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14<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;
15</font>a
16<b>pa</b>rallelized
17<b>L</b>ES <b>m</b>odel
18<br><hr width="100%">
19<br><font size="+2">technical/numerical documentation</font>
20<br>&nbsp;
21<br>&nbsp;
22<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
23</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
24</span></td> </tr>
25<tr nosave=""> <td nosave=""><b>Last
26change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 497 2010-03-02 01:15:19Z raasch $</b></td> </tr>
27</tbody>
28</table><hr width="100%">
29<p><font size="+2">Table of contents</font>
30<br>&nbsp;
31<br>&nbsp;
32</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
33History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
34How to change the source
35code and how to document modifications<br>
36 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
37Description of selected model numerics<br>
38&nbsp;</p>
39</ul><b></b><br>
40
41<h2><a name="Kapitel1.0"></a>1.0&nbsp;
42History of changes</h2>
43The 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>
44<br>
45Entries in the fifth column specify the type of the change:
46change&nbsp;
47of existing code (C), new code (N) or bugfix (B). More detailed
48information
49about the changes may sometimes be found in the header comment lines of the
50respective
51routines.
52<br>&nbsp;
53<br>
54<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
55  <tbody>
56    <tr>
57      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
58      </td>
59      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
60      </td>
61      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
62      </td>
63      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
64      </td>
65      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
66      </td>
67      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
68      </td>
69      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
70      </td>
71    </tr>
72   
73   
74   
75   
76   
77   
78   
79   
80   
81   
82    <tr>
83      <td style="vertical-align: top;">02/03/10<br>
84      </td>
85      <td style="vertical-align: top;">SR<br>
86      </td>
87      <td style="vertical-align: top;">496<br>
88      </td>
89      <td style="vertical-align: top;">3.7a<br>
90      </td>
91      <td style="vertical-align: top;">C<br>
92      </td>
93      <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>
94      </td>
95      <td style="vertical-align: top;">palm<br>
96      </td>
97    </tr>
98<tr>
99      <td style="vertical-align: top;">01/03/10<br>
100      </td>
101      <td style="vertical-align: top;">SR<br>
102      </td>
103      <td style="vertical-align: top;">494<br>
104      </td>
105      <td style="vertical-align: top;">3.7a<br>
106      </td>
107      <td style="vertical-align: top;">N<br>
108      </td>
109      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
110      <br>
111NetCDF4 allows for parallel I/O. Also, variables are not limited in
112size any more (i.e. arrays can be larger than 2GB). The new
113d3par-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>
114only affects 2d- and 3d-output, i.e. there is no parallel output for
115profiles, time series, spectra, and particles. Parallel output of
116particle data may realized in the future.<br>
117      <br>
118In 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>
119(merging data from single files - one per PE - into one file) is not
120neccessary. 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>
121      <br>
122Using NetCDF4 format requires a NetCDF4/HDF library. Respective
123settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
124HLRN 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>
125      <br>
126      <span style="font-weight: bold;">Attention:</span><br>
127So far, NetCDF parallel I/O has only been tested a little. Further
128performance optimizations may be required, especially in case of large
129data 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>
130      <br>
131      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
132      <br>
133Modules 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>
134      <br>
135      <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>
136      <br>
137This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
138      <br>
139      <span style="font-weight: bold;">WARNING:</span><br>
140      <span style="font-weight: bold;">All fixed settings of modules in the scripts mbuild, mrun, and subjob have been removed! Please set the <span style="font-family: Courier New,Courier,monospace;">modules</span> variable appropriately and remove the mpilib variable in your configuration file.<br>
141      <br>
142</span>Compilation time can be reduced be using parallel make. The
143number of allowed simultaneous compiler calls (threads) is set in the
144configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
145      <br>
146      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
147      <br>
148allows a maximum of 4 routines to be compiled simultaneously (provided
149that the makefile does not show any dependencies between these
150routines).<span style="font-weight: bold;"><br>
151      </span>
152      </td>
153      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
154      <br>
155combine_plot_fields<br>
156      <br>
157mbuild, mrun, subjob<br>
158      </td>
159    </tr>
160    <tr>
161      <td style="vertical-align: top;"><br>
162      </td>
163      <td style="vertical-align: top;"><br>
164      </td>
165      <td style="vertical-align: top;"><br>
166      </td>
167      <td style="vertical-align: top;"><br>
168      </td>
169      <td style="vertical-align: top;">C<br>
170      </td>
171      <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>
172for choosing the NetCDF 64bit-offset format (this is the default from
173now on). The offset-format can not be set independently for the
1743d-output-data any more.<br>
175      <br>
176d3par-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>
177      </td>
178      <td style="vertical-align: top;">check_open, close_file,<br>
179data_output_mask, header, init_masks, modules, parin<br>
180      <br>
181      </td>
182    </tr>
183    <tr>
184      <td style="vertical-align: top;"><br>
185      </td>
186      <td style="vertical-align: top;"><br>
187      </td>
188      <td style="vertical-align: top;"><br>
189      </td>
190      <td style="vertical-align: top;"><br>
191      </td>
192      <td style="vertical-align: top;">B<br>
193      </td>
194      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
195      <br>
196Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
197      </td>
198      <td style="vertical-align: top;">user_statistics<br>
199      <br>
200trunk/UTIL/Makefile<br>
201      </td>
202    </tr>
203<tr>
204      <td style="vertical-align: top;">05/02/10<br>
205      </td>
206      <td style="vertical-align: top;">SR<br>
207      </td>
208      <td style="vertical-align: top;">485<br>
209      </td>
210      <td style="vertical-align: top;">3.7a<br>
211      </td>
212      <td style="vertical-align: top;">B<br>
213      </td>
214      <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>
215changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
216some global statistics (e.g. total kinetic energy) have wrong values.<br>
217      </td>
218      <td style="vertical-align: top;">init_3d_model, modules<br>
219      </td>
220    </tr>
221    <tr>
222      <td style="vertical-align: top;">05/02/10<br>
223      </td>
224      <td style="vertical-align: top;">SR<br>
225      </td>
226      <td style="vertical-align: top;">484<br>
227      </td>
228      <td style="vertical-align: top;">3.7a<br>
229      </td>
230      <td style="vertical-align: top;">B<br>
231      </td>
232      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
233      </td>
234      <td style="vertical-align: top;">many<br>
235      </td>
236    </tr>
237<tr>
238      <td style="vertical-align: top; width: 27px;">05/02/10<br>
239      </td>
240      <td style="vertical-align: top; width: 38px;">SR<br>
241      </td>
242      <td style="vertical-align: top; width: 42px;">483<br>
243      </td>
244      <td style="vertical-align: top; width: 40px;">3.7a<br>
245      </td>
246      <td style="vertical-align: top; width: 27px;">N<br>
247      </td>
248      <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>
249      <br>
250make 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>
251      <br>
252      <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;">
253wall_scalarflux</span> are the corresponding new inipar parameters.<br>
254(<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>
255      <br>
256Large scale vertical motion (subsidence/ascent) can be added as
257additional source to the prognostic equation for potential temperature.
258See 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>
259      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
260      <br>
261A 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>
262      <br>
263Masked data output has been implemented but it is not documented in the
264user manual so far. This feature can already use NetCDF4 file format.
265(check_open, check_parameters, close_file, modules, netcdf, parin,
266time_integration, user_parin, new: data_output_mask, init_masks,
267user_data_output_mask)<br>
268      </td>
269      <td style="vertical-align: top; width: 189px;">check_open, check
270parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
271netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
272      <br><span style="font-weight: bold;">
273new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
274<br>
275      </td>
276    </tr>
277    <tr>
278      <td style="vertical-align: top; width: 27px;"><br>
279      </td>
280      <td style="vertical-align: top; width: 38px;"><br>
281      </td>
282      <td style="vertical-align: top; width: 42px;"><br>
283      </td>
284      <td style="vertical-align: top; width: 40px;"><br>
285      </td>
286      <td style="vertical-align: top; width: 27px;">C<br>
287      </td>
288      <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>
289      <br><span style="font-family: Courier New,Courier,monospace;">
290var_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>
291      <br>
292Every cloud droplet has now an own weighting factor and can be deleted
293due to collisions. Condensation and collision of cloud droplets are
294adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
295      <br>
296Collision 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>
297      </td>
298      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
299      </td>
300    </tr>
301    <tr>
302      <td style="vertical-align: top; width: 27px;"><br>
303      </td>
304      <td style="vertical-align: top; width: 38px;"><br>
305      </td>
306      <td style="vertical-align: top; width: 42px;"><br>
307      </td>
308      <td style="vertical-align: top; width: 40px;"><br>
309      </td>
310      <td style="vertical-align: top; width: 27px;">B<br>
311      </td>
312      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
313      <br>
314Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
315      <br>
316Dimension 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>
317      <br>
318Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
319      <br>
320Bugfix: 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>
321      <br>
322Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
323      <br>
324Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
325      <br>
326Bugfix: 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>
327      <br>
328Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
329      <br>
330Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
331      <br>
332Bugfix 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>
333      </td>
334      <td style="vertical-align: top; width: 189px;">advec_particles,
335calc_precipitation, collision_efficiency, disturb_field, header,
336modules, poisfft_hybrid, subjob, sum_up_3d_data,
337time_integration<br>
338<br>
339      </td>
340    </tr>
341    <tr>
342      <td style="vertical-align: top; width: 27px;">23/09/09<br>
343      </td>
344      <td style="vertical-align: top; width: 38px;">SR<br>
345      </td>
346      <td style="vertical-align: top; width: 42px;">392<br>
347      </td>
348      <td style="vertical-align: top; width: 40px;">3.7<br>
349      </td>
350      <td style="vertical-align: top; width: 27px;">N<br>
351      </td>
352      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
353important changes:</span>
354atmosphere-ocean coupling has been improved and steering of
355dvr-software is more user-friendly now. Beside that, the release
356contains a lot of optimizations, changes, and bugfixes which have
357accumulated over the last months.<br>
358
359      <br>
360
361The atmosphere-ocean coupling allows to use independent precursor runs
362in order to account for different spin-up times. The time when coupling
363has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
364The 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
365order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
366output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
367      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
368      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
369      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
370      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
371      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
372      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
373      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
374      <span style="font-family: Courier New,Courier,monospace;">header</span>,
375      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
376      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
377      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
378      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
379      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
380      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
381      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
382      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
383
384      <br>
385
386Clipping of dvrp output implemented. Default colourtable for particles
387implemented, particle attributes (color, dvrp_size) can be set with new
388parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
389      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
390      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
391      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
392Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
393and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
394(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
395      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
396      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
397      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
398      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
399
400      <br>
401
402Polygon reduction for topography and ground plate isosurface. Reduction
403level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
404
405      <br>
406
407Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
408/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
409in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
410
411      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
412for speed optimization. This gives a significant speedup of more than
41310%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
414      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
415      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
416      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
417      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
418
419      <br>
420
421Scripts 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>
422
423      <br>
424
425Additional timestep criterion in case of simulations with plant canopy.
426(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
427
428      <br>
429
430Check 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
431exceed <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>
432
433      <br>
434
435External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
436      <span style="font-family: Courier New,Courier,monospace;">header</span>,
437      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
438      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
439      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
440      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
441      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
442      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
443
444      <br>
445
446New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
447(<span style="font-family: Courier New,Courier,monospace;">header</span>,
448      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
449      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
450      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
451      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
452      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
453      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
454      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
455      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
456
457      <br>
458
459Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
460(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
461      <span style="font-family: Courier New,Courier,monospace;">header</span>,
462      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
463      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
464      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
465      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
466      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
467
468      <br>
469
470Option 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>,
471      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
472
473      <br>
474
475xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
476      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
477      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
478      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
479      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
480      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
481      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
482      <td style="vertical-align: top; width: 189px;">average_3d_data,
483check_for_restart, check_parameters, data_output_2d, data_output_3d,
484data_output_dvrp, data_output_profiles, data_output_ptseries,
485data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
486diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
487header, mbuild, modules, mrun, package_parin, parin,
488prognostic_equations, read_3d_binary, read_var_list, subjob,
489sum_up_3d_data, surface_coupler, timestep, time_integration,
490user_check_parameters, user_data_output_2d, user_data_output_dvrp,
491user_header, user_init_grid, write_3d_binary, write_var_list<br>
492
493      <br>
494
495      <span style="font-weight: bold;">new:</span>
496set_particle_attributes, set_slicer_attributes_dvrp</td>
497    </tr>
498    <tr>
499      <td style="vertical-align: top; width: 27px;"><br>
500      </td>
501      <td style="vertical-align: top; width: 38px;"><br>
502      </td>
503      <td style="vertical-align: top; width: 42px;"><br>
504      </td>
505      <td style="vertical-align: top; width: 40px;"><br>
506      </td>
507      <td style="vertical-align: top; width: 27px;">C<br>
508      </td>
509      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
510message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
511      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
512      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
513      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
514      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
515      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
516      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
517      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
518      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
519      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
520      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
521      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
522      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
523      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
524      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
525      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
526      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
527      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
528      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
529      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
530      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
531      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
532      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
533      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
534      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
535      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
536      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
537      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
538      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
539      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
540      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
541      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
542      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
543      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
544      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
545      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
546      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
547      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
548      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
549      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
550
551      <br>
552
553Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
554      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
555      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
556      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
557      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
558      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
559      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
560      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
561      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
562
563      <br>
564
565__lcmuk changed to __lc to avoid problems with Intel compiler on
566sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
567
568      <br>
569
570For extended NetCDF files, the updated title attribute includes an
571update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
572
573      <br>
574
575In case of restart runs without extension, initial profiles are not
576written to NetCDF-file anymore. So far, time axis always started at
577t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
578      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
579      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
580      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
581
582      <br>
583
584      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
585'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
586can now <br>
587
588be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
589(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
590      <span style="font-family: Courier New,Courier,monospace;">header</span>,
591      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
592
593      <br>
594
5952 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
596
597      <br>
598
599A link to the webspage appendix_a.html is printed for further
600information about possible reasons of the error that appeared. (message)<br>
601
602      <br>
603
604Temperature gradient criterion for estimating the boundary layer height
605replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
606
607      <br>
608
609NetCDF unit attribute in timeseries output in case of statistic regions
610added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
611
612      <br>
613
614Maximum number of tails is calculated from maximum number of particles
615and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
616(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
617
618      <br>
619
620Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
621is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
622      <span style="font-family: Courier New,Courier,monospace;">header</span>,
623      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
624      <br>
625
626      <br>
627
628First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
629defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
630
631      <br>
632
633Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
634moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
635to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
636(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
637
638      <br>
639
640      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
641moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
642to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
643(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
644      <span style="font-family: Courier New,Courier,monospace;">header</span>,
645      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
646      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
647      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
648      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
649      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
650      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
651      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
652
653      <br>
654
655Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
656changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
657
658      <br>
659
660Adjustments for runs on lcxt4 (necessary due to a software update on
661CRAY) 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>
662      <td style="vertical-align: top; width: 189px;">advec_particles,
663advec_s_bc,
664buoyancy, calc_spectra, check_for_restart, check_open,
665check_parameters, close_file, coriolis, cpu_log, data_output_2d,
666data_output_3d, data_output_dvrp, data_output_profiles,
667data_output_ptseries, data_output_spectra, data_output_tseries,
668eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
669init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
670message, mrun, netcdf, package_parin, parin, plant_canopy_model,
671poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
672surface_coupler, temperton_fft, timestep,
673user_actions,user_check_parameters, user_data_output_dvrp,
674user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
675user_parin, user_read_restart_data, user_spectra, write_var_list </td>
676    </tr>
677    <tr>
678      <td style="vertical-align: top; width: 27px;"><br>
679      </td>
680      <td style="vertical-align: top; width: 38px;"><br>
681      </td>
682      <td style="vertical-align: top; width: 42px;"><br>
683      </td>
684      <td style="vertical-align: top; width: 40px;"><br>
685      </td>
686      <td style="vertical-align: top; width: 27px;">B<br>
687      </td>
688      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
689pressure profile in case of ocean runs is now calculated in 5 iteration
690steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
691
692      <br>
693
694Bugfix: wrong sign in buoyancy production of ocean part in case of not
695using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
696(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
697
698      <br>
699
700Bugfix: output of averaged 2d/3d quantities requires that an avaraging
701interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
702
703      <br>
704
705Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
706(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
707
708      <br>
709
710Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
711(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
712
713      <br>
714
715Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
716if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
717is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
718and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
719calls. This implies a possible performance loss; an alternative
720strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
721
722      <br>
723
724Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
725
726      <br>
727
728Bugfix: 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>
729
730      <br>
731
732Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
733=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
734for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
735      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
736
737      <br>
738
739Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
740becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
741
742      <br>
743
744Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
745
746      <br>
747
748Bugfix: error in check, if particles moved further than one subdomain
749length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
750
751      <br>
752
753Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
754is only written to file if its third index is &gt; 0, arrays for tails
755are allocated with a minimum size of 10 tails if there is no tail
756initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
757      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
758
759      <br>
760
761Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
762
763      <br>
764
765Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
766changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
767NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
768
769      <br>
770
771Bugfix: output of particle time series only if particle advection is
772switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
773
774      <br>
775
776Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
777= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
778(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
779
780      <br>
781
782Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
783z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
784
785      <br>
786
787Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
788
789      <br>
790
791If the inversion height calculated by the prerun is zero,
792inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
793
794      <br>
795
796Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
797
798      <br>
799
800Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
801removed from the restart file, because otherwise, no change from a
802fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
803      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
804
805      <br>
806
807Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
808in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
809      <td style="vertical-align: top; width: 189px;">advec_particles,
810check_parameters, cpu_log, data_output_2d, data_output_3d, header,
811init_3d_model, init_particles, init_ocean, modules, netcdf,
812prandtl_fluxes, production_e, read_var_list, time_integration,
813user_last_actions, write_var_list<br>
814
815      </td>
816    </tr>
817    <tr>
818      <td style="vertical-align: top; width: 27px;">02/02/09<br>
819      </td>
820      <td style="vertical-align: top; width: 38px;">SR<br>
821      </td>
822      <td style="vertical-align: top; width: 42px;">228<br>
823      </td>
824      <td style="vertical-align: top; width: 40px;">3.6<br>
825      </td>
826      <td style="vertical-align: top; width: 27px;">N<br>
827      </td>
828      <td style="vertical-align: top; width: 497px;">This
829release contains further additions, changes, and bugfixes for the
830SGI-ICE system, as well as important changes like the splitting of the
831user-interface into single files, a complete revision of the
832pre-compiling mechanism allowing to use different make-depositories
833simultaneously, and a revision of the reading-mechanism from restart
834files, which has no more restrictions in case that the previous and
835current run have different domain/subdomain sizes. A new handling of
836all kind of output messages is introduced with this release and will be
837applied to all existing messages within the next releases.<br>
838
839      <br>
840
841      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
842
843      <br>
844
845Restart runs on SGI-ICE are working. (mrun)<br>
846
8472d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
848
849      <br>
850
851Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
852case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
853"<span style="font-style: italic;">-K parallel</span>" for coupling.
854Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
855      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
856for lcxt4.<br>
857
858      <br>
859
860DVRP arguments changed to single precision, mode pathlines added.<br>
861
862      <br>
863
864User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
865
866      <br>
867
868User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
869      <td style="vertical-align: top; width: 189px;">check_for_restart,
870check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
871modules, package_parin, palm, surface_coupler, timestep<br>
872
873      <br>
874
875Makefile,&nbsp;mbuild, mrun, subjob<br>
876
877      <br>
878
879      <span style="font-weight: bold;">new:</span><br>
880
881init_coupling, user_additional_routines, user_check_parameters</td>
882    </tr>
883    <tr>
884      <td style="vertical-align: top; width: 27px;"><br>
885      </td>
886      <td style="vertical-align: top; width: 38px;"><br>
887      </td>
888      <td style="vertical-align: top; width: 42px;"><br>
889      </td>
890      <td style="vertical-align: top; width: 40px;"><br>
891      </td>
892      <td style="vertical-align: top; width: 27px;">C<br>
893      </td>
894      <td style="vertical-align: top; width: 497px;">User interface has been
895split into single files.<br>
896
897      <br>
898
899Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
900changed to INTEGER(8) in order to avoid "out of range" problems, which
901result in measured negative time intervals. (cpu_log, local_tremain,
902local_tremain_ini)<br>
903
904      <br>
905
906Reading mechanism from restart files
907completely revised. The subdomain/total domain size is now allowed to
908vary arbitrarily between the current and previous run. (read_var_list,
909read_3d_binary, user_read_restart_data)<br>
910
911      <br>
912
913Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
914completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
915One depository per block (given in the config-file) is created. Always
916all files from the source directory are copied to the respective
917depository. No additional file checks are done any more (mrun version
9182.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
919"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
920(mbuild, mrun)<br>
921
922      <br>
923
924Output messages (including required stop of execution) can now be
925handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
926All output messages will be replaced by this routine step by step
927within the next revisions.<br>
928
929      <br>
930
931Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
932explicitly set for better reading, although this has been already done
933in boundary_conds. (advec_s_bc)<br>
934
935      <br>
936
937Origin of the xy-coordinate system shifted from the center of the first
938grid 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
939south-left corner of this cell. (netcdf) Topography definition
940according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
941(init_grid, modules, user_header, user_init_grid, user_parin)</td>
942      <td style="vertical-align: top; width: 189px;">advec_s_bc,
943check_parameters, cpu_log, init_grid, local_stop, local_tremain,
944local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
945user_read_restart_data<br>
946
947      <br>
948
949Makefile, mbuild, mrun<br>
950
951      <br>
952
953      <span style="font-weight: bold;">removed:</span><br>
954
955user_interface<br>
956
957      <br>
958
959      <span style="font-weight: bold;">new:</span><br>
960
961message,
962user_3d_data_averaging, user_actions, user_advec_particles,
963user_check_data_output, user_check_data_output_pr, user_data_output_2d,
964user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
965user_dvrp_coltab, user_header, user_init_3d_model, user_init,
966user_init_grid, user_init_particles, user_init_plant_canopy,
967user_last_actions, user_parin, user_parin, user_particle_attributes,
968user_read_restart_data, user_spectra, user_statistics</td>
969    </tr>
970    <tr>
971      <td style="vertical-align: top; width: 27px;"><br>
972      </td>
973      <td style="vertical-align: top; width: 38px;"><br>
974      </td>
975      <td style="vertical-align: top; width: 42px;"><br>
976      </td>
977      <td style="vertical-align: top; width: 40px;"><br>
978      </td>
979      <td style="vertical-align: top; width: 27px;">B<br>
980      </td>
981      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
982reallocated in case that multigrid is used. (calc_spectra)<br>
983
984      <br>
985
986Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
987inflow_turbulence,&nbsp;timestep)<br>
988
989      <br>
990
991Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
992      </span>adjusted to the required output size (1 gridpoint less,
993along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
994in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
995compiler. (combine_plot_fields)<br>
996
997      <br>
998
999Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1000case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1001(header)<br>
1002
1003      <br>
1004
1005Inconsistency
1006removed: as the thermal stratification is not taken into account for
1007the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1008      <span style="font-family: Courier New,Courier,monospace;">km</span>
1009must 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>.
1010(production_e)<br>
1011
1012      <br>
1013
1014Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1015case of oceans runs. (sort_particles)<br>
1016
1017      <br>
1018
1019Bugfix: no output of particle concentration and radius unless particles
1020have been started. (data_output_2d)<br>
1021
1022      <br>
1023
1024Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1025from restart files ignored if total numbers of grid points do not
1026match. (read_3d_binary)<br>
1027
1028      <br>
1029
1030Bugfix: abort in case that absolute temperature is below zero.
1031(init_cloud_physics)</td>
1032      <td style="vertical-align: top; width: 189px;">advec_particles,
1033calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1034header, inflow_turbulence, init_cloud_physics, production_e,
1035read_3d_binary, timestep<br>
1036
1037      <br>
1038
1039combine_plot_fields</td>
1040    </tr>
1041  </tbody>
1042</table>
1043<b><blink></blink></b><br>&nbsp;
1044<br>&nbsp;
1045<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1046to change the source
1047code and how to document modifications<br>
1048</h2>Currently
1049(Sep 23rd, 2009), only selected users are allowed to commit changes to
1050the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1051<br>
1052<ol>
1053  <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>".
1054Additionally, document all changes in a local file (e.g.
1055~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1056have been changed. Classify changes in three cases, new (N), changed
1057(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>
1058    <br>
1059  </li>
1060  <li>Test the changed version, unless it works sufficiently.<br>
1061    <br>
1062  </li>
1063 
1064  <li>Commit the changes to the repository<br>
1065    <br>
1066    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1067    </span><br>
1068where "<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>
1069    <br>
1070Alternatively, in case that you have made quite a lot of changes, you
1071can also give the contents of your file CURRENT_MODIFICATIONS as the
1072log message:<br>
1073    <br>
1074    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1075    <br>
1076  </li>
1077
1078  <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>
1079    <br>
1080  </li>
1081  <li>Move the change comments in the file headers from "Current
1082revisions:" to "Former revisions:". Set the current svn id in front of
1083that.<br>
1084    <br>
1085    <span style="font-weight: bold;">Example:</span><br>
1086    <br>
1087    <span style="font-weight: bold;">before move:</span><br>
1088    <br>
1089    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1090    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1091    <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;">
1092    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1093    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1094    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1095    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 497 2010-03-02 01:15:19Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1096    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1097    <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;">
1098    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1099    <br>
1100    <span style="font-weight: bold;">after move:</span><br>
1101    <br>
1102    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1103
1104    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1105
1106    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1107
1108    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1109
1110    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1111
1112    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1113
1114    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 497 2010-03-02 01:15:19Z raasch $<br>
1115!</span><br style="font-family: Courier New,Courier,monospace;">
1116    <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>
1117! </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;">
1118
1119    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1120
1121    <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;">
1122
1123    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1124 </span><br>
1125  </li>
1126  <li>Commit the changes in the technical documentation and the file headers:<br>
1127    <br>
1128    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1129    <br>
1130 <br>
1131  </li>
1132</ol>
1133
1134<h2>
1135<a name="Kapitel3.0"></a>3.0&nbsp; Description
1136of selected parts of the
1137model source code</h2>
1138<b></b>
1139<p>This section gives links to existing descriptions about special
1140parts of the PALM code, e.g. special numerical methods that are used
1141(including mathematical background). Documents are stored in single
1142files with different formats. Some are in German (sorry for the
1143inconvenience).
1144<br>&nbsp;
1145</p><ul> <li> <a name="UPS"></a>upstream-spline
1146advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1147, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1148physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1149)</li> 
1150  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1151  </li>
1152  <li>Runge-Kutta
1153time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1154, only in German)</li>
1155
1156</ul><br>
1157&nbsp;
1158<br>&nbsp;
1159<br>&nbsp;
1160<br>&nbsp;
1161<br>&nbsp;
1162<br>&nbsp;
1163<br>&nbsp;
1164<br>&nbsp;
1165</body></html>
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