source: palm/trunk/DOC/tec/technical_documentation.html @ 493

Last change on this file since 493 was 493, checked in by raasch, 14 years ago

New:
---
Output in NetCDF4-format. New d3par-parameter netcdf_data_format.

(check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin)

Modules to be loaded for compilation (mbuild) or job execution (mrun)
can be given in the configuration file using variable modules. Example:

%modules ifort/11.0.069:netcdf lcsgih parallel

This method replaces the (undocumented) mpilib-variable.

WARNING: All fixed settings of modules in the scripts mbuild, mrun, and subjob
have been removed! Please set the modules variable appropriately in your
configuration file. (mbuild, mrun, subjob)

Changed:


Parameters netcdf_64bit and netcdf_64bit_3d have been removed. Use
netcdf_data_format = 2 for choosing the classic 64bit-offset format (this is
the default). The offset-format can not be set independently for the
3d-output-data any more.

Parameters netcdf_format_mask, netcdf_format_mask_av, and variables
nc_format_mask, format_parallel_io removed. They are replaced by the new
parameter netcdf_data_format. (check_open, close_file,
data_output_mask, header, init_masks, modules, parin)

Errors:


bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config

Bugfix: timeseries data have to be collected by PE0 (user_statistics)

  • Property svn:keywords set to Id
File size: 54.5 KB
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1<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
2<html><head>
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11<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;
12</font>a
13<b>pa</b>rallelized
14<b>L</b>ES <b>m</b>odel
15<br><hr width="100%">
16<br><font size="+2">technical/numerical documentation</font>
17<br>&nbsp;
18<br>&nbsp;
19<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>&nbsp; <br> </caption><tbody>
20</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
21</span></td> </tr>
22<tr nosave=""> <td nosave=""><b>Last
23change of this document</b>:&nbsp;</td> <td nosave=""><b>$Id: technical_documentation.html 493 2010-03-01 08:30:24Z raasch $</b></td> </tr>
24</tbody>
25</table><hr width="100%">
26<p><font size="+2">Table of contents</font>
27<br>&nbsp;
28<br>&nbsp;
29</p><ul> <a href="#Kapitel1.0">1.0</a>&nbsp;
30History of changes <p><a href="#Kapitel2.0">2.0</a>&nbsp;
31How to change the source
32code and how to document modifications<br>
33 </p> <p><a href="#Kapitel3.0">3.0</a>&nbsp;
34Description of selected model numerics<br>
35&nbsp;</p>
36</ul><b></b><br>
37
38<h2><a name="Kapitel1.0"></a>1.0&nbsp;
39History of changes</h2>
40The 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>
41<br>
42Entries in the fifth column specify the type of the change:
43change&nbsp;
44of existing code (C), new code (N) or bugfix (B). More detailed
45information
46about the changes may sometimes be found in the header comment lines of the
47respective
48routines.
49<br>&nbsp;
50<br>
51<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
52  <tbody>
53    <tr>
54      <td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
55      </td>
56      <td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
57      </td>
58      <td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
59      </td>
60      <td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
61      </td>
62      <td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
63      </td>
64      <td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
65      </td>
66      <td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
67      </td>
68    </tr>
69   
70   
71   
72   
73   
74   
75   
76   
77   
78   
79    <tr>
80      <td style="vertical-align: top;">05/02/10<br>
81      </td>
82      <td style="vertical-align: top;">SR<br>
83      </td>
84      <td style="vertical-align: top;">485<br>
85      </td>
86      <td style="vertical-align: top;"><br>
87      </td>
88      <td style="vertical-align: top;"><br>
89      </td>
90      <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>
91changed to 64 bit. Otherwise, on large grids &gt; 2*10**9 grid points
92some global statistics (e.g. total kinetic energy) have wrong values.<br>
93      </td>
94      <td style="vertical-align: top;">init_3d_model, modules<br>
95      </td>
96    </tr>
97    <tr>
98      <td style="vertical-align: top;">05/02/10<br>
99      </td>
100      <td style="vertical-align: top;">SR<br>
101      </td>
102      <td style="vertical-align: top;">484<br>
103      </td>
104      <td style="vertical-align: top;"><br>
105      </td>
106      <td style="vertical-align: top;">B<br>
107      </td>
108      <td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
109      </td>
110      <td style="vertical-align: top;">many<br>
111      </td>
112    </tr>
113<tr>
114      <td style="vertical-align: top; width: 27px;">05/02/10<br>
115      </td>
116      <td style="vertical-align: top; width: 38px;">SR<br>
117      </td>
118      <td style="vertical-align: top; width: 42px;">483<br>
119      </td>
120      <td style="vertical-align: top; width: 40px;">3.7a<br>
121      </td>
122      <td style="vertical-align: top; width: 27px;">N<br>
123      </td>
124      <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>
125      <br>
126make 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>
127      <br>
128      <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;">
129wall_scalarflux</span> are the corresponding new inipar parameters.<br>
130(<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>
131      <br>
132Large scale vertical motion (subsidence/ascent) can be added as
133additional source to the prognostic equation for potential temperature.
134See 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>
135      <br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
136      <br>
137A 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>
138      <br>
139Masked data output has been implemented but it is not documented in the
140user manual so far. This feature can already use NetCDF4 file format.
141(check_open, check_parameters, close_file, modules, netcdf, parin,
142time_integration, user_parin, new: data_output_mask, init_masks,
143user_data_output_mask)<br>
144      </td>
145      <td style="vertical-align: top; width: 189px;">check_open, check
146parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
147netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
148      <br><span style="font-weight: bold;">
149new:</span> data_output_mask,&nbsp; init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
150<br>
151      </td>
152    </tr>
153    <tr>
154      <td style="vertical-align: top; width: 27px;"><br>
155      </td>
156      <td style="vertical-align: top; width: 38px;"><br>
157      </td>
158      <td style="vertical-align: top; width: 42px;"><br>
159      </td>
160      <td style="vertical-align: top; width: 40px;"><br>
161      </td>
162      <td style="vertical-align: top; width: 27px;">C<br>
163      </td>
164      <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>
165      <br><span style="font-family: Courier New,Courier,monospace;">
166var_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>
167      <br>
168Every cloud droplet has now an own weighting factor and can be deleted
169due to collisions. Condensation and collision of cloud droplets are
170adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
171      <br>
172Collision 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>
173      </td>
174      <td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
175      </td>
176    </tr>
177    <tr>
178      <td style="vertical-align: top; width: 27px;"><br>
179      </td>
180      <td style="vertical-align: top; width: 38px;"><br>
181      </td>
182      <td style="vertical-align: top; width: 42px;"><br>
183      </td>
184      <td style="vertical-align: top; width: 40px;"><br>
185      </td>
186      <td style="vertical-align: top; width: 27px;">B<br>
187      </td>
188      <td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
189      <br>
190Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
191      <br>
192Dimension 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>
193      <br>
194Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
195      <br>
196Bugfix: 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>
197      <br>
198Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
199      <br>
200Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
201      <br>
202Bugfix: 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>
203      <br>
204Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
205      <br>
206Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
207      <br>
208Bugfix 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>
209      </td>
210      <td style="vertical-align: top; width: 189px;">advec_particles,
211calc_precipitation, collision_efficiency, disturb_field, header,
212modules, poisfft_hybrid, subjob, sum_up_3d_data,
213time_integration<br>
214<br>
215      </td>
216    </tr>
217    <tr>
218      <td style="vertical-align: top; width: 27px;">23/09/09<br>
219      </td>
220      <td style="vertical-align: top; width: 38px;">SR<br>
221      </td>
222      <td style="vertical-align: top; width: 42px;">392<br>
223      </td>
224      <td style="vertical-align: top; width: 40px;">3.7<br>
225      </td>
226      <td style="vertical-align: top; width: 27px;">N<br>
227      </td>
228      <td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
229important changes:</span>
230atmosphere-ocean coupling has been improved and steering of
231dvr-software is more user-friendly now. Beside that, the release
232contains a lot of optimizations, changes, and bugfixes which have
233accumulated over the last months.<br>
234
235      <br>
236
237The atmosphere-ocean coupling allows to use independent precursor runs
238in order to account for different spin-up times. The time when coupling
239has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
240The 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
241order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
242output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
243      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
244      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
245      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
246      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
247      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
248      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
249      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
250      <span style="font-family: Courier New,Courier,monospace;">header</span>,
251      <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
252      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
253      <span style="font-family: Courier New,Courier,monospace;">mrun</span>,
254      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
255      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
256      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
257      <span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
258      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
259
260      <br>
261
262Clipping of dvrp output implemented. Default colourtable for particles
263implemented, particle attributes (color, dvrp_size) can be set with new
264parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
265      <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
266      <span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
267      <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
268Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
269and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
270(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
271      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
272      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
273      <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,&nbsp;
274      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
275
276      <br>
277
278Polygon reduction for topography and ground plate isosurface. Reduction
279level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
280
281      <br>
282
283Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
284/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>&nbsp;
285in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
286
287      <span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
288for speed optimization. This gives a significant speedup of more than
28910%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
290      <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
291      <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
292      <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
293      <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
294
295      <br>
296
297Scripts 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>
298
299      <br>
300
301Additional timestep criterion in case of simulations with plant canopy.
302(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
303
304      <br>
305
306Check 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
307exceed <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>
308
309      <br>
310
311External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
312      <span style="font-family: Courier New,Courier,monospace;">header</span>,
313      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
314      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
315      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
316      <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
317      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
318      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
319
320      <br>
321
322New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
323(<span style="font-family: Courier New,Courier,monospace;">header</span>,
324      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
325      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
326      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
327      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
328      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
329      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
330      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
331      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
332
333      <br>
334
335Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
336(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
337      <span style="font-family: Courier New,Courier,monospace;">header</span>,
338      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
339      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
340      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
341      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
342      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
343
344      <br>
345
346Option 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>,
347      <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
348
349      <br>
350
351xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
352      <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
353      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
354      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
355      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
356      <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
357      <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
358      <td style="vertical-align: top; width: 189px;">average_3d_data,
359check_for_restart, check_parameters, data_output_2d, data_output_3d,
360data_output_dvrp, data_output_profiles, data_output_ptseries,
361data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
362diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
363header, mbuild, modules, mrun, package_parin, parin,
364prognostic_equations, read_3d_binary, read_var_list, subjob,
365sum_up_3d_data, surface_coupler, timestep, time_integration,
366user_check_parameters, user_data_output_2d, user_data_output_dvrp,
367user_header, user_init_grid, write_3d_binary, write_var_list<br>
368
369      <br>
370
371      <span style="font-weight: bold;">new:</span>
372set_particle_attributes, set_slicer_attributes_dvrp</td>
373    </tr>
374    <tr>
375      <td style="vertical-align: top; width: 27px;"><br>
376      </td>
377      <td style="vertical-align: top; width: 38px;"><br>
378      </td>
379      <td style="vertical-align: top; width: 42px;"><br>
380      </td>
381      <td style="vertical-align: top; width: 40px;"><br>
382      </td>
383      <td style="vertical-align: top; width: 27px;">C<br>
384      </td>
385      <td style="vertical-align: top; width: 497px;">Output of messages replaced by
386message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
387      <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
388      <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
389      <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
390      <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
391      <span style="font-family: Courier New,Courier,monospace;">check_open</span>,
392      <span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
393      <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
394      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
395      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
396      <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
397      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
398      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
399      <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
400      <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
401      <span style="font-family: Courier New,Courier,monospace;">header</span>,&nbsp;
402      <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
403      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
404      <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
405      <span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
406      <span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
407      <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
408      <span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
409      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
410      <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
411      <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
412      <span style="font-family: Courier New,Courier,monospace;">poismg</span>,
413      <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
414      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
415      <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
416      <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
417      <span style="font-family: Courier New,Courier,monospace;">timestep</span>,
418      <span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
419      <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
420      <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
421      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
422      <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
423      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
424      <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
425      <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
426
427      <br>
428
429Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
430      <span style="font-family: Courier New,Courier,monospace;">close_file</span>,
431      <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
432      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
433      <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
434      <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
435      <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,&nbsp;
436      <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
437      <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
438
439      <br>
440
441__lcmuk changed to __lc to avoid problems with Intel compiler on
442sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
443
444      <br>
445
446For extended NetCDF files, the updated title attribute includes an
447update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
448
449      <br>
450
451In case of restart runs without extension, initial profiles are not
452written to NetCDF-file anymore. So far, time axis always started at
453t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
454      <span style="font-family: Courier New,Courier,monospace;">modules</span>,
455      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
456      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
457
458      <br>
459
460      <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
461'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
462can now <br>
463
464be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
465(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
466      <span style="font-family: Courier New,Courier,monospace;">header</span>,
467      <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
468
469      <br>
470
4712 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
472
473      <br>
474
475A link to the webspage appendix_a.html is printed for further
476information about possible reasons of the error that appeared. (message)<br>
477
478      <br>
479
480Temperature gradient criterion for estimating the boundary layer height
481replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
482
483      <br>
484
485NetCDF unit attribute in timeseries output in case of statistic regions
486added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
487
488      <br>
489
490Maximum number of tails is calculated from maximum number of particles
491and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
492(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
493
494      <br>
495
496Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
497is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
498      <span style="font-family: Courier New,Courier,monospace;">header</span>,
499      <span style="font-family: Courier New,Courier,monospace;">modules</span>)
500      <br>
501
502      <br>
503
504First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
505defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
506
507      <br>
508
509Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
510moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
511to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
512(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
513
514      <br>
515
516      <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
517moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
518to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
519(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
520      <span style="font-family: Courier New,Courier,monospace;">header</span>,
521      <span style="font-family: Courier New,Courier,monospace;">parin</span>,
522      <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
523      <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
524      <span style="font-family: Courier New,Courier,monospace;">user_header</span>,
525      <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
526      <span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
527      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
528
529      <br>
530
531Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
532changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
533
534      <br>
535
536Adjustments for runs on lcxt4 (necessary due to a software update on
537CRAY) 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>
538      <td style="vertical-align: top; width: 189px;">advec_particles,
539advec_s_bc,
540buoyancy, calc_spectra, check_for_restart, check_open,
541check_parameters, close_file, coriolis, cpu_log, data_output_2d,
542data_output_3d, data_output_dvrp, data_output_profiles,
543data_output_ptseries, data_output_spectra, data_output_tseries,
544eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
545init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
546message, mrun, netcdf, package_parin, parin, plant_canopy_model,
547poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
548surface_coupler, temperton_fft, timestep,
549user_actions,user_check_parameters, user_data_output_dvrp,
550user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
551user_parin, user_read_restart_data, user_spectra, write_var_list </td>
552    </tr>
553    <tr>
554      <td style="vertical-align: top; width: 27px;"><br>
555      </td>
556      <td style="vertical-align: top; width: 38px;"><br>
557      </td>
558      <td style="vertical-align: top; width: 42px;"><br>
559      </td>
560      <td style="vertical-align: top; width: 40px;"><br>
561      </td>
562      <td style="vertical-align: top; width: 27px;">B<br>
563      </td>
564      <td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
565pressure profile in case of ocean runs is now calculated in 5 iteration
566steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
567
568      <br>
569
570Bugfix: wrong sign in buoyancy production of ocean part in case of not
571using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
572(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
573
574      <br>
575
576Bugfix: output of averaged 2d/3d quantities requires that an avaraging
577interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
578
579      <br>
580
581Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
582(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
583
584      <br>
585
586Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
587(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
588
589      <br>
590
591Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
592if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
593is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
594and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
595calls. This implies a possible performance loss; an alternative
596strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
597
598      <br>
599
600Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
601
602      <br>
603
604Bugfix: 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>
605
606      <br>
607
608Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
609=&gt; <span style="font-family: Courier New,Courier,monospace;">s_av</span>
610for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
611      <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
612
613      <br>
614
615Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
616becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
617
618      <br>
619
620Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
621
622      <br>
623
624Bugfix: error in check, if particles moved further than one subdomain
625length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
626
627      <br>
628
629Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
630is only written to file if its third index is &gt; 0, arrays for tails
631are allocated with a minimum size of 10 tails if there is no tail
632initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
633      <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
634
635      <br>
636
637Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
638
639      <br>
640
641Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
642changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
643NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
644
645      <br>
646
647Bugfix: output of particle time series only if particle advection is
648switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
649
650      <br>
651
652Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
653= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
654(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
655
656      <br>
657
658Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
659z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
660
661      <br>
662
663Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
664
665      <br>
666
667If the inversion height calculated by the prerun is zero,
668inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
669
670      <br>
671
672Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
673
674      <br>
675
676Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
677removed from the restart file, because otherwise, no change from a
678fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
679      <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
680
681      <br>
682
683Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
684in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
685      <td style="vertical-align: top; width: 189px;">advec_particles,
686check_parameters, cpu_log, data_output_2d, data_output_3d, header,
687init_3d_model, init_particles, init_ocean, modules, netcdf,
688prandtl_fluxes, production_e, read_var_list, time_integration,
689user_last_actions, write_var_list<br>
690
691      </td>
692    </tr>
693    <tr>
694      <td style="vertical-align: top; width: 27px;">02/02/09<br>
695      </td>
696      <td style="vertical-align: top; width: 38px;">SR<br>
697      </td>
698      <td style="vertical-align: top; width: 42px;">228<br>
699      </td>
700      <td style="vertical-align: top; width: 40px;">3.6<br>
701      </td>
702      <td style="vertical-align: top; width: 27px;">N<br>
703      </td>
704      <td style="vertical-align: top; width: 497px;">This
705release contains further additions, changes, and bugfixes for the
706SGI-ICE system, as well as important changes like the splitting of the
707user-interface into single files, a complete revision of the
708pre-compiling mechanism allowing to use different make-depositories
709simultaneously, and a revision of the reading-mechanism from restart
710files, which has no more restrictions in case that the previous and
711current run have different domain/subdomain sizes. A new handling of
712all kind of output messages is introduced with this release and will be
713applied to all existing messages within the next releases.<br>
714
715      <br>
716
717      <span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
718
719      <br>
720
721Restart runs on SGI-ICE are working. (mrun)<br>
722
7232d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
724
725      <br>
726
727Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
728case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
729"<span style="font-style: italic;">-K parallel</span>" for coupling.
730Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
731      <span style="font-family: Courier New,Courier,monospace;">subjob</span>
732for lcxt4.<br>
733
734      <br>
735
736DVRP arguments changed to single precision, mode pathlines added.<br>
737
738      <br>
739
740User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
741
742      <br>
743
744User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
745      <td style="vertical-align: top; width: 189px;">check_for_restart,
746check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
747modules, package_parin, palm, surface_coupler, timestep<br>
748
749      <br>
750
751Makefile,&nbsp;mbuild, mrun, subjob<br>
752
753      <br>
754
755      <span style="font-weight: bold;">new:</span><br>
756
757init_coupling, user_additional_routines, user_check_parameters</td>
758    </tr>
759    <tr>
760      <td style="vertical-align: top; width: 27px;"><br>
761      </td>
762      <td style="vertical-align: top; width: 38px;"><br>
763      </td>
764      <td style="vertical-align: top; width: 42px;"><br>
765      </td>
766      <td style="vertical-align: top; width: 40px;"><br>
767      </td>
768      <td style="vertical-align: top; width: 27px;">C<br>
769      </td>
770      <td style="vertical-align: top; width: 497px;">User interface has been
771split into single files.<br>
772
773      <br>
774
775Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
776changed to INTEGER(8) in order to avoid "out of range" problems, which
777result in measured negative time intervals. (cpu_log, local_tremain,
778local_tremain_ini)<br>
779
780      <br>
781
782Reading mechanism from restart files
783completely revised. The subdomain/total domain size is now allowed to
784vary arbitrarily between the current and previous run. (read_var_list,
785read_3d_binary, user_read_restart_data)<br>
786
787      <br>
788
789Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
790completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
791One depository per block (given in the config-file) is created. Always
792all files from the source directory are copied to the respective
793depository. No additional file checks are done any more (mrun version
7942.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
795"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
796(mbuild, mrun)<br>
797
798      <br>
799
800Output messages (including required stop of execution) can now be
801handled with the new subroutine&nbsp;<span style="font-family: Courier New,Courier,monospace;">message</span>.
802All output messages will be replaced by this routine step by step
803within the next revisions.<br>
804
805      <br>
806
807Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
808explicitly set for better reading, although this has been already done
809in boundary_conds. (advec_s_bc)<br>
810
811      <br>
812
813Origin of the xy-coordinate system shifted from the center of the first
814grid 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
815south-left corner of this cell. (netcdf) Topography definition
816according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
817(init_grid, modules, user_header, user_init_grid, user_parin)</td>
818      <td style="vertical-align: top; width: 189px;">advec_s_bc,
819check_parameters, cpu_log, init_grid, local_stop, local_tremain,
820local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
821user_read_restart_data<br>
822
823      <br>
824
825Makefile, mbuild, mrun<br>
826
827      <br>
828
829      <span style="font-weight: bold;">removed:</span><br>
830
831user_interface<br>
832
833      <br>
834
835      <span style="font-weight: bold;">new:</span><br>
836
837message,
838user_3d_data_averaging, user_actions, user_advec_particles,
839user_check_data_output, user_check_data_output_pr, user_data_output_2d,
840user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
841user_dvrp_coltab, user_header, user_init_3d_model, user_init,
842user_init_grid, user_init_particles, user_init_plant_canopy,
843user_last_actions, user_parin, user_parin, user_particle_attributes,
844user_read_restart_data, user_spectra, user_statistics</td>
845    </tr>
846    <tr>
847      <td style="vertical-align: top; width: 27px;"><br>
848      </td>
849      <td style="vertical-align: top; width: 38px;"><br>
850      </td>
851      <td style="vertical-align: top; width: 42px;"><br>
852      </td>
853      <td style="vertical-align: top; width: 40px;"><br>
854      </td>
855      <td style="vertical-align: top; width: 27px;">B<br>
856      </td>
857      <td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
858reallocated in case that multigrid is used. (calc_spectra)<br>
859
860      <br>
861
862Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
863inflow_turbulence,&nbsp;timestep)<br>
864
865      <br>
866
867Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
868      </span>adjusted to the required output size (1 gridpoint less,
869along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
870in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
871compiler. (combine_plot_fields)<br>
872
873      <br>
874
875Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
876case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
877(header)<br>
878
879      <br>
880
881Inconsistency
882removed: as the thermal stratification is not taken into account for
883the evaluation of the wall fluxes at vertical walls, the eddy viscosity
884      <span style="font-family: Courier New,Courier,monospace;">km</span>
885must 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>.
886(production_e)<br>
887
888      <br>
889
890Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
891case of oceans runs. (sort_particles)<br>
892
893      <br>
894
895Bugfix: no output of particle concentration and radius unless particles
896have been started. (data_output_2d)<br>
897
898      <br>
899
900Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x|y</span>
901from restart files ignored if total numbers of grid points do not
902match. (read_3d_binary)<br>
903
904      <br>
905
906Bugfix: abort in case that absolute temperature is below zero.
907(init_cloud_physics)</td>
908      <td style="vertical-align: top; width: 189px;">advec_particles,
909calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
910header, inflow_turbulence, init_cloud_physics, production_e,
911read_3d_binary, timestep<br>
912
913      <br>
914
915combine_plot_fields</td>
916    </tr>
917  </tbody>
918</table>
919<b><blink></blink></b><br>&nbsp;
920<br>&nbsp;
921<h2><a name="Kapitel2.0"></a>2.0&nbsp; How
922to change the source
923code and how to document modifications<br>
924</h2>Currently
925(Sep 23rd, 2009), only selected users are allowed to commit changes to
926the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
927<br>
928<ol>
929  <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>".
930Additionally, document all changes in a local file (e.g.
931~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
932have been changed. Classify changes in three cases, new (N), changed
933(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>
934    <br>
935  </li>
936  <li>Test the changed version, unless it works sufficiently.<br>
937    <br>
938  </li>
939 
940  <li>Commit the changes to the repository<br>
941    <br>
942    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "message string" trunk<br>
943    </span><br>
944where "<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>
945    <br>
946Alternatively, in case that you have made quite a lot of changes, you
947can also give the contents of your file CURRENT_MODIFICATIONS as the
948log message:<br>
949    <br>
950    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
951    <br>
952  </li>
953
954  <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>
955    <br>
956  </li>
957  <li>Move the change comments in the file headers from "Current
958revisions:" to "Former revisions:". Set the current svn id in front of
959that.<br>
960    <br>
961    <span style="font-weight: bold;">Example:</span><br>
962    <br>
963    <span style="font-weight: bold;">before move:</span><br>
964    <br>
965    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
966    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
967    <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;">
968    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
969    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
970    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
971    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 493 2010-03-01 08:30:24Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
972    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
973    <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;">
974    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
975    <br>
976    <span style="font-weight: bold;">after move:</span><br>
977    <br>
978    <span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
979
980    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
981
982    <span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
983
984    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
985
986    <span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
987
988    <span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
989
990    <span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 493 2010-03-01 08:30:24Z raasch $<br>
991!</span><br style="font-family: Courier New,Courier,monospace;">
992    <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>
993! </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;">
994
995    <span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
996
997    <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;">
998
999    <span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
1000 </span><br>
1001  </li>
1002  <li>Commit the changes in the technical documentation and the file headers:<br>
1003    <br>
1004    <span style="font-family: Courier New,Courier,monospace;">&nbsp;&nbsp; svn commit -m "last commit documented" trunk</span><br>
1005    <br>
1006 <br>
1007  </li>
1008</ol>
1009
1010<h2>
1011<a name="Kapitel3.0"></a>3.0&nbsp; Description
1012of selected parts of the
1013model source code</h2>
1014<b></b>
1015<p>This section gives links to existing descriptions about special
1016parts of the PALM code, e.g. special numerical methods that are used
1017(including mathematical background). Documents are stored in single
1018files with different formats. Some are in German (sorry for the
1019inconvenience).
1020<br>&nbsp;
1021</p><ul> <li> <a name="UPS"></a>upstream-spline
1022advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
1023, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
1024physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
1025)</li> 
1026  <li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
1027  </li>
1028  <li>Runge-Kutta
1029time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
1030, only in German)</li>
1031
1032</ul><br>
1033&nbsp;
1034<br>&nbsp;
1035<br>&nbsp;
1036<br>&nbsp;
1037<br>&nbsp;
1038<br>&nbsp;
1039<br>&nbsp;
1040<br>&nbsp;
1041</body></html>
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