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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
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15<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;
16</font>a
17<b>pa</b>rallelized
18<b>L</b>ES <b>m</b>odel
19<br><hr width="100%">
20<br><font size="+2">technical/numerical documentation</font>
21<br>&nbsp;
22<br>&nbsp;
23<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
24</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
25</span></td> </tr>
26<tr nosave=""> <td nosave=""><b>Last
27change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $</b></td> </tr>
28</tbody>
29</table><hr width="100%">
30<p><font size="+2">Table of contents</font>
31<br>&nbsp;
32<br>&nbsp;
33</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
34History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
35How to change the source
36code and how to document modifications<br>
37 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
38Description of selected model numerics<br>
39&nbsp;</p>
40</ul><b></b><br>
41
42<h2><a name="Kapitel1.0"></a>1.0&nbsp;
43History of changes</h2>
44The 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>
45<br>
46Entries in the fifth column specify the type of the change:
47change&nbsp;
48of existing code (C), new code (N) or bugfix (B). More detailed
49information
50about the changes may sometimes be found in the header comment lines of the
51respective
52routines.
53<br>&nbsp;
54<br>
55<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
56  <tbody>
57    <tr>
58      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
59      </td>
60      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
61      </td>
62      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
63      </td>
64      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
65      </td>
66      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
67      </td>
68      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
69      </td>
70      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
71      </td>
72    </tr>
73   
74   
75   
76   
77   
78   
79   
80   
81   
82   
83    <tr>
84      <td style="vertical-align: top;">03/03/10<br>
85      </td>
86      <td style="vertical-align: top;">SR<br>
87      </td>
88      <td style="vertical-align: top;">504<br>
89      </td>
90      <td style="vertical-align: top;">3.7a<br>
91      </td>
92      <td style="vertical-align: top;">C<br>
93      </td>
94      <td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> is now directly called within <span style="font-weight: bold;">mrun</span> and must not be given by an output command in the configuration file any more. Please remove the respective output command (<span style="font-family: Courier New,Courier,monospace;">OC:combine_plot_fields.x</span>) from your configuration file!<br>
95      <br>
96Utility programs (<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>, <span style="font-family: Courier New,Courier,monospace;">interpret_config</span>) are created by <span style="font-weight: bold;">mbuild</span> separately for each block in the configuration file. Depending on option <span style="font-family: Courier New,Courier,monospace;">-K</span>, <span style="font-weight: bold;">mrun</span> is using the utility programs for the respective block.<br>
97      <br>
98Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
99      <br>
100Default configuration files updated.<br>
101      </td>
102      <td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
103      </td>
104    </tr>
105<tr>
106      <td style="vertical-align: top;">02/03/10<br>
107      </td>
108      <td style="vertical-align: top;">SR<br>
109      </td>
110      <td style="vertical-align: top;">496<br>
111      </td>
112      <td style="vertical-align: top;">3.7a<br>
113      </td>
114      <td style="vertical-align: top;">C<br>
115      </td>
116      <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>
117      </td>
118      <td style="vertical-align: top;">palm<br>
119      </td>
120    </tr>
121<tr>
122      <td style="vertical-align: top;">01/03/10<br>
123      </td>
124      <td style="vertical-align: top;">SR<br>
125      </td>
126      <td style="vertical-align: top;">494<br>
127      </td>
128      <td style="vertical-align: top;">3.7a<br>
129      </td>
130      <td style="vertical-align: top;">N<br>
131      </td>
132      <td style="vertical-align: top;">Output in NetCDF4-format.<br>
133      <br>
134NetCDF4 allows for parallel I/O. Also, variables are not limited in
135size any more (i.e. arrays can be larger than 2GB). The new
136d3par-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>
137only affects 2d- and 3d-output, i.e. there is no parallel output for
138profiles, time series, spectra, and particles. Parallel output of
139particle data may realized in the future.<br>
140      <br>
141In 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>
142(merging data from single files - one per PE - into one file) is not
143neccessary. 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>
144      <br>
145Using NetCDF4 format requires a NetCDF4/HDF library. Respective
146settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
147HLRN 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>
148      <br>
149      <span style="font-weight: bold;">Attention:</span><br>
150So far, NetCDF parallel I/O has only been tested a little. Further
151performance optimizations may be required, especially in case of large
152data 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>
153      <br>
154      <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
155      <br>
156Modules 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>
157      <br>
158      <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>
159      <br>
160This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
161      <br>
162      <span style="font-weight: bold;">WARNING:</span><br>
163      <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>
164      <br>
165</span>Compilation time can be reduced be using parallel make. The
166number of allowed simultaneous compiler calls (threads) is set in the
167configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
168      <br>
169      <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; %mopts&nbsp; -j:4 &nbsp; lcsgih parallel</span><br>
170      <br>
171allows a maximum of 4 routines to be compiled simultaneously (provided
172that the makefile does not show any dependencies between these
173routines).<span style="font-weight: bold;"><br>
174      </span>
175      </td>
176      <td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
177      <br>
178combine_plot_fields<br>
179      <br>
180mbuild, mrun, subjob<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;">C<br>
193      </td>
194      <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>
195for choosing the NetCDF 64bit-offset format (this is the default from
196now on). The offset-format can not be set independently for the
1973d-output-data any more.<br>
198      <br>
199d3par-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>
200      </td>
201      <td style="vertical-align: top;">check_open, close_file,<br>
202data_output_mask, header, init_masks, modules, parin<br>
203      <br>
204      </td>
205    </tr>
206    <tr>
207      <td style="vertical-align: top;"><br>
208      </td>
209      <td style="vertical-align: top;"><br>
210      </td>
211      <td style="vertical-align: top;"><br>
212      </td>
213      <td style="vertical-align: top;"><br>
214      </td>
215      <td style="vertical-align: top;">B<br>
216      </td>
217      <td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
218      <br>
219Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
220      </td>
221      <td style="vertical-align: top;">user_statistics<br>
222      <br>
223trunk/UTIL/Makefile<br>
224      </td>
225    </tr>
226<tr>
227      <td style="vertical-align: top;">05/02/10<br>
228      </td>
229      <td style="vertical-align: top;">SR<br>
230      </td>
231      <td style="vertical-align: top;">485<br>
232      </td>
233      <td style="vertical-align: top;">3.7a<br>
234      </td>
235      <td style="vertical-align: top;">B<br>
236      </td>
237      <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>
238changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
239some global statistics (e.g. total kinetic energy) have wrong values.<br>
240      </td>
241      <td style="vertical-align: top;">init_3d_model, modules<br>
242      </td>
243    </tr>
244    <tr>
245      <td style="vertical-align: top;">05/02/10<br>
246      </td>
247      <td style="vertical-align: top;">SR<br>
248      </td>
249      <td style="vertical-align: top;">484<br>
250      </td>
251      <td style="vertical-align: top;">3.7a<br>
252      </td>
253      <td style="vertical-align: top;">B<br>
254      </td>
255      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
256      </td>
257      <td style="vertical-align: top;">many<br>
258      </td>
259    </tr>
260<tr>
261      <td style="vertical-align: top; width: 27px;">05/02/10<br>
262      </td>
263      <td style="vertical-align: top; width: 38px;">SR<br>
264      </td>
265      <td style="vertical-align: top; width: 42px;">483<br>
266      </td>
267      <td style="vertical-align: top; width: 40px;">3.7a<br>
268      </td>
269      <td style="vertical-align: top; width: 27px;">N<br>
270      </td>
271      <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>
272      <br>
273make 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>
274      <br>
275      <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;">
276wall_scalarflux</span> are the corresponding new inipar parameters.<br>
277(<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>
278      <br>
279Large scale vertical motion (subsidence/ascent) can be added as
280additional source to the prognostic equation for potential temperature.
281See 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>
282      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
283      <br>
284A 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>
285      <br>
286Masked data output has been implemented but it is not documented in the
287user manual so far. This feature can already use NetCDF4 file format.
288(check_open, check_parameters, close_file, modules, netcdf, parin,
289time_integration, user_parin, new: data_output_mask, init_masks,
290user_data_output_mask)<br>
291      </td>
292      <td style="vertical-align: top; width: 189px;">check_open, check
293parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
294netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
295      <br><span style="font-weight: bold;">
296new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
297<br>
298      </td>
299    </tr>
300    <tr>
301      <td style="vertical-align: top; width: 27px;"><br>
302      </td>
303      <td style="vertical-align: top; width: 38px;"><br>
304      </td>
305      <td style="vertical-align: top; width: 42px;"><br>
306      </td>
307      <td style="vertical-align: top; width: 40px;"><br>
308      </td>
309      <td style="vertical-align: top; width: 27px;">C<br>
310      </td>
311      <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>
312      <br><span style="font-family: Courier New,Courier,monospace;">
313var_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>
314      <br>
315Every cloud droplet has now an own weighting factor and can be deleted
316due to collisions. Condensation and collision of cloud droplets are
317adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
318      <br>
319Collision 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>
320      </td>
321      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
322      </td>
323    </tr>
324    <tr>
325      <td style="vertical-align: top; width: 27px;"><br>
326      </td>
327      <td style="vertical-align: top; width: 38px;"><br>
328      </td>
329      <td style="vertical-align: top; width: 42px;"><br>
330      </td>
331      <td style="vertical-align: top; width: 40px;"><br>
332      </td>
333      <td style="vertical-align: top; width: 27px;">B<br>
334      </td>
335      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
336      <br>
337Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
338      <br>
339Dimension 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>
340      <br>
341Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
342      <br>
343Bugfix: 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>
344      <br>
345Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
346      <br>
347Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
348      <br>
349Bugfix: 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>
350      <br>
351Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
352      <br>
353Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
354      <br>
355Bugfix 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>
356      </td>
357      <td style="vertical-align: top; width: 189px;">advec_particles,
358calc_precipitation, collision_efficiency, disturb_field, header,
359modules, poisfft_hybrid, subjob, sum_up_3d_data,
360time_integration<br>
361<br>
362      </td>
363    </tr>
364    <tr>
365      <td style="vertical-align: top; width: 27px;">23/09/09<br>
366      </td>
367      <td style="vertical-align: top; width: 38px;">SR<br>
368      </td>
369      <td style="vertical-align: top; width: 42px;">392<br>
370      </td>
371      <td style="vertical-align: top; width: 40px;">3.7<br>
372      </td>
373      <td style="vertical-align: top; width: 27px;">N<br>
374      </td>
375      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
376important changes:</span>
377atmosphere-ocean coupling has been improved and steering of
378dvr-software is more user-friendly now. Beside that, the release
379contains a lot of optimizations, changes, and bugfixes which have
380accumulated over the last months.<br>
381
382      <br>
383
384The atmosphere-ocean coupling allows to use independent precursor runs
385in order to account for different spin-up times. The time when coupling
386has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
387The 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
388order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
389output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
390      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
391      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
392      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
393      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
394      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
395      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
396      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
397      <span style="font-family: Courier New,Courier,monospace;">header</span>,
398      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
399      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
400      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
401      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
402      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
403      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
404      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
405      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
406
407      <br>
408
409Clipping of dvrp output implemented. Default colourtable for particles
410implemented, particle attributes (color, dvrp_size) can be set with new
411parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
412      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
413      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
414      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
415Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
416and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
417(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
418      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
419      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
420      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
421      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
422
423      <br>
424
425Polygon reduction for topography and ground plate isosurface. Reduction
426level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
427
428      <br>
429
430Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
431/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
432in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
433
434      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
435for speed optimization. This gives a significant speedup of more than
43610%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
437      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
438      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
439      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
440      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
441
442      <br>
443
444Scripts 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>
445
446      <br>
447
448Additional timestep criterion in case of simulations with plant canopy.
449(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
450
451      <br>
452
453Check 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
454exceed <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>
455
456      <br>
457
458External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
459      <span style="font-family: Courier New,Courier,monospace;">header</span>,
460      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
461      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
462      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
463      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
464      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
465      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
466
467      <br>
468
469New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
470(<span style="font-family: Courier New,Courier,monospace;">header</span>,
471      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
472      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
473      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
474      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
475      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
476      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
477      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
478      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
479
480      <br>
481
482Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
483(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
484      <span style="font-family: Courier New,Courier,monospace;">header</span>,
485      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
486      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
487      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
488      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
489      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
490
491      <br>
492
493Option 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>,
494      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
495
496      <br>
497
498xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
499      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
500      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
501      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
502      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
503      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
504      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
505      <td style="vertical-align: top; width: 189px;">average_3d_data,
506check_for_restart, check_parameters, data_output_2d, data_output_3d,
507data_output_dvrp, data_output_profiles, data_output_ptseries,
508data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
509diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
510header, mbuild, modules, mrun, package_parin, parin,
511prognostic_equations, read_3d_binary, read_var_list, subjob,
512sum_up_3d_data, surface_coupler, timestep, time_integration,
513user_check_parameters, user_data_output_2d, user_data_output_dvrp,
514user_header, user_init_grid, write_3d_binary, write_var_list<br>
515
516      <br>
517
518      <span style="font-weight: bold;">new:</span>
519set_particle_attributes, set_slicer_attributes_dvrp</td>
520    </tr>
521    <tr>
522      <td style="vertical-align: top; width: 27px;"><br>
523      </td>
524      <td style="vertical-align: top; width: 38px;"><br>
525      </td>
526      <td style="vertical-align: top; width: 42px;"><br>
527      </td>
528      <td style="vertical-align: top; width: 40px;"><br>
529      </td>
530      <td style="vertical-align: top; width: 27px;">C<br>
531      </td>
532      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
533message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
534      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
535      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
536      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
537      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
538      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
539      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
540      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
541      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
542      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
543      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
544      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
545      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
546      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
547      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
548      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
549      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
550      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
551      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
552      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
553      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
554      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
555      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
556      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
557      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
558      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
559      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
560      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
561      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
562      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
563      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
564      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
565      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
566      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
567      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
568      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
569      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
570      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
571      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
572      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
573
574      <br>
575
576Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
577      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
578      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
579      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
580      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
581      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
582      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
583      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
584      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
585
586      <br>
587
588__lcmuk changed to __lc to avoid problems with Intel compiler on
589sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
590
591      <br>
592
593For extended NetCDF files, the updated title attribute includes an
594update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
595
596      <br>
597
598In case of restart runs without extension, initial profiles are not
599written to NetCDF-file anymore. So far, time axis always started at
600t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
601      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
602      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
603      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
604
605      <br>
606
607      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
608'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
609can now <br>
610
611be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
612(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
613      <span style="font-family: Courier New,Courier,monospace;">header</span>,
614      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
615
616      <br>
617
6182 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
619
620      <br>
621
622A link to the webspage appendix_a.html is printed for further
623information about possible reasons of the error that appeared. (message)<br>
624
625      <br>
626
627Temperature gradient criterion for estimating the boundary layer height
628replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
629
630      <br>
631
632NetCDF unit attribute in timeseries output in case of statistic regions
633added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
634
635      <br>
636
637Maximum number of tails is calculated from maximum number of particles
638and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
639(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
640
641      <br>
642
643Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
644is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
645      <span style="font-family: Courier New,Courier,monospace;">header</span>,
646      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
647      <br>
648
649      <br>
650
651First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
652defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
653
654      <br>
655
656Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
657moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
658to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
659(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
660
661      <br>
662
663      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
664moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
665to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
666(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
667      <span style="font-family: Courier New,Courier,monospace;">header</span>,
668      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
669      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
670      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
671      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
672      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
673      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
674      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
675
676      <br>
677
678Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
679changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
680
681      <br>
682
683Adjustments for runs on lcxt4 (necessary due to a software update on
684CRAY) 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>
685      <td style="vertical-align: top; width: 189px;">advec_particles,
686advec_s_bc,
687buoyancy, calc_spectra, check_for_restart, check_open,
688check_parameters, close_file, coriolis, cpu_log, data_output_2d,
689data_output_3d, data_output_dvrp, data_output_profiles,
690data_output_ptseries, data_output_spectra, data_output_tseries,
691eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
692init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
693message, mrun, netcdf, package_parin, parin, plant_canopy_model,
694poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
695surface_coupler, temperton_fft, timestep,
696user_actions,user_check_parameters, user_data_output_dvrp,
697user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
698user_parin, user_read_restart_data, user_spectra, write_var_list </td>
699    </tr>
700    <tr>
701      <td style="vertical-align: top; width: 27px;"><br>
702      </td>
703      <td style="vertical-align: top; width: 38px;"><br>
704      </td>
705      <td style="vertical-align: top; width: 42px;"><br>
706      </td>
707      <td style="vertical-align: top; width: 40px;"><br>
708      </td>
709      <td style="vertical-align: top; width: 27px;">B<br>
710      </td>
711      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
712pressure profile in case of ocean runs is now calculated in 5 iteration
713steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
714
715      <br>
716
717Bugfix: wrong sign in buoyancy production of ocean part in case of not
718using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
719(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
720
721      <br>
722
723Bugfix: output of averaged 2d/3d quantities requires that an avaraging
724interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
725
726      <br>
727
728Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
729(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
730
731      <br>
732
733Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
734(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
735
736      <br>
737
738Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
739if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
740is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
741and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
742calls. This implies a possible performance loss; an alternative
743strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
744
745      <br>
746
747Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
748
749      <br>
750
751Bugfix: 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>
752
753      <br>
754
755Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
756=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
757for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
758      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
759
760      <br>
761
762Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
763becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
764
765      <br>
766
767Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
768
769      <br>
770
771Bugfix: error in check, if particles moved further than one subdomain
772length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
773
774      <br>
775
776Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
777is only written to file if its third index is &gt; 0, arrays for tails
778are allocated with a minimum size of 10 tails if there is no tail
779initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
780      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
781
782      <br>
783
784Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
785
786      <br>
787
788Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
789changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
790NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
791
792      <br>
793
794Bugfix: output of particle time series only if particle advection is
795switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
796
797      <br>
798
799Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
800= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
801(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
802
803      <br>
804
805Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
806z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
807
808      <br>
809
810Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
811
812      <br>
813
814If the inversion height calculated by the prerun is zero,
815inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
816
817      <br>
818
819Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
820
821      <br>
822
823Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
824removed from the restart file, because otherwise, no change from a
825fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
826      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
827
828      <br>
829
830Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
831in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
832      <td style="vertical-align: top; width: 189px;">advec_particles,
833check_parameters, cpu_log, data_output_2d, data_output_3d, header,
834init_3d_model, init_particles, init_ocean, modules, netcdf,
835prandtl_fluxes, production_e, read_var_list, time_integration,
836user_last_actions, write_var_list<br>
837
838      </td>
839    </tr>
840    <tr>
841      <td style="vertical-align: top; width: 27px;">02/02/09<br>
842      </td>
843      <td style="vertical-align: top; width: 38px;">SR<br>
844      </td>
845      <td style="vertical-align: top; width: 42px;">228<br>
846      </td>
847      <td style="vertical-align: top; width: 40px;">3.6<br>
848      </td>
849      <td style="vertical-align: top; width: 27px;">N<br>
850      </td>
851      <td style="vertical-align: top; width: 497px;">This
852release contains further additions, changes, and bugfixes for the
853SGI-ICE system, as well as important changes like the splitting of the
854user-interface into single files, a complete revision of the
855pre-compiling mechanism allowing to use different make-depositories
856simultaneously, and a revision of the reading-mechanism from restart
857files, which has no more restrictions in case that the previous and
858current run have different domain/subdomain sizes. A new handling of
859all kind of output messages is introduced with this release and will be
860applied to all existing messages within the next releases.<br>
861
862      <br>
863
864      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
865
866      <br>
867
868Restart runs on SGI-ICE are working. (mrun)<br>
869
8702d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
871
872      <br>
873
874Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
875case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
876"<span style="font-style: italic;">-K parallel</span>" for coupling.
877Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
878      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
879for lcxt4.<br>
880
881      <br>
882
883DVRP arguments changed to single precision, mode pathlines added.<br>
884
885      <br>
886
887User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
888
889      <br>
890
891User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
892      <td style="vertical-align: top; width: 189px;">check_for_restart,
893check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
894modules, package_parin, palm, surface_coupler, timestep<br>
895
896      <br>
897
898Makefile,&nbsp;mbuild, mrun, subjob<br>
899
900      <br>
901
902      <span style="font-weight: bold;">new:</span><br>
903
904init_coupling, user_additional_routines, user_check_parameters</td>
905    </tr>
906    <tr>
907      <td style="vertical-align: top; width: 27px;"><br>
908      </td>
909      <td style="vertical-align: top; width: 38px;"><br>
910      </td>
911      <td style="vertical-align: top; width: 42px;"><br>
912      </td>
913      <td style="vertical-align: top; width: 40px;"><br>
914      </td>
915      <td style="vertical-align: top; width: 27px;">C<br>
916      </td>
917      <td style="vertical-align: top; width: 497px;">User interface has been
918split into single files.<br>
919
920      <br>
921
922Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
923changed to INTEGER(8) in order to avoid "out of range" problems, which
924result in measured negative time intervals. (cpu_log, local_tremain,
925local_tremain_ini)<br>
926
927      <br>
928
929Reading mechanism from restart files
930completely revised. The subdomain/total domain size is now allowed to
931vary arbitrarily between the current and previous run. (read_var_list,
932read_3d_binary, user_read_restart_data)<br>
933
934      <br>
935
936Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
937completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
938One depository per block (given in the config-file) is created. Always
939all files from the source directory are copied to the respective
940depository. No additional file checks are done any more (mrun version
9412.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
942"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
943(mbuild, mrun)<br>
944
945      <br>
946
947Output messages (including required stop of execution) can now be
948handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
949All output messages will be replaced by this routine step by step
950within the next revisions.<br>
951
952      <br>
953
954Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
955explicitly set for better reading, although this has been already done
956in boundary_conds. (advec_s_bc)<br>
957
958      <br>
959
960Origin of the xy-coordinate system shifted from the center of the first
961grid 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
962south-left corner of this cell. (netcdf) Topography definition
963according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
964(init_grid, modules, user_header, user_init_grid, user_parin)</td>
965      <td style="vertical-align: top; width: 189px;">advec_s_bc,
966check_parameters, cpu_log, init_grid, local_stop, local_tremain,
967local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
968user_read_restart_data<br>
969
970      <br>
971
972Makefile, mbuild, mrun<br>
973
974      <br>
975
976      <span style="font-weight: bold;">removed:</span><br>
977
978user_interface<br>
979
980      <br>
981
982      <span style="font-weight: bold;">new:</span><br>
983
984message,
985user_3d_data_averaging, user_actions, user_advec_particles,
986user_check_data_output, user_check_data_output_pr, user_data_output_2d,
987user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
988user_dvrp_coltab, user_header, user_init_3d_model, user_init,
989user_init_grid, user_init_particles, user_init_plant_canopy,
990user_last_actions, user_parin, user_parin, user_particle_attributes,
991user_read_restart_data, user_spectra, user_statistics</td>
992    </tr>
993    <tr>
994      <td style="vertical-align: top; width: 27px;"><br>
995      </td>
996      <td style="vertical-align: top; width: 38px;"><br>
997      </td>
998      <td style="vertical-align: top; width: 42px;"><br>
999      </td>
1000      <td style="vertical-align: top; width: 40px;"><br>
1001      </td>
1002      <td style="vertical-align: top; width: 27px;">B<br>
1003      </td>
1004      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
1005reallocated in case that multigrid is used. (calc_spectra)<br>
1006
1007      <br>
1008
1009Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
1010inflow_turbulence,&nbsp;timestep)<br>
1011
1012      <br>
1013
1014Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
1015      </span>adjusted to the required output size (1 gridpoint less,
1016along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
1017in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
1018compiler. (combine_plot_fields)<br>
1019
1020      <br>
1021
1022Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
1023case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
1024(header)<br>
1025
1026      <br>
1027
1028Inconsistency
1029removed: as the thermal stratification is not taken into account for
1030the evaluation of the wall fluxes at vertical walls, the eddy viscosity
1031      <span style="font-family: Courier New,Courier,monospace;">km</span>
1032must 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>.
1033(production_e)<br>
1034
1035      <br>
1036
1037Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
1038case of oceans runs. (sort_particles)<br>
1039
1040      <br>
1041
1042Bugfix: no output of particle concentration and radius unless particles
1043have been started. (data_output_2d)<br>
1044
1045      <br>
1046
1047Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
1048from restart files ignored if total numbers of grid points do not
1049match. (read_3d_binary)<br>
1050
1051      <br>
1052
1053Bugfix: abort in case that absolute temperature is below zero.
1054(init_cloud_physics)</td>
1055      <td style="vertical-align: top; width: 189px;">advec_particles,
1056calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
1057header, inflow_turbulence, init_cloud_physics, production_e,
1058read_3d_binary, timestep<br>
1059
1060      <br>
1061
1062combine_plot_fields</td>
1063    </tr>
1064  </tbody>
1065</table>
1066<b><blink></blink></b><br>&nbsp;
1067<br>&nbsp;
1068<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
1069to change the source
1070code and how to document modifications<br>
1071</h2>Currently
1072(Sep 23rd, 2009), only selected users are allowed to commit changes to
1073the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
1074<br>
1075<ol>
1076  <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>".
1077Additionally, document all changes in a local file (e.g.
1078~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
1079have been changed. Classify changes in three cases, new (N), changed
1080(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>
1081    <br>
1082  </li>
1083  <li>Test the changed version, unless it works sufficiently.<br>
1084    <br>
1085  </li>
1086 
1087  <li>Commit the changes to the repository<br>
1088    <br>
1089    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
1090    </span><br>
1091where "<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>
1092    <br>
1093Alternatively, in case that you have made quite a lot of changes, you
1094can also give the contents of your file CURRENT_MODIFICATIONS as the
1095log message:<br>
1096    <br>
1097    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
1098    <br>
1099  </li>
1100
1101  <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>
1102    <br>
1103  </li>
1104  <li>Move the change comments in the file headers from "Current
1105revisions:" to "Former revisions:". Set the current svn id in front of
1106that.<br>
1107    <br>
1108    <span style="font-weight: bold;">Example:</span><br>
1109    <br>
1110    <span style="font-weight: bold;">before move:</span><br>
1111    <br>
1112    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1113    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1114    <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;">
1115    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1116    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1117    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1118    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
1119    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1120    <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;">
1121    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
1122    <br>
1123    <span style="font-weight: bold;">after move:</span><br>
1124    <br>
1125    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1126
1127    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1128
1129    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
1130
1131    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1132
1133    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
1134
1135    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
1136
1137    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $<br>
1138!</span><br style="font-family: Courier New,Courier,monospace;">
1139    <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>
1140! </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;">
1141
1142    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
1143
1144    <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;">
1145
1146    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1147 </span><br>
1148  </li>
1149  <li>Commit the changes in the technical documentation and the file headers:<br>
1150    <br>
1151    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1152    <br>
1153 <br>
1154  </li>
1155</ol>
1156
1157<h2>
1158<a name="Kapitel3.0"></a>3.0&nbsp; Description
1159of selected parts of the
1160model source code</h2>
1161<b></b>
1162<p>This section gives links to existing descriptions about special
1163parts of the PALM code, e.g. special numerical methods that are used
1164(including mathematical background). Documents are stored in single
1165files with different formats. Some are in German (sorry for the
1166inconvenience).
1167<br>&nbsp;
1168</p><ul> <li> <a name="UPS"></a>upstream-spline
1169advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1170, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1171physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1172)</li> 
1173  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1174  </li>
1175  <li>Runge-Kutta
1176time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1177, only in German)</li>
1178
1179</ul><br>
1180&nbsp;
1181<br>&nbsp;
1182<br>&nbsp;
1183<br>&nbsp;
1184<br>&nbsp;
1185<br>&nbsp;
1186<br>&nbsp;
1187<br>&nbsp;
1188</body></html>
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