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several parameters for masked output are replaced by arrays
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1	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
2	<HTML>
3	<HEAD>
4	<META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8">
5	<TITLE>PALM technical/numerical documentation</TITLE>
6	<META NAME="GENERATOR" CONTENT="OpenOffice.org 3.0 (Unix)">
7	<META NAME="AUTHOR" CONTENT="Siegfried Raasch">
8	<META NAME="CREATED" CONTENT="0;0">
9	<META NAME="CHANGED" CONTENT="20100901;15562900">
10	<META NAME="KEYWORDS" CONTENT="parallel LES model">
11	</HEAD>
12	<BODY LANG="en-US" DIR="LTR">
13	<P STYLE="margin-bottom: 0in"><FONT SIZE=7>PALM   </FONT>a
14	<B>pa</B>rallelized <B>L</B>ES <B>m</B>odel
15	</P>
16	<HR>
17	<P STYLE="margin-bottom: 0in"><BR><FONT SIZE=5>technical/numerical
18	documentation</FONT> <BR>  <BR>
19	</P>
20	<P ALIGN=CENTER STYLE="margin-bottom: 0in">
21	</P>
22	<TABLE CELLPADDING=0 CELLSPACING=0>
23	<TR>
24	<TD>
25	<P><B>Current fixed release:</B></P>
26	</TD>
27	<TD>
28	<P><B>3.7a</B></P>
29	</TD>
30	</TR>
31	<TR>
32	<TD>
33	<P><B>Last change of this document</B>: </P>
34	</TD>
35	<TD>
36	<P><B>$Id: technical_documentation.html 544 2010-08-17 10:44:58Z
37	maronga $</B></P>
38	</TD>
39	</TR>
40	</TABLE>
41	<HR>
42	<P><FONT SIZE=5>Table of contents</FONT> <BR>  <BR>
43	</P>
44	<UL>
45	<P><A HREF="#Kapitel1.0">1.0</A>  History of changes
46	</P>
47	<P><A HREF="#Kapitel2.0">2.0</A>  How to change the source code
48	and how to document modifications</P>
49	<P><A HREF="#Kapitel3.0">3.0</A>  Description of selected model
50	numerics<BR> </P>
51	</UL>
52	<P><BR><BR>
53	</P>
54	<H2><A NAME="Kapitel1.0"></A>1.0  History of changes</H2>
55	<P STYLE="margin-bottom: 0in">The following table documents all
56	changes to the PALM repository since 2009. Older changes can be found
57	<A HREF="tec_doc_1998-2008.html">here</A>.<BR><BR>Entries in the
58	fifth column specify the type of the change: change  of existing
59	code (C), new code (N) or bugfix (B). More detailed information about
60	the changes may sometimes be found in the header comment lines of the
61	respective routines. <BR>
62	</P>
63	<TABLE WIDTH=1223 BORDER=1 CELLPADDING=2 CELLSPACING=3>
64	<COL WIDTH=37>
65	<COL WIDTH=56>
66	<COL WIDTH=68>
67	<COL WIDTH=62>
68	<COL WIDTH=36>
69	<COL WIDTH=518>
70	<COL WIDTH=393>
71	<TR>
72	<TD WIDTH=37>
73	<P><FONT SIZE=4><B>date</B></FONT></P>
74	</TD>
75	<TD WIDTH=56>
76	<P><FONT SIZE=4><B>author</B></FONT></P>
77	</TD>
78	<TD WIDTH=68>
79	<P><FONT SIZE=4><B>svn revision</B></FONT></P>
80	</TD>
81	<TD WIDTH=62>
82	<P><FONT SIZE=4><B>last release</B></FONT></P>
83	</TD>
84	<TD WIDTH=36>
85	<P><FONT SIZE=4><B>type</B></FONT></P>
86	</TD>
87	<TD WIDTH=518>
88	<P><FONT SIZE=4><B>description</B></FONT></P>
89	</TD>
90	<TD WIDTH=393>
91	<P><FONT SIZE=4><B>affected routines</B></FONT></P>
92	</TD>
93	</TR>
94	<TR>
95	<TD WIDTH=37 SDVAL="40187" SDNUM="1033;0;MM/DD/YY">
96	<P STYLE="font-weight: normal"><FONT SIZE=3>01/09/10</FONT></P>
97	</TD>
98	<TD WIDTH=56>
99	<P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P>
100	</TD>
101	<TD WIDTH=68 SDVAL="553" SDNUM="1033;">
102	<P STYLE="font-weight: normal"><FONT SIZE=3>553</FONT></P>
103	</TD>
104	<TD WIDTH=62>
105	<P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P>
106	</TD>
107	<TD WIDTH=36>
108	<P STYLE="font-weight: normal"><FONT SIZE=3>C</FONT></P>
109	</TD>
110	<TD WIDTH=518>
111	<P STYLE="font-weight: normal"><FONT SIZE=3>d3dpar-parameters for
112	masked output <FONT FACE="Courier New, monospace">data_output_mask_*,
113	data_output_mask_user_, mask__x, mask__y, mask__z,
114	mask__x_loop, mask__y_loop </FONT><FONT FACE="Times New Roman, serif">and
115	</FONT><FONT FACE="Courier New, monospace">mask_*_z_loop </FONT>have
116	been replaced by corresponding arrays <FONT FACE="Courier New, monospace">data_output_masks,
117	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
118	mask_y_loop </FONT><FONT FACE="Times New Roman, serif">and</FONT><FONT FACE="Courier New, monospace">
119	mask_z_loop</FONT></FONT></P>
120	<P STYLE="font-weight: normal"><FONT SIZE=3>inipar-parameter <FONT FACE="Courier New, monospace">masks</FONT>
121	has been removed. </FONT>
122	</P>
123	<P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
124	the masked data output, which is still not documented.</FONT></P>
125	</TD>
126	<TD WIDTH=393>
127	<P STYLE="font-weight: normal"><FONT SIZE=3>check_parameters,
128	init_masks, modules, parin, user_parin</FONT></P>
129	</TD>
130	</TR>
131	<TR>
132	<TD WIDTH=37>
133	<P>17/08/10</P>
134	</TD>
135	<TD WIDTH=56>
136	<P>BM</P>
137	</TD>
138	<TD WIDTH=68>
139	<P>544</P>
140	</TD>
141	<TD WIDTH=62>
142	<P>3.7a</P>
143	</TD>
144	<TD WIDTH=36>
145	<P>B/C/N</P>
146	</TD>
147	<TD WIDTH=518>
148	<P>adjustments for lcxt4; bugfix (mbuild): loading of user-defined
149	modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</P>
150	</TD>
151	<TD WIDTH=393>
152	<P>mrun, mbuild, subjob</P>
153	</TD>
154	</TR>
155	<TR>
156	<TD WIDTH=37>
157	<P>15/06/10</P>
158	</TD>
159	<TD WIDTH=56>
160	<P>RH</P>
161	</TD>
162	<TD WIDTH=68>
163	<P>540</P>
164	</TD>
165	<TD WIDTH=62>
166	<P>3.7a</P>
167	</TD>
168	<TD WIDTH=36>
169	<P>C</P>
170	</TD>
171	<TD WIDTH=518>
172	<P>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is
173	done using the names hicegate0/bicegate0 instead of the IP
174	addresses</P>
175	</TD>
176	<TD WIDTH=393>
177	<P>mrun</P>
178	</TD>
179	</TR>
180	<TR>
181	<TD WIDTH=37>
182	<P>21/04/10</P>
183	</TD>
184	<TD WIDTH=56>
185	<P>RH</P>
186	</TD>
187	<TD WIDTH=68>
188	<P>532</P>
189	</TD>
190	<TD WIDTH=62>
191	<P>3.7a</P>
192	</TD>
193	<TD WIDTH=36>
194	<P>C</P>
195	</TD>
196	<TD WIDTH=518>
197	<P>Large scale vertical motion (subsidence/ascent) can be added as
198	additional source to the prognostic equation for humidity/passive
199	scalar<BR> <BR>character length for dopr_unit
200	enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
201	of png files
202	</P>
203	</TD>
204	<TD WIDTH=393>
205	<P>modules, prognostic_equations<BR><BR>.ncl.config.default,
206	cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</P>
207	</TD>
208	</TR>
209	<TR>
210	<TD WIDTH=37>
211	<P><BR>
212	</P>
213	</TD>
214	<TD WIDTH=56>
215	<P><BR>
216	</P>
217	</TD>
218	<TD WIDTH=68>
219	<P><BR>
220	</P>
221	</TD>
222	<TD WIDTH=62>
223	<P><BR>
224	</P>
225	</TD>
226	<TD WIDTH=36>
227	<P>B</P>
228	</TD>
229	<TD WIDTH=518>
230	<P>Bugfix: unit of hyp changed to dbar</P>
231	</TD>
232	<TD WIDTH=393>
233	<P>check_parameters</P>
234	</TD>
235	</TR>
236	<TR>
237	<TD WIDTH=37>
238	<P>01/04/10</P>
239	</TD>
240	<TD WIDTH=56>
241	<P>RH</P>
242	</TD>
243	<TD WIDTH=68>
244	<P>530</P>
245	</TD>
246	<TD WIDTH=62>
247	<P>3.7a</P>
248	</TD>
249	<TD WIDTH=36>
250	<P>B</P>
251	</TD>
252	<TD WIDTH=518>
253	<P>Bugfix: treatment of special character * in NCL variables
254	containing lists corrected</P>
255	</TD>
256	<TD WIDTH=393>
257	<P>palmplot</P>
258	</TD>
259	</TR>
260	<TR>
261	<TD WIDTH=37>
262	<P>31/03/10</P>
263	</TD>
264	<TD WIDTH=56>
265	<P>RH</P>
266	</TD>
267	<TD WIDTH=68>
268	<P>529</P>
269	</TD>
270	<TD WIDTH=62>
271	<P>3.7a</P>
272	</TD>
273	<TD WIDTH=36>
274	<P>C</P>
275	</TD>
276	<TD WIDTH=518>
277	<P>List of variable names have to specified using blank separated
278	lists and single quotes</P>
279	</TD>
280	<TD WIDTH=393>
281	<P>palmplot</P>
282	</TD>
283	</TR>
284	<TR>
285	<TD WIDTH=37>
286	<P>30/03/10</P>
287	</TD>
288	<TD WIDTH=56>
289	<P>RH</P>
290	</TD>
291	<TD WIDTH=68>
292	<P>526</P>
293	</TD>
294	<TD WIDTH=62>
295	<P>3.7a</P>
296	</TD>
297	<TD WIDTH=36>
298	<P>C</P>
299	</TD>
300	<TD WIDTH=518>
301	<P>Adjustment of the NCL scripts and <FONT FACE="Courier New, Courier, monospace">palmplot
302	</FONT>to allow for special characters in NetCDF variable names
303	</P>
304	</TD>
305	<TD WIDTH=393>
306	<P>palmplot, .ncl.config.default, cross_sections.ncl,
307	profiles.ncl, timeseries.ncl, spectra.ncl</P>
308	</TD>
309	</TR>
310	<TR>
311	<TD WIDTH=37>
312	<P>30/03/10</P>
313	</TD>
314	<TD WIDTH=56>
315	<P>SR</P>
316	</TD>
317	<TD WIDTH=68>
318	<P>525</P>
319	</TD>
320	<TD WIDTH=62>
321	<P>3.7a</P>
322	</TD>
323	<TD WIDTH=36>
324	<P>B</P>
325	</TD>
326	<TD WIDTH=518>
327	<P>Bugfix: "/" in netcdf profile variable names replaced
328	by ":"</P>
329	</TD>
330	<TD WIDTH=393>
331	<P>check_parameters</P>
332	</TD>
333	</TR>
334	<TR>
335	<TD WIDTH=37>
336	<P>19/03/10</P>
337	</TD>
338	<TD WIDTH=56>
339	<P>SR</P>
340	</TD>
341	<TD WIDTH=68>
342	<P>520</P>
343	</TD>
344	<TD WIDTH=62>
345	<P>3.7a</P>
346	</TD>
347	<TD WIDTH=36>
348	<P>N</P>
349	</TD>
350	<TD WIDTH=518>
351	<P>NetCDF4 support for particle data. Total number of particles is
352	allowed to increase during the run, when netcdf_data_format > <I>2</I>
353	is used.</P>
354	</TD>
355	<TD WIDTH=393>
356	<P>advec_particles, check_open, netcdf</P>
357	</TD>
358	</TR>
359	<TR>
360	<TD WIDTH=37>
361	<P><BR>
362	</P>
363	</TD>
364	<TD WIDTH=56>
365	<P><BR>
366	</P>
367	</TD>
368	<TD WIDTH=68>
369	<P><BR>
370	</P>
371	</TD>
372	<TD WIDTH=62>
373	<P><BR>
374	</P>
375	</TD>
376	<TD WIDTH=36>
377	<P>C</P>
378	</TD>
379	<TD WIDTH=518>
380	<P>Special characters like * and " are now allowed for NetCDF
381	variable names. Replacement of these characters has been removed
382	(routine clean_netcdf_varname removed)</P>
383	</TD>
384	<TD WIDTH=393>
385	<P><BR>
386	</P>
387	</TD>
388	</TR>
389	<TR>
390	<TD WIDTH=37>
391	<P>18/03/10</P>
392	</TD>
393	<TD WIDTH=56>
394	<P>SR</P>
395	</TD>
396	<TD WIDTH=68>
397	<P>516</P>
398	</TD>
399	<TD WIDTH=62>
400	<P>3.7a</P>
401	</TD>
402	<TD WIDTH=36>
403	<P>N</P>
404	</TD>
405	<TD WIDTH=518>
406	<P>Simple installation method has been documented (see chapter
407	5.0). Respective scripts and configuration files have been
408	updated.</P>
409	</TD>
410	<TD WIDTH=393>
411	<P>palm_simple_install, palm_simple_run</P>
412	</TD>
413	</TR>
414	<TR>
415	<TD WIDTH=37>
416	<P><BR>
417	</P>
418	</TD>
419	<TD WIDTH=56>
420	<P><BR>
421	</P>
422	</TD>
423	<TD WIDTH=68>
424	<P><BR>
425	</P>
426	</TD>
427	<TD WIDTH=62>
428	<P><BR>
429	</P>
430	</TD>
431	<TD WIDTH=36>
432	<P>B</P>
433	</TD>
434	<TD WIDTH=518>
435	<P>opt=1 is forced for PGI-compiler in routine <FONT FACE="Courier New, Courier, monospace">buoyancy
436	</FONT>by compiler-directive. Otherwise, program aborts with
437	SIGFPE.</P>
438	</TD>
439	<TD WIDTH=393>
440	<P>buoyancy</P>
441	</TD>
442	</TR>
443	<TR>
444	<TD WIDTH=37>
445	<P>16/03/10</P>
446	</TD>
447	<TD WIDTH=56>
448	<P>RH</P>
449	</TD>
450	<TD WIDTH=68>
451	<P>513</P>
452	</TD>
453	<TD WIDTH=62>
454	<P>3.7a</P>
455	</TD>
456	<TD WIDTH=36>
457	<P>N</P>
458	</TD>
459	<TD WIDTH=518>
460	<P>NCL scripts can be run with the shell script <FONT FACE="Courier New, Courier, monospace">palmplot.</FONT></P>
461	</TD>
462	<TD WIDTH=393>
463	<P>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</P>
464	</TD>
465	</TR>
466	<TR>
467	<TD WIDTH=37>
468	<P>12/03/10</P>
469	</TD>
470	<TD WIDTH=56>
471	<P>SR</P>
472	</TD>
473	<TD WIDTH=68>
474	<P>509</P>
475	</TD>
476	<TD WIDTH=62>
477	<P>3.7a</P>
478	</TD>
479	<TD WIDTH=36>
480	<P>B</P>
481	</TD>
482	<TD WIDTH=518>
483	<P>bugfix for rev 504: remode_md was given a wrong value</P>
484	</TD>
485	<TD WIDTH=393>
486	<P>mbuild</P>
487	</TD>
488	</TR>
489	<TR>
490	<TD WIDTH=37>
491	<P>08/03/10</P>
492	</TD>
493	<TD WIDTH=56>
494	<P>SR</P>
495	</TD>
496	<TD WIDTH=68>
497	<P>506</P>
498	</TD>
499	<TD WIDTH=62>
500	<P>3.7a</P>
501	</TD>
502	<TD WIDTH=36>
503	<P>C</P>
504	</TD>
505	<TD WIDTH=518>
506	<P>hack for better usage of <B>mrun</B> on Kyoto computing center
507	machine (<FONT FACE="Courier New, Courier, monospace">lckyoto</FONT>)</P>
508	</TD>
509	<TD WIDTH=393>
510	<P>mrun</P>
511	</TD>
512	</TR>
513	<TR>
514	<TD WIDTH=37>
515	<P>03/03/10</P>
516	</TD>
517	<TD WIDTH=56>
518	<P>SR</P>
519	</TD>
520	<TD WIDTH=68>
521	<P>504</P>
522	</TD>
523	<TD WIDTH=62>
524	<P>3.7a</P>
525	</TD>
526	<TD WIDTH=36>
527	<P>C</P>
528	</TD>
529	<TD WIDTH=518>
530	<P><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
531	is now directly called within <B>mrun</B> and must not be given by
532	an output command in the configuration file any more. Please
533	remove the respective output command (<FONT FACE="Courier New, Courier, monospace">OC:combine_plot_fields.x</FONT>)
534	from your configuration file!<BR><BR>Utility programs
535	(<FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>,
536	<FONT FACE="Courier New, Courier, monospace">interpret_config</FONT>)
537	are created by <B>mbuild</B> separately for each block in the
538	configuration file. Depending on option <FONT FACE="Courier New, Courier, monospace">-K</FONT>,
539	<B>mrun</B> is using the utility programs for the respective
540	block.<BR><BR>Utility programs are also compiled in parallel,
541	depending on variable <FONT FACE="Courier New, Courier, monospace">%mopts</FONT>
542	in the configuration file..<BR><BR>Default configuration files
543	updated.</P>
544	</TD>
545	<TD WIDTH=393>
546	<P>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</P>
547	</TD>
548	</TR>
549	<TR>
550	<TD WIDTH=37>
551	<P>02/03/10</P>
552	</TD>
553	<TD WIDTH=56>
554	<P>SR</P>
555	</TD>
556	<TD WIDTH=68>
557	<P>496</P>
558	</TD>
559	<TD WIDTH=62>
560	<P>3.7a</P>
561	</TD>
562	<TD WIDTH=36>
563	<P>C</P>
564	</TD>
565	<TD WIDTH=518>
566	<P>Particle data for restart runs are only written if environment
567	variable <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>
568	= <I>.T.</I>, i.e. particle data are now handled in the same way
569	as the other restart data.</P>
570	</TD>
571	<TD WIDTH=393>
572	<P>palm</P>
573	</TD>
574	</TR>
575	<TR>
576	<TD WIDTH=37>
577	<P>01/03/10</P>
578	</TD>
579	<TD WIDTH=56>
580	<P>SR</P>
581	</TD>
582	<TD WIDTH=68>
583	<P>494</P>
584	</TD>
585	<TD WIDTH=62>
586	<P>3.7a</P>
587	</TD>
588	<TD WIDTH=36>
589	<P>N</P>
590	</TD>
591	<TD WIDTH=518>
592	<P>Output in NetCDF4-format.<BR><BR>NetCDF4 allows for parallel
593	I/O. Also, variables are not limited in size any more (i.e. arrays
594	can be larger than 2GB). The new d3par-parameter
595	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.can
596	be used to select among the different NetCDF file formats (<I>1</I>:
597	classic format, <I>2</I>: 64-bit-offset format (this is now the
598	default), <I>3</I>: NetCDF4/HDF5 format, <I>4</I>: NetCDF4 format
599	with NF90_CLASSIC_MODEL bit set). Setting <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
600	> <I>2</I> only affects 2d- and 3d-output, i.e. there is no
601	parallel output for profiles, time series, spectra, and particles.
602	Parallel output of particle data may realized in the future.<BR><BR>In
603	case of parallel output, all PEs write into one file, which means
604	that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
605	(merging data from single files - one per PE - into one file) is
606	not neccessary. In this case, flag files are automatically set,
607	telling <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
608	that nothing is to be done.<BR><BR>Using NetCDF4 format requires a
609	NetCDF4/HDF library. Respective settings for -I, -L, and -l
610	compiler/loader options for the SGI-ICE at HLRN can be found in
611	the new example configuration file
612	<FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
613	far, NetCDF parallel I/O has only been tested a little. Further
614	performance optimizations may be required, especially in case of
615	large data sets (e.g. data chunking, or lustre file system
616	settings with <FONT FACE="Courier New, Courier, monospace">lfs
617	setstripe</FONT>). <B>Please report bugs and performance problems
618	immediately!</B><BR><BR><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
619	outputs cpu-time needed for file merging.<BR><BR>Modules to be
620	loaded for compilation (mbuild) or job execution (mrun) can/should
621	now be given in the configuration file (<FONT FACE="Courier New, Courier, monospace">.mrun.config</FONT>)
622	using variable <FONT FACE="Courier New, Courier, monospace">modules</FONT>.
623	Example:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">%modules
624	ifort/11.0.069:netcdf       lcsgih
625	parallel</FONT><BR><BR>This method replaces the (undocumented)
626	<FONT FACE="Courier New, Courier, monospace">mpilib</FONT>-variable.<BR><BR><B>WARNING:</B><BR><B>All
627	fixed settings of modules in the scripts mbuild, mrun, and subjob
628	have been removed! Please set the </B><FONT FACE="Courier New, Courier, monospace"><B>modules</B></FONT><B>
629	variable appropriately and remove the mpilib variable in your
630	configuration file.<BR><BR></B>Compilation time can be reduced be
631	using parallel make. The number of allowed simultaneous compiler
632	calls (threads) is set in the configuration file using variable
633	<FONT FACE="Courier New, Courier, monospace">mopt</FONT>, e.g.<BR><BR>
634	<FONT FACE="Courier New, Courier, monospace">%mopts  -j:4
635	lcsgih parallel</FONT><BR><BR>allows a maximum of 4 routines to be
636	compiled simultaneously (provided that the makefile does not show
637	any dependencies between these routines).</P>
638	</TD>
639	<TD WIDTH=393>
640	<P>check_open, check_parameters, close_file, data_output_2d,
641	data_output_3d, header, modules, netcdf,
642	parin<BR><BR>combine_plot_fields<BR><BR>mbuild, mrun, subjob</P>
643	</TD>
644	</TR>
645	<TR>
646	<TD WIDTH=37>
647	<P><BR>
648	</P>
649	</TD>
650	<TD WIDTH=56>
651	<P><BR>
652	</P>
653	</TD>
654	<TD WIDTH=68>
655	<P><BR>
656	</P>
657	</TD>
658	<TD WIDTH=62>
659	<P><BR>
660	</P>
661	</TD>
662	<TD WIDTH=36>
663	<P>C</P>
664	</TD>
665	<TD WIDTH=518>
666	<P>d3par-parameters <FONT FACE="Courier New, Courier, monospace">netcdf_64bit</FONT>
667	and <FONT FACE="Courier New, Courier, monospace">netcdf_64bit_3d</FONT>
668	have been removed. Use the new d3par-variable <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
669	= <I>2</I> for choosing the NetCDF 64bit-offset format (this is
670	the default from now on). The offset-format can not be set
671	independently for the 3d-output-data any more.<BR><BR>d3par-parameters
672	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask</FONT>,
673	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask_av</FONT>,
674	and variables <FONT FACE="Courier New, Courier, monospace">nc_format_mask</FONT>,
675	<FONT FACE="Courier New, Courier, monospace">format_parallel_io</FONT>
676	removed. They are replaced by the new parameter
677	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
678	This change concerns the masked data output, which is still not
679	documented.</P>
680	</TD>
681	<TD WIDTH=393>
682	<P>check_open, close_file,<BR>data_output_mask, header,
683	init_masks, modules, parin</P>
684	</TD>
685	</TR>
686	<TR>
687	<TD WIDTH=37>
688	<P><BR>
689	</P>
690	</TD>
691	<TD WIDTH=56>
692	<P><BR>
693	</P>
694	</TD>
695	<TD WIDTH=68>
696	<P><BR>
697	</P>
698	</TD>
699	<TD WIDTH=62>
700	<P><BR>
701	</P>
702	</TD>
703	<TD WIDTH=36>
704	<P>B</P>
705	</TD>
706	<TD WIDTH=518>
707	<P>Bugfix in trunk/UTIL/Makefile: forgot to compile for
708	interpret_config.<BR><BR>Bugfix: timeseries data have to be
709	collected by PE0 (user_statistics).</P>
710	</TD>
711	<TD WIDTH=393>
712	<P>user_statistics<BR><BR>trunk/UTIL/Makefile</P>
713	</TD>
714	</TR>
715	<TR>
716	<TD WIDTH=37>
717	<P>05/02/10</P>
718	</TD>
719	<TD WIDTH=56>
720	<P>SR</P>
721	</TD>
722	<TD WIDTH=68>
723	<P>485</P>
724	</TD>
725	<TD WIDTH=62>
726	<P>3.7a</P>
727	</TD>
728	<TD WIDTH=36>
729	<P>B</P>
730	</TD>
731	<TD WIDTH=518>
732	<P><FONT FACE="Courier New, Courier, monospace">ngp_3d</FONT>,
733	<FONT FACE="Courier New, Courier, monospace">ngp_3d_inner</FONT>
734	changed to 64 bit. Otherwise, on large grids > 210*9 grid
735	points some global statistics (e.g. total kinetic energy) have
736	wrong values.</P>
737	</TD>
738	<TD WIDTH=393>
739	<P>init_3d_model, modules</P>
740	</TD>
741	</TR>
742	<TR>
743	<TD WIDTH=37>
744	<P>05/02/10</P>
745	</TD>
746	<TD WIDTH=56>
747	<P>SR</P>
748	</TD>
749	<TD WIDTH=68>
750	<P>484</P>
751	</TD>
752	<TD WIDTH=62>
753	<P>3.7a</P>
754	</TD>
755	<TD WIDTH=36>
756	<P>B</P>
757	</TD>
758	<TD WIDTH=518>
759	<P>Typo in file headers removed ("current" instead of
760	"actual").</P>
761	</TD>
762	<TD WIDTH=393>
763	<P>many</P>
764	</TD>
765	</TR>
766	<TR>
767	<TD WIDTH=37>
768	<P>05/02/10</P>
769	</TD>
770	<TD WIDTH=56>
771	<P>SR</P>
772	</TD>
773	<TD WIDTH=68>
774	<P>483</P>
775	</TD>
776	<TD WIDTH=62>
777	<P>3.7a</P>
778	</TD>
779	<TD WIDTH=36>
780	<P>N</P>
781	</TD>
782	<TD WIDTH=518>
783	<P><FONT FACE="Courier New, Courier, monospace">compare_palm_logs
784	</FONT>is additionally compiled with <B>mbuild</B> <FONT FACE="Courier New, Courier, monospace">-u</FONT>
785	. (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT> in
786	<FONT FACE="Courier New, Courier, monospace">trunk/UTIL</FONT>)<BR><BR>make
787	options (<FONT FACE="Courier New, Courier, monospace">mopts</FONT>)
788	to be set by configuration file implemented. (<B>mrun</B>,
789	<B>mbuild</B>)<BR><BR><FONT FACE="Courier New, Courier, monospace">humidity</FONT>
790	= <I>.T.</I> can be used for runs with topography.
791	<FONT FACE="Courier New, Courier, monospace">wall_humidityflux</FONT>
792	and<BR><FONT FACE="Courier New, Courier, monospace">wall_scalarflux</FONT>
793	are the corresponding new inipar parameters.<BR>(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
794	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
795	<FONT FACE="Courier New, Courier, monospace">parin</FONT>)<BR><BR>Large
796	scale vertical motion (subsidence/ascent) can be added as
797	additional source to the prognostic equation for potential
798	temperature. See new parameters <FONT FACE="Courier New, Courier, monospace">large_scale_subsidence</FONT>,
799	<FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient</FONT>,
800	and <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient_level</FONT>.
801	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
802	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
803	<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>,
804	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
805	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
806	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
807	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
808	<FONT FACE="Courier New, Courier, monospace">subsidence</FONT>,
809	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Scripts
810	have been updated for Cray-XT5 machine (lcxt5m) and
811	Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
812	and running palm (with limited features) has been added.
813	(<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, new
814	scripts <B>palm_simple_install</B>, <B>palm_simple_run</B>)<BR><BR>Masked
815	data output has been implemented but it is not documented in the
816	user manual so far. This feature can already use NetCDF4 file
817	format. (check_open, check_parameters, close_file, modules,
818	netcdf, parin, time_integration, user_parin, new:
819	data_output_mask, init_masks, user_data_output_mask)</P>
820	</TD>
821	<TD WIDTH=393>
822	<P>check_open, check parameters, close_file, header,
823	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
824	prognostic_equations, read_var_list, time_integration, user_parin,
825	write_var_list<BR><BR><B>new:</B> data_output_mask,
826	init_masks, palm_simple_install, palm_simple_run, subsidence,
827	user_data_output_mask</P>
828	</TD>
829	</TR>
830	<TR>
831	<TD WIDTH=37>
832	<P><BR>
833	</P>
834	</TD>
835	<TD WIDTH=56>
836	<P><BR>
837	</P>
838	</TD>
839	<TD WIDTH=68>
840	<P><BR>
841	</P>
842	</TD>
843	<TD WIDTH=62>
844	<P><BR>
845	</P>
846	</TD>
847	<TD WIDTH=36>
848	<P>C</P>
849	</TD>
850	<TD WIDTH=518>
851	<P>2d-decomposition is default for Cray-XT machines.
852	(<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">var_ts</FONT>
853	is replaced by <FONT FACE="Courier New, Courier, monospace">dots_max</FONT>.
854	(<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
855	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Every
856	cloud droplet has now an own weighting factor and can be deleted
857	due to collisions. Condensation and collision of cloud droplets
858	are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
859	efficiency for large cloud droplets has changed according to table
860	of Rogers and Yau. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
861	</TD>
862	<TD WIDTH=393>
863	<P>advec_particles, collision_efficiency, init_3d_model,
864	init_pegrid, modules</P>
865	</TD>
866	</TR>
867	<TR>
868	<TD WIDTH=37>
869	<P><BR>
870	</P>
871	</TD>
872	<TD WIDTH=56>
873	<P><BR>
874	</P>
875	</TD>
876	<TD WIDTH=68>
877	<P><BR>
878	</P>
879	</TD>
880	<TD WIDTH=62>
881	<P><BR>
882	</P>
883	</TD>
884	<TD WIDTH=36>
885	<P>B</P>
886	</TD>
887	<TD WIDTH=518>
888	<P>Bugfix for generating serial jobs. (<B>subjob</B>)<BR><BR>Bugfix:
889	index problem concerning gradient_level indices removed.
890	(<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
891	of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
892	in cascade change to prevent type problems with mpi2 libraries.
893	(<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
894	was split to make runs reproducible when using ifort compiler.
895	(<FONT FACE="Courier New, Courier, monospace">disturb_field</FONT>)<BR><BR>Bugfix:
896	exchange of ghost points for <FONT FACE="Courier New, Courier, monospace">prho</FONT>
897	included. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix
898	in calculation of time-averaged surface heatfluxes.
899	(<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
900	in calculation of precipitation_rate.
901	(<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
902	initial data assignments to some dvrp arrays changed due to error
903	messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
904	in calculation of cloud droplet velocity.
905	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
906	in transfer of particles at south/left edge.
907	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
908	in calculation of collision efficiency. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
909	</TD>
910	<TD WIDTH=393>
911	<P>advec_particles, calc_precipitation, collision_efficiency,
912	disturb_field, header, modules, poisfft_hybrid, subjob,
913	sum_up_3d_data, time_integration</P>
914	</TD>
915	</TR>
916	<TR>
917	<TD WIDTH=37>
918	<P>23/09/09</P>
919	</TD>
920	<TD WIDTH=56>
921	<P>SR</P>
922	</TD>
923	<TD WIDTH=68>
924	<P>392</P>
925	</TD>
926	<TD WIDTH=62>
927	<P>3.7</P>
928	</TD>
929	<TD WIDTH=36>
930	<P>N</P>
931	</TD>
932	<TD WIDTH=518>
933	<P><B>Most important changes:</B> atmosphere-ocean coupling has
934	been improved and steering of dvr-software is more user-friendly
935	now. Beside that, the release contains a lot of optimizations,
936	changes, and bugfixes which have accumulated over the last
937	months.<BR><BR>The atmosphere-ocean coupling allows to use
938	independent precursor runs in order to account for different
939	spin-up times. The time when coupling has to be started is given
940	by new inipar parameter <FONT FACE="Courier New, Courier, monospace">coupling_start_time</FONT>.
941	The precursor ocean run has to be started using new <B>mrun</B>
942	option "<FONT FACE="Courier New, Courier, monospace">-y</FONT>"
943	in order to add the appendix "<FONT FACE="Courier New, Courier, monospace">_O</FONT>"
944	to all output files. (<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
945	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
946	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
947	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
948	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
949	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
950	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
951	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
952	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
953	<FONT FACE="Courier New, Courier, monospace">init_coupling</FONT>,
954	<FONT FACE="Courier New, Courier, monospace">modules</FONT>, <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
955	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
956	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
957	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
958	<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>,
959	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Clipping
960	of dvrp output implemented. Default colourtable for particles
961	implemented, particle attributes (color, dvrp_size) can be set
962	with new parameters <FONT FACE="Courier New, Courier, monospace">particle_color</FONT>,
963	<FONT FACE="Courier New, Courier, monospace">particle_dvrpsize</FONT>,
964	<FONT FACE="Courier New, Courier, monospace">color_interval</FONT>,
965	<FONT FACE="Courier New, Courier, monospace">dvrpsize_interval</FONT>.
966	Slicer attributes (dvrp) are set with new routine
967	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>
968	and are controlled with existing parameters <FONT FACE="Courier New, Courier, monospace">slicer_range_limits</FONT>.
969	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
970	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
971	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
972	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>,
973	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>)<BR><BR>Polygon
974	reduction for topography and ground plate isosurface. Reduction
975	level for buildings can be chosen with parameter cluster_size.
976	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>)<BR><BR>Variables
977	<FONT FACE="Courier New, Courier, monospace">bc_lr</FONT> / <FONT FACE="Courier New, Courier, monospace">bc_ns</FONT>
978	in most subroutines replaced by LOGICAL variables
979	<FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
980	for speed optimization. This gives a significant speedup of more
981	than 10%. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
982	<FONT FACE="Courier New, Courier, monospace">diffusion_u</FONT>,
983	<FONT FACE="Courier New, Courier, monospace">diffusion_v</FONT>,
984	<FONT FACE="Courier New, Courier, monospace">diffusion_w</FONT>,
985	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Scripts
986	have been adapted for machine lck (Yonsei Univ.). (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
987	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>,
988	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)<BR><BR>Additional
989	timestep criterion in case of simulations with plant canopy.
990	(<FONT FACE="Courier New, Courier, monospace">timestep</FONT>)<BR><BR>Check
991	for illegal entries in <FONT FACE="Courier New, Courier, monospace">section_xy</FONT>\|<FONT FACE="Courier New, Courier, monospace">xz</FONT>\|<FONT FACE="Courier New, Courier, monospace">yz</FONT>
992	that exceed <FONT FACE="Courier New, Courier, monospace">nz+1</FONT>\|<FONT FACE="Courier New, Courier, monospace">ny+1</FONT>\|<FONT FACE="Courier New, Courier, monospace">nx+1</FONT>.
993	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>External
994	pressure gradient can be used as driving force. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
995	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
996	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
997	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
998	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
999	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
1000	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1001	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>New
1002	topography case '<I>single_street_canyon</I>'. (<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1003	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1004	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1005	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1006	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1007	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1008	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1009	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1010	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1011	to predefine a target bulk velocity for <FONT FACE="Courier New, Courier, monospace">conserve_volume_flow</FONT>.
1012	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1013	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1014	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1015	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1016	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1017	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1018	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1019	for user defined 2D data output in xy cross sections at z=<FONT FACE="Courier New, Courier, monospace">nzb</FONT>+1.
1020	(<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1021	<FONT FACE="Courier New, Courier, monospace">user_data_output_2d</FONT>)<BR><BR>xy
1022	cross section output of surface heatfluxes (sensible and latent).
1023	(<FONT FACE="Courier New, Courier, monospace">average_3d_data</FONT>,
1024	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1025	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1026	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1027	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1028	<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>,
1029	<FONT FACE="Courier New, Courier, monospace">write_3d_binary</FONT>)</P>
1030	</TD>
1031	<TD WIDTH=393>
1032	<P>average_3d_data, check_for_restart, check_parameters,
1033	data_output_2d, data_output_3d, data_output_dvrp,
1034	data_output_profiles, data_output_ptseries, data_output_spectra,
1035	data_output_tseries, diffusion_u, diffusion_v, diffusion_w,
1036	init_coupling, init_dvrp, init_grid, init_3d_model, header,
1037	mbuild, modules, mrun, package_parin, parin, prognostic_equations,
1038	read_3d_binary, read_var_list, subjob, sum_up_3d_data,
1039	surface_coupler, timestep, time_integration,
1040	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
1041	user_header, user_init_grid, write_3d_binary, write_var_list<BR><BR><B>new:</B>
1042	set_particle_attributes, set_slicer_attributes_dvrp</P>
1043	</TD>
1044	</TR>
1045	<TR>
1046	<TD WIDTH=37>
1047	<P><BR>
1048	</P>
1049	</TD>
1050	<TD WIDTH=56>
1051	<P><BR>
1052	</P>
1053	</TD>
1054	<TD WIDTH=68>
1055	<P><BR>
1056	</P>
1057	</TD>
1058	<TD WIDTH=62>
1059	<P><BR>
1060	</P>
1061	</TD>
1062	<TD WIDTH=36>
1063	<P>C</P>
1064	</TD>
1065	<TD WIDTH=518>
1066	<P>Output of messages replaced by message handling routine.
1067	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1068	<FONT FACE="Courier New, Courier, monospace">advec_s_bc</FONT>,
1069	<FONT FACE="Courier New, Courier, monospace">buoyancy</FONT>,
1070	<FONT FACE="Courier New, Courier, monospace">calc_spectra</FONT>,
1071	<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
1072	<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1073	<FONT FACE="Courier New, Courier, monospace">coriolis</FONT>,
1074	<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>,
1075	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1076	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1077	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
1078	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1079	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1080	<FONT FACE="Courier New, Courier, monospace">fft_xy</FONT>,
1081	<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>,
1082	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1083	<FONT FACE="Courier New, Courier, monospace">init_1d_model</FONT>,
1084	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1085	<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
1086	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1087	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>,
1088	<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>,
1089	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1090	<FONT FACE="Courier New, Courier, monospace">plant_canopy_model</FONT>,
1091	<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>,
1092	<FONT FACE="Courier New, Courier, monospace">poismg</FONT>,
1093	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1094	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1095	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
1096	<FONT FACE="Courier New, Courier, monospace">temperton_fft</FONT>,
1097	<FONT FACE="Courier New, Courier, monospace">timestep</FONT>,
1098	<FONT FACE="Courier New, Courier, monospace">user_actions</FONT>,
1099	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>,
1100	<FONT FACE="Courier New, Courier, monospace">user_dvrp_coltab</FONT>,
1101	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1102	<FONT FACE="Courier New, Courier, monospace">user_init_plant_canopy</FONT>,
1103	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1104	<FONT FACE="Courier New, Courier, monospace">user_read_restart_data</FONT>,
1105	<FONT FACE="Courier New, Courier, monospace">user_spectra</FONT>)<BR><BR>Output
1106	of NetCDF messages with aid of message handling routine.
1107	(<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1108	<FONT FACE="Courier New, Courier, monospace">close_file</FONT>,
1109	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1110	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1111	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1112	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
1113	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1114	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
1115	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>__lcmuk
1116	changed to __lc to avoid problems with Intel compiler on sgi-ice.
1117	(<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
1118	extended NetCDF files, the updated title attribute includes an
1119	update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
1120	case of restart runs without extension, initial profiles are not
1121	written to NetCDF-file anymore. So far, time axis always started
1122	at t=0. (<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1123	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1124	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1125	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">initializing_actions</FONT>='<I>read_data_for_recycling</I>'
1126	renamed to '<I>cyclic_fill</I>'. A cyclic fill can now <BR>be used
1127	independent of <FONT FACE="Courier New, Courier, monospace">turbulent_inflow</FONT>.
1128	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1129	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1130	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>2
1131	NetCDF error numbers changed. (<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>A
1132	link to the webspage appendix_a.html is printed for further
1133	information about possible reasons of the error that appeared.
1134	(message)<BR><BR>Temperature gradient criterion for estimating the
1135	boundary layer height replaced by the gradient criterion of
1136	Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
1137	unit attribute in timeseries output in case of statistic regions
1138	added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
1139	number of tails is calculated from maximum number of particles and
1140	<FONT FACE="Courier New, Courier, monospace">skip_particles_for_tail</FONT>.
1141	(<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Value
1142	of <FONT FACE="Courier New, Courier, monospace">vertical_particle_advection</FONT>
1143	is allowed to differ for each particle group. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1144	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1145	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)
1146	<BR><BR>First constant in array <FONT FACE="Courier New, Courier, monospace">den</FONT>
1147	also defined as type double. (<FONT FACE="Courier New, Courier, monospace">eqn_state_seawater</FONT>)<BR><BR>Parameter
1148	<FONT FACE="Courier New, Courier, monospace">dvrp_psize</FONT>
1149	moved from <FONT FACE="Courier New, Courier, monospace">particles_par</FONT>
1150	to <FONT FACE="Courier New, Courier, monospace">dvrp_graphics_par</FONT>.
1151	(<FONT FACE="Courier New, Courier, monospace">package_parin</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>
1152	moved from <FONT FACE="Courier New, Courier, monospace">userpar</FONT>
1153	to <FONT FACE="Courier New, Courier, monospace">inipar</FONT>
1154	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1155	<FONT FACE="Courier New, Courier, monospace">header</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1156	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1157	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1158	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1159	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1160	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1161	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Default
1162	value of <FONT FACE="Courier New, Courier, monospace">grid_matching</FONT>
1163	changed to '<I>strict</I>'. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Adjustments
1164	for runs on lcxt4 (necessary due to a software update on CRAY) and
1165	for coupled runs on ibmy. (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1166	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)</P>
1167	</TD>
1168	<TD WIDTH=393>
1169	<P>advec_particles, advec_s_bc, buoyancy, calc_spectra,
1170	check_for_restart, check_open, check_parameters, close_file,
1171	coriolis, cpu_log, data_output_2d, data_output_3d,
1172	data_output_dvrp, data_output_profiles, data_output_ptseries,
1173	data_output_spectra, data_output_tseries, eqn_state_seawater,
1174	fft_xy, flow_statistics, header, init_1d_model, init_3d_model,
1175	init_dvrp, init_grid, init_particles, init_pegrid, message, mrun,
1176	netcdf, package_parin, parin, plant_canopy_model, poisfft,
1177	poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
1178	surface_coupler, temperton_fft, timestep,
1179	user_actions,user_check_parameters, user_data_output_dvrp,
1180	user_dvrp_coltab, user_header, user_init_grid,
1181	user_init_plant_canopy, user_parin, user_read_restart_data,
1182	user_spectra, write_var_list
1183	</P>
1184	</TD>
1185	</TR>
1186	<TR>
1187	<TD WIDTH=37>
1188	<P><BR>
1189	</P>
1190	</TD>
1191	<TD WIDTH=56>
1192	<P><BR>
1193	</P>
1194	</TD>
1195	<TD WIDTH=68>
1196	<P><BR>
1197	</P>
1198	</TD>
1199	<TD WIDTH=62>
1200	<P><BR>
1201	</P>
1202	</TD>
1203	<TD WIDTH=36>
1204	<P>B</P>
1205	</TD>
1206	<TD WIDTH=518>
1207	<P>Bugfix: Initial hydrostatic pressure profile in case of ocean
1208	runs is now calculated in 5 iteration steps. (<FONT FACE="Courier New, Courier, monospace">init_ocean</FONT>)<BR><BR>Bugfix:
1209	wrong sign in buoyancy production of ocean part in case of not
1210	using the reference density (only in 3D routine <FONT FACE="Courier New, Courier, monospace">production_e</FONT>).
1211	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix:
1212	output of averaged 2d/3d quantities requires that an avaraging
1213	interval has been set, respective error message is included.
1214	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1215	Output on unit 14 only if requested by <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>.
1216	(<FONT FACE="Courier New, Courier, monospace">user_last_actions</FONT>)<BR><BR>Bugfix
1217	to avoid zero division by <FONT FACE="Courier New, Courier, monospace">km_neutral</FONT>.
1218	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix
1219	for extended NetCDF files: In order to avoid 'data mode' errors if
1220	updated attributes are larger than their original size,
1221	<FONT FACE="Courier New, Courier, monospace">NF90_PUT_ATT</FONT>
1222	is called in 'define mode' enclosed by <FONT FACE="Courier New, Courier, monospace">NF90_REDEF</FONT>
1223	and <FONT FACE="Courier New, Courier, monospace">NF90_ENDDEF</FONT>
1224	calls. This implies a possible performance loss; an alternative
1225	strategy would be to ensure equal attribute size in a job chain.
1226	(<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
1227	correction of initial volume flow for non-flat topography.
1228	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1229	zero initialization of arrays within buildings for '<I>cyclic_fill</I>'.
1230	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1231	<FONT FACE="Courier New, Courier, monospace">to_be_resorted</FONT>
1232	=> <FONT FACE="Courier New, Courier, monospace">s_av</FONT> for
1233	time-averaged scalars. (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1234	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>Bugfix:
1235	avoid that <FONT FACE="Courier New, Courier, monospace">ngp_2dh_s_inner</FONT>
1236	becomes zero. (<FONT FACE="Courier New, Courier, monospace">init_3_model</FONT>)<BR><BR>Typographical
1237	error: unit of wpt in dots_unit. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix:
1238	error in check, if particles moved further than one subdomain
1239	length. This check must not be applied for newly released
1240	particles. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix:
1241	several tail counters are initialized, <FONT FACE="Courier New, Courier, monospace">particle_tail_coordinates</FONT>
1242	is only written to file if its third index is > 0, arrays for
1243	tails are allocated with a minimum size of 10 tails if there is no
1244	tail initially. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1245	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Bugfix:
1246	pressure included for profile output. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1247	Type of <FONT FACE="Courier New, Courier, monospace">count</FONT>
1248	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1249	changed to default <FONT FACE="Courier New, Courier, monospace">INTEGER</FONT>
1250	on NEC machines. (<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>)<BR><BR>Bugfix:
1251	output of particle time series only if particle advection is
1252	switched on. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix:
1253	qsws was calculated in case of <FONT FACE="Courier New, Courier, monospace">constant
1254	heatflux</FONT> = <FONT FACE="Courier New, Courier, monospace">.FALSE.</FONT>.
1255	(<FONT FACE="Courier New, Courier, monospace">prandtl_fluxes</FONT>)<BR><BR>Bugfix:
1256	averaging along z is not allowed for 2d quantities (e.g. u* and
1257	z0). (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>)<BR><BR>Typographical
1258	errors. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>If
1259	the inversion height calculated by the prerun is zero,
1260	inflow_damping_height must be explicitly specified.
1261	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Small
1262	bugfix concerning 3d 64bit netcdf output format. (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Bugfix:
1263	<FONT FACE="Courier New, Courier, monospace">dt_fixed</FONT>
1264	removed from the restart file, because otherwise, no change from a
1265	fixed to a variable timestep would be possible in restart runs.
1266	(<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1267	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Bugfix:
1268	initial setting of <FONT FACE="Courier New, Courier, monospace">time_coupling</FONT>
1269	in coupled restart runs. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)</P>
1270	</TD>
1271	<TD WIDTH=393>
1272	<P>advec_particles, check_parameters, cpu_log, data_output_2d,
1273	data_output_3d, header, init_3d_model, init_particles, init_ocean,
1274	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
1275	time_integration, user_last_actions, write_var_list</P>
1276	</TD>
1277	</TR>
1278	<TR>
1279	<TD WIDTH=37>
1280	<P>02/02/09</P>
1281	</TD>
1282	<TD WIDTH=56>
1283	<P>SR</P>
1284	</TD>
1285	<TD WIDTH=68>
1286	<P>228</P>
1287	</TD>
1288	<TD WIDTH=62>
1289	<P>3.6</P>
1290	</TD>
1291	<TD WIDTH=36>
1292	<P>N</P>
1293	</TD>
1294	<TD WIDTH=518>
1295	<P>This release contains further additions, changes, and bugfixes
1296	for the SGI-ICE system, as well as important changes like the
1297	splitting of the user-interface into single files, a complete
1298	revision of the pre-compiling mechanism allowing to use different
1299	make-depositories simultaneously, and a revision of the
1300	reading-mechanism from restart files, which has no more
1301	restrictions in case that the previous and current run have
1302	different domain/subdomain sizes. A new handling of all kind of
1303	output messages is introduced with this release and will be
1304	applied to all existing messages within the next releases.<BR><BR><B>New
1305	features are:</B><BR><BR>Restart runs on SGI-ICE are working.
1306	(mrun)<BR>2d-decomposition is default on SGI-ICE systems.
1307	(init_pegrid)<BR><BR>Ocean-atmosphere coupling realized with
1308	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
1309	called with <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1310	"<I>-K parallel</I>" for coupling. Adjustments in <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1311	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, and
1312	<FONT FACE="Courier New, Courier, monospace">subjob</FONT> for
1313	lcxt4.<BR><BR>DVRP arguments changed to single precision, mode
1314	pathlines added.<BR><BR>User can add additional routines in files
1315	<FONT FACE="Courier New, Courier, monospace">user_additional_routines</FONT>.<BR><BR>User
1316	can check user parameters and deduce further quantities in
1317	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT></P>
1318	</TD>
1319	<TD WIDTH=393>
1320	<P>check_for_restart, check_parameters, data_output_dvrp,
1321	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
1322	surface_coupler, timestep<BR><BR>Makefile, mbuild, mrun,
1323	subjob<BR><BR><B>new:</B><BR>init_coupling,
1324	user_additional_routines, user_check_parameters</P>
1325	</TD>
1326	</TR>
1327	<TR>
1328	<TD WIDTH=37>
1329	<P><BR>
1330	</P>
1331	</TD>
1332	<TD WIDTH=56>
1333	<P><BR>
1334	</P>
1335	</TD>
1336	<TD WIDTH=68>
1337	<P><BR>
1338	</P>
1339	</TD>
1340	<TD WIDTH=62>
1341	<P><BR>
1342	</P>
1343	</TD>
1344	<TD WIDTH=36>
1345	<P>C</P>
1346	</TD>
1347	<TD WIDTH=518>
1348	<P>User interface has been split into single files.<BR><BR>Type of
1349	variables <FONT FACE="Courier New, Courier, monospace">count</FONT>
1350	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1351	changed to INTEGER(8) in order to avoid "out of range"
1352	problems, which result in measured negative time intervals.
1353	(cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
1354	mechanism from restart files completely revised. The
1355	subdomain/total domain size is now allowed to vary arbitrarily
1356	between the current and previous run. (read_var_list,
1357	read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
1358	mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
1359	completely revised: the source-tarfile remains in the source
1360	directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
1361	One depository per block (given in the config-file) is created.
1362	Always all files from the source directory are copied to the
1363	respective depository. No additional file checks are done any more
1364	(mrun version 2.1). The depository name used contains the
1365	conditions given by <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1366	"<FONT FACE="Courier New, Courier, monospace">-K</FONT>".
1367	(mbuild, mrun)<BR><BR>Output messages (including required stop of
1368	execution) can now be handled with the new subroutine <FONT FACE="Courier New, Courier, monospace">message</FONT>.
1369	All output messages will be replaced by this routine step by step
1370	within the next revisions.<BR><BR>Neumann boundary condition at
1371	<FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
1372	explicitly set for better reading, although this has been already
1373	done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
1374	xy-coordinate system shifted from the center of the first grid
1375	cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
1376	<FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
1377	south-left corner of this cell. (netcdf) Topography definition
1378	according to new user parameter <FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>.
1379	(init_grid, modules, user_header, user_init_grid, user_parin)</P>
1380	</TD>
1381	<TD WIDTH=393>
1382	<P>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop,
1383	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
1384	read_var_list, user_read_restart_data<BR><BR>Makefile, mbuild,
1385	mrun<BR><BR><B>removed:</B><BR>user_interface<BR><BR><B>new:</B><BR>message,
1386	user_3d_data_averaging, user_actions, user_advec_particles,
1387	user_check_data_output, user_check_data_output_pr,
1388	user_data_output_2d, user_data_output_3d, user_data_output_dvrp,
1389	user_define_netcdf_grid, user_dvrp_coltab, user_header,
1390	user_init_3d_model, user_init, user_init_grid,
1391	user_init_particles, user_init_plant_canopy, user_last_actions,
1392	user_parin, user_parin, user_particle_attributes,
1393	user_read_restart_data, user_spectra, user_statistics</P>
1394	</TD>
1395	</TR>
1396	<TR>
1397	<TD WIDTH=37>
1398	<P><BR>
1399	</P>
1400	</TD>
1401	<TD WIDTH=56>
1402	<P><BR>
1403	</P>
1404	</TD>
1405	<TD WIDTH=68>
1406	<P><BR>
1407	</P>
1408	</TD>
1409	<TD WIDTH=62>
1410	<P><BR>
1411	</P>
1412	</TD>
1413	<TD WIDTH=36>
1414	<P>B</P>
1415	</TD>
1416	<TD WIDTH=518>
1417	<P>Bugfix: array <FONT FACE="Courier New, Courier, monospace">d</FONT>
1418	is reallocated in case that multigrid is used.
1419	(calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
1420	(check_for_restart, cpu_statistics,
1421	inflow_turbulence, timestep)<BR><BR>Size of <FONT FACE="Courier New, Courier, monospace">pf3d
1422	</FONT>adjusted to the required output size (1 gridpoint less,
1423	along all three dimensions), because output of a subset of the
1424	data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
1425	in the NF90_PUT_VAR statement caused segmentation fault with the
1426	INTEL compiler. (combine_plot_fields)<BR><BR>Bugfix: error in <FONT FACE="Courier New, Courier, monospace">zu</FONT>
1427	index in case of <FONT FACE="Courier New, Courier, monospace">section_xy=-1</FONT>.
1428	(header)<BR><BR>Inconsistency removed: as the thermal
1429	stratification is not taken into account for the evaluation of the
1430	wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
1431	must not be used for the evaluation of the velocity gradients
1432	<FONT FACE="Courier New, Courier, monospace">dudy</FONT>, <FONT FACE="Courier New, Courier, monospace">dwdy</FONT>,
1433	<FONT FACE="Courier New, Courier, monospace">dvdx</FONT> and <FONT FACE="Courier New, Courier, monospace">dwdx</FONT>.
1434	(production_e)<BR><BR>Bugfix in calculating <FONT FACE="Courier New, Courier, monospace">k</FONT>
1435	index in case of oceans runs. (sort_particles)<BR><BR>Bugfix: no
1436	output of particle concentration and radius unless particles have
1437	been started. (data_output_2d)<BR><BR>Bugfix: reading of
1438	<FONT FACE="Courier New, Courier, monospace">spectrum_x\|y</FONT>
1439	from restart files ignored if total numbers of grid points do not
1440	match. (read_3d_binary)<BR><BR>Bugfix: abort in case that absolute
1441	temperature is below zero. (init_cloud_physics)</P>
1442	</TD>
1443	<TD WIDTH=393>
1444	<P>advec_particles, calc_spectra, check_for_restart,
1445	cpu_statistics, data_output_2d, header, inflow_turbulence,
1446	init_cloud_physics, production_e, read_3d_binary,
1447	timestep<BR><BR>combine_plot_fields</P>
1448	</TD>
1449	</TR>
1450	</TABLE>
1451	<P><BR>  <BR>
1452	</P>
1453	<H2><A NAME="Kapitel2.0"></A>2.0  How to change the source code
1454	and how to document modifications</H2>
1455	<P>Currently (Sep 23rd, 2009), only selected users are allowed to
1456	commit changes to the repository. Rules given below are preliminary,
1457	until we have switched to the "trac"-System.</P>
1458	<OL>
1459	<LI><P>Change source code in your current working copy. Document
1460	changes in the respective file headers unter "<FONT FACE="Courier New, Courier, monospace">Current
1461	revisions:</FONT>". Additionally, document all changes in a
1462	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
1463	including the files that have been changed. Classify changes in
1464	three cases, new (N), changed (C), and bugfix (B). <B>Try to be as
1465	short and as precise as possible in describing the changes!</B></P>
1466	<LI><P>Test the changed version, unless it works sufficiently.</P>
1467	<LI><P>Commit the changes to the repository<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1468	commit -m "message string" trunk<BR></FONT><BR>where
1469	"<FONT FACE="Courier New, Courier, monospace">message string</FONT>"
1470	is a short, <B>meaningful</B> summary of the
1471	changes.<BR><BR>Alternatively, in case that you have made quite a
1472	lot of changes, you can also give the contents of your file
1473	CURRENT_MODIFICATIONS as the log message:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1474	commit -F CURRENT_MODIFICATIONS trunk</FONT></P>
1475	<LI><P>Enter the changes into the technical documentation (under
1476	<FONT FACE="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</FONT>).</P>
1477	<LI><P>Move the change comments in the file headers from "Current
1478	revisions:" to "Former revisions:". Set the current
1479	svn id in front of that.<BR><BR><B>Example:</B><BR><BR><B>before
1480	move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1481	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1482	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1483	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1484	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1485	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1486	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1487	Ã¯Â¿ÂœId: init_3d_model.f90 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1488	2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace">
1489	Ã¯Â¿Âœ</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1490	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1491	var_ts is replaced by dots_max </FONT><BR><BR><B>after move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1492	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1493	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1494	</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1495	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1496	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1497	Ã¯Â¿ÂœId: init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</FONT>
1498	<FONT FACE="Courier New, Courier, monospace">Ã¯Â¿Âœ<BR>!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1499	</FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1500	2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"><BR>!
1501	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1502	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1503	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1504	var_ts is replaced by dots_max<BR><BR></FONT><FONT FACE="Times New Roman, Times, serif">Note
1505	that the "</FONT><FONT FACE="Courier New, Courier, monospace">Ã¯Â¿Âœ</FONT><FONT FACE="Times New Roman, Times, serif">"
1506	in this example should read "$", but "$" cannot
1507	be used here, because otherwise svn would replace these entries
1508	after every change to this technical documentation.</FONT></P>
1509	<LI><P>Commit the changes in the technical documentation and the
1510	file headers:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1511	commit -m "last commit documented" trunk</FONT><BR><BR><BR>
1512	</P>
1513	</OL>
1514	<H2><A NAME="Kapitel3.0"></A>3.0  Description of selected parts
1515	of the model source code</H2>
1516	<P>This section gives links to existing descriptions about special
1517	parts of the PALM code, e.g. special numerical methods that are used
1518	(including mathematical background). Documents are stored in single
1519	files with different formats. Some are in German (sorry for the
1520	inconvenience). <BR>
1521	</P>
1522	<UL>
1523	<LI><P STYLE="margin-bottom: 0in"><A NAME="UPS"></A>upstream-spline
1524	advection scheme ( <A HREF="methods/upstream_spline/ups.pdf">.pdf</A>
1525	, only in German)
1526	</P>
1527	<LI><P STYLE="margin-bottom: 0in"><A NAME="Cloud_physics"></A>cloud
1528	physics module ( <A HREF="methods/cloud_physics/cloud_physics.pdf">.pdf</A>
1529	)
1530	</P>
1531	<LI><P STYLE="margin-bottom: 0in"><A NAME="Bitkompression"></A>data
1532	compression with <A HREF="methods/bit_compression/bit_compression.html">bit
1533	shifting method</A> (only in German)</P>
1534	<LI><P>Runge-Kutta time integration scheme ( <A HREF="methods/runge_kutta/runge_kutta.pdf">.pdf</A>
1535	, only in German)
1536	</P>
1537	</UL>
1538	<P><BR>  <BR>  <BR>  <BR>  <BR>  <BR>
1539	<BR>  <BR>
1540	</P>
1541	</BODY>
1542	</HTML>

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