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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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16<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;
17</font>a
18<b>pa</b>rallelized
19<b>L</b>ES <b>m</b>odel
20<br><hr width="100%">
21<br><font size="+2">technical/numerical documentation</font>
22<br>&nbsp;
23<br>&nbsp;
24<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
25</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
26</span></td> </tr>
27<tr nosave=""> <td nosave=""><b>Last
28change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $</b></td> </tr>
29</tbody>
30</table><hr width="100%">
31<p><font size="+2">Table of contents</font>
32<br>&nbsp;
33<br>&nbsp;
34</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
35History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
36How to change the source
37code and how to document modifications<br>
38 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
39Description of selected model numerics<br>
40&nbsp;</p>
41</ul><b></b><br>
42
43<h2><a name="Kapitel1.0"></a>1.0&nbsp;
44History of changes</h2>
45The 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>
46<br>
47Entries in the fifth column specify the type of the change:
48change&nbsp;
49of existing code (C), new code (N) or bugfix (B). More detailed
50information
51about the changes may sometimes be found in the header comment lines of the
52respective
53routines.
54<br>&nbsp;
55<br>
56<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
57  <tbody>
58    <tr>
59      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
60      </td>
61      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
62      </td>
63      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
64      </td>
65      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
66      </td>
67      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
68      </td>
69      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
70      </td>
71      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
72      </td>
73    </tr>
74   
75   
76   
77   
78   
79   
80   
81   
82   
83   
84    <tr>
85      <td style="vertical-align: top;">08/03/10<br>
86      </td>
87      <td style="vertical-align: top;">SR<br>
88      </td>
89      <td style="vertical-align: top;">506<br>
90      </td>
91      <td style="vertical-align: top;">3.7a<br>
92      </td>
93      <td style="vertical-align: top;">C<br>
94      </td>
95      <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>
96      </td>
97      <td style="vertical-align: top;">mrun<br>
98      </td>
99    </tr>
100<tr>
101      <td style="vertical-align: top;">03/03/10<br>
102      </td>
103      <td style="vertical-align: top;">SR<br>
104      </td>
105      <td style="vertical-align: top;">504<br>
106      </td>
107      <td style="vertical-align: top;">3.7a<br>
108      </td>
109      <td style="vertical-align: top;">C<br>
110      </td>
111      <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>
112      <br>
113Utility 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>
114      <br>
115Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
116      <br>
117Default configuration files updated.<br>
118      </td>
119      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
120      </td>
121    </tr>
122<tr>
123      <td style="vertical-align: top;">02/03/10<br>
124      </td>
125      <td style="vertical-align: top;">SR<br>
126      </td>
127      <td style="vertical-align: top;">496<br>
128      </td>
129      <td style="vertical-align: top;">3.7a<br>
130      </td>
131      <td style="vertical-align: top;">C<br>
132      </td>
133      <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>
134      </td>
135      <td style="vertical-align: top;">palm<br>
136      </td>
137    </tr>
138<tr>
139      <td style="vertical-align: top;">01/03/10<br>
140      </td>
141      <td style="vertical-align: top;">SR<br>
142      </td>
143      <td style="vertical-align: top;">494<br>
144      </td>
145      <td style="vertical-align: top;">3.7a<br>
146      </td>
147      <td style="vertical-align: top;">N<br>
148      </td>
149      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
150      <br>
151NetCDF4 allows for parallel I/O. Also, variables are not limited in
152size any more (i.e. arrays can be larger than 2GB). The new
153d3par-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>
154only affects 2d- and 3d-output, i.e. there is no parallel output for
155profiles, time series, spectra, and particles. Parallel output of
156particle data may realized in the future.<br>
157      <br>
158In 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>
159(merging data from single files - one per PE - into one file) is not
160neccessary. 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>
161      <br>
162Using NetCDF4 format requires a NetCDF4/HDF library. Respective
163settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
164HLRN 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>
165      <br>
166      <span style="font-weight: bold;">Attention:</span><br>
167So far, NetCDF parallel I/O has only been tested a little. Further
168performance optimizations may be required, especially in case of large
169data 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>
170      <br>
171      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
172      <br>
173Modules 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>
174      <br>
175      <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>
176      <br>
177This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
178      <br>
179      <span style="font-weight: bold;">WARNING:</span><br>
180      <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>
181      <br>
182</span>Compilation time can be reduced be using parallel make. The
183number of allowed simultaneous compiler calls (threads) is set in the
184configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
185      <br>
186      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
187      <br>
188allows a maximum of 4 routines to be compiled simultaneously (provided
189that the makefile does not show any dependencies between these
190routines).<span style="font-weight: bold;"><br>
191      </span>
192      </td>
193      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
194      <br>
195combine_plot_fields<br>
196      <br>
197mbuild, mrun, subjob<br>
198      </td>
199    </tr>
200    <tr>
201      <td style="vertical-align: top;"><br>
202      </td>
203      <td style="vertical-align: top;"><br>
204      </td>
205      <td style="vertical-align: top;"><br>
206      </td>
207      <td style="vertical-align: top;"><br>
208      </td>
209      <td style="vertical-align: top;">C<br>
210      </td>
211      <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>
212for choosing the NetCDF 64bit-offset format (this is the default from
213now on). The offset-format can not be set independently for the
2143d-output-data any more.<br>
215      <br>
216d3par-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>
217      </td>
218      <td style="vertical-align: top;">check_open, close_file,<br>
219data_output_mask, header, init_masks, modules, parin<br>
220      <br>
221      </td>
222    </tr>
223    <tr>
224      <td style="vertical-align: top;"><br>
225      </td>
226      <td style="vertical-align: top;"><br>
227      </td>
228      <td style="vertical-align: top;"><br>
229      </td>
230      <td style="vertical-align: top;"><br>
231      </td>
232      <td style="vertical-align: top;">B<br>
233      </td>
234      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
235      <br>
236Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
237      </td>
238      <td style="vertical-align: top;">user_statistics<br>
239      <br>
240trunk/UTIL/Makefile<br>
241      </td>
242    </tr>
243<tr>
244      <td style="vertical-align: top;">05/02/10<br>
245      </td>
246      <td style="vertical-align: top;">SR<br>
247      </td>
248      <td style="vertical-align: top;">485<br>
249      </td>
250      <td style="vertical-align: top;">3.7a<br>
251      </td>
252      <td style="vertical-align: top;">B<br>
253      </td>
254      <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>
255changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
256some global statistics (e.g. total kinetic energy) have wrong values.<br>
257      </td>
258      <td style="vertical-align: top;">init_3d_model, modules<br>
259      </td>
260    </tr>
261    <tr>
262      <td style="vertical-align: top;">05/02/10<br>
263      </td>
264      <td style="vertical-align: top;">SR<br>
265      </td>
266      <td style="vertical-align: top;">484<br>
267      </td>
268      <td style="vertical-align: top;">3.7a<br>
269      </td>
270      <td style="vertical-align: top;">B<br>
271      </td>
272      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
273      </td>
274      <td style="vertical-align: top;">many<br>
275      </td>
276    </tr>
277<tr>
278      <td style="vertical-align: top; width: 27px;">05/02/10<br>
279      </td>
280      <td style="vertical-align: top; width: 38px;">SR<br>
281      </td>
282      <td style="vertical-align: top; width: 42px;">483<br>
283      </td>
284      <td style="vertical-align: top; width: 40px;">3.7a<br>
285      </td>
286      <td style="vertical-align: top; width: 27px;">N<br>
287      </td>
288      <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>
289      <br>
290make 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>
291      <br>
292      <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;">
293wall_scalarflux</span> are the corresponding new inipar parameters.<br>
294(<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>
295      <br>
296Large scale vertical motion (subsidence/ascent) can be added as
297additional source to the prognostic equation for potential temperature.
298See 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>
299      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
300      <br>
301A 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>
302      <br>
303Masked data output has been implemented but it is not documented in the
304user manual so far. This feature can already use NetCDF4 file format.
305(check_open, check_parameters, close_file, modules, netcdf, parin,
306time_integration, user_parin, new: data_output_mask, init_masks,
307user_data_output_mask)<br>
308      </td>
309      <td style="vertical-align: top; width: 189px;">check_open, check
310parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
311netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
312      <br><span style="font-weight: bold;">
313new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
314<br>
315      </td>
316    </tr>
317    <tr>
318      <td style="vertical-align: top; width: 27px;"><br>
319      </td>
320      <td style="vertical-align: top; width: 38px;"><br>
321      </td>
322      <td style="vertical-align: top; width: 42px;"><br>
323      </td>
324      <td style="vertical-align: top; width: 40px;"><br>
325      </td>
326      <td style="vertical-align: top; width: 27px;">C<br>
327      </td>
328      <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>
329      <br><span style="font-family: Courier New,Courier,monospace;">
330var_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>
331      <br>
332Every cloud droplet has now an own weighting factor and can be deleted
333due to collisions. Condensation and collision of cloud droplets are
334adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
335      <br>
336Collision 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>
337      </td>
338      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
339      </td>
340    </tr>
341    <tr>
342      <td style="vertical-align: top; width: 27px;"><br>
343      </td>
344      <td style="vertical-align: top; width: 38px;"><br>
345      </td>
346      <td style="vertical-align: top; width: 42px;"><br>
347      </td>
348      <td style="vertical-align: top; width: 40px;"><br>
349      </td>
350      <td style="vertical-align: top; width: 27px;">B<br>
351      </td>
352      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
353      <br>
354Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
355      <br>
356Dimension 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>
357      <br>
358Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
359      <br>
360Bugfix: 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>
361      <br>
362Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
363      <br>
364Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
365      <br>
366Bugfix: 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>
367      <br>
368Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
369      <br>
370Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
371      <br>
372Bugfix 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>
373      </td>
374      <td style="vertical-align: top; width: 189px;">advec_particles,
375calc_precipitation, collision_efficiency, disturb_field, header,
376modules, poisfft_hybrid, subjob, sum_up_3d_data,
377time_integration<br>
378<br>
379      </td>
380    </tr>
381    <tr>
382      <td style="vertical-align: top; width: 27px;">23/09/09<br>
383      </td>
384      <td style="vertical-align: top; width: 38px;">SR<br>
385      </td>
386      <td style="vertical-align: top; width: 42px;">392<br>
387      </td>
388      <td style="vertical-align: top; width: 40px;">3.7<br>
389      </td>
390      <td style="vertical-align: top; width: 27px;">N<br>
391      </td>
392      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
393important changes:</span>
394atmosphere-ocean coupling has been improved and steering of
395dvr-software is more user-friendly now. Beside that, the release
396contains a lot of optimizations, changes, and bugfixes which have
397accumulated over the last months.<br>
398
399      <br>
400
401The atmosphere-ocean coupling allows to use independent precursor runs
402in order to account for different spin-up times. The time when coupling
403has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
404The 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
405order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
406output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
407      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
408      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
409      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
410      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
411      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
412      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
413      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
414      <span style="font-family: Courier New,Courier,monospace;">header</span>,
415      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
416      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
417      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
418      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
419      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
420      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
421      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
422      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
423
424      <br>
425
426Clipping of dvrp output implemented. Default colourtable for particles
427implemented, particle attributes (color, dvrp_size) can be set with new
428parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
429      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
430      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
431      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
432Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
433and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
434(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
435      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
436      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
437      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
438      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
439
440      <br>
441
442Polygon reduction for topography and ground plate isosurface. Reduction
443level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
444
445      <br>
446
447Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
448/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
449in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
450
451      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
452for speed optimization. This gives a significant speedup of more than
45310%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
454      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
455      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
456      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
457      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
458
459      <br>
460
461Scripts 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>
462
463      <br>
464
465Additional timestep criterion in case of simulations with plant canopy.
466(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
467
468      <br>
469
470Check 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
471exceed <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>
472
473      <br>
474
475External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
476      <span style="font-family: Courier New,Courier,monospace;">header</span>,
477      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
478      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
479      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
480      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
481      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
482      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
483
484      <br>
485
486New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
487(<span style="font-family: Courier New,Courier,monospace;">header</span>,
488      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
489      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
490      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
491      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
492      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
493      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
494      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
495      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
496
497      <br>
498
499Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
500(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
501      <span style="font-family: Courier New,Courier,monospace;">header</span>,
502      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
503      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
504      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
505      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
506      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
507
508      <br>
509
510Option 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>,
511      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
512
513      <br>
514
515xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
516      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
517      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
518      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
519      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
520      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
521      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
522      <td style="vertical-align: top; width: 189px;">average_3d_data,
523check_for_restart, check_parameters, data_output_2d, data_output_3d,
524data_output_dvrp, data_output_profiles, data_output_ptseries,
525data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
526diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
527header, mbuild, modules, mrun, package_parin, parin,
528prognostic_equations, read_3d_binary, read_var_list, subjob,
529sum_up_3d_data, surface_coupler, timestep, time_integration,
530user_check_parameters, user_data_output_2d, user_data_output_dvrp,
531user_header, user_init_grid, write_3d_binary, write_var_list<br>
532
533      <br>
534
535      <span style="font-weight: bold;">new:</span>
536set_particle_attributes, set_slicer_attributes_dvrp</td>
537    </tr>
538    <tr>
539      <td style="vertical-align: top; width: 27px;"><br>
540      </td>
541      <td style="vertical-align: top; width: 38px;"><br>
542      </td>
543      <td style="vertical-align: top; width: 42px;"><br>
544      </td>
545      <td style="vertical-align: top; width: 40px;"><br>
546      </td>
547      <td style="vertical-align: top; width: 27px;">C<br>
548      </td>
549      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
550message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
551      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
552      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
553      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
554      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
555      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
556      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
557      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
558      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
559      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
560      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
561      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
562      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
563      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
564      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
565      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
566      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
567      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
568      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
569      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
570      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
571      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
572      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
573      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
574      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
575      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
576      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
577      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
578      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
579      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
580      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
581      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
582      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
583      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
584      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
585      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
586      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
587      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
588      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
589      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
590
591      <br>
592
593Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
594      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
595      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
596      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
597      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
598      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
599      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
600      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
601      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
602
603      <br>
604
605__lcmuk changed to __lc to avoid problems with Intel compiler on
606sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
607
608      <br>
609
610For extended NetCDF files, the updated title attribute includes an
611update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
612
613      <br>
614
615In case of restart runs without extension, initial profiles are not
616written to NetCDF-file anymore. So far, time axis always started at
617t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
618      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
619      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
620      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
621
622      <br>
623
624      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
625'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
626can now <br>
627
628be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
629(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
630      <span style="font-family: Courier New,Courier,monospace;">header</span>,
631      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
632
633      <br>
634
6352 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
636
637      <br>
638
639A link to the webspage appendix_a.html is printed for further
640information about possible reasons of the error that appeared. (message)<br>
641
642      <br>
643
644Temperature gradient criterion for estimating the boundary layer height
645replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
646
647      <br>
648
649NetCDF unit attribute in timeseries output in case of statistic regions
650added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
651
652      <br>
653
654Maximum number of tails is calculated from maximum number of particles
655and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
656(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
657
658      <br>
659
660Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
661is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
662      <span style="font-family: Courier New,Courier,monospace;">header</span>,
663      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
664      <br>
665
666      <br>
667
668First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
669defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
670
671      <br>
672
673Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
674moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
675to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
676(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
677
678      <br>
679
680      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
681moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
682to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
683(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
684      <span style="font-family: Courier New,Courier,monospace;">header</span>,
685      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
686      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
687      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
688      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
689      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
690      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
691      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
692
693      <br>
694
695Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
696changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
697
698      <br>
699
700Adjustments for runs on lcxt4 (necessary due to a software update on
701CRAY) 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>
702      <td style="vertical-align: top; width: 189px;">advec_particles,
703advec_s_bc,
704buoyancy, calc_spectra, check_for_restart, check_open,
705check_parameters, close_file, coriolis, cpu_log, data_output_2d,
706data_output_3d, data_output_dvrp, data_output_profiles,
707data_output_ptseries, data_output_spectra, data_output_tseries,
708eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
709init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
710message, mrun, netcdf, package_parin, parin, plant_canopy_model,
711poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
712surface_coupler, temperton_fft, timestep,
713user_actions,user_check_parameters, user_data_output_dvrp,
714user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
715user_parin, user_read_restart_data, user_spectra, write_var_list </td>
716    </tr>
717    <tr>
718      <td style="vertical-align: top; width: 27px;"><br>
719      </td>
720      <td style="vertical-align: top; width: 38px;"><br>
721      </td>
722      <td style="vertical-align: top; width: 42px;"><br>
723      </td>
724      <td style="vertical-align: top; width: 40px;"><br>
725      </td>
726      <td style="vertical-align: top; width: 27px;">B<br>
727      </td>
728      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
729pressure profile in case of ocean runs is now calculated in 5 iteration
730steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
731
732      <br>
733
734Bugfix: wrong sign in buoyancy production of ocean part in case of not
735using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
736(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
737
738      <br>
739
740Bugfix: output of averaged 2d/3d quantities requires that an avaraging
741interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
742
743      <br>
744
745Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
746(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
747
748      <br>
749
750Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
751(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
752
753      <br>
754
755Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
756if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
757is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
758and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
759calls. This implies a possible performance loss; an alternative
760strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
761
762      <br>
763
764Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
765
766      <br>
767
768Bugfix: 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>
769
770      <br>
771
772Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
773=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
774for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
775      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
776
777      <br>
778
779Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
780becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
781
782      <br>
783
784Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
785
786      <br>
787
788Bugfix: error in check, if particles moved further than one subdomain
789length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
790
791      <br>
792
793Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
794is only written to file if its third index is &gt; 0, arrays for tails
795are allocated with a minimum size of 10 tails if there is no tail
796initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
797      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
798
799      <br>
800
801Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
802
803      <br>
804
805Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
806changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
807NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
808
809      <br>
810
811Bugfix: output of particle time series only if particle advection is
812switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
813
814      <br>
815
816Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
817= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
818(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
819
820      <br>
821
822Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
823z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
824
825      <br>
826
827Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
828
829      <br>
830
831If the inversion height calculated by the prerun is zero,
832inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
833
834      <br>
835
836Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
837
838      <br>
839
840Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
841removed from the restart file, because otherwise, no change from a
842fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
843      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
844
845      <br>
846
847Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
848in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
849      <td style="vertical-align: top; width: 189px;">advec_particles,
850check_parameters, cpu_log, data_output_2d, data_output_3d, header,
851init_3d_model, init_particles, init_ocean, modules, netcdf,
852prandtl_fluxes, production_e, read_var_list, time_integration,
853user_last_actions, write_var_list<br>
854
855      </td>
856    </tr>
857    <tr>
858      <td style="vertical-align: top; width: 27px;">02/02/09<br>
859      </td>
860      <td style="vertical-align: top; width: 38px;">SR<br>
861      </td>
862      <td style="vertical-align: top; width: 42px;">228<br>
863      </td>
864      <td style="vertical-align: top; width: 40px;">3.6<br>
865      </td>
866      <td style="vertical-align: top; width: 27px;">N<br>
867      </td>
868      <td style="vertical-align: top; width: 497px;">This
869release contains further additions, changes, and bugfixes for the
870SGI-ICE system, as well as important changes like the splitting of the
871user-interface into single files, a complete revision of the
872pre-compiling mechanism allowing to use different make-depositories
873simultaneously, and a revision of the reading-mechanism from restart
874files, which has no more restrictions in case that the previous and
875current run have different domain/subdomain sizes. A new handling of
876all kind of output messages is introduced with this release and will be
877applied to all existing messages within the next releases.<br>
878
879      <br>
880
881      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
882
883      <br>
884
885Restart runs on SGI-ICE are working. (mrun)<br>
886
8872d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
888
889      <br>
890
891Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
892case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
893"<span style="font-style: italic;">-K parallel</span>" for coupling.
894Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
895      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
896for lcxt4.<br>
897
898      <br>
899
900DVRP arguments changed to single precision, mode pathlines added.<br>
901
902      <br>
903
904User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
905
906      <br>
907
908User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
909      <td style="vertical-align: top; width: 189px;">check_for_restart,
910check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
911modules, package_parin, palm, surface_coupler, timestep<br>
912
913      <br>
914
915Makefile,&nbsp;mbuild, mrun, subjob<br>
916
917      <br>
918
919      <span style="font-weight: bold;">new:</span><br>
920
921init_coupling, user_additional_routines, user_check_parameters</td>
922    </tr>
923    <tr>
924      <td style="vertical-align: top; width: 27px;"><br>
925      </td>
926      <td style="vertical-align: top; width: 38px;"><br>
927      </td>
928      <td style="vertical-align: top; width: 42px;"><br>
929      </td>
930      <td style="vertical-align: top; width: 40px;"><br>
931      </td>
932      <td style="vertical-align: top; width: 27px;">C<br>
933      </td>
934      <td style="vertical-align: top; width: 497px;">User interface has been
935split into single files.<br>
936
937      <br>
938
939Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
940changed to INTEGER(8) in order to avoid "out of range" problems, which
941result in measured negative time intervals. (cpu_log, local_tremain,
942local_tremain_ini)<br>
943
944      <br>
945
946Reading mechanism from restart files
947completely revised. The subdomain/total domain size is now allowed to
948vary arbitrarily between the current and previous run. (read_var_list,
949read_3d_binary, user_read_restart_data)<br>
950
951      <br>
952
953Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
954completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
955One depository per block (given in the config-file) is created. Always
956all files from the source directory are copied to the respective
957depository. No additional file checks are done any more (mrun version
9582.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
959"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
960(mbuild, mrun)<br>
961
962      <br>
963
964Output messages (including required stop of execution) can now be
965handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
966All output messages will be replaced by this routine step by step
967within the next revisions.<br>
968
969      <br>
970
971Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
972explicitly set for better reading, although this has been already done
973in boundary_conds. (advec_s_bc)<br>
974
975      <br>
976
977Origin of the xy-coordinate system shifted from the center of the first
978grid 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
979south-left corner of this cell. (netcdf) Topography definition
980according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
981(init_grid, modules, user_header, user_init_grid, user_parin)</td>
982      <td style="vertical-align: top; width: 189px;">advec_s_bc,
983check_parameters, cpu_log, init_grid, local_stop, local_tremain,
984local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
985user_read_restart_data<br>
986
987      <br>
988
989Makefile, mbuild, mrun<br>
990
991      <br>
992
993      <span style="font-weight: bold;">removed:</span><br>
994
995user_interface<br>
996
997      <br>
998
999      <span style="font-weight: bold;">new:</span><br>
1000
1001message,
1002user_3d_data_averaging, user_actions, user_advec_particles,
1003user_check_data_output, user_check_data_output_pr, user_data_output_2d,
1004user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
1005user_dvrp_coltab, user_header, user_init_3d_model, user_init,
1006user_init_grid, user_init_particles, user_init_plant_canopy,
1007user_last_actions, user_parin, user_parin, user_particle_attributes,
1008user_read_restart_data, user_spectra, user_statistics</td>
1009    </tr>
1010    <tr>
1011      <td style="vertical-align: top; width: 27px;"><br>
1012      </td>
1013      <td style="vertical-align: top; width: 38px;"><br>
1014      </td>
1015      <td style="vertical-align: top; width: 42px;"><br>
1016      </td>
1017      <td style="vertical-align: top; width: 40px;"><br>
1018      </td>
1019      <td style="vertical-align: top; width: 27px;">B<br>
1020      </td>
1021      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1022reallocated in case that multigrid is used. (calc_spectra)<br>
1023
1024      <br>
1025
1026Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1027inflow_turbulence,&nbsp;timestep)<br>
1028
1029      <br>
1030
1031Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1032      </span>adjusted to the required output size (1 gridpoint less,
1033along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1034in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1035compiler. (combine_plot_fields)<br>
1036
1037      <br>
1038
1039Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1040case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1041(header)<br>
1042
1043      <br>
1044
1045Inconsistency
1046removed: as the thermal stratification is not taken into account for
1047the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1048      <span style="font-family: Courier New,Courier,monospace;">km</span>
1049must 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>.
1050(production_e)<br>
1051
1052      <br>
1053
1054Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1055case of oceans runs. (sort_particles)<br>
1056
1057      <br>
1058
1059Bugfix: no output of particle concentration and radius unless particles
1060have been started. (data_output_2d)<br>
1061
1062      <br>
1063
1064Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1065from restart files ignored if total numbers of grid points do not
1066match. (read_3d_binary)<br>
1067
1068      <br>
1069
1070Bugfix: abort in case that absolute temperature is below zero.
1071(init_cloud_physics)</td>
1072      <td style="vertical-align: top; width: 189px;">advec_particles,
1073calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1074header, inflow_turbulence, init_cloud_physics, production_e,
1075read_3d_binary, timestep<br>
1076
1077      <br>
1078
1079combine_plot_fields</td>
1080    </tr>
1081  </tbody>
1082</table>
1083<b><blink></blink></b><br>&nbsp;
1084<br>&nbsp;
1085<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1086to change the source
1087code and how to document modifications<br>
1088</h2>Currently
1089(Sep 23rd, 2009), only selected users are allowed to commit changes to
1090the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1091<br>
1092<ol>
1093  <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>".
1094Additionally, document all changes in a local file (e.g.
1095~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1096have been changed. Classify changes in three cases, new (N), changed
1097(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>
1098    <br>
1099  </li>
1100  <li>Test the changed version, unless it works sufficiently.<br>
1101    <br>
1102  </li>
1103 
1104  <li>Commit the changes to the repository<br>
1105    <br>
1106    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1107    </span><br>
1108where "<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>
1109    <br>
1110Alternatively, in case that you have made quite a lot of changes, you
1111can also give the contents of your file CURRENT_MODIFICATIONS as the
1112log message:<br>
1113    <br>
1114    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1115    <br>
1116  </li>
1117
1118  <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>
1119    <br>
1120  </li>
1121  <li>Move the change comments in the file headers from "Current
1122revisions:" to "Former revisions:". Set the current svn id in front of
1123that.<br>
1124    <br>
1125    <span style="font-weight: bold;">Example:</span><br>
1126    <br>
1127    <span style="font-weight: bold;">before move:</span><br>
1128    <br>
1129    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1130    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1131    <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;">
1132    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1133    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1134    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1135    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1136    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1137    <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;">
1138    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1139    <br>
1140    <span style="font-weight: bold;">after move:</span><br>
1141    <br>
1142    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1143
1144    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1145
1146    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1147
1148    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1149
1150    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1151
1152    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1153
1154    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $<br>
1155!</span><br style="font-family: Courier New,Courier,monospace;">
1156    <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>
1157! </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;">
1158
1159    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1160
1161    <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;">
1162
1163    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1164 </span><br>
1165  </li>
1166  <li>Commit the changes in the technical documentation and the file headers:<br>
1167    <br>
1168    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1169    <br>
1170 <br>
1171  </li>
1172</ol>
1173
1174<h2>
1175<a name="Kapitel3.0"></a>3.0&nbsp; Description
1176of selected parts of the
1177model source code</h2>
1178<b></b>
1179<p>This section gives links to existing descriptions about special
1180parts of the PALM code, e.g. special numerical methods that are used
1181(including mathematical background). Documents are stored in single
1182files with different formats. Some are in German (sorry for the
1183inconvenience).
1184<br>&nbsp;
1185</p><ul> <li> <a name="UPS"></a>upstream-spline
1186advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1187, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1188physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1189)</li> 
1190  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1191  </li>
1192  <li>Runge-Kutta
1193time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1194, only in German)</li>
1195
1196</ul><br>
1197&nbsp;
1198<br>&nbsp;
1199<br>&nbsp;
1200<br>&nbsp;
1201<br>&nbsp;
1202<br>&nbsp;
1203<br>&nbsp;
1204<br>&nbsp;
1205</body></html>
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