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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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17<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;
18</font>a
19<b>pa</b>rallelized
20<b>L</b>ES <b>m</b>odel
21<br><hr width="100%">
22<br><font size="+2">technical/numerical documentation</font>
23<br>&nbsp;
24<br>&nbsp;
25<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
26</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
27</span></td> </tr>
28<tr nosave=""> <td nosave=""><b>Last
29change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 509 2010-03-12 00:31:47Z raasch $</b></td> </tr>
30</tbody>
31</table><hr width="100%">
32<p><font size="+2">Table of contents</font>
33<br>&nbsp;
34<br>&nbsp;
35</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
36History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
37How to change the source
38code and how to document modifications<br>
39 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
40Description of selected model numerics<br>
41&nbsp;</p>
42</ul><b></b><br>
43
44<h2><a name="Kapitel1.0"></a>1.0&nbsp;
45History of changes</h2>
46The 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>
47<br>
48Entries in the fifth column specify the type of the change:
49change&nbsp;
50of existing code (C), new code (N) or bugfix (B). More detailed
51information
52about the changes may sometimes be found in the header comment lines of the
53respective
54routines.
55<br>&nbsp;
56<br>
57<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
58  <tbody>
59    <tr>
60      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
61      </td>
62      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
63      </td>
64      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
65      </td>
66      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
67      </td>
68      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
69      </td>
70      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
71      </td>
72      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
73      </td>
74    </tr>
75   
76   
77   
78   
79   
80   
81   
82   
83   
84   
85    <tr>
86      <td style="vertical-align: top;">12/03/09<br>
87      </td>
88      <td style="vertical-align: top;">SR<br>
89      </td>
90      <td style="vertical-align: top;">509<br>
91      </td>
92      <td style="vertical-align: top;">3.7a<br>
93      </td>
94      <td style="vertical-align: top;">E<br>
95      </td>
96      <td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
97      </td>
98      <td style="vertical-align: top;">mbuild<br>
99      </td>
100    </tr>
101<tr>
102      <td style="vertical-align: top;">08/03/10<br>
103      </td>
104      <td style="vertical-align: top;">SR<br>
105      </td>
106      <td style="vertical-align: top;">506<br>
107      </td>
108      <td style="vertical-align: top;">3.7a<br>
109      </td>
110      <td style="vertical-align: top;">C<br>
111      </td>
112      <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>
113      </td>
114      <td style="vertical-align: top;">mrun<br>
115      </td>
116    </tr>
117<tr>
118      <td style="vertical-align: top;">03/03/10<br>
119      </td>
120      <td style="vertical-align: top;">SR<br>
121      </td>
122      <td style="vertical-align: top;">504<br>
123      </td>
124      <td style="vertical-align: top;">3.7a<br>
125      </td>
126      <td style="vertical-align: top;">C<br>
127      </td>
128      <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>
129      <br>
130Utility 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>
131      <br>
132Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
133      <br>
134Default configuration files updated.<br>
135      </td>
136      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
137      </td>
138    </tr>
139<tr>
140      <td style="vertical-align: top;">02/03/10<br>
141      </td>
142      <td style="vertical-align: top;">SR<br>
143      </td>
144      <td style="vertical-align: top;">496<br>
145      </td>
146      <td style="vertical-align: top;">3.7a<br>
147      </td>
148      <td style="vertical-align: top;">C<br>
149      </td>
150      <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>
151      </td>
152      <td style="vertical-align: top;">palm<br>
153      </td>
154    </tr>
155<tr>
156      <td style="vertical-align: top;">01/03/10<br>
157      </td>
158      <td style="vertical-align: top;">SR<br>
159      </td>
160      <td style="vertical-align: top;">494<br>
161      </td>
162      <td style="vertical-align: top;">3.7a<br>
163      </td>
164      <td style="vertical-align: top;">N<br>
165      </td>
166      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
167      <br>
168NetCDF4 allows for parallel I/O. Also, variables are not limited in
169size any more (i.e. arrays can be larger than 2GB). The new
170d3par-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>
171only affects 2d- and 3d-output, i.e. there is no parallel output for
172profiles, time series, spectra, and particles. Parallel output of
173particle data may realized in the future.<br>
174      <br>
175In 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>
176(merging data from single files - one per PE - into one file) is not
177neccessary. 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>
178      <br>
179Using NetCDF4 format requires a NetCDF4/HDF library. Respective
180settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
181HLRN 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>
182      <br>
183      <span style="font-weight: bold;">Attention:</span><br>
184So far, NetCDF parallel I/O has only been tested a little. Further
185performance optimizations may be required, especially in case of large
186data 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>
187      <br>
188      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
189      <br>
190Modules 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>
191      <br>
192      <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>
193      <br>
194This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
195      <br>
196      <span style="font-weight: bold;">WARNING:</span><br>
197      <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>
198      <br>
199</span>Compilation time can be reduced be using parallel make. The
200number of allowed simultaneous compiler calls (threads) is set in the
201configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
202      <br>
203      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
204      <br>
205allows a maximum of 4 routines to be compiled simultaneously (provided
206that the makefile does not show any dependencies between these
207routines).<span style="font-weight: bold;"><br>
208      </span>
209      </td>
210      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
211      <br>
212combine_plot_fields<br>
213      <br>
214mbuild, mrun, subjob<br>
215      </td>
216    </tr>
217    <tr>
218      <td style="vertical-align: top;"><br>
219      </td>
220      <td style="vertical-align: top;"><br>
221      </td>
222      <td style="vertical-align: top;"><br>
223      </td>
224      <td style="vertical-align: top;"><br>
225      </td>
226      <td style="vertical-align: top;">C<br>
227      </td>
228      <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>
229for choosing the NetCDF 64bit-offset format (this is the default from
230now on). The offset-format can not be set independently for the
2313d-output-data any more.<br>
232      <br>
233d3par-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>
234      </td>
235      <td style="vertical-align: top;">check_open, close_file,<br>
236data_output_mask, header, init_masks, modules, parin<br>
237      <br>
238      </td>
239    </tr>
240    <tr>
241      <td style="vertical-align: top;"><br>
242      </td>
243      <td style="vertical-align: top;"><br>
244      </td>
245      <td style="vertical-align: top;"><br>
246      </td>
247      <td style="vertical-align: top;"><br>
248      </td>
249      <td style="vertical-align: top;">B<br>
250      </td>
251      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
252      <br>
253Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
254      </td>
255      <td style="vertical-align: top;">user_statistics<br>
256      <br>
257trunk/UTIL/Makefile<br>
258      </td>
259    </tr>
260<tr>
261      <td style="vertical-align: top;">05/02/10<br>
262      </td>
263      <td style="vertical-align: top;">SR<br>
264      </td>
265      <td style="vertical-align: top;">485<br>
266      </td>
267      <td style="vertical-align: top;">3.7a<br>
268      </td>
269      <td style="vertical-align: top;">B<br>
270      </td>
271      <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>
272changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
273some global statistics (e.g. total kinetic energy) have wrong values.<br>
274      </td>
275      <td style="vertical-align: top;">init_3d_model, modules<br>
276      </td>
277    </tr>
278    <tr>
279      <td style="vertical-align: top;">05/02/10<br>
280      </td>
281      <td style="vertical-align: top;">SR<br>
282      </td>
283      <td style="vertical-align: top;">484<br>
284      </td>
285      <td style="vertical-align: top;">3.7a<br>
286      </td>
287      <td style="vertical-align: top;">B<br>
288      </td>
289      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
290      </td>
291      <td style="vertical-align: top;">many<br>
292      </td>
293    </tr>
294<tr>
295      <td style="vertical-align: top; width: 27px;">05/02/10<br>
296      </td>
297      <td style="vertical-align: top; width: 38px;">SR<br>
298      </td>
299      <td style="vertical-align: top; width: 42px;">483<br>
300      </td>
301      <td style="vertical-align: top; width: 40px;">3.7a<br>
302      </td>
303      <td style="vertical-align: top; width: 27px;">N<br>
304      </td>
305      <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>
306      <br>
307make 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>
308      <br>
309      <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;">
310wall_scalarflux</span> are the corresponding new inipar parameters.<br>
311(<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>
312      <br>
313Large scale vertical motion (subsidence/ascent) can be added as
314additional source to the prognostic equation for potential temperature.
315See 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>
316      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
317      <br>
318A 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>
319      <br>
320Masked data output has been implemented but it is not documented in the
321user manual so far. This feature can already use NetCDF4 file format.
322(check_open, check_parameters, close_file, modules, netcdf, parin,
323time_integration, user_parin, new: data_output_mask, init_masks,
324user_data_output_mask)<br>
325      </td>
326      <td style="vertical-align: top; width: 189px;">check_open, check
327parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
328netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
329      <br><span style="font-weight: bold;">
330new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
331<br>
332      </td>
333    </tr>
334    <tr>
335      <td style="vertical-align: top; width: 27px;"><br>
336      </td>
337      <td style="vertical-align: top; width: 38px;"><br>
338      </td>
339      <td style="vertical-align: top; width: 42px;"><br>
340      </td>
341      <td style="vertical-align: top; width: 40px;"><br>
342      </td>
343      <td style="vertical-align: top; width: 27px;">C<br>
344      </td>
345      <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>
346      <br><span style="font-family: Courier New,Courier,monospace;">
347var_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>
348      <br>
349Every cloud droplet has now an own weighting factor and can be deleted
350due to collisions. Condensation and collision of cloud droplets are
351adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
352      <br>
353Collision 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>
354      </td>
355      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
356      </td>
357    </tr>
358    <tr>
359      <td style="vertical-align: top; width: 27px;"><br>
360      </td>
361      <td style="vertical-align: top; width: 38px;"><br>
362      </td>
363      <td style="vertical-align: top; width: 42px;"><br>
364      </td>
365      <td style="vertical-align: top; width: 40px;"><br>
366      </td>
367      <td style="vertical-align: top; width: 27px;">B<br>
368      </td>
369      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
370      <br>
371Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
372      <br>
373Dimension 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>
374      <br>
375Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
376      <br>
377Bugfix: 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>
378      <br>
379Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
380      <br>
381Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
382      <br>
383Bugfix: 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>
384      <br>
385Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
386      <br>
387Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
388      <br>
389Bugfix 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>
390      </td>
391      <td style="vertical-align: top; width: 189px;">advec_particles,
392calc_precipitation, collision_efficiency, disturb_field, header,
393modules, poisfft_hybrid, subjob, sum_up_3d_data,
394time_integration<br>
395<br>
396      </td>
397    </tr>
398    <tr>
399      <td style="vertical-align: top; width: 27px;">23/09/09<br>
400      </td>
401      <td style="vertical-align: top; width: 38px;">SR<br>
402      </td>
403      <td style="vertical-align: top; width: 42px;">392<br>
404      </td>
405      <td style="vertical-align: top; width: 40px;">3.7<br>
406      </td>
407      <td style="vertical-align: top; width: 27px;">N<br>
408      </td>
409      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
410important changes:</span>
411atmosphere-ocean coupling has been improved and steering of
412dvr-software is more user-friendly now. Beside that, the release
413contains a lot of optimizations, changes, and bugfixes which have
414accumulated over the last months.<br>
415
416      <br>
417
418The atmosphere-ocean coupling allows to use independent precursor runs
419in order to account for different spin-up times. The time when coupling
420has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
421The 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
422order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
423output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
424      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
425      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
426      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
427      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
428      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
429      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
430      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
431      <span style="font-family: Courier New,Courier,monospace;">header</span>,
432      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
433      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
434      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
435      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
436      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
437      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
438      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
439      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
440
441      <br>
442
443Clipping of dvrp output implemented. Default colourtable for particles
444implemented, particle attributes (color, dvrp_size) can be set with new
445parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
446      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
447      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
448      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
449Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
450and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
451(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
452      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
453      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
454      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
455      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
456
457      <br>
458
459Polygon reduction for topography and ground plate isosurface. Reduction
460level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
461
462      <br>
463
464Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
465/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
466in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
467
468      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
469for speed optimization. This gives a significant speedup of more than
47010%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
471      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
472      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
473      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
474      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
475
476      <br>
477
478Scripts 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>
479
480      <br>
481
482Additional timestep criterion in case of simulations with plant canopy.
483(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
484
485      <br>
486
487Check 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
488exceed <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>
489
490      <br>
491
492External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
493      <span style="font-family: Courier New,Courier,monospace;">header</span>,
494      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
495      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
496      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
497      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
498      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
499      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
500
501      <br>
502
503New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
504(<span style="font-family: Courier New,Courier,monospace;">header</span>,
505      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
506      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
507      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
508      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
509      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
510      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
511      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
512      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
513
514      <br>
515
516Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
517(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
518      <span style="font-family: Courier New,Courier,monospace;">header</span>,
519      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
520      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
521      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
522      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
523      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
524
525      <br>
526
527Option 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>,
528      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
529
530      <br>
531
532xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
533      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
534      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
535      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
536      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
537      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
538      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
539      <td style="vertical-align: top; width: 189px;">average_3d_data,
540check_for_restart, check_parameters, data_output_2d, data_output_3d,
541data_output_dvrp, data_output_profiles, data_output_ptseries,
542data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
543diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
544header, mbuild, modules, mrun, package_parin, parin,
545prognostic_equations, read_3d_binary, read_var_list, subjob,
546sum_up_3d_data, surface_coupler, timestep, time_integration,
547user_check_parameters, user_data_output_2d, user_data_output_dvrp,
548user_header, user_init_grid, write_3d_binary, write_var_list<br>
549
550      <br>
551
552      <span style="font-weight: bold;">new:</span>
553set_particle_attributes, set_slicer_attributes_dvrp</td>
554    </tr>
555    <tr>
556      <td style="vertical-align: top; width: 27px;"><br>
557      </td>
558      <td style="vertical-align: top; width: 38px;"><br>
559      </td>
560      <td style="vertical-align: top; width: 42px;"><br>
561      </td>
562      <td style="vertical-align: top; width: 40px;"><br>
563      </td>
564      <td style="vertical-align: top; width: 27px;">C<br>
565      </td>
566      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
567message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
568      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
569      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
570      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
571      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
572      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
573      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
574      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
575      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
576      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
577      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
578      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
579      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
580      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
581      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
582      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
583      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
584      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
585      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
586      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
587      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
588      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
589      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
590      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
591      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
592      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
593      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
594      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
595      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
596      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
597      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
598      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
599      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
600      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
601      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
602      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
603      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
604      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
605      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
606      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
607
608      <br>
609
610Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
611      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
612      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
613      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
614      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
615      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
616      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
617      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
618      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
619
620      <br>
621
622__lcmuk changed to __lc to avoid problems with Intel compiler on
623sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
624
625      <br>
626
627For extended NetCDF files, the updated title attribute includes an
628update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
629
630      <br>
631
632In case of restart runs without extension, initial profiles are not
633written to NetCDF-file anymore. So far, time axis always started at
634t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
635      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
636      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
637      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
638
639      <br>
640
641      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
642'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
643can now <br>
644
645be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
646(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
647      <span style="font-family: Courier New,Courier,monospace;">header</span>,
648      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
649
650      <br>
651
6522 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
653
654      <br>
655
656A link to the webspage appendix_a.html is printed for further
657information about possible reasons of the error that appeared. (message)<br>
658
659      <br>
660
661Temperature gradient criterion for estimating the boundary layer height
662replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
663
664      <br>
665
666NetCDF unit attribute in timeseries output in case of statistic regions
667added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
668
669      <br>
670
671Maximum number of tails is calculated from maximum number of particles
672and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
673(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
674
675      <br>
676
677Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
678is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
679      <span style="font-family: Courier New,Courier,monospace;">header</span>,
680      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
681      <br>
682
683      <br>
684
685First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
686defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
687
688      <br>
689
690Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
691moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
692to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
693(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
694
695      <br>
696
697      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
698moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
699to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
700(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
701      <span style="font-family: Courier New,Courier,monospace;">header</span>,
702      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
703      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
704      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
705      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
706      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
707      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
708      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
709
710      <br>
711
712Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
713changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
714
715      <br>
716
717Adjustments for runs on lcxt4 (necessary due to a software update on
718CRAY) 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>
719      <td style="vertical-align: top; width: 189px;">advec_particles,
720advec_s_bc,
721buoyancy, calc_spectra, check_for_restart, check_open,
722check_parameters, close_file, coriolis, cpu_log, data_output_2d,
723data_output_3d, data_output_dvrp, data_output_profiles,
724data_output_ptseries, data_output_spectra, data_output_tseries,
725eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
726init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
727message, mrun, netcdf, package_parin, parin, plant_canopy_model,
728poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
729surface_coupler, temperton_fft, timestep,
730user_actions,user_check_parameters, user_data_output_dvrp,
731user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
732user_parin, user_read_restart_data, user_spectra, write_var_list </td>
733    </tr>
734    <tr>
735      <td style="vertical-align: top; width: 27px;"><br>
736      </td>
737      <td style="vertical-align: top; width: 38px;"><br>
738      </td>
739      <td style="vertical-align: top; width: 42px;"><br>
740      </td>
741      <td style="vertical-align: top; width: 40px;"><br>
742      </td>
743      <td style="vertical-align: top; width: 27px;">B<br>
744      </td>
745      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
746pressure profile in case of ocean runs is now calculated in 5 iteration
747steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
748
749      <br>
750
751Bugfix: wrong sign in buoyancy production of ocean part in case of not
752using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
753(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
754
755      <br>
756
757Bugfix: output of averaged 2d/3d quantities requires that an avaraging
758interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
759
760      <br>
761
762Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
763(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
764
765      <br>
766
767Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
768(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
769
770      <br>
771
772Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
773if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
774is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
775and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
776calls. This implies a possible performance loss; an alternative
777strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
778
779      <br>
780
781Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
782
783      <br>
784
785Bugfix: 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>
786
787      <br>
788
789Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
790=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
791for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
792      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
793
794      <br>
795
796Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
797becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
798
799      <br>
800
801Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
802
803      <br>
804
805Bugfix: error in check, if particles moved further than one subdomain
806length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
807
808      <br>
809
810Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
811is only written to file if its third index is &gt; 0, arrays for tails
812are allocated with a minimum size of 10 tails if there is no tail
813initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
814      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
815
816      <br>
817
818Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
819
820      <br>
821
822Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
823changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
824NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
825
826      <br>
827
828Bugfix: output of particle time series only if particle advection is
829switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
830
831      <br>
832
833Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
834= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
835(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
836
837      <br>
838
839Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
840z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
841
842      <br>
843
844Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
845
846      <br>
847
848If the inversion height calculated by the prerun is zero,
849inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
850
851      <br>
852
853Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
854
855      <br>
856
857Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
858removed from the restart file, because otherwise, no change from a
859fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
860      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
861
862      <br>
863
864Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
865in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
866      <td style="vertical-align: top; width: 189px;">advec_particles,
867check_parameters, cpu_log, data_output_2d, data_output_3d, header,
868init_3d_model, init_particles, init_ocean, modules, netcdf,
869prandtl_fluxes, production_e, read_var_list, time_integration,
870user_last_actions, write_var_list<br>
871
872      </td>
873    </tr>
874    <tr>
875      <td style="vertical-align: top; width: 27px;">02/02/09<br>
876      </td>
877      <td style="vertical-align: top; width: 38px;">SR<br>
878      </td>
879      <td style="vertical-align: top; width: 42px;">228<br>
880      </td>
881      <td style="vertical-align: top; width: 40px;">3.6<br>
882      </td>
883      <td style="vertical-align: top; width: 27px;">N<br>
884      </td>
885      <td style="vertical-align: top; width: 497px;">This
886release contains further additions, changes, and bugfixes for the
887SGI-ICE system, as well as important changes like the splitting of the
888user-interface into single files, a complete revision of the
889pre-compiling mechanism allowing to use different make-depositories
890simultaneously, and a revision of the reading-mechanism from restart
891files, which has no more restrictions in case that the previous and
892current run have different domain/subdomain sizes. A new handling of
893all kind of output messages is introduced with this release and will be
894applied to all existing messages within the next releases.<br>
895
896      <br>
897
898      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
899
900      <br>
901
902Restart runs on SGI-ICE are working. (mrun)<br>
903
9042d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
905
906      <br>
907
908Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
909case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
910"<span style="font-style: italic;">-K parallel</span>" for coupling.
911Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
912      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
913for lcxt4.<br>
914
915      <br>
916
917DVRP arguments changed to single precision, mode pathlines added.<br>
918
919      <br>
920
921User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
922
923      <br>
924
925User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
926      <td style="vertical-align: top; width: 189px;">check_for_restart,
927check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
928modules, package_parin, palm, surface_coupler, timestep<br>
929
930      <br>
931
932Makefile,&nbsp;mbuild, mrun, subjob<br>
933
934      <br>
935
936      <span style="font-weight: bold;">new:</span><br>
937
938init_coupling, user_additional_routines, user_check_parameters</td>
939    </tr>
940    <tr>
941      <td style="vertical-align: top; width: 27px;"><br>
942      </td>
943      <td style="vertical-align: top; width: 38px;"><br>
944      </td>
945      <td style="vertical-align: top; width: 42px;"><br>
946      </td>
947      <td style="vertical-align: top; width: 40px;"><br>
948      </td>
949      <td style="vertical-align: top; width: 27px;">C<br>
950      </td>
951      <td style="vertical-align: top; width: 497px;">User interface has been
952split into single files.<br>
953
954      <br>
955
956Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
957changed to INTEGER(8) in order to avoid "out of range" problems, which
958result in measured negative time intervals. (cpu_log, local_tremain,
959local_tremain_ini)<br>
960
961      <br>
962
963Reading mechanism from restart files
964completely revised. The subdomain/total domain size is now allowed to
965vary arbitrarily between the current and previous run. (read_var_list,
966read_3d_binary, user_read_restart_data)<br>
967
968      <br>
969
970Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
971completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
972One depository per block (given in the config-file) is created. Always
973all files from the source directory are copied to the respective
974depository. No additional file checks are done any more (mrun version
9752.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
976"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
977(mbuild, mrun)<br>
978
979      <br>
980
981Output messages (including required stop of execution) can now be
982handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
983All output messages will be replaced by this routine step by step
984within the next revisions.<br>
985
986      <br>
987
988Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
989explicitly set for better reading, although this has been already done
990in boundary_conds. (advec_s_bc)<br>
991
992      <br>
993
994Origin of the xy-coordinate system shifted from the center of the first
995grid 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
996south-left corner of this cell. (netcdf) Topography definition
997according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
998(init_grid, modules, user_header, user_init_grid, user_parin)</td>
999      <td style="vertical-align: top; width: 189px;">advec_s_bc,
1000check_parameters, cpu_log, init_grid, local_stop, local_tremain,
1001local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
1002user_read_restart_data<br>
1003
1004      <br>
1005
1006Makefile, mbuild, mrun<br>
1007
1008      <br>
1009
1010      <span style="font-weight: bold;">removed:</span><br>
1011
1012user_interface<br>
1013
1014      <br>
1015
1016      <span style="font-weight: bold;">new:</span><br>
1017
1018message,
1019user_3d_data_averaging, user_actions, user_advec_particles,
1020user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1021user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1022user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1023user_init_grid, user_init_particles, user_init_plant_canopy,
1024user_last_actions, user_parin, user_parin, user_particle_attributes,
1025user_read_restart_data, user_spectra, user_statistics</td>
1026    </tr>
1027    <tr>
1028      <td style="vertical-align: top; width: 27px;"><br>
1029      </td>
1030      <td style="vertical-align: top; width: 38px;"><br>
1031      </td>
1032      <td style="vertical-align: top; width: 42px;"><br>
1033      </td>
1034      <td style="vertical-align: top; width: 40px;"><br>
1035      </td>
1036      <td style="vertical-align: top; width: 27px;">B<br>
1037      </td>
1038      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1039reallocated in case that multigrid is used. (calc_spectra)<br>
1040
1041      <br>
1042
1043Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1044inflow_turbulence,&nbsp;timestep)<br>
1045
1046      <br>
1047
1048Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1049      </span>adjusted to the required output size (1 gridpoint less,
1050along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1051in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1052compiler. (combine_plot_fields)<br>
1053
1054      <br>
1055
1056Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1057case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1058(header)<br>
1059
1060      <br>
1061
1062Inconsistency
1063removed: as the thermal stratification is not taken into account for
1064the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1065      <span style="font-family: Courier New,Courier,monospace;">km</span>
1066must 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>.
1067(production_e)<br>
1068
1069      <br>
1070
1071Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1072case of oceans runs. (sort_particles)<br>
1073
1074      <br>
1075
1076Bugfix: no output of particle concentration and radius unless particles
1077have been started. (data_output_2d)<br>
1078
1079      <br>
1080
1081Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1082from restart files ignored if total numbers of grid points do not
1083match. (read_3d_binary)<br>
1084
1085      <br>
1086
1087Bugfix: abort in case that absolute temperature is below zero.
1088(init_cloud_physics)</td>
1089      <td style="vertical-align: top; width: 189px;">advec_particles,
1090calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1091header, inflow_turbulence, init_cloud_physics, production_e,
1092read_3d_binary, timestep<br>
1093
1094      <br>
1095
1096combine_plot_fields</td>
1097    </tr>
1098  </tbody>
1099</table>
1100<b><blink></blink></b><br>&nbsp;
1101<br>&nbsp;
1102<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1103to change the source
1104code and how to document modifications<br>
1105</h2>Currently
1106(Sep 23rd, 2009), only selected users are allowed to commit changes to
1107the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1108<br>
1109<ol>
1110  <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>".
1111Additionally, document all changes in a local file (e.g.
1112~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1113have been changed. Classify changes in three cases, new (N), changed
1114(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>
1115    <br>
1116  </li>
1117  <li>Test the changed version, unless it works sufficiently.<br>
1118    <br>
1119  </li>
1120 
1121  <li>Commit the changes to the repository<br>
1122    <br>
1123    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1124    </span><br>
1125where "<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>
1126    <br>
1127Alternatively, in case that you have made quite a lot of changes, you
1128can also give the contents of your file CURRENT_MODIFICATIONS as the
1129log message:<br>
1130    <br>
1131    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1132    <br>
1133  </li>
1134
1135  <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>
1136    <br>
1137  </li>
1138  <li>Move the change comments in the file headers from "Current
1139revisions:" to "Former revisions:". Set the current svn id in front of
1140that.<br>
1141    <br>
1142    <span style="font-weight: bold;">Example:</span><br>
1143    <br>
1144    <span style="font-weight: bold;">before move:</span><br>
1145    <br>
1146    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1147    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1148    <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;">
1149    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1150    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1151    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1152    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 509 2010-03-12 00:31:47Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1153    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1154    <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;">
1155    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1156    <br>
1157    <span style="font-weight: bold;">after move:</span><br>
1158    <br>
1159    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1160
1161    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1162
1163    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1164
1165    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1166
1167    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1168
1169    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1170
1171    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 509 2010-03-12 00:31:47Z raasch $<br>
1172!</span><br style="font-family: Courier New,Courier,monospace;">
1173    <span style="font-family: Courier New,Courier,monospace;">! </span><span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold; color: rgb(51, 51, 255);">377 2008-08-30 11:03:41Z raasch</span><br>
1174! </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;">
1175
1176    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1177
1178    <span style="font-family: Courier New,Courier,monospace;">! 359 2008-06-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
1179
1180    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1181 </span><br>
1182  </li>
1183  <li>Commit the changes in the technical documentation and the file headers:<br>
1184    <br>
1185    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1186    <br>
1187 <br>
1188  </li>
1189</ol>
1190
1191<h2>
1192<a name="Kapitel3.0"></a>3.0&nbsp; Description
1193of selected parts of the
1194model source code</h2>
1195<b></b>
1196<p>This section gives links to existing descriptions about special
1197parts of the PALM code, e.g. special numerical methods that are used
1198(including mathematical background). Documents are stored in single
1199files with different formats. Some are in German (sorry for the
1200inconvenience).
1201<br>&nbsp;
1202</p><ul> <li> <a name="UPS"></a>upstream-spline
1203advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1204, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1205physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1206)</li> 
1207  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1208  </li>
1209  <li>Runge-Kutta
1210time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1211, only in German)</li>
1212
1213</ul><br>
1214&nbsp;
1215<br>&nbsp;
1216<br>&nbsp;
1217<br>&nbsp;
1218<br>&nbsp;
1219<br>&nbsp;
1220<br>&nbsp;
1221<br>&nbsp;
1222</body></html>
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