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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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20<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;
21</font>a
22<b>pa</b>rallelized
23<b>L</b>ES <b>m</b>odel
24<br><hr width="100%">
25<br><font size="+2">technical/numerical documentation</font>
26<br>&nbsp;
27<br>&nbsp;
28<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
29</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
30</span></td> </tr>
31<tr nosave=""> <td nosave=""><b>Last
32change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 516 2010-03-18 02:53:00Z heinze $</b></td> </tr>
33</tbody>
34</table><hr width="100%">
35<p><font size="+2">Table of contents</font>
36<br>&nbsp;
37<br>&nbsp;
38</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
39History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
40How to change the source
41code and how to document modifications<br>
42 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
43Description of selected model numerics<br>
44&nbsp;</p>
45</ul><b></b><br>
46
47<h2><a name="Kapitel1.0"></a>1.0&nbsp;
48History of changes</h2>
49The 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>
50<br>
51Entries in the fifth column specify the type of the change:
52change&nbsp;
53of existing code (C), new code (N) or bugfix (B). More detailed
54information
55about the changes may sometimes be found in the header comment lines of the
56respective
57routines.
58<br>&nbsp;
59<br>
60<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
61  <tbody>
62    <tr>
63      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
64      </td>
65      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
66      </td>
67      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
68      </td>
69      <td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
70      </td>
71      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
72      </td>
73      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
74      </td>
75      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
76      </td>
77    </tr>
78   
79   
80   
81   
82   
83   
84   
85   
86   
87   
88    <tr>
89      <td style="vertical-align: top;">18/03/10<br>
90      </td>
91      <td style="vertical-align: top;">SR<br>
92      </td>
93      <td style="vertical-align: top;">516<br>
94      </td>
95      <td style="vertical-align: top;">3.7a<br>
96      </td>
97      <td style="vertical-align: top;">N<br>
98      </td>
99      <td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
100      </td>
101      <td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
102      </td>
103    </tr>
104    <tr>
105      <td style="vertical-align: top;"><br>
106      </td>
107      <td style="vertical-align: top;"><br>
108      </td>
109      <td style="vertical-align: top;"><br>
110      </td>
111      <td style="vertical-align: top;"><br>
112      </td>
113      <td style="vertical-align: top;">B<br>
114      </td>
115      <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>
116      </td>
117      <td style="vertical-align: top;">buoyancy<br>
118      </td>
119    </tr>
120<tr>
121      <td style="vertical-align: top;">16/03/10<br>
122      </td>
123      <td style="vertical-align: top;">RH<br>
124      </td>
125      <td style="vertical-align: top;">513<br>
126      </td>
127      <td style="vertical-align: top;">3.7a<br>
128      </td>
129      <td style="vertical-align: top;">N<br>
130      </td>
131      <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>
132      </td>
133      <td style="vertical-align: top;">palmplot .ncl.config.default cross_sections.ncl profiles.ncl<br>
134      </td>
135    </tr>
136<tr>
137      <td style="vertical-align: top;">12/03/10<br>
138      </td>
139      <td style="vertical-align: top;">SR<br>
140      </td>
141      <td style="vertical-align: top;">509<br>
142      </td>
143      <td style="vertical-align: top;">3.7a<br>
144      </td>
145      <td style="vertical-align: top;">E<br>
146      </td>
147      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
148      </td>
149      <td style="vertical-align: top;">mbuild<br>
150      </td>
151    </tr>
152<tr>
153      <td style="vertical-align: top;">08/03/10<br>
154      </td>
155      <td style="vertical-align: top;">SR<br>
156      </td>
157      <td style="vertical-align: top;">506<br>
158      </td>
159      <td style="vertical-align: top;">3.7a<br>
160      </td>
161      <td style="vertical-align: top;">C<br>
162      </td>
163      <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>
164      </td>
165      <td style="vertical-align: top;">mrun<br>
166      </td>
167    </tr>
168<tr>
169      <td style="vertical-align: top;">03/03/10<br>
170      </td>
171      <td style="vertical-align: top;">SR<br>
172      </td>
173      <td style="vertical-align: top;">504<br>
174      </td>
175      <td style="vertical-align: top;">3.7a<br>
176      </td>
177      <td style="vertical-align: top;">C<br>
178      </td>
179      <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>
180      <br>
181Utility 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>
182      <br>
183Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
184      <br>
185Default configuration files updated.<br>
186      </td>
187      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
188      </td>
189    </tr>
190<tr>
191      <td style="vertical-align: top;">02/03/10<br>
192      </td>
193      <td style="vertical-align: top;">SR<br>
194      </td>
195      <td style="vertical-align: top;">496<br>
196      </td>
197      <td style="vertical-align: top;">3.7a<br>
198      </td>
199      <td style="vertical-align: top;">C<br>
200      </td>
201      <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>
202      </td>
203      <td style="vertical-align: top;">palm<br>
204      </td>
205    </tr>
206<tr>
207      <td style="vertical-align: top;">01/03/10<br>
208      </td>
209      <td style="vertical-align: top;">SR<br>
210      </td>
211      <td style="vertical-align: top;">494<br>
212      </td>
213      <td style="vertical-align: top;">3.7a<br>
214      </td>
215      <td style="vertical-align: top;">N<br>
216      </td>
217      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
218      <br>
219NetCDF4 allows for parallel I/O. Also, variables are not limited in
220size any more (i.e. arrays can be larger than 2GB). The new
221d3par-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>
222only affects 2d- and 3d-output, i.e. there is no parallel output for
223profiles, time series, spectra, and particles. Parallel output of
224particle data may realized in the future.<br>
225      <br>
226In 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>
227(merging data from single files - one per PE - into one file) is not
228neccessary. 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>
229      <br>
230Using NetCDF4 format requires a NetCDF4/HDF library. Respective
231settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
232HLRN 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>
233      <br>
234      <span style="font-weight: bold;">Attention:</span><br>
235So far, NetCDF parallel I/O has only been tested a little. Further
236performance optimizations may be required, especially in case of large
237data 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>
238      <br>
239      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
240      <br>
241Modules 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>
242      <br>
243      <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>
244      <br>
245This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
246      <br>
247      <span style="font-weight: bold;">WARNING:</span><br>
248      <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>
249      <br>
250</span>Compilation time can be reduced be using parallel make. The
251number of allowed simultaneous compiler calls (threads) is set in the
252configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
253      <br>
254      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
255      <br>
256allows a maximum of 4 routines to be compiled simultaneously (provided
257that the makefile does not show any dependencies between these
258routines).<span style="font-weight: bold;"><br>
259      </span>
260      </td>
261      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
262      <br>
263combine_plot_fields<br>
264      <br>
265mbuild, mrun, subjob<br>
266      </td>
267    </tr>
268    <tr>
269      <td style="vertical-align: top;"><br>
270      </td>
271      <td style="vertical-align: top;"><br>
272      </td>
273      <td style="vertical-align: top;"><br>
274      </td>
275      <td style="vertical-align: top;"><br>
276      </td>
277      <td style="vertical-align: top;">C<br>
278      </td>
279      <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>
280for choosing the NetCDF 64bit-offset format (this is the default from
281now on). The offset-format can not be set independently for the
2823d-output-data any more.<br>
283      <br>
284d3par-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>
285      </td>
286      <td style="vertical-align: top;">check_open, close_file,<br>
287data_output_mask, header, init_masks, modules, parin<br>
288      <br>
289      </td>
290    </tr>
291    <tr>
292      <td style="vertical-align: top;"><br>
293      </td>
294      <td style="vertical-align: top;"><br>
295      </td>
296      <td style="vertical-align: top;"><br>
297      </td>
298      <td style="vertical-align: top;"><br>
299      </td>
300      <td style="vertical-align: top;">B<br>
301      </td>
302      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
303      <br>
304Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
305      </td>
306      <td style="vertical-align: top;">user_statistics<br>
307      <br>
308trunk/UTIL/Makefile<br>
309      </td>
310    </tr>
311<tr>
312      <td style="vertical-align: top;">05/02/10<br>
313      </td>
314      <td style="vertical-align: top;">SR<br>
315      </td>
316      <td style="vertical-align: top;">485<br>
317      </td>
318      <td style="vertical-align: top;">3.7a<br>
319      </td>
320      <td style="vertical-align: top;">B<br>
321      </td>
322      <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>
323changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
324some global statistics (e.g. total kinetic energy) have wrong values.<br>
325      </td>
326      <td style="vertical-align: top;">init_3d_model, modules<br>
327      </td>
328    </tr>
329    <tr>
330      <td style="vertical-align: top;">05/02/10<br>
331      </td>
332      <td style="vertical-align: top;">SR<br>
333      </td>
334      <td style="vertical-align: top;">484<br>
335      </td>
336      <td style="vertical-align: top;">3.7a<br>
337      </td>
338      <td style="vertical-align: top;">B<br>
339      </td>
340      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
341      </td>
342      <td style="vertical-align: top;">many<br>
343      </td>
344    </tr>
345<tr>
346      <td style="vertical-align: top; width: 27px;">05/02/10<br>
347      </td>
348      <td style="vertical-align: top; width: 38px;">SR<br>
349      </td>
350      <td style="vertical-align: top; width: 42px;">483<br>
351      </td>
352      <td style="vertical-align: top; width: 40px;">3.7a<br>
353      </td>
354      <td style="vertical-align: top; width: 27px;">N<br>
355      </td>
356      <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>
357      <br>
358make 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>
359      <br>
360      <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;">
361wall_scalarflux</span> are the corresponding new inipar parameters.<br>
362(<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>
363      <br>
364Large scale vertical motion (subsidence/ascent) can be added as
365additional source to the prognostic equation for potential temperature.
366See 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>
367      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
368      <br>
369A 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>
370      <br>
371Masked data output has been implemented but it is not documented in the
372user manual so far. This feature can already use NetCDF4 file format.
373(check_open, check_parameters, close_file, modules, netcdf, parin,
374time_integration, user_parin, new: data_output_mask, init_masks,
375user_data_output_mask)<br>
376      </td>
377      <td style="vertical-align: top; width: 189px;">check_open, check
378parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
379netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
380      <br><span style="font-weight: bold;">
381new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
382<br>
383      </td>
384    </tr>
385    <tr>
386      <td style="vertical-align: top; width: 27px;"><br>
387      </td>
388      <td style="vertical-align: top; width: 38px;"><br>
389      </td>
390      <td style="vertical-align: top; width: 42px;"><br>
391      </td>
392      <td style="vertical-align: top; width: 40px;"><br>
393      </td>
394      <td style="vertical-align: top; width: 27px;">C<br>
395      </td>
396      <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>
397      <br><span style="font-family: Courier New,Courier,monospace;">
398var_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>
399      <br>
400Every cloud droplet has now an own weighting factor and can be deleted
401due to collisions. Condensation and collision of cloud droplets are
402adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
403      <br>
404Collision 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>
405      </td>
406      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
407      </td>
408    </tr>
409    <tr>
410      <td style="vertical-align: top; width: 27px;"><br>
411      </td>
412      <td style="vertical-align: top; width: 38px;"><br>
413      </td>
414      <td style="vertical-align: top; width: 42px;"><br>
415      </td>
416      <td style="vertical-align: top; width: 40px;"><br>
417      </td>
418      <td style="vertical-align: top; width: 27px;">B<br>
419      </td>
420      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
421      <br>
422Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
423      <br>
424Dimension 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>
425      <br>
426Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
427      <br>
428Bugfix: 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>
429      <br>
430Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
431      <br>
432Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
433      <br>
434Bugfix: 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>
435      <br>
436Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
437      <br>
438Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
439      <br>
440Bugfix 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>
441      </td>
442      <td style="vertical-align: top; width: 189px;">advec_particles,
443calc_precipitation, collision_efficiency, disturb_field, header,
444modules, poisfft_hybrid, subjob, sum_up_3d_data,
445time_integration<br>
446<br>
447      </td>
448    </tr>
449    <tr>
450      <td style="vertical-align: top; width: 27px;">23/09/09<br>
451      </td>
452      <td style="vertical-align: top; width: 38px;">SR<br>
453      </td>
454      <td style="vertical-align: top; width: 42px;">392<br>
455      </td>
456      <td style="vertical-align: top; width: 40px;">3.7<br>
457      </td>
458      <td style="vertical-align: top; width: 27px;">N<br>
459      </td>
460      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
461important changes:</span>
462atmosphere-ocean coupling has been improved and steering of
463dvr-software is more user-friendly now. Beside that, the release
464contains a lot of optimizations, changes, and bugfixes which have
465accumulated over the last months.<br>
466
467      <br>
468
469The atmosphere-ocean coupling allows to use independent precursor runs
470in order to account for different spin-up times. The time when coupling
471has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
472The 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
473order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
474output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
475      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
476      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
477      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
478      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
479      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
480      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
481      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
482      <span style="font-family: Courier New,Courier,monospace;">header</span>,
483      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
484      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
485      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
486      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
487      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
488      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
489      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
490      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
491
492      <br>
493
494Clipping of dvrp output implemented. Default colourtable for particles
495implemented, particle attributes (color, dvrp_size) can be set with new
496parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
497      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
498      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
499      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
500Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
501and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
502(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
503      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
504      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
505      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
506      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
507
508      <br>
509
510Polygon reduction for topography and ground plate isosurface. Reduction
511level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
512
513      <br>
514
515Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
516/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
517in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
518
519      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
520for speed optimization. This gives a significant speedup of more than
52110%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
522      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
523      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
524      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
525      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
526
527      <br>
528
529Scripts 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>
530
531      <br>
532
533Additional timestep criterion in case of simulations with plant canopy.
534(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
535
536      <br>
537
538Check 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
539exceed <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>
540
541      <br>
542
543External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
544      <span style="font-family: Courier New,Courier,monospace;">header</span>,
545      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
546      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
547      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
548      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
549      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
550      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
551
552      <br>
553
554New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
555(<span style="font-family: Courier New,Courier,monospace;">header</span>,
556      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
557      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
558      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
559      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
560      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
561      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
562      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
563      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
564
565      <br>
566
567Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
568(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
569      <span style="font-family: Courier New,Courier,monospace;">header</span>,
570      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
571      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
572      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
573      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
574      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
575
576      <br>
577
578Option 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>,
579      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
580
581      <br>
582
583xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
584      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
585      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
586      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
587      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
588      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
589      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
590      <td style="vertical-align: top; width: 189px;">average_3d_data,
591check_for_restart, check_parameters, data_output_2d, data_output_3d,
592data_output_dvrp, data_output_profiles, data_output_ptseries,
593data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
594diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
595header, mbuild, modules, mrun, package_parin, parin,
596prognostic_equations, read_3d_binary, read_var_list, subjob,
597sum_up_3d_data, surface_coupler, timestep, time_integration,
598user_check_parameters, user_data_output_2d, user_data_output_dvrp,
599user_header, user_init_grid, write_3d_binary, write_var_list<br>
600
601      <br>
602
603      <span style="font-weight: bold;">new:</span>
604set_particle_attributes, set_slicer_attributes_dvrp</td>
605    </tr>
606    <tr>
607      <td style="vertical-align: top; width: 27px;"><br>
608      </td>
609      <td style="vertical-align: top; width: 38px;"><br>
610      </td>
611      <td style="vertical-align: top; width: 42px;"><br>
612      </td>
613      <td style="vertical-align: top; width: 40px;"><br>
614      </td>
615      <td style="vertical-align: top; width: 27px;">C<br>
616      </td>
617      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
618message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
619      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
620      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
621      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
622      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
623      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
624      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
625      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
626      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
627      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
628      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
629      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
630      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
631      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
632      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
633      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
634      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
635      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
636      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
637      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
638      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
639      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
640      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
641      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
642      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
643      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
644      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
645      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
646      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
647      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
648      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
649      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
650      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
651      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
652      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
653      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
654      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
655      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
656      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
657      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
658
659      <br>
660
661Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
662      <span style="font-family: Courier New,Courier,monospace;">close_file</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_profiles</span>,
666      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
667      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
668      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
669      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
670
671      <br>
672
673__lcmuk changed to __lc to avoid problems with Intel compiler on
674sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
675
676      <br>
677
678For extended NetCDF files, the updated title attribute includes an
679update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
680
681      <br>
682
683In case of restart runs without extension, initial profiles are not
684written to NetCDF-file anymore. So far, time axis always started at
685t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
686      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
687      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
688      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
689
690      <br>
691
692      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
693'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
694can now <br>
695
696be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
697(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
698      <span style="font-family: Courier New,Courier,monospace;">header</span>,
699      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
700
701      <br>
702
7032 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
704
705      <br>
706
707A link to the webspage appendix_a.html is printed for further
708information about possible reasons of the error that appeared. (message)<br>
709
710      <br>
711
712Temperature gradient criterion for estimating the boundary layer height
713replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
714
715      <br>
716
717NetCDF unit attribute in timeseries output in case of statistic regions
718added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
719
720      <br>
721
722Maximum number of tails is calculated from maximum number of particles
723and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
724(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
725
726      <br>
727
728Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
729is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
730      <span style="font-family: Courier New,Courier,monospace;">header</span>,
731      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
732      <br>
733
734      <br>
735
736First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
737defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
738
739      <br>
740
741Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
742moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
743to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
744(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
745
746      <br>
747
748      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
749moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
750to <span style="font-family: Courier New,Courier,monospace;">inipar</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;">parin</span>,
754      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
755      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
756      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
757      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
758      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
759      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
760
761      <br>
762
763Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
764changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
765
766      <br>
767
768Adjustments for runs on lcxt4 (necessary due to a software update on
769CRAY) 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>
770      <td style="vertical-align: top; width: 189px;">advec_particles,
771advec_s_bc,
772buoyancy, calc_spectra, check_for_restart, check_open,
773check_parameters, close_file, coriolis, cpu_log, data_output_2d,
774data_output_3d, data_output_dvrp, data_output_profiles,
775data_output_ptseries, data_output_spectra, data_output_tseries,
776eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
777init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
778message, mrun, netcdf, package_parin, parin, plant_canopy_model,
779poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
780surface_coupler, temperton_fft, timestep,
781user_actions,user_check_parameters, user_data_output_dvrp,
782user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
783user_parin, user_read_restart_data, user_spectra, write_var_list </td>
784    </tr>
785    <tr>
786      <td style="vertical-align: top; width: 27px;"><br>
787      </td>
788      <td style="vertical-align: top; width: 38px;"><br>
789      </td>
790      <td style="vertical-align: top; width: 42px;"><br>
791      </td>
792      <td style="vertical-align: top; width: 40px;"><br>
793      </td>
794      <td style="vertical-align: top; width: 27px;">B<br>
795      </td>
796      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
797pressure profile in case of ocean runs is now calculated in 5 iteration
798steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
799
800      <br>
801
802Bugfix: wrong sign in buoyancy production of ocean part in case of not
803using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
804(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
805
806      <br>
807
808Bugfix: output of averaged 2d/3d quantities requires that an avaraging
809interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
810
811      <br>
812
813Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
814(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
815
816      <br>
817
818Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
819(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
820
821      <br>
822
823Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
824if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
825is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
826and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
827calls. This implies a possible performance loss; an alternative
828strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
829
830      <br>
831
832Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
833
834      <br>
835
836Bugfix: 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>
837
838      <br>
839
840Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
841=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
842for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
843      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
844
845      <br>
846
847Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
848becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
849
850      <br>
851
852Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
853
854      <br>
855
856Bugfix: error in check, if particles moved further than one subdomain
857length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
858
859      <br>
860
861Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
862is only written to file if its third index is &gt; 0, arrays for tails
863are allocated with a minimum size of 10 tails if there is no tail
864initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
865      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
866
867      <br>
868
869Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
870
871      <br>
872
873Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
874changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
875NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
876
877      <br>
878
879Bugfix: output of particle time series only if particle advection is
880switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
881
882      <br>
883
884Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
885= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
886(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
887
888      <br>
889
890Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
891z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
892
893      <br>
894
895Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
896
897      <br>
898
899If the inversion height calculated by the prerun is zero,
900inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
901
902      <br>
903
904Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
905
906      <br>
907
908Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
909removed from the restart file, because otherwise, no change from a
910fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
911      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
912
913      <br>
914
915Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
916in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
917      <td style="vertical-align: top; width: 189px;">advec_particles,
918check_parameters, cpu_log, data_output_2d, data_output_3d, header,
919init_3d_model, init_particles, init_ocean, modules, netcdf,
920prandtl_fluxes, production_e, read_var_list, time_integration,
921user_last_actions, write_var_list<br>
922
923      </td>
924    </tr>
925    <tr>
926      <td style="vertical-align: top; width: 27px;">02/02/09<br>
927      </td>
928      <td style="vertical-align: top; width: 38px;">SR<br>
929      </td>
930      <td style="vertical-align: top; width: 42px;">228<br>
931      </td>
932      <td style="vertical-align: top; width: 40px;">3.6<br>
933      </td>
934      <td style="vertical-align: top; width: 27px;">N<br>
935      </td>
936      <td style="vertical-align: top; width: 497px;">This
937release contains further additions, changes, and bugfixes for the
938SGI-ICE system, as well as important changes like the splitting of the
939user-interface into single files, a complete revision of the
940pre-compiling mechanism allowing to use different make-depositories
941simultaneously, and a revision of the reading-mechanism from restart
942files, which has no more restrictions in case that the previous and
943current run have different domain/subdomain sizes. A new handling of
944all kind of output messages is introduced with this release and will be
945applied to all existing messages within the next releases.<br>
946
947      <br>
948
949      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
950
951      <br>
952
953Restart runs on SGI-ICE are working. (mrun)<br>
954
9552d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
956
957      <br>
958
959Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
960case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
961"<span style="font-style: italic;">-K parallel</span>" for coupling.
962Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
963      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
964for lcxt4.<br>
965
966      <br>
967
968DVRP arguments changed to single precision, mode pathlines added.<br>
969
970      <br>
971
972User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
973
974      <br>
975
976User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
977      <td style="vertical-align: top; width: 189px;">check_for_restart,
978check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
979modules, package_parin, palm, surface_coupler, timestep<br>
980
981      <br>
982
983Makefile,&nbsp;mbuild, mrun, subjob<br>
984
985      <br>
986
987      <span style="font-weight: bold;">new:</span><br>
988
989init_coupling, user_additional_routines, user_check_parameters</td>
990    </tr>
991    <tr>
992      <td style="vertical-align: top; width: 27px;"><br>
993      </td>
994      <td style="vertical-align: top; width: 38px;"><br>
995      </td>
996      <td style="vertical-align: top; width: 42px;"><br>
997      </td>
998      <td style="vertical-align: top; width: 40px;"><br>
999      </td>
1000      <td style="vertical-align: top; width: 27px;">C<br>
1001      </td>
1002      <td style="vertical-align: top; width: 497px;">User interface has been
1003split into single files.<br>
1004
1005      <br>
1006
1007Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
1008changed to INTEGER(8) in order to avoid "out of range" problems, which
1009result in measured negative time intervals. (cpu_log, local_tremain,
1010local_tremain_ini)<br>
1011
1012      <br>
1013
1014Reading mechanism from restart files
1015completely revised. The subdomain/total domain size is now allowed to
1016vary arbitrarily between the current and previous run. (read_var_list,
1017read_3d_binary, user_read_restart_data)<br>
1018
1019      <br>
1020
1021Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
1022completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
1023One depository per block (given in the config-file) is created. Always
1024all files from the source directory are copied to the respective
1025depository. No additional file checks are done any more (mrun version
10262.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
1027"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
1028(mbuild, mrun)<br>
1029
1030      <br>
1031
1032Output messages (including required stop of execution) can now be
1033handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
1034All output messages will be replaced by this routine step by step
1035within the next revisions.<br>
1036
1037      <br>
1038
1039Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
1040explicitly set for better reading, although this has been already done
1041in boundary_conds. (advec_s_bc)<br>
1042
1043      <br>
1044
1045Origin of the xy-coordinate system shifted from the center of the first
1046grid 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
1047south-left corner of this cell. (netcdf) Topography definition
1048according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
1049(init_grid, modules, user_header, user_init_grid, user_parin)</td>
1050      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1051check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1052local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1053user_read_restart_data<br>
1054
1055      <br>
1056
1057Makefile, mbuild, mrun<br>
1058
1059      <br>
1060
1061      <span style="font-weight: bold;">removed:</span><br>
1062
1063user_interface<br>
1064
1065      <br>
1066
1067      <span style="font-weight: bold;">new:</span><br>
1068
1069message,
1070user_3d_data_averaging, user_actions, user_advec_particles,
1071user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1072user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1073user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1074user_init_grid, user_init_particles, user_init_plant_canopy,
1075user_last_actions, user_parin, user_parin, user_particle_attributes,
1076user_read_restart_data, user_spectra, user_statistics</td>
1077    </tr>
1078    <tr>
1079      <td style="vertical-align: top; width: 27px;"><br>
1080      </td>
1081      <td style="vertical-align: top; width: 38px;"><br>
1082      </td>
1083      <td style="vertical-align: top; width: 42px;"><br>
1084      </td>
1085      <td style="vertical-align: top; width: 40px;"><br>
1086      </td>
1087      <td style="vertical-align: top; width: 27px;">B<br>
1088      </td>
1089      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1090reallocated in case that multigrid is used. (calc_spectra)<br>
1091
1092      <br>
1093
1094Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1095inflow_turbulence,&nbsp;timestep)<br>
1096
1097      <br>
1098
1099Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1100      </span>adjusted to the required output size (1 gridpoint less,
1101along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1102in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1103compiler. (combine_plot_fields)<br>
1104
1105      <br>
1106
1107Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1108case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1109(header)<br>
1110
1111      <br>
1112
1113Inconsistency
1114removed: as the thermal stratification is not taken into account for
1115the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1116      <span style="font-family: Courier New,Courier,monospace;">km</span>
1117must 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>.
1118(production_e)<br>
1119
1120      <br>
1121
1122Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1123case of oceans runs. (sort_particles)<br>
1124
1125      <br>
1126
1127Bugfix: no output of particle concentration and radius unless particles
1128have been started. (data_output_2d)<br>
1129
1130      <br>
1131
1132Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1133from restart files ignored if total numbers of grid points do not
1134match. (read_3d_binary)<br>
1135
1136      <br>
1137
1138Bugfix: abort in case that absolute temperature is below zero.
1139(init_cloud_physics)</td>
1140      <td style="vertical-align: top; width: 189px;">advec_particles,
1141calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1142header, inflow_turbulence, init_cloud_physics, production_e,
1143read_3d_binary, timestep<br>
1144
1145      <br>
1146
1147combine_plot_fields</td>
1148    </tr>
1149  </tbody>
1150</table>
1151<b><blink></blink></b><br>&nbsp;
1152<br>&nbsp;
1153<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1154to change the source
1155code and how to document modifications<br>
1156</h2>Currently
1157(Sep 23rd, 2009), only selected users are allowed to commit changes to
1158the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1159<br>
1160<ol>
1161  <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>".
1162Additionally, document all changes in a local file (e.g.
1163~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1164have been changed. Classify changes in three cases, new (N), changed
1165(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>
1166    <br>
1167  </li>
1168  <li>Test the changed version, unless it works sufficiently.<br>
1169    <br>
1170  </li>
1171 
1172  <li>Commit the changes to the repository<br>
1173    <br>
1174    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1175    </span><br>
1176where "<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>
1177    <br>
1178Alternatively, in case that you have made quite a lot of changes, you
1179can also give the contents of your file CURRENT_MODIFICATIONS as the
1180log message:<br>
1181    <br>
1182    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1183    <br>
1184  </li>
1185
1186  <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>
1187    <br>
1188  </li>
1189  <li>Move the change comments in the file headers from "Current
1190revisions:" to "Former revisions:". Set the current svn id in front of
1191that.<br>
1192    <br>
1193    <span style="font-weight: bold;">Example:</span><br>
1194    <br>
1195    <span style="font-weight: bold;">before move:</span><br>
1196    <br>
1197    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1198    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1199    <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;">
1200    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1201    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1202    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1203    <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;">
1204    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1205    <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;">
1206    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1207    <br>
1208    <span style="font-weight: bold;">after move:</span><br>
1209    <br>
1210    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1211
1212    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1213
1214    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1215
1216    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1217
1218    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1219
1220    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1221
1222    <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>
1223!</span><br style="font-family: Courier New,Courier,monospace;">
1224    <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>
1225! </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;">
1226
1227    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1228
1229    <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;">
1230
1231    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1232    <br>
1233    <span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">§</span>"
1234in this example should read "$", but "$" cannot be used here, because
1235otherwise svn would replace these entries after every change to this
1236technical documentation.</span><br>
1237 </span><br>
1238  </li>
1239  <li>Commit the changes in the technical documentation and the file headers:<br>
1240    <br>
1241    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1242    <br>
1243 <br>
1244  </li>
1245</ol>
1246
1247<h2>
1248<a name="Kapitel3.0"></a>3.0&nbsp; Description
1249of selected parts of the
1250model source code</h2>
1251<b></b>
1252<p>This section gives links to existing descriptions about special
1253parts of the PALM code, e.g. special numerical methods that are used
1254(including mathematical background). Documents are stored in single
1255files with different formats. Some are in German (sorry for the
1256inconvenience).
1257<br>&nbsp;
1258</p><ul> <li> <a name="UPS"></a>upstream-spline
1259advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1260, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1261physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1262)</li> 
1263  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1264  </li>
1265  <li>Runge-Kutta
1266time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1267, only in German)</li>
1268
1269</ul><br>
1270&nbsp;
1271<br>&nbsp;
1272<br>&nbsp;
1273<br>&nbsp;
1274<br>&nbsp;
1275<br>&nbsp;
1276<br>&nbsp;
1277<br>&nbsp;
1278</body></html>
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