>
422    <tr>
423      <td style="vertical-align: top; width: 27px;"><br>
424      </td>
425      <td style="vertical-align: top; width: 38px;"><br>
426      </td>
427      <td style="vertical-align: top; width: 42px;"><br>
428      </td>
429      <td style="vertical-align: top; width: 40px;"><br>
430      </td>
431      <td style="vertical-align: top; width: 27px;">C<br>
432      </td>
433      <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>
434      <br><span style="font-family: Courier New,Courier,monospace;">
435var_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>
436      <br>
437Every cloud droplet has now an own weighting factor and can be deleted
438due to collisions. Condensation and collision of cloud droplets are
439adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
440      <br>
441Collision 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>
442      </td>
443      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
444      </td>
445    </tr>
446    <tr>
447      <td style="vertical-align: top; width: 27px;"><br>
448      </td>
449      <td style="vertical-align: top; width: 38px;"><br>
450      </td>
451      <td style="vertical-align: top; width: 42px;"><br>
452      </td>
453      <td style="vertical-align: top; width: 40px;"><br>
454      </td>
455      <td style="vertical-align: top; width: 27px;">B<br>
456      </td>
457      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
458      <br>
459Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
460      <br>
461Dimension 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>
462      <br>
463Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
464      <br>
465Bugfix: 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>
466      <br>
467Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
468      <br>
469Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
470      <br>
471Bugfix: 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>
472      <br>
473Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
474      <br>
475Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
476      <br>
477Bugfix 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>
478      </td>
479      <td style="vertical-align: top; width: 189px;">advec_particles,
480calc_precipitation, collision_efficiency, disturb_field, header,
481modules, poisfft_hybrid, subjob, sum_up_3d_data,
482time_integration<br>
483<br>
484      </td>
485    </tr>
486    <tr>
487      <td style="vertical-align: top; width: 27px;">23/09/09<br>
488      </td>
489      <td style="vertical-align: top; width: 38px;">SR<br>
490      </td>
491      <td style="vertical-align: top; width: 42px;">392<br>
492      </td>
493      <td style="vertical-align: top; width: 40px;">3.7<br>
494      </td>
495      <td style="vertical-align: top; width: 27px;">N<br>
496      </td>
497      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
498important changes:</span>
499atmosphere-ocean coupling has been improved and steering of
500dvr-software is more user-friendly now. Beside that, the release
501contains a lot of optimizations, changes, and bugfixes which have
502accumulated over the last months.<br>
503
504      <br>
505
506The atmosphere-ocean coupling allows to use independent precursor runs
507in order to account for different spin-up times. The time when coupling
508has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
509The 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
510order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
511output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
512      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
513      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
514      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
515      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
516      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
517      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
518      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
519      <span style="font-family: Courier New,Courier,monospace;">header</span>,
520      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
521      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
522      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
523      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
524      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
525      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
526      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
527      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
528
529      <br>
530
531Clipping of dvrp output implemented. Default colourtable for particles
532implemented, particle attributes (color, dvrp_size) can be set with new
533parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
534      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
535      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
536      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
537Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
538and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
539(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
540      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
541      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
542      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
543      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
544
545      <br>
546
547Polygon reduction for topography and ground plate isosurface. Reduction
548level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
549
550      <br>
551
552Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
553/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
554in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
555
556      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
557for speed optimization. This gives a significant speedup of more than
55810%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
559      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
560      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
561      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
562      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
563
564      <br>
565
566Scripts 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>
567
568      <br>
569
570Additional timestep criterion in case of simulations with plant canopy.
571(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
572
573      <br>
574
575Check 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
576exceed <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>
577
578      <br>
579
580External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
581      <span style="font-family: Courier New,Courier,monospace;">header</span>,
582      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
583      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
584      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
585      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
586      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
587      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
588
589      <br>
590
591New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
592(<span style="font-family: Courier New,Courier,monospace;">header</span>,
593      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
594      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
595      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
596      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
597      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
598      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
599      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
600      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
601
602      <br>
603
604Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
605(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
606      <span style="font-family: Courier New,Courier,monospace;">header</span>,
607      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
608      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
609      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
610      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
611      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
612
613      <br>
614
615Option 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>,
616      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
617
618      <br>
619
620xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
621      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
622      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
623      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
624      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
625      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
626      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
627      <td style="vertical-align: top; width: 189px;">average_3d_data,
628check_for_restart, check_parameters, data_output_2d, data_output_3d,
629data_output_dvrp, data_output_profiles, data_output_ptseries,
630data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
631diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
632header, mbuild, modules, mrun, package_parin, parin,
633prognostic_equations, read_3d_binary, read_var_list, subjob,
634sum_up_3d_data, surface_coupler, timestep, time_integration,
635user_check_parameters, user_data_output_2d, user_data_output_dvrp,
636user_header, user_init_grid, write_3d_binary, write_var_list<br>
637
638      <br>
639
640      <span style="font-weight: bold;">new:</span>
641set_particle_attributes, set_slicer_attributes_dvrp</td>
642    </tr>
643    <tr>
644      <td style="vertical-align: top; width: 27px;"><br>
645      </td>
646      <td style="vertical-align: top; width: 38px;"><br>
647      </td>
648      <td style="vertical-align: top; width: 42px;"><br>
649      </td>
650      <td style="vertical-align: top; width: 40px;"><br>
651      </td>
652      <td style="vertical-align: top; width: 27px;">C<br>
653      </td>
654      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
655message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
656      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
657      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
658      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
659      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
660      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
661      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
662      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
663      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
664      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
665      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
666      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
667      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
668      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
669      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
670      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
671      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
672      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
673      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
674      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
675      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
676      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
677      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
678      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
679      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
680      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
681      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
682      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
683      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
684      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
685      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
686      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
687      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
688      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
689      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
690      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
691      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
692      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
693      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
694      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
695
696      <br>
697
698Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
699      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
700      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
701      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
702      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
703      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
704      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
705      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
706      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
707
708      <br>
709
710__lcmuk changed to __lc to avoid problems with Intel compiler on
711sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
712
713      <br>
714
715For extended NetCDF files, the updated title attribute includes an
716update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
717
718      <br>
719
720In case of restart runs without extension, initial profiles are not
721written to NetCDF-file anymore. So far, time axis always started at
722t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
723      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
724      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
725      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
726
727      <br>
728
729      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
730'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
731can now <br>
732
733be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
734(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
735      <span style="font-family: Courier New,Courier,monospace;">header</span>,
736      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
737
738      <br>
739
7402 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
741
742      <br>
743
744A link to the webspage appendix_a.html is printed for further
745information about possible reasons of the error that appeared. (message)<br>
746
747      <br>
748
749Temperature gradient criterion for estimating the boundary layer height
750replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
751
752      <br>
753
754NetCDF unit attribute in timeseries output in case of statistic regions
755added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
756
757      <br>
758
759Maximum number of tails is calculated from maximum number of particles
760and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
761(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
762
763      <br>
764
765Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
766is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
767      <span style="font-family: Courier New,Courier,monospace;">header</span>,
768      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
769      <br>
770
771      <br>
772
773First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
774defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
775
776      <br>
777
778Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
779moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
780to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
781(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
782
783      <br>
784
785      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
786moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
787to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
788(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
789      <span style="font-family: Courier New,Courier,monospace;">header</span>,
790      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
791      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
792      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
793      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
794      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
795      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
796      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
797
798      <br>
799
800Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
801changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
802
803      <br>
804
805Adjustments for runs on lcxt4 (necessary due to a software update on
806CRAY) 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>
807      <td style="vertical-align: top; width: 189px;">advec_particles,
808advec_s_bc,
809buoyancy, calc_spectra, check_for_restart, check_open,
810check_parameters, close_file, coriolis, cpu_log, data_output_2d,
811data_output_3d, data_output_dvrp, data_output_profiles,
812data_output_ptseries, data_output_spectra, data_output_tseries,
813eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
814init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
815message, mrun, netcdf, package_parin, parin, plant_canopy_model,
816poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
817surface_coupler, temperton_fft, timestep,
818user_actions,user_check_parameters, user_data_output_dvrp,
819user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
820user_parin, user_read_restart_data, user_spectra, write_var_list </td>
821    </tr>
822    <tr>
823      <td style="vertical-align: top; width: 27px;"><br>
824      </td>
825      <td style="vertical-align: top; width: 38px;"><br>
826      </td>
827      <td style="vertical-align: top; width: 42px;"><br>
828      </td>
829      <td style="vertical-align: top; width: 40px;"><br>
830      </td>
831      <td style="vertical-align: top; width: 27px;">B<br>
832      </td>
833      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
834pressure profile in case of ocean runs is now calculated in 5 iteration
835steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
836
837      <br>
838
839Bugfix: wrong sign in buoyancy production of ocean part in case of not
840using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
841(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
842
843      <br>
844
845Bugfix: output of averaged 2d/3d quantities requires that an avaraging
846interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
847
848      <br>
849
850Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
851(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
852
853      <br>
854
855Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
856(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
857
858      <br>
859
860Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
861if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
862is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
863and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
864calls. This implies a possible performance loss; an alternative
865strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
866
867      <br>
868
869Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
870
871      <br>
872
873Bugfix: 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>
874
875      <br>
876
877Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
878=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
879for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
880      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
881
882      <br>
883
884Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
885becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
886
887      <br>
888
889Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
890
891      <br>
892
893Bugfix: error in check, if particles moved further than one subdomain
894length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
895
896      <br>
897
898Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
899is only written to file if its third index is &gt; 0, arrays for tails
900are allocated with a minimum size of 10 tails if there is no tail
901initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
902      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
903
904      <br>
905
906Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
907
908      <br>
909
910Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
911changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
912NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
913
914      <br>
915
916Bugfix: output of particle time series only if particle advection is
917switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
918
919      <br>
920
921Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
922= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
923(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
924
925      <br>
926
927Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
928z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
929
930      <br>
931
932Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
933
934      <br>
935
936If the inversion height calculated by the prerun is zero,
937inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
938
939      <br>
940
941Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
942
943      <br>
944
945Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
946removed from the restart file, because otherwise, no change from a
947fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
948      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
949
950      <br>
951
952Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
953in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
954      <td style="vertical-align: top; width: 189px;">advec_particles,
955check_parameters, cpu_log, data_output_2d, data_output_3d, header,
956init_3d_model, init_particles, init_ocean, modules, netcdf,
957prandtl_fluxes, production_e, read_var_list, time_integration,
958user_last_actions, write_var_list<br>
959
960      </td>
961    </tr>
962    <tr>
963      <td style="vertical-align: top; width: 27px;">02/02/09<br>
964      </td>
965      <td style="vertical-align: top; width: 38px;">SR<br>
966      </td>
967      <td style="vertical-align: top; width: 42px;">228<br>
968      </td>
969      <td style="vertical-align: top; width: 40px;">3.6<br>
970      </td>
971      <td style="vertical-align: top; width: 27px;">N<br>
972      </td>
973      <td style="vertical-align: top; width: 497px;">This
974release contains further additions, changes, and bugfixes for the
975SGI-ICE system, as well as important changes like the splitting of the
976user-interface into single files, a complete revision of the
977pre-compiling mechanism allowing to use different make-depositories
978simultaneously, and a revision of the reading-mechanism from restart
979files, which has no more restrictions in case that the previous and
980current run have different domain/subdomain sizes. A new handling of
981all kind of output messages is introduced with this release and will be
982applied to all existing messages within the next releases.<br>
983
984      <br>
985
986      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
987
988      <br>
989
990Restart runs on SGI-ICE are working. (mrun)<br>
991
9922d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
993
994      <br>
995
996Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
997case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
998"<span style="font-style: italic;">-K parallel</span>" for coupling.
999Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
1000      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
1001for lcxt4.<br>
1002
1003      <br>
1004
1005DVRP arguments changed to single precision, mode pathlines added.<br>
1006
1007      <br>
1008
1009User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
1010
1011      <br>
1012
1013User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
1014      <td style="vertical-align: top; width: 189px;">check_for_restart,
1015check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
1016modules, package_parin, palm, surface_coupler, timestep<br>
1017
1018      <br>
1019
1020Makefile,&nbsp;mbuild, mrun, subjob<br>
1021
1022      <br>
1023
1024      <span style="font-weight: bold;">new:</span><br>
1025
1026init_coupling, user_additional_routines, user_check_parameters</td>
1027    </tr>
1028    <tr>
1029      <td style="vertical-align: top; width: 27px;"><br>
1030      </td>
1031      <td style="vertical-align: top; width: 38px;"><br>
1032      </td>
1033      <td style="vertical-align: top; width: 42px;"><br>
1034      </td>
1035      <td style="vertical-align: top; width: 40px;"><br>
1036      </td>
1037      <td style="vertical-align: top; width: 27px;">C<br>
1038      </td>
1039      <td style="vertical-align: top; width: 497px;">User interface has been
1040split into single files.<br>
1041
1042      <br>
1043
1044Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
1045changed to INTEGER(8) in order to avoid "out of range" problems, which
1046result in measured negative time intervals. (cpu_log, local_tremain,
1047local_tremain_ini)<br>
1048
1049      <br>
1050
1051Reading mechanism from restart files
1052completely revised. The subdomain/total domain size is now allowed to
1053vary arbitrarily between the current and previous run. (read_var_list,
1054read_3d_binary, user_read_restart_data)<br>
1055
1056      <br>
1057
1058Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
1059completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
1060One depository per block (given in the config-file) is created. Always
1061all files from the source directory are copied to the respective
1062depository. No additional file checks are done any more (mrun version
10632.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1064"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
1065(mbuild, mrun)<br>
1066
1067      <br>
1068
1069Output messages (including required stop of execution) can now be
1070handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
1071All output messages will be replaced by this routine step by step
1072within the next revisions.<br>
1073
1074      <br>
1075
1076Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
1077explicitly set for better reading, although this has been already done
1078in boundary_conds. (advec_s_bc)<br>
1079
1080      <br>
1081
1082Origin of the xy-coordinate system shifted from the center of the first
1083grid 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
1084south-left corner of this cell. (netcdf) Topography definition
1085according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
1086(init_grid, modules, user_header, user_init_grid, user_parin)</td>
1087      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1088check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1089local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1090user_read_restart_data<br>
1091
1092      <br>
1093
1094Makefile, mbuild, mrun<br>
1095
1096      <br>
1097
1098      <span style="font-weight: bold;">removed:</span><br>
1099
1100user_interface<br>
1101
1102      <br>
1103
1104      <span style="font-weight: bold;">new:</span><br>
1105
1106message,
1107user_3d_data_averaging, user_actions, user_advec_particles,
1108user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1109user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1110user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1111user_init_grid, user_init_particles, user_init_plant_canopy,
1112user_last_actions, user_parin, user_parin, user_particle_attributes,
1113user_read_restart_data, user_spectra, user_statistics</td>
1114    </tr>
1115    <tr>
1116      <td style="vertical-align: top; width: 27px;"><br>
1117      </td>
1118      <td style="vertical-align: top; width: 38px;"><br>
1119      </td>
1120      <td style="vertical-align: top; width: 42px;"><br>
1121      </td>
1122      <td style="vertical-align: top; width: 40px;"><br>
1123      </td>
1124      <td style="vertical-align: top; width: 27px;">B<br>
1125      </td>
1126      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1127reallocated in case that multigrid is used. (calc_spectra)<br>
1128
1129      <br>
1130
1131Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1132inflow_turbulence,&nbsp;timestep)<br>
1133
1134      <br>
1135
1136Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1137      </span>adjusted to the required output size (1 gridpoint less,
1138along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1139in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1140compiler. (combine_plot_fields)<br>
1141
1142      <br>
1143
1144Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1145case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1146(header)<br>
1147
1148      <br>
1149
1150Inconsistency
1151removed: as the thermal stratification is not taken into account for
1152the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1153      <span style="font-family: Courier New,Courier,monospace;">km</span>
1154must 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>.
1155(production_e)<br>
1156
1157      <br>
1158
1159Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1160case of oceans runs. (sort_particles)<br>
1161
1162      <br>
1163
1164Bugfix: no output of particle concentration and radius unless particles
1165have been started. (data_output_2d)<br>
1166
1167      <br>
1168
1169Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1170from restart files ignored if total numbers of grid points do not
1171match. (read_3d_binary)<br>
1172
1173      <br>
1174
1175Bugfix: abort in case that absolute temperature is below zero.
1176(init_cloud_physics)</td>
1177      <td style="vertical-align: top; width: 189px;">advec_particles,
1178calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1179header, inflow_turbulence, init_cloud_physics, production_e,
1180read_3d_binary, timestep<br>
1181
1182      <br>
1183
1184combine_plot_fields</td>
1185    </tr>
1186  </tbody>
1187</table>
1188<b><blink></blink></b><br>&nbsp;
1189<br>&nbsp;
1190<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1191to change the source
1192code and how to document modifications<br>
1193</h2>Currently
1194(Sep 23rd, 2009), only selected users are allowed to commit changes to
1195the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1196<br>
1197<ol>
1198  <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>".
1199Additionally, document all changes in a local file (e.g.
1200~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1201have been changed. Classify changes in three cases, new (N), changed
1202(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>
1203    <br>
1204  </li>
1205  <li>Test the changed version, unless it works sufficiently.<br>
1206    <br>
1207  </li>
1208 
1209  <li>Commit the changes to the repository<br>
1210    <br>
1211    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1212    </span><br>
1213where "<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>
1214    <br>
1215Alternatively, in case that you have made quite a lot of changes, you
1216can also give the contents of your file CURRENT_MODIFICATIONS as the
1217log message:<br>
1218    <br>
1219    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1220    <br>
1221  </li>
1222
1223  <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>
1224    <br>
1225  </li>
1226  <li>Move the change comments in the file headers from "Current
1227revisions:" to "Former revisions:". Set the current svn id in front of
1228that.<br>
1229    <br>
1230    <span style="font-weight: bold;">Example:</span><br>
1231    <br>
1232    <span style="font-weight: bold;">before move:</span><br>
1233    <br>
1234    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1235    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1236    <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;">
1237    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1238    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1239    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1240    <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;">
1241    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1242    <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;">
1243    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1244    <br>
1245    <span style="font-weight: bold;">after move:</span><br>
1246    <br>
1247    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1248
1249    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1250
1251    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1252
1253    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1254
1255    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1256
1257    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1258
1259    <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>
1260!</span><br style="font-family: Courier New,Courier,monospace;">
1261    <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>
1262! </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;">
1263
1264    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1265
1266    <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;">
1267
1268    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1269    <br>
1270    <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">§</span>"
1271in this example should read "$", but "$" cannot be used here, because
1272otherwise svn would replace these entries after every change to this
1273technical documentation.</span><br>
1274 </span><br>
1275  </li>
1276  <li>Commit the changes in the technical documentation and the file headers:<br>
1277    <br>
1278    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1279    <br>
1280 <br>
1281  </li>
1282</ol>
1283
1284<h2>
1285<a name="Kapitel3.0"></a>3.0&nbsp; Description
1286of selected parts of the
1287model source code</h2>
1288<b></b>
1289<p>This section gives links to existing descriptions about special
1290parts of the PALM code, e.g. special numerical methods that are used
1291(including mathematical background). Documents are stored in single
1292files with different formats. Some are in German (sorry for the
1293inconvenience).
1294<br>&nbsp;
1295</p><ul> <li> <a name="UPS"></a>upstream-spline
1296advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1297, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1298physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1299)</li> 
1300  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1301  </li>
1302  <li>Runge-Kutta
1303time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1304, only in German)</li>
1305
1306</ul><br>
1307&nbsp;
1308<br>&nbsp;
1309<br>&nbsp;
1310<br>&nbsp;
1311<br>&nbsp;
1312<br>&nbsp;
1313<br>&nbsp;
1314<br>&nbsp;
1315</body></html>
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