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source: palm/trunk/DOC/tec/technical_documentation.html @ 494

Last change on this file since 494 was 494, checked in by raasch, 15 years ago

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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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12<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;
13</font>a
14<b>pa</b>rallelized
15<b>L</b>ES <b>m</b>odel
16<br><hr width="100%">
17<br><font size="+2">technical/numerical documentation</font>
18<br>&nbsp;
19<br>&nbsp;
20<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
21</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
22</span></td> </tr>
23<tr nosave=""> <td nosave=""><b>Last
24change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 494 2010-03-01 12:23:32Z raasch $</b></td> </tr>
25</tbody>
26</table><hr width="100%">
27<p><font size="+2">Table of contents</font>
28<br>&nbsp;
29<br>&nbsp;
30</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
31History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
32How to change the source
33code and how to document modifications<br>
34 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
35Description of selected model numerics<br>
36&nbsp;</p>
37</ul><b></b><br>
38
39<h2><a name="Kapitel1.0"></a>1.0&nbsp;
40History of changes</h2>
41The 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>
42<br>
43Entries in the fifth column specify the type of the change:
44change&nbsp;
45of existing code (C), new code (N) or bugfix (B). More detailed
46information
47about the changes may sometimes be found in the header comment lines of the
48respective
49routines.
50<br>&nbsp;
51<br>
52<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
53  <tbody>
54    <tr>
55      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
56      </td>
57      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
58      </td>
59      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
60      </td>
61      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
62      </td>
63      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
64      </td>
65      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
66      </td>
67      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
68      </td>
69    </tr>
70   
71   
72   
73   
74   
75   
76   
77   
78   
79   
80    <tr>
81      <td style="vertical-align: top;">01/03/10<br>
82      </td>
83      <td style="vertical-align: top;">SR<br>
84      </td>
85      <td style="vertical-align: top;">494<br>
86      </td>
87      <td style="vertical-align: top;">3.7a<br>
88      </td>
89      <td style="vertical-align: top;">N<br>
90      </td>
91      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
92      <br>
93NetCDF4 allows for parallel I/O. Also, variables are not limited in
94size any more (i.e. arrays can be larger than 2GB). The new
95d3par-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>
96only affects 2d- and 3d-output, i.e. there is no parallel output for
97profiles, time series, spectra, and particles. Parallel output of
98particle data may realized in the future.<br>
99      <br>
100In 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>
101(merging data from single files - one per PE - into one file) is not
102neccessary. 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>
103      <br>
104Using NetCDF4 format requires a NetCDF4/HDF library. Respective
105settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
106HLRN 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>
107      <br>
108      <span style="font-weight: bold;">Attention:</span><br>
109So far, NetCDF parallel I/O has only been tested a little. Further
110performance optimizations may be required, especially in case of large
111data 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>
112      <br>
113      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
114      <br>
115Modules 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>
116      <br>
117      <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>
118      <br>
119This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
120      <br>
121      <span style="font-weight: bold;">WARNING:</span><br>
122      <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>
123      </td>
124      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
125      <br>
126combine_plot_fields<br>
127      <br>
128mbuild, mrun, subjob<br>
129      </td>
130    </tr>
131    <tr>
132      <td style="vertical-align: top;"><br>
133      </td>
134      <td style="vertical-align: top;"><br>
135      </td>
136      <td style="vertical-align: top;"><br>
137      </td>
138      <td style="vertical-align: top;"><br>
139      </td>
140      <td style="vertical-align: top;">C<br>
141      </td>
142      <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>
143for choosing the NetCDF 64bit-offset format (this is the default from
144now on). The offset-format can not be set independently for the
1453d-output-data any more.<br>
146      <br>
147d3par-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>
148      </td>
149      <td style="vertical-align: top;">check_open, close_file,<br>
150data_output_mask, header, init_masks, modules, parin<br>
151      <br>
152      </td>
153    </tr>
154    <tr>
155      <td style="vertical-align: top;"><br>
156      </td>
157      <td style="vertical-align: top;"><br>
158      </td>
159      <td style="vertical-align: top;"><br>
160      </td>
161      <td style="vertical-align: top;"><br>
162      </td>
163      <td style="vertical-align: top;">B<br>
164      </td>
165      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
166      <br>
167Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
168      </td>
169      <td style="vertical-align: top;">user_statistics<br>
170      <br>
171trunk/UTIL/Makefile<br>
172      </td>
173    </tr>
174<tr>
175      <td style="vertical-align: top;">05/02/10<br>
176      </td>
177      <td style="vertical-align: top;">SR<br>
178      </td>
179      <td style="vertical-align: top;">485<br>
180      </td>
181      <td style="vertical-align: top;">3.7a<br>
182      </td>
183      <td style="vertical-align: top;">B<br>
184      </td>
185      <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>
186changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
187some global statistics (e.g. total kinetic energy) have wrong values.<br>
188      </td>
189      <td style="vertical-align: top;">init_3d_model, modules<br>
190      </td>
191    </tr>
192    <tr>
193      <td style="vertical-align: top;">05/02/10<br>
194      </td>
195      <td style="vertical-align: top;">SR<br>
196      </td>
197      <td style="vertical-align: top;">484<br>
198      </td>
199      <td style="vertical-align: top;">3.7a<br>
200      </td>
201      <td style="vertical-align: top;">B<br>
202      </td>
203      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
204      </td>
205      <td style="vertical-align: top;">many<br>
206      </td>
207    </tr>
208<tr>
209      <td style="vertical-align: top; width: 27px;">05/02/10<br>
210      </td>
211      <td style="vertical-align: top; width: 38px;">SR<br>
212      </td>
213      <td style="vertical-align: top; width: 42px;">483<br>
214      </td>
215      <td style="vertical-align: top; width: 40px;">3.7a<br>
216      </td>
217      <td style="vertical-align: top; width: 27px;">N<br>
218      </td>
219      <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>
220      <br>
221make 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>
222      <br>
223      <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;">
224wall_scalarflux</span> are the corresponding new inipar parameters.<br>
225(<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>
226      <br>
227Large scale vertical motion (subsidence/ascent) can be added as
228additional source to the prognostic equation for potential temperature.
229See 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>
230      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
231      <br>
232A 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>
233      <br>
234Masked data output has been implemented but it is not documented in the
235user manual so far. This feature can already use NetCDF4 file format.
236(check_open, check_parameters, close_file, modules, netcdf, parin,
237time_integration, user_parin, new: data_output_mask, init_masks,
238user_data_output_mask)<br>
239      </td>
240      <td style="vertical-align: top; width: 189px;">check_open, check
241parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
242netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
243      <br><span style="font-weight: bold;">
244new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
245<br>
246      </td>
247    </tr>
248    <tr>
249      <td style="vertical-align: top; width: 27px;"><br>
250      </td>
251      <td style="vertical-align: top; width: 38px;"><br>
252      </td>
253      <td style="vertical-align: top; width: 42px;"><br>
254      </td>
255      <td style="vertical-align: top; width: 40px;"><br>
256      </td>
257      <td style="vertical-align: top; width: 27px;">C<br>
258      </td>
259      <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>
260      <br><span style="font-family: Courier New,Courier,monospace;">
261var_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>
262      <br>
263Every cloud droplet has now an own weighting factor and can be deleted
264due to collisions. Condensation and collision of cloud droplets are
265adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
266      <br>
267Collision 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>
268      </td>
269      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
270      </td>
271    </tr>
272    <tr>
273      <td style="vertical-align: top; width: 27px;"><br>
274      </td>
275      <td style="vertical-align: top; width: 38px;"><br>
276      </td>
277      <td style="vertical-align: top; width: 42px;"><br>
278      </td>
279      <td style="vertical-align: top; width: 40px;"><br>
280      </td>
281      <td style="vertical-align: top; width: 27px;">B<br>
282      </td>
283      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
284      <br>
285Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
286      <br>
287Dimension 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>
288      <br>
289Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
290      <br>
291Bugfix: 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>
292      <br>
293Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
294      <br>
295Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
296      <br>
297Bugfix: 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>
298      <br>
299Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
300      <br>
301Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
302      <br>
303Bugfix 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>
304      </td>
305      <td style="vertical-align: top; width: 189px;">advec_particles,
306calc_precipitation, collision_efficiency, disturb_field, header,
307modules, poisfft_hybrid, subjob, sum_up_3d_data,
308time_integration<br>
309<br>
310      </td>
311    </tr>
312    <tr>
313      <td style="vertical-align: top; width: 27px;">23/09/09<br>
314      </td>
315      <td style="vertical-align: top; width: 38px;">SR<br>
316      </td>
317      <td style="vertical-align: top; width: 42px;">392<br>
318      </td>
319      <td style="vertical-align: top; width: 40px;">3.7<br>
320      </td>
321      <td style="vertical-align: top; width: 27px;">N<br>
322      </td>
323      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
324important changes:</span>
325atmosphere-ocean coupling has been improved and steering of
326dvr-software is more user-friendly now. Beside that, the release
327contains a lot of optimizations, changes, and bugfixes which have
328accumulated over the last months.<br>
329
330      <br>
331
332The atmosphere-ocean coupling allows to use independent precursor runs
333in order to account for different spin-up times. The time when coupling
334has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
335The 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
336order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
337output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
338      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
339      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
340      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
341      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
342      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
343      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
344      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
345      <span style="font-family: Courier New,Courier,monospace;">header</span>,
346      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
347      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
348      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
349      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
350      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
351      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
352      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
353      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
354
355      <br>
356
357Clipping of dvrp output implemented. Default colourtable for particles
358implemented, particle attributes (color, dvrp_size) can be set with new
359parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
360      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
361      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
362      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
363Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
364and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
365(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
366      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
367      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
368      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
369      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
370
371      <br>
372
373Polygon reduction for topography and ground plate isosurface. Reduction
374level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
375
376      <br>
377
378Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
379/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
380in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
381
382      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
383for speed optimization. This gives a significant speedup of more than
38410%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
385      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
386      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
387      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
388      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
389
390      <br>
391
392Scripts 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>
393
394      <br>
395
396Additional timestep criterion in case of simulations with plant canopy.
397(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
398
399      <br>
400
401Check 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
402exceed <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>
403
404      <br>
405
406External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
407      <span style="font-family: Courier New,Courier,monospace;">header</span>,
408      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
409      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
410      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
411      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
412      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
413      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
414
415      <br>
416
417New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
418(<span style="font-family: Courier New,Courier,monospace;">header</span>,
419      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
420      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
421      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
422      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
423      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
424      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
425      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
426      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
427
428      <br>
429
430Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
431(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
432      <span style="font-family: Courier New,Courier,monospace;">header</span>,
433      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
434      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
435      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
436      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
437      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
438
439      <br>
440
441Option 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>,
442      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
443
444      <br>
445
446xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
447      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
448      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
449      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
450      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
451      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
452      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
453      <td style="vertical-align: top; width: 189px;">average_3d_data,
454check_for_restart, check_parameters, data_output_2d, data_output_3d,
455data_output_dvrp, data_output_profiles, data_output_ptseries,
456data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
457diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
458header, mbuild, modules, mrun, package_parin, parin,
459prognostic_equations, read_3d_binary, read_var_list, subjob,
460sum_up_3d_data, surface_coupler, timestep, time_integration,
461user_check_parameters, user_data_output_2d, user_data_output_dvrp,
462user_header, user_init_grid, write_3d_binary, write_var_list<br>
463
464      <br>
465
466      <span style="font-weight: bold;">new:</span>
467set_particle_attributes, set_slicer_attributes_dvrp</td>
468    </tr>
469    <tr>
470      <td style="vertical-align: top; width: 27px;"><br>
471      </td>
472      <td style="vertical-align: top; width: 38px;"><br>
473      </td>
474      <td style="vertical-align: top; width: 42px;"><br>
475      </td>
476      <td style="vertical-align: top; width: 40px;"><br>
477      </td>
478      <td style="vertical-align: top; width: 27px;">C<br>
479      </td>
480      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
481message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
482      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
483      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
484      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
485      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
486      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
487      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
488      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
489      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
490      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
491      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
492      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
493      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
494      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
495      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
496      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
497      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
498      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
499      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
500      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
501      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
502      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
503      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
504      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
505      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
506      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
507      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
508      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
509      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
510      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
511      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
512      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
513      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
514      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
515      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
516      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
517      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
518      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
519      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
520      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
521
522      <br>
523
524Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
525      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
526      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
527      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
528      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
529      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
530      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
531      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
532      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
533
534      <br>
535
536__lcmuk changed to __lc to avoid problems with Intel compiler on
537sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
538
539      <br>
540
541For extended NetCDF files, the updated title attribute includes an
542update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
543
544      <br>
545
546In case of restart runs without extension, initial profiles are not
547written to NetCDF-file anymore. So far, time axis always started at
548t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
549      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
550      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
551      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
552
553      <br>
554
555      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
556'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
557can now <br>
558
559be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
560(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
561      <span style="font-family: Courier New,Courier,monospace;">header</span>,
562      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
563
564      <br>
565
5662 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
567
568      <br>
569
570A link to the webspage appendix_a.html is printed for further
571information about possible reasons of the error that appeared. (message)<br>
572
573      <br>
574
575Temperature gradient criterion for estimating the boundary layer height
576replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
577
578      <br>
579
580NetCDF unit attribute in timeseries output in case of statistic regions
581added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
582
583      <br>
584
585Maximum number of tails is calculated from maximum number of particles
586and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
587(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
588
589      <br>
590
591Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
592is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
593      <span style="font-family: Courier New,Courier,monospace;">header</span>,
594      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
595      <br>
596
597      <br>
598
599First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
600defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
601
602      <br>
603
604Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
605moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
606to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
607(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
608
609      <br>
610
611      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
612moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
613to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
614(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
615      <span style="font-family: Courier New,Courier,monospace;">header</span>,
616      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
617      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
618      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
619      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
620      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
621      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
622      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
623
624      <br>
625
626Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
627changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
628
629      <br>
630
631Adjustments for runs on lcxt4 (necessary due to a software update on
632CRAY) 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>
633      <td style="vertical-align: top; width: 189px;">advec_particles,
634advec_s_bc,
635buoyancy, calc_spectra, check_for_restart, check_open,
636check_parameters, close_file, coriolis, cpu_log, data_output_2d,
637data_output_3d, data_output_dvrp, data_output_profiles,
638data_output_ptseries, data_output_spectra, data_output_tseries,
639eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
640init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
641message, mrun, netcdf, package_parin, parin, plant_canopy_model,
642poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
643surface_coupler, temperton_fft, timestep,
644user_actions,user_check_parameters, user_data_output_dvrp,
645user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
646user_parin, user_read_restart_data, user_spectra, write_var_list </td>
647    </tr>
648    <tr>
649      <td style="vertical-align: top; width: 27px;"><br>
650      </td>
651      <td style="vertical-align: top; width: 38px;"><br>
652      </td>
653      <td style="vertical-align: top; width: 42px;"><br>
654      </td>
655      <td style="vertical-align: top; width: 40px;"><br>
656      </td>
657      <td style="vertical-align: top; width: 27px;">B<br>
658      </td>
659      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
660pressure profile in case of ocean runs is now calculated in 5 iteration
661steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
662
663      <br>
664
665Bugfix: wrong sign in buoyancy production of ocean part in case of not
666using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
667(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
668
669      <br>
670
671Bugfix: output of averaged 2d/3d quantities requires that an avaraging
672interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
673
674      <br>
675
676Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
677(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
678
679      <br>
680
681Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
682(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
683
684      <br>
685
686Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
687if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
688is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
689and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
690calls. This implies a possible performance loss; an alternative
691strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
692
693      <br>
694
695Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
696
697      <br>
698
699Bugfix: 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>
700
701      <br>
702
703Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
704=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
705for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
706      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
707
708      <br>
709
710Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
711becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
712
713      <br>
714
715Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
716
717      <br>
718
719Bugfix: error in check, if particles moved further than one subdomain
720length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
721
722      <br>
723
724Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
725is only written to file if its third index is &gt; 0, arrays for tails
726are allocated with a minimum size of 10 tails if there is no tail
727initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
728      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
729
730      <br>
731
732Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
733
734      <br>
735
736Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
737changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
738NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
739
740      <br>
741
742Bugfix: output of particle time series only if particle advection is
743switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
744
745      <br>
746
747Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
748= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
749(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
750
751      <br>
752
753Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
754z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
755
756      <br>
757
758Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
759
760      <br>
761
762If the inversion height calculated by the prerun is zero,
763inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
764
765      <br>
766
767Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
768
769      <br>
770
771Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
772removed from the restart file, because otherwise, no change from a
773fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
774      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
775
776      <br>
777
778Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
779in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
780      <td style="vertical-align: top; width: 189px;">advec_particles,
781check_parameters, cpu_log, data_output_2d, data_output_3d, header,
782init_3d_model, init_particles, init_ocean, modules, netcdf,
783prandtl_fluxes, production_e, read_var_list, time_integration,
784user_last_actions, write_var_list<br>
785
786      </td>
787    </tr>
788    <tr>
789      <td style="vertical-align: top; width: 27px;">02/02/09<br>
790      </td>
791      <td style="vertical-align: top; width: 38px;">SR<br>
792      </td>
793      <td style="vertical-align: top; width: 42px;">228<br>
794      </td>
795      <td style="vertical-align: top; width: 40px;">3.6<br>
796      </td>
797      <td style="vertical-align: top; width: 27px;">N<br>
798      </td>
799      <td style="vertical-align: top; width: 497px;">This
800release contains further additions, changes, and bugfixes for the
801SGI-ICE system, as well as important changes like the splitting of the
802user-interface into single files, a complete revision of the
803pre-compiling mechanism allowing to use different make-depositories
804simultaneously, and a revision of the reading-mechanism from restart
805files, which has no more restrictions in case that the previous and
806current run have different domain/subdomain sizes. A new handling of
807all kind of output messages is introduced with this release and will be
808applied to all existing messages within the next releases.<br>
809
810      <br>
811
812      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
813
814      <br>
815
816Restart runs on SGI-ICE are working. (mrun)<br>
817
8182d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
819
820      <br>
821
822Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
823case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
824"<span style="font-style: italic;">-K parallel</span>" for coupling.
825Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
826      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
827for lcxt4.<br>
828
829      <br>
830
831DVRP arguments changed to single precision, mode pathlines added.<br>
832
833      <br>
834
835User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
836
837      <br>
838
839User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
840      <td style="vertical-align: top; width: 189px;">check_for_restart,
841check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
842modules, package_parin, palm, surface_coupler, timestep<br>
843
844      <br>
845
846Makefile,&nbsp;mbuild, mrun, subjob<br>
847
848      <br>
849
850      <span style="font-weight: bold;">new:</span><br>
851
852init_coupling, user_additional_routines, user_check_parameters</td>
853    </tr>
854    <tr>
855      <td style="vertical-align: top; width: 27px;"><br>
856      </td>
857      <td style="vertical-align: top; width: 38px;"><br>
858      </td>
859      <td style="vertical-align: top; width: 42px;"><br>
860      </td>
861      <td style="vertical-align: top; width: 40px;"><br>
862      </td>
863      <td style="vertical-align: top; width: 27px;">C<br>
864      </td>
865      <td style="vertical-align: top; width: 497px;">User interface has been
866split into single files.<br>
867
868      <br>
869
870Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
871changed to INTEGER(8) in order to avoid "out of range" problems, which
872result in measured negative time intervals. (cpu_log, local_tremain,
873local_tremain_ini)<br>
874
875      <br>
876
877Reading mechanism from restart files
878completely revised. The subdomain/total domain size is now allowed to
879vary arbitrarily between the current and previous run. (read_var_list,
880read_3d_binary, user_read_restart_data)<br>
881
882      <br>
883
884Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
885completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
886One depository per block (given in the config-file) is created. Always
887all files from the source directory are copied to the respective
888depository. No additional file checks are done any more (mrun version
8892.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
890"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
891(mbuild, mrun)<br>
892
893      <br>
894
895Output messages (including required stop of execution) can now be
896handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
897All output messages will be replaced by this routine step by step
898within the next revisions.<br>
899
900      <br>
901
902Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
903explicitly set for better reading, although this has been already done
904in boundary_conds. (advec_s_bc)<br>
905
906      <br>
907
908Origin of the xy-coordinate system shifted from the center of the first
909grid 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
910south-left corner of this cell. (netcdf) Topography definition
911according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
912(init_grid, modules, user_header, user_init_grid, user_parin)</td>
913      <td style="vertical-align: top; width: 189px;">advec_s_bc,
914check_parameters, cpu_log, init_grid, local_stop, local_tremain,
915local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
916user_read_restart_data<br>
917
918      <br>
919
920Makefile, mbuild, mrun<br>
921
922      <br>
923
924      <span style="font-weight: bold;">removed:</span><br>
925
926user_interface<br>
927
928      <br>
929
930      <span style="font-weight: bold;">new:</span><br>
931
932message,
933user_3d_data_averaging, user_actions, user_advec_particles,
934user_check_data_output, user_check_data_output_pr, user_data_output_2d,
935user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
936user_dvrp_coltab, user_header, user_init_3d_model, user_init,
937user_init_grid, user_init_particles, user_init_plant_canopy,
938user_last_actions, user_parin, user_parin, user_particle_attributes,
939user_read_restart_data, user_spectra, user_statistics</td>
940    </tr>
941    <tr>
942      <td style="vertical-align: top; width: 27px;"><br>
943      </td>
944      <td style="vertical-align: top; width: 38px;"><br>
945      </td>
946      <td style="vertical-align: top; width: 42px;"><br>
947      </td>
948      <td style="vertical-align: top; width: 40px;"><br>
949      </td>
950      <td style="vertical-align: top; width: 27px;">B<br>
951      </td>
952      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
953reallocated in case that multigrid is used. (calc_spectra)<br>
954
955      <br>
956
957Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
958inflow_turbulence,&nbsp;timestep)<br>
959
960      <br>
961
962Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
963      </span>adjusted to the required output size (1 gridpoint less,
964along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
965in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
966compiler. (combine_plot_fields)<br>
967
968      <br>
969
970Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
971case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
972(header)<br>
973
974      <br>
975
976Inconsistency
977removed: as the thermal stratification is not taken into account for
978the evaluation of the wall fluxes at vertical walls, the eddy viscosity
979      <span style="font-family: Courier New,Courier,monospace;">km</span>
980must 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>.
981(production_e)<br>
982
983      <br>
984
985Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
986case of oceans runs. (sort_particles)<br>
987
988      <br>
989
990Bugfix: no output of particle concentration and radius unless particles
991have been started. (data_output_2d)<br>
992
993      <br>
994
995Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
996from restart files ignored if total numbers of grid points do not
997match. (read_3d_binary)<br>
998
999      <br>
1000
1001Bugfix: abort in case that absolute temperature is below zero.
1002(init_cloud_physics)</td>
1003      <td style="vertical-align: top; width: 189px;">advec_particles,
1004calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1005header, inflow_turbulence, init_cloud_physics, production_e,
1006read_3d_binary, timestep<br>
1007
1008      <br>
1009
1010combine_plot_fields</td>
1011    </tr>
1012  </tbody>
1013</table>
1014<b><blink></blink></b><br>&nbsp;
1015<br>&nbsp;
1016<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1017to change the source
1018code and how to document modifications<br>
1019</h2>Currently
1020(Sep 23rd, 2009), only selected users are allowed to commit changes to
1021the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1022<br>
1023<ol>
1024  <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>".
1025Additionally, document all changes in a local file (e.g.
1026~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1027have been changed. Classify changes in three cases, new (N), changed
1028(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>
1029    <br>
1030  </li>
1031  <li>Test the changed version, unless it works sufficiently.<br>
1032    <br>
1033  </li>
1034 
1035  <li>Commit the changes to the repository<br>
1036    <br>
1037    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1038    </span><br>
1039where "<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>
1040    <br>
1041Alternatively, in case that you have made quite a lot of changes, you
1042can also give the contents of your file CURRENT_MODIFICATIONS as the
1043log message:<br>
1044    <br>
1045    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1046    <br>
1047  </li>
1048
1049  <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>
1050    <br>
1051  </li>
1052  <li>Move the change comments in the file headers from "Current
1053revisions:" to "Former revisions:". Set the current svn id in front of
1054that.<br>
1055    <br>
1056    <span style="font-weight: bold;">Example:</span><br>
1057    <br>
1058    <span style="font-weight: bold;">before move:</span><br>
1059    <br>
1060    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1061    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1062    <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;">
1063    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1064    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1065    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1066    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 494 2010-03-01 12:23:32Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1067    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1068    <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;">
1069    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1070    <br>
1071    <span style="font-weight: bold;">after move:</span><br>
1072    <br>
1073    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1074
1075    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1076
1077    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1078
1079    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1080
1081    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1082
1083    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1084
1085    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 494 2010-03-01 12:23:32Z raasch $<br>
1086!</span><br style="font-family: Courier New,Courier,monospace;">
1087    <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>
1088! </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;">
1089
1090    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1091
1092    <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;">
1093
1094    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1095 </span><br>
1096  </li>
1097  <li>Commit the changes in the technical documentation and the file headers:<br>
1098    <br>
1099    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1100    <br>
1101 <br>
1102  </li>
1103</ol>
1104
1105<h2>
1106<a name="Kapitel3.0"></a>3.0&nbsp; Description
1107of selected parts of the
1108model source code</h2>
1109<b></b>
1110<p>This section gives links to existing descriptions about special
1111parts of the PALM code, e.g. special numerical methods that are used
1112(including mathematical background). Documents are stored in single
1113files with different formats. Some are in German (sorry for the
1114inconvenience).
1115<br>&nbsp;
1116</p><ul> <li> <a name="UPS"></a>upstream-spline
1117advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1118, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1119physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1120)</li> 
1121  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1122  </li>
1123  <li>Runge-Kutta
1124time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1125, only in German)</li>
1126
1127</ul><br>
1128&nbsp;
1129<br>&nbsp;
1130<br>&nbsp;
1131<br>&nbsp;
1132<br>&nbsp;
1133<br>&nbsp;
1134<br>&nbsp;
1135<br>&nbsp;
1136</body></html>
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