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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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13<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;
14</font>a
15<b>pa</b>rallelized
16<b>L</b>ES <b>m</b>odel
17<br><hr width="100%">
18<br><font size="+2">technical/numerical documentation</font>
19<br>&nbsp;
20<br>&nbsp;
21<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
22</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
23</span></td> </tr>
24<tr nosave=""> <td nosave=""><b>Last
25change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 496 2010-03-02 00:41:44Z raasch $</b></td> </tr>
26</tbody>
27</table><hr width="100%">
28<p><font size="+2">Table of contents</font>
29<br>&nbsp;
30<br>&nbsp;
31</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
32History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
33How to change the source
34code and how to document modifications<br>
35 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
36Description of selected model numerics<br>
37&nbsp;</p>
38</ul><b></b><br>
39
40<h2><a name="Kapitel1.0"></a>1.0&nbsp;
41History of changes</h2>
42The 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>
43<br>
44Entries in the fifth column specify the type of the change:
45change&nbsp;
46of existing code (C), new code (N) or bugfix (B). More detailed
47information
48about the changes may sometimes be found in the header comment lines of the
49respective
50routines.
51<br>&nbsp;
52<br>
53<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
54  <tbody>
55    <tr>
56      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
57      </td>
58      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
59      </td>
60      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
61      </td>
62      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
63      </td>
64      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
65      </td>
66      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
67      </td>
68      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
69      </td>
70    </tr>
71   
72   
73   
74   
75   
76   
77   
78   
79   
80   
81    <tr>
82      <td style="vertical-align: top;">02/03/10<br>
83      </td>
84      <td style="vertical-align: top;">SR<br>
85      </td>
86      <td style="vertical-align: top;">496<br>
87      </td>
88      <td style="vertical-align: top;">3.7a<br>
89      </td>
90      <td style="vertical-align: top;">C<br>
91      </td>
92      <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>
93      </td>
94      <td style="vertical-align: top;">palm<br>
95      </td>
96    </tr>
97<tr>
98      <td style="vertical-align: top;">01/03/10<br>
99      </td>
100      <td style="vertical-align: top;">SR<br>
101      </td>
102      <td style="vertical-align: top;">494<br>
103      </td>
104      <td style="vertical-align: top;">3.7a<br>
105      </td>
106      <td style="vertical-align: top;">N<br>
107      </td>
108      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
109      <br>
110NetCDF4 allows for parallel I/O. Also, variables are not limited in
111size any more (i.e. arrays can be larger than 2GB). The new
112d3par-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>
113only affects 2d- and 3d-output, i.e. there is no parallel output for
114profiles, time series, spectra, and particles. Parallel output of
115particle data may realized in the future.<br>
116      <br>
117In 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>
118(merging data from single files - one per PE - into one file) is not
119neccessary. 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>
120      <br>
121Using NetCDF4 format requires a NetCDF4/HDF library. Respective
122settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
123HLRN 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>
124      <br>
125      <span style="font-weight: bold;">Attention:</span><br>
126So far, NetCDF parallel I/O has only been tested a little. Further
127performance optimizations may be required, especially in case of large
128data 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>
129      <br>
130      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
131      <br>
132Modules 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>
133      <br>
134      <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>
135      <br>
136This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
137      <br>
138      <span style="font-weight: bold;">WARNING:</span><br>
139      <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.</span><br>
140      </td>
141      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
142      <br>
143combine_plot_fields<br>
144      <br>
145mbuild, mrun, subjob<br>
146      </td>
147    </tr>
148    <tr>
149      <td style="vertical-align: top;"><br>
150      </td>
151      <td style="vertical-align: top;"><br>
152      </td>
153      <td style="vertical-align: top;"><br>
154      </td>
155      <td style="vertical-align: top;"><br>
156      </td>
157      <td style="vertical-align: top;">C<br>
158      </td>
159      <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>
160for choosing the NetCDF 64bit-offset format (this is the default from
161now on). The offset-format can not be set independently for the
1623d-output-data any more.<br>
163      <br>
164d3par-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>
165      </td>
166      <td style="vertical-align: top;">check_open, close_file,<br>
167data_output_mask, header, init_masks, modules, parin<br>
168      <br>
169      </td>
170    </tr>
171    <tr>
172      <td style="vertical-align: top;"><br>
173      </td>
174      <td style="vertical-align: top;"><br>
175      </td>
176      <td style="vertical-align: top;"><br>
177      </td>
178      <td style="vertical-align: top;"><br>
179      </td>
180      <td style="vertical-align: top;">B<br>
181      </td>
182      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
183      <br>
184Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
185      </td>
186      <td style="vertical-align: top;">user_statistics<br>
187      <br>
188trunk/UTIL/Makefile<br>
189      </td>
190    </tr>
191<tr>
192      <td style="vertical-align: top;">05/02/10<br>
193      </td>
194      <td style="vertical-align: top;">SR<br>
195      </td>
196      <td style="vertical-align: top;">485<br>
197      </td>
198      <td style="vertical-align: top;">3.7a<br>
199      </td>
200      <td style="vertical-align: top;">B<br>
201      </td>
202      <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>
203changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
204some global statistics (e.g. total kinetic energy) have wrong values.<br>
205      </td>
206      <td style="vertical-align: top;">init_3d_model, modules<br>
207      </td>
208    </tr>
209    <tr>
210      <td style="vertical-align: top;">05/02/10<br>
211      </td>
212      <td style="vertical-align: top;">SR<br>
213      </td>
214      <td style="vertical-align: top;">484<br>
215      </td>
216      <td style="vertical-align: top;">3.7a<br>
217      </td>
218      <td style="vertical-align: top;">B<br>
219      </td>
220      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
221      </td>
222      <td style="vertical-align: top;">many<br>
223      </td>
224    </tr>
225<tr>
226      <td style="vertical-align: top; width: 27px;">05/02/10<br>
227      </td>
228      <td style="vertical-align: top; width: 38px;">SR<br>
229      </td>
230      <td style="vertical-align: top; width: 42px;">483<br>
231      </td>
232      <td style="vertical-align: top; width: 40px;">3.7a<br>
233      </td>
234      <td style="vertical-align: top; width: 27px;">N<br>
235      </td>
236      <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>
237      <br>
238make 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>
239      <br>
240      <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;">
241wall_scalarflux</span> are the corresponding new inipar parameters.<br>
242(<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>
243      <br>
244Large scale vertical motion (subsidence/ascent) can be added as
245additional source to the prognostic equation for potential temperature.
246See 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>
247      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
248      <br>
249A 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>
250      <br>
251Masked data output has been implemented but it is not documented in the
252user manual so far. This feature can already use NetCDF4 file format.
253(check_open, check_parameters, close_file, modules, netcdf, parin,
254time_integration, user_parin, new: data_output_mask, init_masks,
255user_data_output_mask)<br>
256      </td>
257      <td style="vertical-align: top; width: 189px;">check_open, check
258parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
259netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
260      <br><span style="font-weight: bold;">
261new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
262<br>
263      </td>
264    </tr>
265    <tr>
266      <td style="vertical-align: top; width: 27px;"><br>
267      </td>
268      <td style="vertical-align: top; width: 38px;"><br>
269      </td>
270      <td style="vertical-align: top; width: 42px;"><br>
271      </td>
272      <td style="vertical-align: top; width: 40px;"><br>
273      </td>
274      <td style="vertical-align: top; width: 27px;">C<br>
275      </td>
276      <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>
277      <br><span style="font-family: Courier New,Courier,monospace;">
278var_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>
279      <br>
280Every cloud droplet has now an own weighting factor and can be deleted
281due to collisions. Condensation and collision of cloud droplets are
282adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
283      <br>
284Collision 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>
285      </td>
286      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
287      </td>
288    </tr>
289    <tr>
290      <td style="vertical-align: top; width: 27px;"><br>
291      </td>
292      <td style="vertical-align: top; width: 38px;"><br>
293      </td>
294      <td style="vertical-align: top; width: 42px;"><br>
295      </td>
296      <td style="vertical-align: top; width: 40px;"><br>
297      </td>
298      <td style="vertical-align: top; width: 27px;">B<br>
299      </td>
300      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
301      <br>
302Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
303      <br>
304Dimension 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>
305      <br>
306Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
307      <br>
308Bugfix: 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>
309      <br>
310Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
311      <br>
312Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
313      <br>
314Bugfix: 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>
315      <br>
316Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
317      <br>
318Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
319      <br>
320Bugfix 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>
321      </td>
322      <td style="vertical-align: top; width: 189px;">advec_particles,
323calc_precipitation, collision_efficiency, disturb_field, header,
324modules, poisfft_hybrid, subjob, sum_up_3d_data,
325time_integration<br>
326<br>
327      </td>
328    </tr>
329    <tr>
330      <td style="vertical-align: top; width: 27px;">23/09/09<br>
331      </td>
332      <td style="vertical-align: top; width: 38px;">SR<br>
333      </td>
334      <td style="vertical-align: top; width: 42px;">392<br>
335      </td>
336      <td style="vertical-align: top; width: 40px;">3.7<br>
337      </td>
338      <td style="vertical-align: top; width: 27px;">N<br>
339      </td>
340      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
341important changes:</span>
342atmosphere-ocean coupling has been improved and steering of
343dvr-software is more user-friendly now. Beside that, the release
344contains a lot of optimizations, changes, and bugfixes which have
345accumulated over the last months.<br>
346
347      <br>
348
349The atmosphere-ocean coupling allows to use independent precursor runs
350in order to account for different spin-up times. The time when coupling
351has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
352The 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
353order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
354output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
355      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
356      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
357      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
358      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
359      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
360      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
361      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
362      <span style="font-family: Courier New,Courier,monospace;">header</span>,
363      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
364      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
365      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
366      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
367      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
368      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
369      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
370      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
371
372      <br>
373
374Clipping of dvrp output implemented. Default colourtable for particles
375implemented, particle attributes (color, dvrp_size) can be set with new
376parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
377      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
378      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
379      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
380Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
381and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
382(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
383      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
384      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
385      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
386      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
387
388      <br>
389
390Polygon reduction for topography and ground plate isosurface. Reduction
391level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
392
393      <br>
394
395Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
396/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
397in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
398
399      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
400for speed optimization. This gives a significant speedup of more than
40110%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
402      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
403      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
404      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
405      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
406
407      <br>
408
409Scripts 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>
410
411      <br>
412
413Additional timestep criterion in case of simulations with plant canopy.
414(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
415
416      <br>
417
418Check 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
419exceed <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>
420
421      <br>
422
423External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
424      <span style="font-family: Courier New,Courier,monospace;">header</span>,
425      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
426      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
427      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
428      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
429      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
430      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
431
432      <br>
433
434New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
435(<span style="font-family: Courier New,Courier,monospace;">header</span>,
436      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
437      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
438      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
439      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
440      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
441      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
442      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
443      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
444
445      <br>
446
447Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
448(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
449      <span style="font-family: Courier New,Courier,monospace;">header</span>,
450      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
451      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
452      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
453      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
454      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
455
456      <br>
457
458Option 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>,
459      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
460
461      <br>
462
463xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
464      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
465      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
466      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
467      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
468      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
469      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
470      <td style="vertical-align: top; width: 189px;">average_3d_data,
471check_for_restart, check_parameters, data_output_2d, data_output_3d,
472data_output_dvrp, data_output_profiles, data_output_ptseries,
473data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
474diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
475header, mbuild, modules, mrun, package_parin, parin,
476prognostic_equations, read_3d_binary, read_var_list, subjob,
477sum_up_3d_data, surface_coupler, timestep, time_integration,
478user_check_parameters, user_data_output_2d, user_data_output_dvrp,
479user_header, user_init_grid, write_3d_binary, write_var_list<br>
480
481      <br>
482
483      <span style="font-weight: bold;">new:</span>
484set_particle_attributes, set_slicer_attributes_dvrp</td>
485    </tr>
486    <tr>
487      <td style="vertical-align: top; width: 27px;"><br>
488      </td>
489      <td style="vertical-align: top; width: 38px;"><br>
490      </td>
491      <td style="vertical-align: top; width: 42px;"><br>
492      </td>
493      <td style="vertical-align: top; width: 40px;"><br>
494      </td>
495      <td style="vertical-align: top; width: 27px;">C<br>
496      </td>
497      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
498message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
499      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
500      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
501      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
502      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
503      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
504      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
505      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
506      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
507      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
508      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
509      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
510      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
511      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
512      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
513      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
514      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
515      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
516      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
517      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
518      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
519      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
520      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
521      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
522      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
523      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
524      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
525      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
526      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
527      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
528      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
529      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
530      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
531      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
532      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
533      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
534      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
535      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
536      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
537      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
538
539      <br>
540
541Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
542      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
543      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
544      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
545      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
546      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
547      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
548      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
549      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
550
551      <br>
552
553__lcmuk changed to __lc to avoid problems with Intel compiler on
554sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
555
556      <br>
557
558For extended NetCDF files, the updated title attribute includes an
559update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
560
561      <br>
562
563In case of restart runs without extension, initial profiles are not
564written to NetCDF-file anymore. So far, time axis always started at
565t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
566      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
567      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
568      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
569
570      <br>
571
572      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
573'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
574can now <br>
575
576be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
577(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
578      <span style="font-family: Courier New,Courier,monospace;">header</span>,
579      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
580
581      <br>
582
5832 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
584
585      <br>
586
587A link to the webspage appendix_a.html is printed for further
588information about possible reasons of the error that appeared. (message)<br>
589
590      <br>
591
592Temperature gradient criterion for estimating the boundary layer height
593replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
594
595      <br>
596
597NetCDF unit attribute in timeseries output in case of statistic regions
598added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
599
600      <br>
601
602Maximum number of tails is calculated from maximum number of particles
603and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
604(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
605
606      <br>
607
608Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
609is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
610      <span style="font-family: Courier New,Courier,monospace;">header</span>,
611      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
612      <br>
613
614      <br>
615
616First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
617defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
618
619      <br>
620
621Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
622moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
623to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
624(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
625
626      <br>
627
628      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
629moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
630to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
631(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
632      <span style="font-family: Courier New,Courier,monospace;">header</span>,
633      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
634      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
635      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
636      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
637      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
638      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
639      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
640
641      <br>
642
643Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
644changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
645
646      <br>
647
648Adjustments for runs on lcxt4 (necessary due to a software update on
649CRAY) 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>
650      <td style="vertical-align: top; width: 189px;">advec_particles,
651advec_s_bc,
652buoyancy, calc_spectra, check_for_restart, check_open,
653check_parameters, close_file, coriolis, cpu_log, data_output_2d,
654data_output_3d, data_output_dvrp, data_output_profiles,
655data_output_ptseries, data_output_spectra, data_output_tseries,
656eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
657init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
658message, mrun, netcdf, package_parin, parin, plant_canopy_model,
659poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
660surface_coupler, temperton_fft, timestep,
661user_actions,user_check_parameters, user_data_output_dvrp,
662user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
663user_parin, user_read_restart_data, user_spectra, write_var_list </td>
664    </tr>
665    <tr>
666      <td style="vertical-align: top; width: 27px;"><br>
667      </td>
668      <td style="vertical-align: top; width: 38px;"><br>
669      </td>
670      <td style="vertical-align: top; width: 42px;"><br>
671      </td>
672      <td style="vertical-align: top; width: 40px;"><br>
673      </td>
674      <td style="vertical-align: top; width: 27px;">B<br>
675      </td>
676      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
677pressure profile in case of ocean runs is now calculated in 5 iteration
678steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
679
680      <br>
681
682Bugfix: wrong sign in buoyancy production of ocean part in case of not
683using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
684(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
685
686      <br>
687
688Bugfix: output of averaged 2d/3d quantities requires that an avaraging
689interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
690
691      <br>
692
693Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
694(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
695
696      <br>
697
698Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
699(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
700
701      <br>
702
703Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
704if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
705is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
706and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
707calls. This implies a possible performance loss; an alternative
708strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
709
710      <br>
711
712Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
713
714      <br>
715
716Bugfix: 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>
717
718      <br>
719
720Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
721=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
722for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
723      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
724
725      <br>
726
727Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
728becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
729
730      <br>
731
732Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
733
734      <br>
735
736Bugfix: error in check, if particles moved further than one subdomain
737length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
738
739      <br>
740
741Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
742is only written to file if its third index is &gt; 0, arrays for tails
743are allocated with a minimum size of 10 tails if there is no tail
744initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
745      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
746
747      <br>
748
749Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
750
751      <br>
752
753Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
754changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
755NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
756
757      <br>
758
759Bugfix: output of particle time series only if particle advection is
760switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
761
762      <br>
763
764Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
765= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
766(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
767
768      <br>
769
770Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
771z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
772
773      <br>
774
775Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
776
777      <br>
778
779If the inversion height calculated by the prerun is zero,
780inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
781
782      <br>
783
784Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
785
786      <br>
787
788Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
789removed from the restart file, because otherwise, no change from a
790fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
791      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
792
793      <br>
794
795Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
796in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
797      <td style="vertical-align: top; width: 189px;">advec_particles,
798check_parameters, cpu_log, data_output_2d, data_output_3d, header,
799init_3d_model, init_particles, init_ocean, modules, netcdf,
800prandtl_fluxes, production_e, read_var_list, time_integration,
801user_last_actions, write_var_list<br>
802
803      </td>
804    </tr>
805    <tr>
806      <td style="vertical-align: top; width: 27px;">02/02/09<br>
807      </td>
808      <td style="vertical-align: top; width: 38px;">SR<br>
809      </td>
810      <td style="vertical-align: top; width: 42px;">228<br>
811      </td>
812      <td style="vertical-align: top; width: 40px;">3.6<br>
813      </td>
814      <td style="vertical-align: top; width: 27px;">N<br>
815      </td>
816      <td style="vertical-align: top; width: 497px;">This
817release contains further additions, changes, and bugfixes for the
818SGI-ICE system, as well as important changes like the splitting of the
819user-interface into single files, a complete revision of the
820pre-compiling mechanism allowing to use different make-depositories
821simultaneously, and a revision of the reading-mechanism from restart
822files, which has no more restrictions in case that the previous and
823current run have different domain/subdomain sizes. A new handling of
824all kind of output messages is introduced with this release and will be
825applied to all existing messages within the next releases.<br>
826
827      <br>
828
829      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
830
831      <br>
832
833Restart runs on SGI-ICE are working. (mrun)<br>
834
8352d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
836
837      <br>
838
839Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
840case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
841"<span style="font-style: italic;">-K parallel</span>" for coupling.
842Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
843      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
844for lcxt4.<br>
845
846      <br>
847
848DVRP arguments changed to single precision, mode pathlines added.<br>
849
850      <br>
851
852User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
853
854      <br>
855
856User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
857      <td style="vertical-align: top; width: 189px;">check_for_restart,
858check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
859modules, package_parin, palm, surface_coupler, timestep<br>
860
861      <br>
862
863Makefile,&nbsp;mbuild, mrun, subjob<br>
864
865      <br>
866
867      <span style="font-weight: bold;">new:</span><br>
868
869init_coupling, user_additional_routines, user_check_parameters</td>
870    </tr>
871    <tr>
872      <td style="vertical-align: top; width: 27px;"><br>
873      </td>
874      <td style="vertical-align: top; width: 38px;"><br>
875      </td>
876      <td style="vertical-align: top; width: 42px;"><br>
877      </td>
878      <td style="vertical-align: top; width: 40px;"><br>
879      </td>
880      <td style="vertical-align: top; width: 27px;">C<br>
881      </td>
882      <td style="vertical-align: top; width: 497px;">User interface has been
883split into single files.<br>
884
885      <br>
886
887Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
888changed to INTEGER(8) in order to avoid "out of range" problems, which
889result in measured negative time intervals. (cpu_log, local_tremain,
890local_tremain_ini)<br>
891
892      <br>
893
894Reading mechanism from restart files
895completely revised. The subdomain/total domain size is now allowed to
896vary arbitrarily between the current and previous run. (read_var_list,
897read_3d_binary, user_read_restart_data)<br>
898
899      <br>
900
901Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
902completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
903One depository per block (given in the config-file) is created. Always
904all files from the source directory are copied to the respective
905depository. No additional file checks are done any more (mrun version
9062.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
907"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
908(mbuild, mrun)<br>
909
910      <br>
911
912Output messages (including required stop of execution) can now be
913handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
914All output messages will be replaced by this routine step by step
915within the next revisions.<br>
916
917      <br>
918
919Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
920explicitly set for better reading, although this has been already done
921in boundary_conds. (advec_s_bc)<br>
922
923      <br>
924
925Origin of the xy-coordinate system shifted from the center of the first
926grid 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
927south-left corner of this cell. (netcdf) Topography definition
928according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
929(init_grid, modules, user_header, user_init_grid, user_parin)</td>
930      <td style="vertical-align: top; width: 189px;">advec_s_bc,
931check_parameters, cpu_log, init_grid, local_stop, local_tremain,
932local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
933user_read_restart_data<br>
934
935      <br>
936
937Makefile, mbuild, mrun<br>
938
939      <br>
940
941      <span style="font-weight: bold;">removed:</span><br>
942
943user_interface<br>
944
945      <br>
946
947      <span style="font-weight: bold;">new:</span><br>
948
949message,
950user_3d_data_averaging, user_actions, user_advec_particles,
951user_check_data_output, user_check_data_output_pr, user_data_output_2d,
952user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
953user_dvrp_coltab, user_header, user_init_3d_model, user_init,
954user_init_grid, user_init_particles, user_init_plant_canopy,
955user_last_actions, user_parin, user_parin, user_particle_attributes,
956user_read_restart_data, user_spectra, user_statistics</td>
957    </tr>
958    <tr>
959      <td style="vertical-align: top; width: 27px;"><br>
960      </td>
961      <td style="vertical-align: top; width: 38px;"><br>
962      </td>
963      <td style="vertical-align: top; width: 42px;"><br>
964      </td>
965      <td style="vertical-align: top; width: 40px;"><br>
966      </td>
967      <td style="vertical-align: top; width: 27px;">B<br>
968      </td>
969      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
970reallocated in case that multigrid is used. (calc_spectra)<br>
971
972      <br>
973
974Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
975inflow_turbulence,&nbsp;timestep)<br>
976
977      <br>
978
979Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
980      </span>adjusted to the required output size (1 gridpoint less,
981along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
982in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
983compiler. (combine_plot_fields)<br>
984
985      <br>
986
987Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
988case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
989(header)<br>
990
991      <br>
992
993Inconsistency
994removed: as the thermal stratification is not taken into account for
995the evaluation of the wall fluxes at vertical walls, the eddy viscosity
996      <span style="font-family: Courier New,Courier,monospace;">km</span>
997must 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>.
998(production_e)<br>
999
1000      <br>
1001
1002Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1003case of oceans runs. (sort_particles)<br>
1004
1005      <br>
1006
1007Bugfix: no output of particle concentration and radius unless particles
1008have been started. (data_output_2d)<br>
1009
1010      <br>
1011
1012Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1013from restart files ignored if total numbers of grid points do not
1014match. (read_3d_binary)<br>
1015
1016      <br>
1017
1018Bugfix: abort in case that absolute temperature is below zero.
1019(init_cloud_physics)</td>
1020      <td style="vertical-align: top; width: 189px;">advec_particles,
1021calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1022header, inflow_turbulence, init_cloud_physics, production_e,
1023read_3d_binary, timestep<br>
1024
1025      <br>
1026
1027combine_plot_fields</td>
1028    </tr>
1029  </tbody>
1030</table>
1031<b><blink></blink></b><br>&nbsp;
1032<br>&nbsp;
1033<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1034to change the source
1035code and how to document modifications<br>
1036</h2>Currently
1037(Sep 23rd, 2009), only selected users are allowed to commit changes to
1038the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1039<br>
1040<ol>
1041  <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>".
1042Additionally, document all changes in a local file (e.g.
1043~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1044have been changed. Classify changes in three cases, new (N), changed
1045(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>
1046    <br>
1047  </li>
1048  <li>Test the changed version, unless it works sufficiently.<br>
1049    <br>
1050  </li>
1051 
1052  <li>Commit the changes to the repository<br>
1053    <br>
1054    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1055    </span><br>
1056where "<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>
1057    <br>
1058Alternatively, in case that you have made quite a lot of changes, you
1059can also give the contents of your file CURRENT_MODIFICATIONS as the
1060log message:<br>
1061    <br>
1062    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1063    <br>
1064  </li>
1065
1066  <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>
1067    <br>
1068  </li>
1069  <li>Move the change comments in the file headers from "Current
1070revisions:" to "Former revisions:". Set the current svn id in front of
1071that.<br>
1072    <br>
1073    <span style="font-weight: bold;">Example:</span><br>
1074    <br>
1075    <span style="font-weight: bold;">before move:</span><br>
1076    <br>
1077    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1078    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1079    <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;">
1080    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1081    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1082    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1083    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 496 2010-03-02 00:41:44Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1084    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1085    <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;">
1086    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1087    <br>
1088    <span style="font-weight: bold;">after move:</span><br>
1089    <br>
1090    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1091
1092    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1093
1094    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1095
1096    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1097
1098    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1099
1100    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1101
1102    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 496 2010-03-02 00:41:44Z raasch $<br>
1103!</span><br style="font-family: Courier New,Courier,monospace;">
1104    <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>
1105! </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;">
1106
1107    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1108
1109    <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;">
1110
1111    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1112 </span><br>
1113  </li>
1114  <li>Commit the changes in the technical documentation and the file headers:<br>
1115    <br>
1116    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1117    <br>
1118 <br>
1119  </li>
1120</ol>
1121
1122<h2>
1123<a name="Kapitel3.0"></a>3.0&nbsp; Description
1124of selected parts of the
1125model source code</h2>
1126<b></b>
1127<p>This section gives links to existing descriptions about special
1128parts of the PALM code, e.g. special numerical methods that are used
1129(including mathematical background). Documents are stored in single
1130files with different formats. Some are in German (sorry for the
1131inconvenience).
1132<br>&nbsp;
1133</p><ul> <li> <a name="UPS"></a>upstream-spline
1134advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1135, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1136physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1137)</li> 
1138  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1139  </li>
1140  <li>Runge-Kutta
1141time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1142, only in German)</li>
1143
1144</ul><br>
1145&nbsp;
1146<br>&nbsp;
1147<br>&nbsp;
1148<br>&nbsp;
1149<br>&nbsp;
1150<br>&nbsp;
1151<br>&nbsp;
1152<br>&nbsp;
1153</body></html>
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