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Last change on this file since 557 was 557, checked in by weinreis, 14 years ago
bugfix message string in set_mask_locations
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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="20100907;16492700">
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=517>
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=517>
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="40368" SDNUM="1033;0;MM/DD/YY">
96	<P STYLE="font-weight: normal"><FONT SIZE=3>07/09/10</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="557" SDNUM="1033;">
102	<P STYLE="font-weight: normal"><FONT SIZE=3>557</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>B</FONT></P>
109	</TD>
110	<TD WIDTH=517>
111	<P STYLE="font-weight: normal"><FONT SIZE=3>Bugfix of message
112	string in if statement (dz_stretch_level) of subroutine
113	set_mask_locations.</FONT></P>
114	<P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
115	the masked data output, which is still not documented.</FONT></P>
116	</TD>
117	<TD WIDTH=393>
118	<P STYLE="font-weight: normal"><FONT SIZE=3>init_masks</FONT></P>
119	</TD>
120	</TR>
121	<TR>
122	<TD WIDTH=37>
123	<P>07/09/10</P>
124	</TD>
125	<TD WIDTH=56>
126	<P>SR</P>
127	</TD>
128	<TD WIDTH=68>
129	<P>556</P>
130	</TD>
131	<TD WIDTH=62>
132	<P>3.7a</P>
133	</TD>
134	<TD WIDTH=36>
135	<P>C</P>
136	</TD>
137	<TD WIDTH=517>
138	<P>Documentation for <FONT FACE="Courier New, Courier, monospace">surface_heatflux
139	</FONT>in case of <FONT FACE="Courier New, Courier, monospace">prandtl_layer
140	</FONT>= <I>.F.</I> improved.<BR><BR>bugfix for wrong netcdf/3.6.3
141	module on lcsgi (mbuild, mrun)</P>
142	</TD>
143	<TD WIDTH=393>
144	<P>mbuild, mrun</P>
145	</TD>
146	</TR>
147	<TR>
148	<TD WIDTH=37>
149	<P><BR>
150	</P>
151	</TD>
152	<TD WIDTH=56>
153	<P><BR>
154	</P>
155	</TD>
156	<TD WIDTH=68>
157	<P><BR>
158	</P>
159	</TD>
160	<TD WIDTH=62>
161	<P><BR>
162	</P>
163	</TD>
164	<TD WIDTH=36>
165	<P>B</P>
166	</TD>
167	<TD WIDTH=517>
168	<P>Bugfix in if statement (disturb_heatflux)<BR><BR>Bugfix: in
169	2201 statement: closing " was missing
170	(interpret_config)<BR><BR>Bugfix: default setting of nzb_local for
171	flat topography (init_grid)<BR><BR>Bugfix: wrong dimension used
172	for ts_value_l (user_statistics)</P>
173	</TD>
174	<TD WIDTH=393>
175	<P>disturb_heatflux, init_grid, user_statistics<BR><BR>interpret_config</P>
176	</TD>
177	</TR>
178	<TR>
179	<TD WIDTH=37 SDVAL="40187" SDNUM="1033;0;MM/DD/YY">
180	<P STYLE="font-weight: normal"><FONT SIZE=3>01/09/10</FONT></P>
181	</TD>
182	<TD WIDTH=56>
183	<P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P>
184	</TD>
185	<TD WIDTH=68 SDVAL="553" SDNUM="1033;">
186	<P STYLE="font-weight: normal"><FONT SIZE=3>553</FONT></P>
187	</TD>
188	<TD WIDTH=62>
189	<P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P>
190	</TD>
191	<TD WIDTH=36>
192	<P STYLE="font-weight: normal"><FONT SIZE=3>C</FONT></P>
193	</TD>
194	<TD WIDTH=517>
195	<P STYLE="font-weight: normal"><FONT SIZE=3>d3dpar-parameters for
196	masked output <FONT FACE="Courier New, monospace">data_output_mask_*,
197	data_output_mask_user_, mask__x, mask__y, mask__z,
198	mask__x_loop, mask__y_loop </FONT><FONT FACE="Times New Roman, serif">and
199	</FONT><FONT FACE="Courier New, monospace">mask_*_z_loop </FONT>have
200	been replaced by corresponding arrays <FONT FACE="Courier New, monospace">data_output_masks,
201	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
202	mask_y_loop </FONT><FONT FACE="Times New Roman, serif">and</FONT>
203	<FONT FACE="Courier New, monospace">mask_z_loop</FONT></FONT></P>
204	<P STYLE="font-weight: normal"><FONT SIZE=3>inipar-parameter <FONT FACE="Courier New, monospace">masks</FONT>
205	has been removed. </FONT>
206	</P>
207	<P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
208	the masked data output, which is still not documented.</FONT></P>
209	</TD>
210	<TD WIDTH=393>
211	<P STYLE="font-weight: normal"><FONT SIZE=3>check_parameters,
212	init_masks, modules, parin, user_parin</FONT></P>
213	</TD>
214	</TR>
215	<TR>
216	<TD WIDTH=37>
217	<P>17/08/10</P>
218	</TD>
219	<TD WIDTH=56>
220	<P>BM</P>
221	</TD>
222	<TD WIDTH=68>
223	<P>544</P>
224	</TD>
225	<TD WIDTH=62>
226	<P>3.7a</P>
227	</TD>
228	<TD WIDTH=36>
229	<P>B/C/N</P>
230	</TD>
231	<TD WIDTH=517>
232	<P>adjustments for lcxt4; bugfix (mbuild): loading of user-defined
233	modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</P>
234	</TD>
235	<TD WIDTH=393>
236	<P>mrun, mbuild, subjob</P>
237	</TD>
238	</TR>
239	<TR>
240	<TD WIDTH=37>
241	<P>15/06/10</P>
242	</TD>
243	<TD WIDTH=56>
244	<P>RH</P>
245	</TD>
246	<TD WIDTH=68>
247	<P>540</P>
248	</TD>
249	<TD WIDTH=62>
250	<P>3.7a</P>
251	</TD>
252	<TD WIDTH=36>
253	<P>C</P>
254	</TD>
255	<TD WIDTH=517>
256	<P>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is
257	done using the names hicegate0/bicegate0 instead of the IP
258	addresses</P>
259	</TD>
260	<TD WIDTH=393>
261	<P>mrun</P>
262	</TD>
263	</TR>
264	<TR>
265	<TD WIDTH=37>
266	<P>21/04/10</P>
267	</TD>
268	<TD WIDTH=56>
269	<P>RH</P>
270	</TD>
271	<TD WIDTH=68>
272	<P>532</P>
273	</TD>
274	<TD WIDTH=62>
275	<P>3.7a</P>
276	</TD>
277	<TD WIDTH=36>
278	<P>C</P>
279	</TD>
280	<TD WIDTH=517>
281	<P>Large scale vertical motion (subsidence/ascent) can be added as
282	additional source to the prognostic equation for humidity/passive
283	scalar<BR> <BR>character length for dopr_unit
284	enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
285	of png files
286	</P>
287	</TD>
288	<TD WIDTH=393>
289	<P>modules, prognostic_equations<BR><BR>.ncl.config.default,
290	cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</P>
291	</TD>
292	</TR>
293	<TR>
294	<TD WIDTH=37>
295	<P><BR>
296	</P>
297	</TD>
298	<TD WIDTH=56>
299	<P><BR>
300	</P>
301	</TD>
302	<TD WIDTH=68>
303	<P><BR>
304	</P>
305	</TD>
306	<TD WIDTH=62>
307	<P><BR>
308	</P>
309	</TD>
310	<TD WIDTH=36>
311	<P>B</P>
312	</TD>
313	<TD WIDTH=517>
314	<P>Bugfix: unit of hyp changed to dbar</P>
315	</TD>
316	<TD WIDTH=393>
317	<P>check_parameters</P>
318	</TD>
319	</TR>
320	<TR>
321	<TD WIDTH=37>
322	<P>01/04/10</P>
323	</TD>
324	<TD WIDTH=56>
325	<P>RH</P>
326	</TD>
327	<TD WIDTH=68>
328	<P>530</P>
329	</TD>
330	<TD WIDTH=62>
331	<P>3.7a</P>
332	</TD>
333	<TD WIDTH=36>
334	<P>B</P>
335	</TD>
336	<TD WIDTH=517>
337	<P>Bugfix: treatment of special character * in NCL variables
338	containing lists corrected</P>
339	</TD>
340	<TD WIDTH=393>
341	<P>palmplot</P>
342	</TD>
343	</TR>
344	<TR>
345	<TD WIDTH=37>
346	<P>31/03/10</P>
347	</TD>
348	<TD WIDTH=56>
349	<P>RH</P>
350	</TD>
351	<TD WIDTH=68>
352	<P>529</P>
353	</TD>
354	<TD WIDTH=62>
355	<P>3.7a</P>
356	</TD>
357	<TD WIDTH=36>
358	<P>C</P>
359	</TD>
360	<TD WIDTH=517>
361	<P>List of variable names have to specified using blank separated
362	lists and single quotes</P>
363	</TD>
364	<TD WIDTH=393>
365	<P>palmplot</P>
366	</TD>
367	</TR>
368	<TR>
369	<TD WIDTH=37>
370	<P>30/03/10</P>
371	</TD>
372	<TD WIDTH=56>
373	<P>RH</P>
374	</TD>
375	<TD WIDTH=68>
376	<P>526</P>
377	</TD>
378	<TD WIDTH=62>
379	<P>3.7a</P>
380	</TD>
381	<TD WIDTH=36>
382	<P>C</P>
383	</TD>
384	<TD WIDTH=517>
385	<P>Adjustment of the NCL scripts and <FONT FACE="Courier New, Courier, monospace">palmplot
386	</FONT>to allow for special characters in NetCDF variable names
387	</P>
388	</TD>
389	<TD WIDTH=393>
390	<P>palmplot, .ncl.config.default, cross_sections.ncl,
391	profiles.ncl, timeseries.ncl, spectra.ncl</P>
392	</TD>
393	</TR>
394	<TR>
395	<TD WIDTH=37>
396	<P>30/03/10</P>
397	</TD>
398	<TD WIDTH=56>
399	<P>SR</P>
400	</TD>
401	<TD WIDTH=68>
402	<P>525</P>
403	</TD>
404	<TD WIDTH=62>
405	<P>3.7a</P>
406	</TD>
407	<TD WIDTH=36>
408	<P>B</P>
409	</TD>
410	<TD WIDTH=517>
411	<P>Bugfix: "/" in netcdf profile variable names replaced
412	by ":"</P>
413	</TD>
414	<TD WIDTH=393>
415	<P>check_parameters</P>
416	</TD>
417	</TR>
418	<TR>
419	<TD WIDTH=37>
420	<P>19/03/10</P>
421	</TD>
422	<TD WIDTH=56>
423	<P>SR</P>
424	</TD>
425	<TD WIDTH=68>
426	<P>520</P>
427	</TD>
428	<TD WIDTH=62>
429	<P>3.7a</P>
430	</TD>
431	<TD WIDTH=36>
432	<P>N</P>
433	</TD>
434	<TD WIDTH=517>
435	<P>NetCDF4 support for particle data. Total number of particles is
436	allowed to increase during the run, when netcdf_data_format > <I>2</I>
437	is used.</P>
438	</TD>
439	<TD WIDTH=393>
440	<P>advec_particles, check_open, netcdf</P>
441	</TD>
442	</TR>
443	<TR>
444	<TD WIDTH=37>
445	<P><BR>
446	</P>
447	</TD>
448	<TD WIDTH=56>
449	<P><BR>
450	</P>
451	</TD>
452	<TD WIDTH=68>
453	<P><BR>
454	</P>
455	</TD>
456	<TD WIDTH=62>
457	<P><BR>
458	</P>
459	</TD>
460	<TD WIDTH=36>
461	<P>C</P>
462	</TD>
463	<TD WIDTH=517>
464	<P>Special characters like * and " are now allowed for NetCDF
465	variable names. Replacement of these characters has been removed
466	(routine clean_netcdf_varname removed)</P>
467	</TD>
468	<TD WIDTH=393>
469	<P><BR>
470	</P>
471	</TD>
472	</TR>
473	<TR>
474	<TD WIDTH=37>
475	<P>18/03/10</P>
476	</TD>
477	<TD WIDTH=56>
478	<P>SR</P>
479	</TD>
480	<TD WIDTH=68>
481	<P>516</P>
482	</TD>
483	<TD WIDTH=62>
484	<P>3.7a</P>
485	</TD>
486	<TD WIDTH=36>
487	<P>N</P>
488	</TD>
489	<TD WIDTH=517>
490	<P>Simple installation method has been documented (see chapter
491	5.0). Respective scripts and configuration files have been
492	updated.</P>
493	</TD>
494	<TD WIDTH=393>
495	<P>palm_simple_install, palm_simple_run</P>
496	</TD>
497	</TR>
498	<TR>
499	<TD WIDTH=37>
500	<P><BR>
501	</P>
502	</TD>
503	<TD WIDTH=56>
504	<P><BR>
505	</P>
506	</TD>
507	<TD WIDTH=68>
508	<P><BR>
509	</P>
510	</TD>
511	<TD WIDTH=62>
512	<P><BR>
513	</P>
514	</TD>
515	<TD WIDTH=36>
516	<P>B</P>
517	</TD>
518	<TD WIDTH=517>
519	<P>opt=1 is forced for PGI-compiler in routine <FONT FACE="Courier New, Courier, monospace">buoyancy
520	</FONT>by compiler-directive. Otherwise, program aborts with
521	SIGFPE.</P>
522	</TD>
523	<TD WIDTH=393>
524	<P>buoyancy</P>
525	</TD>
526	</TR>
527	<TR>
528	<TD WIDTH=37>
529	<P>16/03/10</P>
530	</TD>
531	<TD WIDTH=56>
532	<P>RH</P>
533	</TD>
534	<TD WIDTH=68>
535	<P>513</P>
536	</TD>
537	<TD WIDTH=62>
538	<P>3.7a</P>
539	</TD>
540	<TD WIDTH=36>
541	<P>N</P>
542	</TD>
543	<TD WIDTH=517>
544	<P>NCL scripts can be run with the shell script <FONT FACE="Courier New, Courier, monospace">palmplot.</FONT></P>
545	</TD>
546	<TD WIDTH=393>
547	<P>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</P>
548	</TD>
549	</TR>
550	<TR>
551	<TD WIDTH=37>
552	<P>12/03/10</P>
553	</TD>
554	<TD WIDTH=56>
555	<P>SR</P>
556	</TD>
557	<TD WIDTH=68>
558	<P>509</P>
559	</TD>
560	<TD WIDTH=62>
561	<P>3.7a</P>
562	</TD>
563	<TD WIDTH=36>
564	<P>B</P>
565	</TD>
566	<TD WIDTH=517>
567	<P>bugfix for rev 504: remode_md was given a wrong value</P>
568	</TD>
569	<TD WIDTH=393>
570	<P>mbuild</P>
571	</TD>
572	</TR>
573	<TR>
574	<TD WIDTH=37>
575	<P>08/03/10</P>
576	</TD>
577	<TD WIDTH=56>
578	<P>SR</P>
579	</TD>
580	<TD WIDTH=68>
581	<P>506</P>
582	</TD>
583	<TD WIDTH=62>
584	<P>3.7a</P>
585	</TD>
586	<TD WIDTH=36>
587	<P>C</P>
588	</TD>
589	<TD WIDTH=517>
590	<P>hack for better usage of <B>mrun</B> on Kyoto computing center
591	machine (<FONT FACE="Courier New, Courier, monospace">lckyoto</FONT>)</P>
592	</TD>
593	<TD WIDTH=393>
594	<P>mrun</P>
595	</TD>
596	</TR>
597	<TR>
598	<TD WIDTH=37>
599	<P>03/03/10</P>
600	</TD>
601	<TD WIDTH=56>
602	<P>SR</P>
603	</TD>
604	<TD WIDTH=68>
605	<P>504</P>
606	</TD>
607	<TD WIDTH=62>
608	<P>3.7a</P>
609	</TD>
610	<TD WIDTH=36>
611	<P>C</P>
612	</TD>
613	<TD WIDTH=517>
614	<P><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
615	is now directly called within <B>mrun</B> and must not be given by
616	an output command in the configuration file any more. Please
617	remove the respective output command (<FONT FACE="Courier New, Courier, monospace">OC:combine_plot_fields.x</FONT>)
618	from your configuration file!<BR><BR>Utility programs
619	(<FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>,
620	<FONT FACE="Courier New, Courier, monospace">interpret_config</FONT>)
621	are created by <B>mbuild</B> separately for each block in the
622	configuration file. Depending on option <FONT FACE="Courier New, Courier, monospace">-K</FONT>,
623	<B>mrun</B> is using the utility programs for the respective
624	block.<BR><BR>Utility programs are also compiled in parallel,
625	depending on variable <FONT FACE="Courier New, Courier, monospace">%mopts</FONT>
626	in the configuration file..<BR><BR>Default configuration files
627	updated.</P>
628	</TD>
629	<TD WIDTH=393>
630	<P>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</P>
631	</TD>
632	</TR>
633	<TR>
634	<TD WIDTH=37>
635	<P>02/03/10</P>
636	</TD>
637	<TD WIDTH=56>
638	<P>SR</P>
639	</TD>
640	<TD WIDTH=68>
641	<P>496</P>
642	</TD>
643	<TD WIDTH=62>
644	<P>3.7a</P>
645	</TD>
646	<TD WIDTH=36>
647	<P>C</P>
648	</TD>
649	<TD WIDTH=517>
650	<P>Particle data for restart runs are only written if environment
651	variable <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>
652	= <I>.T.</I>, i.e. particle data are now handled in the same way
653	as the other restart data.</P>
654	</TD>
655	<TD WIDTH=393>
656	<P>palm</P>
657	</TD>
658	</TR>
659	<TR>
660	<TD WIDTH=37>
661	<P>01/03/10</P>
662	</TD>
663	<TD WIDTH=56>
664	<P>SR</P>
665	</TD>
666	<TD WIDTH=68>
667	<P>494</P>
668	</TD>
669	<TD WIDTH=62>
670	<P>3.7a</P>
671	</TD>
672	<TD WIDTH=36>
673	<P>N</P>
674	</TD>
675	<TD WIDTH=517>
676	<P>Output in NetCDF4-format.<BR><BR>NetCDF4 allows for parallel
677	I/O. Also, variables are not limited in size any more (i.e. arrays
678	can be larger than 2GB). The new d3par-parameter
679	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.can
680	be used to select among the different NetCDF file formats (<I>1</I>:
681	classic format, <I>2</I>: 64-bit-offset format (this is now the
682	default), <I>3</I>: NetCDF4/HDF5 format, <I>4</I>: NetCDF4 format
683	with NF90_CLASSIC_MODEL bit set). Setting <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
684	> <I>2</I> only affects 2d- and 3d-output, i.e. there is no
685	parallel output for profiles, time series, spectra, and particles.
686	Parallel output of particle data may realized in the future.<BR><BR>In
687	case of parallel output, all PEs write into one file, which means
688	that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
689	(merging data from single files - one per PE - into one file) is
690	not neccessary. In this case, flag files are automatically set,
691	telling <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
692	that nothing is to be done.<BR><BR>Using NetCDF4 format requires a
693	NetCDF4/HDF library. Respective settings for -I, -L, and -l
694	compiler/loader options for the SGI-ICE at HLRN can be found in
695	the new example configuration file
696	<FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
697	far, NetCDF parallel I/O has only been tested a little. Further
698	performance optimizations may be required, especially in case of
699	large data sets (e.g. data chunking, or lustre file system
700	settings with <FONT FACE="Courier New, Courier, monospace">lfs
701	setstripe</FONT>). <B>Please report bugs and performance problems
702	immediately!</B><BR><BR><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
703	outputs cpu-time needed for file merging.<BR><BR>Modules to be
704	loaded for compilation (mbuild) or job execution (mrun) can/should
705	now be given in the configuration file (<FONT FACE="Courier New, Courier, monospace">.mrun.config</FONT>)
706	using variable <FONT FACE="Courier New, Courier, monospace">modules</FONT>.
707	Example:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">%modules
708	ifort/11.0.069:netcdf       lcsgih
709	parallel</FONT><BR><BR>This method replaces the (undocumented)
710	<FONT FACE="Courier New, Courier, monospace">mpilib</FONT>-variable.<BR><BR><B>WARNING:</B><BR><B>All
711	fixed settings of modules in the scripts mbuild, mrun, and subjob
712	have been removed! Please set the </B><FONT FACE="Courier New, Courier, monospace"><B>modules</B></FONT>
713	<B>variable appropriately and remove the mpilib variable in your
714	configuration file.<BR><BR></B>Compilation time can be reduced be
715	using parallel make. The number of allowed simultaneous compiler
716	calls (threads) is set in the configuration file using variable
717	<FONT FACE="Courier New, Courier, monospace">mopt</FONT>, e.g.<BR><BR>
718	<FONT FACE="Courier New, Courier, monospace">%mopts  -j:4
719	lcsgih parallel</FONT><BR><BR>allows a maximum of 4 routines to be
720	compiled simultaneously (provided that the makefile does not show
721	any dependencies between these routines).</P>
722	</TD>
723	<TD WIDTH=393>
724	<P>check_open, check_parameters, close_file, data_output_2d,
725	data_output_3d, header, modules, netcdf,
726	parin<BR><BR>combine_plot_fields<BR><BR>mbuild, mrun, subjob</P>
727	</TD>
728	</TR>
729	<TR>
730	<TD WIDTH=37>
731	<P><BR>
732	</P>
733	</TD>
734	<TD WIDTH=56>
735	<P><BR>
736	</P>
737	</TD>
738	<TD WIDTH=68>
739	<P><BR>
740	</P>
741	</TD>
742	<TD WIDTH=62>
743	<P><BR>
744	</P>
745	</TD>
746	<TD WIDTH=36>
747	<P>C</P>
748	</TD>
749	<TD WIDTH=517>
750	<P>d3par-parameters <FONT FACE="Courier New, Courier, monospace">netcdf_64bit</FONT>
751	and <FONT FACE="Courier New, Courier, monospace">netcdf_64bit_3d</FONT>
752	have been removed. Use the new d3par-variable <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
753	= <I>2</I> for choosing the NetCDF 64bit-offset format (this is
754	the default from now on). The offset-format can not be set
755	independently for the 3d-output-data any more.<BR><BR>d3par-parameters
756	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask</FONT>,
757	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask_av</FONT>,
758	and variables <FONT FACE="Courier New, Courier, monospace">nc_format_mask</FONT>,
759	<FONT FACE="Courier New, Courier, monospace">format_parallel_io</FONT>
760	removed. They are replaced by the new parameter
761	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
762	This change concerns the masked data output, which is still not
763	documented.</P>
764	</TD>
765	<TD WIDTH=393>
766	<P>check_open, close_file,<BR>data_output_mask, header,
767	init_masks, modules, parin</P>
768	</TD>
769	</TR>
770	<TR>
771	<TD WIDTH=37>
772	<P><BR>
773	</P>
774	</TD>
775	<TD WIDTH=56>
776	<P><BR>
777	</P>
778	</TD>
779	<TD WIDTH=68>
780	<P><BR>
781	</P>
782	</TD>
783	<TD WIDTH=62>
784	<P><BR>
785	</P>
786	</TD>
787	<TD WIDTH=36>
788	<P>B</P>
789	</TD>
790	<TD WIDTH=517>
791	<P>Bugfix in trunk/UTIL/Makefile: forgot to compile for
792	interpret_config.<BR><BR>Bugfix: timeseries data have to be
793	collected by PE0 (user_statistics).</P>
794	</TD>
795	<TD WIDTH=393>
796	<P>user_statistics<BR><BR>trunk/UTIL/Makefile</P>
797	</TD>
798	</TR>
799	<TR>
800	<TD WIDTH=37>
801	<P>05/02/10</P>
802	</TD>
803	<TD WIDTH=56>
804	<P>SR</P>
805	</TD>
806	<TD WIDTH=68>
807	<P>485</P>
808	</TD>
809	<TD WIDTH=62>
810	<P>3.7a</P>
811	</TD>
812	<TD WIDTH=36>
813	<P>B</P>
814	</TD>
815	<TD WIDTH=517>
816	<P><FONT FACE="Courier New, Courier, monospace">ngp_3d</FONT>,
817	<FONT FACE="Courier New, Courier, monospace">ngp_3d_inner</FONT>
818	changed to 64 bit. Otherwise, on large grids > 210*9 grid
819	points some global statistics (e.g. total kinetic energy) have
820	wrong values.</P>
821	</TD>
822	<TD WIDTH=393>
823	<P>init_3d_model, modules</P>
824	</TD>
825	</TR>
826	<TR>
827	<TD WIDTH=37>
828	<P>05/02/10</P>
829	</TD>
830	<TD WIDTH=56>
831	<P>SR</P>
832	</TD>
833	<TD WIDTH=68>
834	<P>484</P>
835	</TD>
836	<TD WIDTH=62>
837	<P>3.7a</P>
838	</TD>
839	<TD WIDTH=36>
840	<P>B</P>
841	</TD>
842	<TD WIDTH=517>
843	<P>Typo in file headers removed ("current" instead of
844	"actual").</P>
845	</TD>
846	<TD WIDTH=393>
847	<P>many</P>
848	</TD>
849	</TR>
850	<TR>
851	<TD WIDTH=37>
852	<P>05/02/10</P>
853	</TD>
854	<TD WIDTH=56>
855	<P>SR</P>
856	</TD>
857	<TD WIDTH=68>
858	<P>483</P>
859	</TD>
860	<TD WIDTH=62>
861	<P>3.7a</P>
862	</TD>
863	<TD WIDTH=36>
864	<P>N</P>
865	</TD>
866	<TD WIDTH=517>
867	<P><FONT FACE="Courier New, Courier, monospace">compare_palm_logs
868	</FONT>is additionally compiled with <B>mbuild</B> <FONT FACE="Courier New, Courier, monospace">-u</FONT>
869	. (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT> in
870	<FONT FACE="Courier New, Courier, monospace">trunk/UTIL</FONT>)<BR><BR>make
871	options (<FONT FACE="Courier New, Courier, monospace">mopts</FONT>)
872	to be set by configuration file implemented. (<B>mrun</B>,
873	<B>mbuild</B>)<BR><BR><FONT FACE="Courier New, Courier, monospace">humidity</FONT>
874	= <I>.T.</I> can be used for runs with topography.
875	<FONT FACE="Courier New, Courier, monospace">wall_humidityflux</FONT>
876	and<BR><FONT FACE="Courier New, Courier, monospace">wall_scalarflux</FONT>
877	are the corresponding new inipar parameters.<BR>(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
878	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
879	<FONT FACE="Courier New, Courier, monospace">parin</FONT>)<BR><BR>Large
880	scale vertical motion (subsidence/ascent) can be added as
881	additional source to the prognostic equation for potential
882	temperature. See new parameters <FONT FACE="Courier New, Courier, monospace">large_scale_subsidence</FONT>,
883	<FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient</FONT>,
884	and <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient_level</FONT>.
885	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
886	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
887	<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>,
888	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
889	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
890	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
891	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
892	<FONT FACE="Courier New, Courier, monospace">subsidence</FONT>,
893	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Scripts
894	have been updated for Cray-XT5 machine (lcxt5m) and
895	Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
896	and running palm (with limited features) has been added.
897	(<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, new
898	scripts <B>palm_simple_install</B>, <B>palm_simple_run</B>)<BR><BR>Masked
899	data output has been implemented but it is not documented in the
900	user manual so far. This feature can already use NetCDF4 file
901	format. (check_open, check_parameters, close_file, modules,
902	netcdf, parin, time_integration, user_parin, new:
903	data_output_mask, init_masks, user_data_output_mask)</P>
904	</TD>
905	<TD WIDTH=393>
906	<P>check_open, check parameters, close_file, header,
907	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
908	prognostic_equations, read_var_list, time_integration, user_parin,
909	write_var_list<BR><BR><B>new:</B> data_output_mask,
910	init_masks, palm_simple_install, palm_simple_run, subsidence,
911	user_data_output_mask</P>
912	</TD>
913	</TR>
914	<TR>
915	<TD WIDTH=37>
916	<P><BR>
917	</P>
918	</TD>
919	<TD WIDTH=56>
920	<P><BR>
921	</P>
922	</TD>
923	<TD WIDTH=68>
924	<P><BR>
925	</P>
926	</TD>
927	<TD WIDTH=62>
928	<P><BR>
929	</P>
930	</TD>
931	<TD WIDTH=36>
932	<P>C</P>
933	</TD>
934	<TD WIDTH=517>
935	<P>2d-decomposition is default for Cray-XT machines.
936	(<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">var_ts</FONT>
937	is replaced by <FONT FACE="Courier New, Courier, monospace">dots_max</FONT>.
938	(<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
939	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Every
940	cloud droplet has now an own weighting factor and can be deleted
941	due to collisions. Condensation and collision of cloud droplets
942	are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
943	efficiency for large cloud droplets has changed according to table
944	of Rogers and Yau. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
945	</TD>
946	<TD WIDTH=393>
947	<P>advec_particles, collision_efficiency, init_3d_model,
948	init_pegrid, modules</P>
949	</TD>
950	</TR>
951	<TR>
952	<TD WIDTH=37>
953	<P><BR>
954	</P>
955	</TD>
956	<TD WIDTH=56>
957	<P><BR>
958	</P>
959	</TD>
960	<TD WIDTH=68>
961	<P><BR>
962	</P>
963	</TD>
964	<TD WIDTH=62>
965	<P><BR>
966	</P>
967	</TD>
968	<TD WIDTH=36>
969	<P>B</P>
970	</TD>
971	<TD WIDTH=517>
972	<P>Bugfix for generating serial jobs. (<B>subjob</B>)<BR><BR>Bugfix:
973	index problem concerning gradient_level indices removed.
974	(<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
975	of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
976	in cascade change to prevent type problems with mpi2 libraries.
977	(<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
978	was split to make runs reproducible when using ifort compiler.
979	(<FONT FACE="Courier New, Courier, monospace">disturb_field</FONT>)<BR><BR>Bugfix:
980	exchange of ghost points for <FONT FACE="Courier New, Courier, monospace">prho</FONT>
981	included. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix
982	in calculation of time-averaged surface heatfluxes.
983	(<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
984	in calculation of precipitation_rate.
985	(<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
986	initial data assignments to some dvrp arrays changed due to error
987	messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
988	in calculation of cloud droplet velocity.
989	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
990	in transfer of particles at south/left edge.
991	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
992	in calculation of collision efficiency. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
993	</TD>
994	<TD WIDTH=393>
995	<P>advec_particles, calc_precipitation, collision_efficiency,
996	disturb_field, header, modules, poisfft_hybrid, subjob,
997	sum_up_3d_data, time_integration</P>
998	</TD>
999	</TR>
1000	<TR>
1001	<TD WIDTH=37>
1002	<P>23/09/09</P>
1003	</TD>
1004	<TD WIDTH=56>
1005	<P>SR</P>
1006	</TD>
1007	<TD WIDTH=68>
1008	<P>392</P>
1009	</TD>
1010	<TD WIDTH=62>
1011	<P>3.7</P>
1012	</TD>
1013	<TD WIDTH=36>
1014	<P>N</P>
1015	</TD>
1016	<TD WIDTH=517>
1017	<P><B>Most important changes:</B> atmosphere-ocean coupling has
1018	been improved and steering of dvr-software is more user-friendly
1019	now. Beside that, the release contains a lot of optimizations,
1020	changes, and bugfixes which have accumulated over the last
1021	months.<BR><BR>The atmosphere-ocean coupling allows to use
1022	independent precursor runs in order to account for different
1023	spin-up times. The time when coupling has to be started is given
1024	by new inipar parameter <FONT FACE="Courier New, Courier, monospace">coupling_start_time</FONT>.
1025	The precursor ocean run has to be started using new <B>mrun</B>
1026	option "<FONT FACE="Courier New, Courier, monospace">-y</FONT>"
1027	in order to add the appendix "<FONT FACE="Courier New, Courier, monospace">_O</FONT>"
1028	to all output files. (<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
1029	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1030	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1031	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1032	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1033	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
1034	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1035	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
1036	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1037	<FONT FACE="Courier New, Courier, monospace">init_coupling</FONT>,
1038	<FONT FACE="Courier New, Courier, monospace">modules</FONT>, <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1039	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1040	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1041	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
1042	<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>,
1043	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Clipping
1044	of dvrp output implemented. Default colourtable for particles
1045	implemented, particle attributes (color, dvrp_size) can be set
1046	with new parameters <FONT FACE="Courier New, Courier, monospace">particle_color</FONT>,
1047	<FONT FACE="Courier New, Courier, monospace">particle_dvrpsize</FONT>,
1048	<FONT FACE="Courier New, Courier, monospace">color_interval</FONT>,
1049	<FONT FACE="Courier New, Courier, monospace">dvrpsize_interval</FONT>.
1050	Slicer attributes (dvrp) are set with new routine
1051	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>
1052	and are controlled with existing parameters <FONT FACE="Courier New, Courier, monospace">slicer_range_limits</FONT>.
1053	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
1054	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
1055	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1056	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>,
1057	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>)<BR><BR>Polygon
1058	reduction for topography and ground plate isosurface. Reduction
1059	level for buildings can be chosen with parameter cluster_size.
1060	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>)<BR><BR>Variables
1061	<FONT FACE="Courier New, Courier, monospace">bc_lr</FONT> / <FONT FACE="Courier New, Courier, monospace">bc_ns</FONT>
1062	in most subroutines replaced by LOGICAL variables
1063	<FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
1064	for speed optimization. This gives a significant speedup of more
1065	than 10%. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1066	<FONT FACE="Courier New, Courier, monospace">diffusion_u</FONT>,
1067	<FONT FACE="Courier New, Courier, monospace">diffusion_v</FONT>,
1068	<FONT FACE="Courier New, Courier, monospace">diffusion_w</FONT>,
1069	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Scripts
1070	have been adapted for machine lck (Yonsei Univ.). (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1071	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>,
1072	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)<BR><BR>Additional
1073	timestep criterion in case of simulations with plant canopy.
1074	(<FONT FACE="Courier New, Courier, monospace">timestep</FONT>)<BR><BR>Check
1075	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>
1076	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>.
1077	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>External
1078	pressure gradient can be used as driving force. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1079	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1080	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1081	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1082	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1083	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
1084	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1085	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>New
1086	topography case '<I>single_street_canyon</I>'. (<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1087	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1088	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1089	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1090	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1091	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1092	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1093	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1094	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1095	to predefine a target bulk velocity for <FONT FACE="Courier New, Courier, monospace">conserve_volume_flow</FONT>.
1096	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1097	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1098	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1099	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1100	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1101	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1102	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1103	for user defined 2D data output in xy cross sections at z=<FONT FACE="Courier New, Courier, monospace">nzb</FONT>+1.
1104	(<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1105	<FONT FACE="Courier New, Courier, monospace">user_data_output_2d</FONT>)<BR><BR>xy
1106	cross section output of surface heatfluxes (sensible and latent).
1107	(<FONT FACE="Courier New, Courier, monospace">average_3d_data</FONT>,
1108	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1109	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1110	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1111	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1112	<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>,
1113	<FONT FACE="Courier New, Courier, monospace">write_3d_binary</FONT>)</P>
1114	</TD>
1115	<TD WIDTH=393>
1116	<P>average_3d_data, check_for_restart, check_parameters,
1117	data_output_2d, data_output_3d, data_output_dvrp,
1118	data_output_profiles, data_output_ptseries, data_output_spectra,
1119	data_output_tseries, diffusion_u, diffusion_v, diffusion_w,
1120	init_coupling, init_dvrp, init_grid, init_3d_model, header,
1121	mbuild, modules, mrun, package_parin, parin, prognostic_equations,
1122	read_3d_binary, read_var_list, subjob, sum_up_3d_data,
1123	surface_coupler, timestep, time_integration,
1124	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
1125	user_header, user_init_grid, write_3d_binary, write_var_list<BR><BR><B>new:</B>
1126	set_particle_attributes, set_slicer_attributes_dvrp</P>
1127	</TD>
1128	</TR>
1129	<TR>
1130	<TD WIDTH=37>
1131	<P><BR>
1132	</P>
1133	</TD>
1134	<TD WIDTH=56>
1135	<P><BR>
1136	</P>
1137	</TD>
1138	<TD WIDTH=68>
1139	<P><BR>
1140	</P>
1141	</TD>
1142	<TD WIDTH=62>
1143	<P><BR>
1144	</P>
1145	</TD>
1146	<TD WIDTH=36>
1147	<P>C</P>
1148	</TD>
1149	<TD WIDTH=517>
1150	<P>Output of messages replaced by message handling routine.
1151	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1152	<FONT FACE="Courier New, Courier, monospace">advec_s_bc</FONT>,
1153	<FONT FACE="Courier New, Courier, monospace">buoyancy</FONT>,
1154	<FONT FACE="Courier New, Courier, monospace">calc_spectra</FONT>,
1155	<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
1156	<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1157	<FONT FACE="Courier New, Courier, monospace">coriolis</FONT>,
1158	<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>,
1159	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1160	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1161	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
1162	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1163	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1164	<FONT FACE="Courier New, Courier, monospace">fft_xy</FONT>,
1165	<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>,
1166	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1167	<FONT FACE="Courier New, Courier, monospace">init_1d_model</FONT>,
1168	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1169	<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
1170	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1171	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>,
1172	<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>,
1173	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1174	<FONT FACE="Courier New, Courier, monospace">plant_canopy_model</FONT>,
1175	<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>,
1176	<FONT FACE="Courier New, Courier, monospace">poismg</FONT>,
1177	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1178	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1179	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
1180	<FONT FACE="Courier New, Courier, monospace">temperton_fft</FONT>,
1181	<FONT FACE="Courier New, Courier, monospace">timestep</FONT>,
1182	<FONT FACE="Courier New, Courier, monospace">user_actions</FONT>,
1183	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>,
1184	<FONT FACE="Courier New, Courier, monospace">user_dvrp_coltab</FONT>,
1185	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1186	<FONT FACE="Courier New, Courier, monospace">user_init_plant_canopy</FONT>,
1187	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1188	<FONT FACE="Courier New, Courier, monospace">user_read_restart_data</FONT>,
1189	<FONT FACE="Courier New, Courier, monospace">user_spectra</FONT>)<BR><BR>Output
1190	of NetCDF messages with aid of message handling routine.
1191	(<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1192	<FONT FACE="Courier New, Courier, monospace">close_file</FONT>,
1193	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1194	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1195	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1196	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
1197	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1198	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
1199	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>__lcmuk
1200	changed to __lc to avoid problems with Intel compiler on sgi-ice.
1201	(<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
1202	extended NetCDF files, the updated title attribute includes an
1203	update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
1204	case of restart runs without extension, initial profiles are not
1205	written to NetCDF-file anymore. So far, time axis always started
1206	at t=0. (<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1207	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1208	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1209	<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>'
1210	renamed to '<I>cyclic_fill</I>'. A cyclic fill can now <BR>be used
1211	independent of <FONT FACE="Courier New, Courier, monospace">turbulent_inflow</FONT>.
1212	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1213	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1214	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>2
1215	NetCDF error numbers changed. (<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>A
1216	link to the webspage appendix_a.html is printed for further
1217	information about possible reasons of the error that appeared.
1218	(message)<BR><BR>Temperature gradient criterion for estimating the
1219	boundary layer height replaced by the gradient criterion of
1220	Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
1221	unit attribute in timeseries output in case of statistic regions
1222	added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
1223	number of tails is calculated from maximum number of particles and
1224	<FONT FACE="Courier New, Courier, monospace">skip_particles_for_tail</FONT>.
1225	(<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Value
1226	of <FONT FACE="Courier New, Courier, monospace">vertical_particle_advection</FONT>
1227	is allowed to differ for each particle group. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1228	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1229	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)
1230	<BR><BR>First constant in array <FONT FACE="Courier New, Courier, monospace">den</FONT>
1231	also defined as type double. (<FONT FACE="Courier New, Courier, monospace">eqn_state_seawater</FONT>)<BR><BR>Parameter
1232	<FONT FACE="Courier New, Courier, monospace">dvrp_psize</FONT>
1233	moved from <FONT FACE="Courier New, Courier, monospace">particles_par</FONT>
1234	to <FONT FACE="Courier New, Courier, monospace">dvrp_graphics_par</FONT>.
1235	(<FONT FACE="Courier New, Courier, monospace">package_parin</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>
1236	moved from <FONT FACE="Courier New, Courier, monospace">userpar</FONT>
1237	to <FONT FACE="Courier New, Courier, monospace">inipar</FONT>
1238	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1239	<FONT FACE="Courier New, Courier, monospace">header</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1240	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1241	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1242	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1243	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1244	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1245	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Default
1246	value of <FONT FACE="Courier New, Courier, monospace">grid_matching</FONT>
1247	changed to '<I>strict</I>'. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Adjustments
1248	for runs on lcxt4 (necessary due to a software update on CRAY) and
1249	for coupled runs on ibmy. (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1250	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)</P>
1251	</TD>
1252	<TD WIDTH=393>
1253	<P>advec_particles, advec_s_bc, buoyancy, calc_spectra,
1254	check_for_restart, check_open, check_parameters, close_file,
1255	coriolis, cpu_log, data_output_2d, data_output_3d,
1256	data_output_dvrp, data_output_profiles, data_output_ptseries,
1257	data_output_spectra, data_output_tseries, eqn_state_seawater,
1258	fft_xy, flow_statistics, header, init_1d_model, init_3d_model,
1259	init_dvrp, init_grid, init_particles, init_pegrid, message, mrun,
1260	netcdf, package_parin, parin, plant_canopy_model, poisfft,
1261	poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
1262	surface_coupler, temperton_fft, timestep,
1263	user_actions,user_check_parameters, user_data_output_dvrp,
1264	user_dvrp_coltab, user_header, user_init_grid,
1265	user_init_plant_canopy, user_parin, user_read_restart_data,
1266	user_spectra, write_var_list
1267	</P>
1268	</TD>
1269	</TR>
1270	<TR>
1271	<TD WIDTH=37>
1272	<P><BR>
1273	</P>
1274	</TD>
1275	<TD WIDTH=56>
1276	<P><BR>
1277	</P>
1278	</TD>
1279	<TD WIDTH=68>
1280	<P><BR>
1281	</P>
1282	</TD>
1283	<TD WIDTH=62>
1284	<P><BR>
1285	</P>
1286	</TD>
1287	<TD WIDTH=36>
1288	<P>B</P>
1289	</TD>
1290	<TD WIDTH=517>
1291	<P>Bugfix: Initial hydrostatic pressure profile in case of ocean
1292	runs is now calculated in 5 iteration steps. (<FONT FACE="Courier New, Courier, monospace">init_ocean</FONT>)<BR><BR>Bugfix:
1293	wrong sign in buoyancy production of ocean part in case of not
1294	using the reference density (only in 3D routine <FONT FACE="Courier New, Courier, monospace">production_e</FONT>).
1295	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix:
1296	output of averaged 2d/3d quantities requires that an avaraging
1297	interval has been set, respective error message is included.
1298	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1299	Output on unit 14 only if requested by <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>.
1300	(<FONT FACE="Courier New, Courier, monospace">user_last_actions</FONT>)<BR><BR>Bugfix
1301	to avoid zero division by <FONT FACE="Courier New, Courier, monospace">km_neutral</FONT>.
1302	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix
1303	for extended NetCDF files: In order to avoid 'data mode' errors if
1304	updated attributes are larger than their original size,
1305	<FONT FACE="Courier New, Courier, monospace">NF90_PUT_ATT</FONT>
1306	is called in 'define mode' enclosed by <FONT FACE="Courier New, Courier, monospace">NF90_REDEF</FONT>
1307	and <FONT FACE="Courier New, Courier, monospace">NF90_ENDDEF</FONT>
1308	calls. This implies a possible performance loss; an alternative
1309	strategy would be to ensure equal attribute size in a job chain.
1310	(<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
1311	correction of initial volume flow for non-flat topography.
1312	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1313	zero initialization of arrays within buildings for '<I>cyclic_fill</I>'.
1314	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1315	<FONT FACE="Courier New, Courier, monospace">to_be_resorted</FONT>
1316	=> <FONT FACE="Courier New, Courier, monospace">s_av</FONT> for
1317	time-averaged scalars. (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1318	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>Bugfix:
1319	avoid that <FONT FACE="Courier New, Courier, monospace">ngp_2dh_s_inner</FONT>
1320	becomes zero. (<FONT FACE="Courier New, Courier, monospace">init_3_model</FONT>)<BR><BR>Typographical
1321	error: unit of wpt in dots_unit. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix:
1322	error in check, if particles moved further than one subdomain
1323	length. This check must not be applied for newly released
1324	particles. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix:
1325	several tail counters are initialized, <FONT FACE="Courier New, Courier, monospace">particle_tail_coordinates</FONT>
1326	is only written to file if its third index is > 0, arrays for
1327	tails are allocated with a minimum size of 10 tails if there is no
1328	tail initially. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1329	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Bugfix:
1330	pressure included for profile output. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1331	Type of <FONT FACE="Courier New, Courier, monospace">count</FONT>
1332	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1333	changed to default <FONT FACE="Courier New, Courier, monospace">INTEGER</FONT>
1334	on NEC machines. (<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>)<BR><BR>Bugfix:
1335	output of particle time series only if particle advection is
1336	switched on. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix:
1337	qsws was calculated in case of <FONT FACE="Courier New, Courier, monospace">constant
1338	heatflux</FONT> = <FONT FACE="Courier New, Courier, monospace">.FALSE.</FONT>.
1339	(<FONT FACE="Courier New, Courier, monospace">prandtl_fluxes</FONT>)<BR><BR>Bugfix:
1340	averaging along z is not allowed for 2d quantities (e.g. u* and
1341	z0). (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>)<BR><BR>Typographical
1342	errors. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>If
1343	the inversion height calculated by the prerun is zero,
1344	inflow_damping_height must be explicitly specified.
1345	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Small
1346	bugfix concerning 3d 64bit netcdf output format. (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Bugfix:
1347	<FONT FACE="Courier New, Courier, monospace">dt_fixed</FONT>
1348	removed from the restart file, because otherwise, no change from a
1349	fixed to a variable timestep would be possible in restart runs.
1350	(<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1351	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Bugfix:
1352	initial setting of <FONT FACE="Courier New, Courier, monospace">time_coupling</FONT>
1353	in coupled restart runs. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)</P>
1354	</TD>
1355	<TD WIDTH=393>
1356	<P>advec_particles, check_parameters, cpu_log, data_output_2d,
1357	data_output_3d, header, init_3d_model, init_particles, init_ocean,
1358	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
1359	time_integration, user_last_actions, write_var_list</P>
1360	</TD>
1361	</TR>
1362	<TR>
1363	<TD WIDTH=37>
1364	<P>02/02/09</P>
1365	</TD>
1366	<TD WIDTH=56>
1367	<P>SR</P>
1368	</TD>
1369	<TD WIDTH=68>
1370	<P>228</P>
1371	</TD>
1372	<TD WIDTH=62>
1373	<P>3.6</P>
1374	</TD>
1375	<TD WIDTH=36>
1376	<P>N</P>
1377	</TD>
1378	<TD WIDTH=517>
1379	<P>This release contains further additions, changes, and bugfixes
1380	for the SGI-ICE system, as well as important changes like the
1381	splitting of the user-interface into single files, a complete
1382	revision of the pre-compiling mechanism allowing to use different
1383	make-depositories simultaneously, and a revision of the
1384	reading-mechanism from restart files, which has no more
1385	restrictions in case that the previous and current run have
1386	different domain/subdomain sizes. A new handling of all kind of
1387	output messages is introduced with this release and will be
1388	applied to all existing messages within the next releases.<BR><BR><B>New
1389	features are:</B><BR><BR>Restart runs on SGI-ICE are working.
1390	(mrun)<BR>2d-decomposition is default on SGI-ICE systems.
1391	(init_pegrid)<BR><BR>Ocean-atmosphere coupling realized with
1392	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
1393	called with <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1394	"<I>-K parallel</I>" for coupling. Adjustments in <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1395	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, and
1396	<FONT FACE="Courier New, Courier, monospace">subjob</FONT> for
1397	lcxt4.<BR><BR>DVRP arguments changed to single precision, mode
1398	pathlines added.<BR><BR>User can add additional routines in files
1399	<FONT FACE="Courier New, Courier, monospace">user_additional_routines</FONT>.<BR><BR>User
1400	can check user parameters and deduce further quantities in
1401	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT></P>
1402	</TD>
1403	<TD WIDTH=393>
1404	<P>check_for_restart, check_parameters, data_output_dvrp,
1405	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
1406	surface_coupler, timestep<BR><BR>Makefile, mbuild, mrun,
1407	subjob<BR><BR><B>new:</B><BR>init_coupling,
1408	user_additional_routines, user_check_parameters</P>
1409	</TD>
1410	</TR>
1411	<TR>
1412	<TD WIDTH=37>
1413	<P><BR>
1414	</P>
1415	</TD>
1416	<TD WIDTH=56>
1417	<P><BR>
1418	</P>
1419	</TD>
1420	<TD WIDTH=68>
1421	<P><BR>
1422	</P>
1423	</TD>
1424	<TD WIDTH=62>
1425	<P><BR>
1426	</P>
1427	</TD>
1428	<TD WIDTH=36>
1429	<P>C</P>
1430	</TD>
1431	<TD WIDTH=517>
1432	<P>User interface has been split into single files.<BR><BR>Type of
1433	variables <FONT FACE="Courier New, Courier, monospace">count</FONT>
1434	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1435	changed to INTEGER(8) in order to avoid "out of range"
1436	problems, which result in measured negative time intervals.
1437	(cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
1438	mechanism from restart files completely revised. The
1439	subdomain/total domain size is now allowed to vary arbitrarily
1440	between the current and previous run. (read_var_list,
1441	read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
1442	mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
1443	completely revised: the source-tarfile remains in the source
1444	directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
1445	One depository per block (given in the config-file) is created.
1446	Always all files from the source directory are copied to the
1447	respective depository. No additional file checks are done any more
1448	(mrun version 2.1). The depository name used contains the
1449	conditions given by <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1450	"<FONT FACE="Courier New, Courier, monospace">-K</FONT>".
1451	(mbuild, mrun)<BR><BR>Output messages (including required stop of
1452	execution) can now be handled with the new subroutine <FONT FACE="Courier New, Courier, monospace">message</FONT>.
1453	All output messages will be replaced by this routine step by step
1454	within the next revisions.<BR><BR>Neumann boundary condition at
1455	<FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
1456	explicitly set for better reading, although this has been already
1457	done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
1458	xy-coordinate system shifted from the center of the first grid
1459	cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
1460	<FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
1461	south-left corner of this cell. (netcdf) Topography definition
1462	according to new user parameter <FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>.
1463	(init_grid, modules, user_header, user_init_grid, user_parin)</P>
1464	</TD>
1465	<TD WIDTH=393>
1466	<P>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop,
1467	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
1468	read_var_list, user_read_restart_data<BR><BR>Makefile, mbuild,
1469	mrun<BR><BR><B>removed:</B><BR>user_interface<BR><BR><B>new:</B><BR>message,
1470	user_3d_data_averaging, user_actions, user_advec_particles,
1471	user_check_data_output, user_check_data_output_pr,
1472	user_data_output_2d, user_data_output_3d, user_data_output_dvrp,
1473	user_define_netcdf_grid, user_dvrp_coltab, user_header,
1474	user_init_3d_model, user_init, user_init_grid,
1475	user_init_particles, user_init_plant_canopy, user_last_actions,
1476	user_parin, user_parin, user_particle_attributes,
1477	user_read_restart_data, user_spectra, user_statistics</P>
1478	</TD>
1479	</TR>
1480	<TR>
1481	<TD WIDTH=37>
1482	<P><BR>
1483	</P>
1484	</TD>
1485	<TD WIDTH=56>
1486	<P><BR>
1487	</P>
1488	</TD>
1489	<TD WIDTH=68>
1490	<P><BR>
1491	</P>
1492	</TD>
1493	<TD WIDTH=62>
1494	<P><BR>
1495	</P>
1496	</TD>
1497	<TD WIDTH=36>
1498	<P>B</P>
1499	</TD>
1500	<TD WIDTH=517>
1501	<P>Bugfix: array <FONT FACE="Courier New, Courier, monospace">d</FONT>
1502	is reallocated in case that multigrid is used.
1503	(calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
1504	(check_for_restart, cpu_statistics,
1505	inflow_turbulence, timestep)<BR><BR>Size of <FONT FACE="Courier New, Courier, monospace">pf3d
1506	</FONT>adjusted to the required output size (1 gridpoint less,
1507	along all three dimensions), because output of a subset of the
1508	data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
1509	in the NF90_PUT_VAR statement caused segmentation fault with the
1510	INTEL compiler. (combine_plot_fields)<BR><BR>Bugfix: error in <FONT FACE="Courier New, Courier, monospace">zu</FONT>
1511	index in case of <FONT FACE="Courier New, Courier, monospace">section_xy=-1</FONT>.
1512	(header)<BR><BR>Inconsistency removed: as the thermal
1513	stratification is not taken into account for the evaluation of the
1514	wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
1515	must not be used for the evaluation of the velocity gradients
1516	<FONT FACE="Courier New, Courier, monospace">dudy</FONT>, <FONT FACE="Courier New, Courier, monospace">dwdy</FONT>,
1517	<FONT FACE="Courier New, Courier, monospace">dvdx</FONT> and <FONT FACE="Courier New, Courier, monospace">dwdx</FONT>.
1518	(production_e)<BR><BR>Bugfix in calculating <FONT FACE="Courier New, Courier, monospace">k</FONT>
1519	index in case of oceans runs. (sort_particles)<BR><BR>Bugfix: no
1520	output of particle concentration and radius unless particles have
1521	been started. (data_output_2d)<BR><BR>Bugfix: reading of
1522	<FONT FACE="Courier New, Courier, monospace">spectrum_x\|y</FONT>
1523	from restart files ignored if total numbers of grid points do not
1524	match. (read_3d_binary)<BR><BR>Bugfix: abort in case that absolute
1525	temperature is below zero. (init_cloud_physics)</P>
1526	</TD>
1527	<TD WIDTH=393>
1528	<P>advec_particles, calc_spectra, check_for_restart,
1529	cpu_statistics, data_output_2d, header, inflow_turbulence,
1530	init_cloud_physics, production_e, read_3d_binary,
1531	timestep<BR><BR>combine_plot_fields</P>
1532	</TD>
1533	</TR>
1534	</TABLE>
1535	<P><BR>  <BR>
1536	</P>
1537	<H2><A NAME="Kapitel2.0"></A>2.0  How to change the source code
1538	and how to document modifications</H2>
1539	<P>Currently (Sep 23rd, 2009), only selected users are allowed to
1540	commit changes to the repository. Rules given below are preliminary,
1541	until we have switched to the "trac"-System.</P>
1542	<OL>
1543	<LI><P>Change source code in your current working copy. Document
1544	changes in the respective file headers unter "<FONT FACE="Courier New, Courier, monospace">Current
1545	revisions:</FONT>". Additionally, document all changes in a
1546	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
1547	including the files that have been changed. Classify changes in
1548	three cases, new (N), changed (C), and bugfix (B). <B>Try to be as
1549	short and as precise as possible in describing the changes!</B></P>
1550	<LI><P>Test the changed version, unless it works sufficiently.</P>
1551	<LI><P>Commit the changes to the repository<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1552	commit -m "message string" trunk<BR></FONT><BR>where
1553	"<FONT FACE="Courier New, Courier, monospace">message string</FONT>"
1554	is a short, <B>meaningful</B> summary of the
1555	changes.<BR><BR>Alternatively, in case that you have made quite a
1556	lot of changes, you can also give the contents of your file
1557	CURRENT_MODIFICATIONS as the log message:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1558	commit -F CURRENT_MODIFICATIONS trunk</FONT></P>
1559	<LI><P>Enter the changes into the technical documentation (under
1560	<FONT FACE="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</FONT>).</P>
1561	<LI><P>Move the change comments in the file headers from "Current
1562	revisions:" to "Former revisions:". Set the current
1563	svn id in front of that.<BR><BR><B>Example:</B><BR><BR><B>before
1564	move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1565	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1566	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1567	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1568	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1569	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1570	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1571	Â§Id: init_3d_model.f90 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1572	2010-02-06 13:37:48Z raasch</B></FONT></FONT> <FONT FACE="Courier New, Courier, monospace">Â§</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1573	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1574	var_ts is replaced by dots_max </FONT><BR><BR><B>after move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1575	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1576	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1577	</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1578	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1579	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1580	Â§Id: init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</FONT> <FONT FACE="Courier New, Courier, monospace">Â§<BR>!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1581	</FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1582	2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"><BR>!
1583	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1584	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1585	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1586	var_ts is replaced by dots_max<BR><BR></FONT><FONT FACE="Times New Roman, Times, serif">Note
1587	that the "</FONT><FONT FACE="Courier New, Courier, monospace">Â§</FONT><FONT FACE="Times New Roman, Times, serif">"
1588	in this example should read "$", but "$" cannot
1589	be used here, because otherwise svn would replace these entries
1590	after every change to this technical documentation.</FONT></P>
1591	<LI><P>Commit the changes in the technical documentation and the
1592	file headers:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1593	commit -m "last commit documented" trunk</FONT><BR><BR><BR>
1594	</P>
1595	</OL>
1596	<H2><A NAME="Kapitel3.0"></A>3.0  Description of selected parts
1597	of the model source code</H2>
1598	<P>This section gives links to existing descriptions about special
1599	parts of the PALM code, e.g. special numerical methods that are used
1600	(including mathematical background). Documents are stored in single
1601	files with different formats. Some are in German (sorry for the
1602	inconvenience). <BR>
1603	</P>
1604	<UL>
1605	<LI><P STYLE="margin-bottom: 0in"><A NAME="UPS"></A>upstream-spline
1606	advection scheme ( <A HREF="methods/upstream_spline/ups.pdf">.pdf</A>
1607	, only in German)
1608	</P>
1609	<LI><P STYLE="margin-bottom: 0in"><A NAME="Cloud_physics"></A>cloud
1610	physics module ( <A HREF="methods/cloud_physics/cloud_physics.pdf">.pdf</A>
1611	)
1612	</P>
1613	<LI><P STYLE="margin-bottom: 0in"><A NAME="Bitkompression"></A>data
1614	compression with <A HREF="methods/bit_compression/bit_compression.html">bit
1615	shifting method</A> (only in German)</P>
1616	<LI><P>Runge-Kutta time integration scheme ( <A HREF="methods/runge_kutta/runge_kutta.pdf">.pdf</A>
1617	, only in German)
1618	</P>
1619	</UL>
1620	<P><BR>  <BR>  <BR>  <BR>  <BR>  <BR>
1621	<BR>  <BR>
1622	</P>
1623	</BODY>
1624	</HTML>

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