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correction of calculating ngp_3d for 64 bit
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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="20100909;12050600">
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="40430" SDNUM="1033;0;MM/DD/YY">
96	<P STYLE="font-weight: normal"><FONT SIZE=3>09/09/10</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="560" SDNUM="1033;">
102	<P STYLE="font-weight: normal"><FONT SIZE=3>560</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 calculating
112	<FONT FACE="Courier New, monospace">ngp_3d</FONT> for 64 bit. So
113	far <FONT FACE="Courier New, monospace">ngp_3d</FONT><FONT FACE="Times New Roman, serif">
114	has not been 64 bit.</FONT></FONT></P>
115	</TD>
116	<TD WIDTH=393>
117	<P STYLE="font-weight: normal"><FONT SIZE=3>init_3d_model</FONT></P>
118	</TD>
119	</TR>
120	<TR>
121	<TD WIDTH=37 SDVAL="40368" SDNUM="1033;0;MM/DD/YY">
122	<P STYLE="font-weight: normal"><FONT SIZE=3>07/09/10</FONT></P>
123	</TD>
124	<TD WIDTH=56>
125	<P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P>
126	</TD>
127	<TD WIDTH=68 SDVAL="557" SDNUM="1033;">
128	<P STYLE="font-weight: normal"><FONT SIZE=3>557</FONT></P>
129	</TD>
130	<TD WIDTH=62>
131	<P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P>
132	</TD>
133	<TD WIDTH=36>
134	<P STYLE="font-weight: normal"><FONT SIZE=3>B</FONT></P>
135	</TD>
136	<TD WIDTH=517>
137	<P STYLE="font-weight: normal"><FONT SIZE=3>Bugfix of message
138	string in if statement (dz_stretch_level) of subroutine
139	set_mask_locations.</FONT></P>
140	<P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
141	the masked data output, which is still not documented.</FONT></P>
142	</TD>
143	<TD WIDTH=393>
144	<P STYLE="font-weight: normal"><FONT SIZE=3>init_masks</FONT></P>
145	</TD>
146	</TR>
147	<TR>
148	<TD WIDTH=37>
149	<P>07/09/10</P>
150	</TD>
151	<TD WIDTH=56>
152	<P>SR</P>
153	</TD>
154	<TD WIDTH=68>
155	<P>556</P>
156	</TD>
157	<TD WIDTH=62>
158	<P>3.7a</P>
159	</TD>
160	<TD WIDTH=36>
161	<P>C</P>
162	</TD>
163	<TD WIDTH=517>
164	<P>Documentation for <FONT FACE="Courier New, Courier, monospace">surface_heatflux
165	</FONT>in case of <FONT FACE="Courier New, Courier, monospace">prandtl_layer
166	</FONT>= <I>.F.</I> improved.<BR><BR>bugfix for wrong netcdf/3.6.3
167	module on lcsgi (mbuild, mrun)</P>
168	</TD>
169	<TD WIDTH=393>
170	<P>mbuild, mrun</P>
171	</TD>
172	</TR>
173	<TR>
174	<TD WIDTH=37>
175	<P><BR>
176	</P>
177	</TD>
178	<TD WIDTH=56>
179	<P><BR>
180	</P>
181	</TD>
182	<TD WIDTH=68>
183	<P><BR>
184	</P>
185	</TD>
186	<TD WIDTH=62>
187	<P><BR>
188	</P>
189	</TD>
190	<TD WIDTH=36>
191	<P>B</P>
192	</TD>
193	<TD WIDTH=517>
194	<P>Bugfix in if statement (disturb_heatflux)<BR><BR>Bugfix: in
195	2201 statement: closing " was missing
196	(interpret_config)<BR><BR>Bugfix: default setting of nzb_local for
197	flat topography (init_grid)<BR><BR>Bugfix: wrong dimension used
198	for ts_value_l (user_statistics)</P>
199	</TD>
200	<TD WIDTH=393>
201	<P>disturb_heatflux, init_grid, user_statistics<BR><BR>interpret_config</P>
202	</TD>
203	</TR>
204	<TR>
205	<TD WIDTH=37 SDVAL="40187" SDNUM="1033;0;MM/DD/YY">
206	<P STYLE="font-weight: normal"><FONT SIZE=3>01/09/10</FONT></P>
207	</TD>
208	<TD WIDTH=56>
209	<P STYLE="font-weight: normal"><FONT SIZE=3>CH</FONT></P>
210	</TD>
211	<TD WIDTH=68 SDVAL="553" SDNUM="1033;">
212	<P STYLE="font-weight: normal"><FONT SIZE=3>553</FONT></P>
213	</TD>
214	<TD WIDTH=62>
215	<P STYLE="font-weight: normal"><FONT SIZE=3>3.7a</FONT></P>
216	</TD>
217	<TD WIDTH=36>
218	<P STYLE="font-weight: normal"><FONT SIZE=3>C</FONT></P>
219	</TD>
220	<TD WIDTH=517>
221	<P STYLE="font-weight: normal"><FONT SIZE=3>d3dpar-parameters for
222	masked output <FONT FACE="Courier New, monospace">data_output_mask_*,
223	data_output_mask_user_, mask__x, mask__y, mask__z,
224	mask__x_loop, mask__y_loop </FONT><FONT FACE="Times New Roman, serif">and
225	</FONT><FONT FACE="Courier New, monospace">mask_*_z_loop </FONT>have
226	been replaced by corresponding arrays <FONT FACE="Courier New, monospace">data_output_masks,
227	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
228	mask_y_loop </FONT><FONT FACE="Times New Roman, serif">and</FONT>
229	<FONT FACE="Courier New, monospace">mask_z_loop</FONT></FONT></P>
230	<P STYLE="font-weight: normal"><FONT SIZE=3>inipar-parameter <FONT FACE="Courier New, monospace">masks</FONT>
231	has been removed. </FONT>
232	</P>
233	<P STYLE="font-weight: normal"><FONT SIZE=3>The changes concern
234	the masked data output, which is still not documented.</FONT></P>
235	</TD>
236	<TD WIDTH=393>
237	<P STYLE="font-weight: normal"><FONT SIZE=3>check_parameters,
238	init_masks, modules, parin, user_parin</FONT></P>
239	</TD>
240	</TR>
241	<TR>
242	<TD WIDTH=37>
243	<P>17/08/10</P>
244	</TD>
245	<TD WIDTH=56>
246	<P>BM</P>
247	</TD>
248	<TD WIDTH=68>
249	<P>544</P>
250	</TD>
251	<TD WIDTH=62>
252	<P>3.7a</P>
253	</TD>
254	<TD WIDTH=36>
255	<P>B/C/N</P>
256	</TD>
257	<TD WIDTH=517>
258	<P>adjustments for lcxt4; bugfix (mbuild): loading of user-defined
259	modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</P>
260	</TD>
261	<TD WIDTH=393>
262	<P>mrun, mbuild, subjob</P>
263	</TD>
264	</TR>
265	<TR>
266	<TD WIDTH=37>
267	<P>15/06/10</P>
268	</TD>
269	<TD WIDTH=56>
270	<P>RH</P>
271	</TD>
272	<TD WIDTH=68>
273	<P>540</P>
274	</TD>
275	<TD WIDTH=62>
276	<P>3.7a</P>
277	</TD>
278	<TD WIDTH=36>
279	<P>C</P>
280	</TD>
281	<TD WIDTH=517>
282	<P>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is
283	done using the names hicegate0/bicegate0 instead of the IP
284	addresses</P>
285	</TD>
286	<TD WIDTH=393>
287	<P>mrun</P>
288	</TD>
289	</TR>
290	<TR>
291	<TD WIDTH=37>
292	<P>21/04/10</P>
293	</TD>
294	<TD WIDTH=56>
295	<P>RH</P>
296	</TD>
297	<TD WIDTH=68>
298	<P>532</P>
299	</TD>
300	<TD WIDTH=62>
301	<P>3.7a</P>
302	</TD>
303	<TD WIDTH=36>
304	<P>C</P>
305	</TD>
306	<TD WIDTH=517>
307	<P>Large scale vertical motion (subsidence/ascent) can be added as
308	additional source to the prognostic equation for humidity/passive
309	scalar<BR> <BR>character length for dopr_unit
310	enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
311	of png files
312	</P>
313	</TD>
314	<TD WIDTH=393>
315	<P>modules, prognostic_equations<BR><BR>.ncl.config.default,
316	cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</P>
317	</TD>
318	</TR>
319	<TR>
320	<TD WIDTH=37>
321	<P><BR>
322	</P>
323	</TD>
324	<TD WIDTH=56>
325	<P><BR>
326	</P>
327	</TD>
328	<TD WIDTH=68>
329	<P><BR>
330	</P>
331	</TD>
332	<TD WIDTH=62>
333	<P><BR>
334	</P>
335	</TD>
336	<TD WIDTH=36>
337	<P>B</P>
338	</TD>
339	<TD WIDTH=517>
340	<P>Bugfix: unit of hyp changed to dbar</P>
341	</TD>
342	<TD WIDTH=393>
343	<P>check_parameters</P>
344	</TD>
345	</TR>
346	<TR>
347	<TD WIDTH=37>
348	<P>01/04/10</P>
349	</TD>
350	<TD WIDTH=56>
351	<P>RH</P>
352	</TD>
353	<TD WIDTH=68>
354	<P>530</P>
355	</TD>
356	<TD WIDTH=62>
357	<P>3.7a</P>
358	</TD>
359	<TD WIDTH=36>
360	<P>B</P>
361	</TD>
362	<TD WIDTH=517>
363	<P>Bugfix: treatment of special character * in NCL variables
364	containing lists corrected</P>
365	</TD>
366	<TD WIDTH=393>
367	<P>palmplot</P>
368	</TD>
369	</TR>
370	<TR>
371	<TD WIDTH=37>
372	<P>31/03/10</P>
373	</TD>
374	<TD WIDTH=56>
375	<P>RH</P>
376	</TD>
377	<TD WIDTH=68>
378	<P>529</P>
379	</TD>
380	<TD WIDTH=62>
381	<P>3.7a</P>
382	</TD>
383	<TD WIDTH=36>
384	<P>C</P>
385	</TD>
386	<TD WIDTH=517>
387	<P>List of variable names have to specified using blank separated
388	lists and single quotes</P>
389	</TD>
390	<TD WIDTH=393>
391	<P>palmplot</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>RH</P>
400	</TD>
401	<TD WIDTH=68>
402	<P>526</P>
403	</TD>
404	<TD WIDTH=62>
405	<P>3.7a</P>
406	</TD>
407	<TD WIDTH=36>
408	<P>C</P>
409	</TD>
410	<TD WIDTH=517>
411	<P>Adjustment of the NCL scripts and <FONT FACE="Courier New, Courier, monospace">palmplot
412	</FONT>to allow for special characters in NetCDF variable names
413	</P>
414	</TD>
415	<TD WIDTH=393>
416	<P>palmplot, .ncl.config.default, cross_sections.ncl,
417	profiles.ncl, timeseries.ncl, spectra.ncl</P>
418	</TD>
419	</TR>
420	<TR>
421	<TD WIDTH=37>
422	<P>30/03/10</P>
423	</TD>
424	<TD WIDTH=56>
425	<P>SR</P>
426	</TD>
427	<TD WIDTH=68>
428	<P>525</P>
429	</TD>
430	<TD WIDTH=62>
431	<P>3.7a</P>
432	</TD>
433	<TD WIDTH=36>
434	<P>B</P>
435	</TD>
436	<TD WIDTH=517>
437	<P>Bugfix: "/" in netcdf profile variable names replaced
438	by ":"</P>
439	</TD>
440	<TD WIDTH=393>
441	<P>check_parameters</P>
442	</TD>
443	</TR>
444	<TR>
445	<TD WIDTH=37>
446	<P>19/03/10</P>
447	</TD>
448	<TD WIDTH=56>
449	<P>SR</P>
450	</TD>
451	<TD WIDTH=68>
452	<P>520</P>
453	</TD>
454	<TD WIDTH=62>
455	<P>3.7a</P>
456	</TD>
457	<TD WIDTH=36>
458	<P>N</P>
459	</TD>
460	<TD WIDTH=517>
461	<P>NetCDF4 support for particle data. Total number of particles is
462	allowed to increase during the run, when netcdf_data_format > <I>2</I>
463	is used.</P>
464	</TD>
465	<TD WIDTH=393>
466	<P>advec_particles, check_open, netcdf</P>
467	</TD>
468	</TR>
469	<TR>
470	<TD WIDTH=37>
471	<P><BR>
472	</P>
473	</TD>
474	<TD WIDTH=56>
475	<P><BR>
476	</P>
477	</TD>
478	<TD WIDTH=68>
479	<P><BR>
480	</P>
481	</TD>
482	<TD WIDTH=62>
483	<P><BR>
484	</P>
485	</TD>
486	<TD WIDTH=36>
487	<P>C</P>
488	</TD>
489	<TD WIDTH=517>
490	<P>Special characters like * and " are now allowed for NetCDF
491	variable names. Replacement of these characters has been removed
492	(routine clean_netcdf_varname removed)</P>
493	</TD>
494	<TD WIDTH=393>
495	<P><BR>
496	</P>
497	</TD>
498	</TR>
499	<TR>
500	<TD WIDTH=37>
501	<P>18/03/10</P>
502	</TD>
503	<TD WIDTH=56>
504	<P>SR</P>
505	</TD>
506	<TD WIDTH=68>
507	<P>516</P>
508	</TD>
509	<TD WIDTH=62>
510	<P>3.7a</P>
511	</TD>
512	<TD WIDTH=36>
513	<P>N</P>
514	</TD>
515	<TD WIDTH=517>
516	<P>Simple installation method has been documented (see chapter
517	5.0). Respective scripts and configuration files have been
518	updated.</P>
519	</TD>
520	<TD WIDTH=393>
521	<P>palm_simple_install, palm_simple_run</P>
522	</TD>
523	</TR>
524	<TR>
525	<TD WIDTH=37>
526	<P><BR>
527	</P>
528	</TD>
529	<TD WIDTH=56>
530	<P><BR>
531	</P>
532	</TD>
533	<TD WIDTH=68>
534	<P><BR>
535	</P>
536	</TD>
537	<TD WIDTH=62>
538	<P><BR>
539	</P>
540	</TD>
541	<TD WIDTH=36>
542	<P>B</P>
543	</TD>
544	<TD WIDTH=517>
545	<P>opt=1 is forced for PGI-compiler in routine <FONT FACE="Courier New, Courier, monospace">buoyancy
546	</FONT>by compiler-directive. Otherwise, program aborts with
547	SIGFPE.</P>
548	</TD>
549	<TD WIDTH=393>
550	<P>buoyancy</P>
551	</TD>
552	</TR>
553	<TR>
554	<TD WIDTH=37>
555	<P>16/03/10</P>
556	</TD>
557	<TD WIDTH=56>
558	<P>RH</P>
559	</TD>
560	<TD WIDTH=68>
561	<P>513</P>
562	</TD>
563	<TD WIDTH=62>
564	<P>3.7a</P>
565	</TD>
566	<TD WIDTH=36>
567	<P>N</P>
568	</TD>
569	<TD WIDTH=517>
570	<P>NCL scripts can be run with the shell script <FONT FACE="Courier New, Courier, monospace">palmplot.</FONT></P>
571	</TD>
572	<TD WIDTH=393>
573	<P>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</P>
574	</TD>
575	</TR>
576	<TR>
577	<TD WIDTH=37>
578	<P>12/03/10</P>
579	</TD>
580	<TD WIDTH=56>
581	<P>SR</P>
582	</TD>
583	<TD WIDTH=68>
584	<P>509</P>
585	</TD>
586	<TD WIDTH=62>
587	<P>3.7a</P>
588	</TD>
589	<TD WIDTH=36>
590	<P>B</P>
591	</TD>
592	<TD WIDTH=517>
593	<P>bugfix for rev 504: remode_md was given a wrong value</P>
594	</TD>
595	<TD WIDTH=393>
596	<P>mbuild</P>
597	</TD>
598	</TR>
599	<TR>
600	<TD WIDTH=37>
601	<P>08/03/10</P>
602	</TD>
603	<TD WIDTH=56>
604	<P>SR</P>
605	</TD>
606	<TD WIDTH=68>
607	<P>506</P>
608	</TD>
609	<TD WIDTH=62>
610	<P>3.7a</P>
611	</TD>
612	<TD WIDTH=36>
613	<P>C</P>
614	</TD>
615	<TD WIDTH=517>
616	<P>hack for better usage of <B>mrun</B> on Kyoto computing center
617	machine (<FONT FACE="Courier New, Courier, monospace">lckyoto</FONT>)</P>
618	</TD>
619	<TD WIDTH=393>
620	<P>mrun</P>
621	</TD>
622	</TR>
623	<TR>
624	<TD WIDTH=37>
625	<P>03/03/10</P>
626	</TD>
627	<TD WIDTH=56>
628	<P>SR</P>
629	</TD>
630	<TD WIDTH=68>
631	<P>504</P>
632	</TD>
633	<TD WIDTH=62>
634	<P>3.7a</P>
635	</TD>
636	<TD WIDTH=36>
637	<P>C</P>
638	</TD>
639	<TD WIDTH=517>
640	<P><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
641	is now directly called within <B>mrun</B> and must not be given by
642	an output command in the configuration file any more. Please
643	remove the respective output command (<FONT FACE="Courier New, Courier, monospace">OC:combine_plot_fields.x</FONT>)
644	from your configuration file!<BR><BR>Utility programs
645	(<FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>,
646	<FONT FACE="Courier New, Courier, monospace">interpret_config</FONT>)
647	are created by <B>mbuild</B> separately for each block in the
648	configuration file. Depending on option <FONT FACE="Courier New, Courier, monospace">-K</FONT>,
649	<B>mrun</B> is using the utility programs for the respective
650	block.<BR><BR>Utility programs are also compiled in parallel,
651	depending on variable <FONT FACE="Courier New, Courier, monospace">%mopts</FONT>
652	in the configuration file..<BR><BR>Default configuration files
653	updated.</P>
654	</TD>
655	<TD WIDTH=393>
656	<P>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</P>
657	</TD>
658	</TR>
659	<TR>
660	<TD WIDTH=37>
661	<P>02/03/10</P>
662	</TD>
663	<TD WIDTH=56>
664	<P>SR</P>
665	</TD>
666	<TD WIDTH=68>
667	<P>496</P>
668	</TD>
669	<TD WIDTH=62>
670	<P>3.7a</P>
671	</TD>
672	<TD WIDTH=36>
673	<P>C</P>
674	</TD>
675	<TD WIDTH=517>
676	<P>Particle data for restart runs are only written if environment
677	variable <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>
678	= <I>.T.</I>, i.e. particle data are now handled in the same way
679	as the other restart data.</P>
680	</TD>
681	<TD WIDTH=393>
682	<P>palm</P>
683	</TD>
684	</TR>
685	<TR>
686	<TD WIDTH=37>
687	<P>01/03/10</P>
688	</TD>
689	<TD WIDTH=56>
690	<P>SR</P>
691	</TD>
692	<TD WIDTH=68>
693	<P>494</P>
694	</TD>
695	<TD WIDTH=62>
696	<P>3.7a</P>
697	</TD>
698	<TD WIDTH=36>
699	<P>N</P>
700	</TD>
701	<TD WIDTH=517>
702	<P>Output in NetCDF4-format.<BR><BR>NetCDF4 allows for parallel
703	I/O. Also, variables are not limited in size any more (i.e. arrays
704	can be larger than 2GB). The new d3par-parameter
705	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.can
706	be used to select among the different NetCDF file formats (<I>1</I>:
707	classic format, <I>2</I>: 64-bit-offset format (this is now the
708	default), <I>3</I>: NetCDF4/HDF5 format, <I>4</I>: NetCDF4 format
709	with NF90_CLASSIC_MODEL bit set). Setting <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
710	> <I>2</I> only affects 2d- and 3d-output, i.e. there is no
711	parallel output for profiles, time series, spectra, and particles.
712	Parallel output of particle data may realized in the future.<BR><BR>In
713	case of parallel output, all PEs write into one file, which means
714	that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
715	(merging data from single files - one per PE - into one file) is
716	not neccessary. In this case, flag files are automatically set,
717	telling <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
718	that nothing is to be done.<BR><BR>Using NetCDF4 format requires a
719	NetCDF4/HDF library. Respective settings for -I, -L, and -l
720	compiler/loader options for the SGI-ICE at HLRN can be found in
721	the new example configuration file
722	<FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
723	far, NetCDF parallel I/O has only been tested a little. Further
724	performance optimizations may be required, especially in case of
725	large data sets (e.g. data chunking, or lustre file system
726	settings with <FONT FACE="Courier New, Courier, monospace">lfs
727	setstripe</FONT>). <B>Please report bugs and performance problems
728	immediately!</B><BR><BR><FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
729	outputs cpu-time needed for file merging.<BR><BR>Modules to be
730	loaded for compilation (mbuild) or job execution (mrun) can/should
731	now be given in the configuration file (<FONT FACE="Courier New, Courier, monospace">.mrun.config</FONT>)
732	using variable <FONT FACE="Courier New, Courier, monospace">modules</FONT>.
733	Example:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">%modules
734	ifort/11.0.069:netcdf       lcsgih
735	parallel</FONT><BR><BR>This method replaces the (undocumented)
736	<FONT FACE="Courier New, Courier, monospace">mpilib</FONT>-variable.<BR><BR><B>WARNING:</B><BR><B>All
737	fixed settings of modules in the scripts mbuild, mrun, and subjob
738	have been removed! Please set the </B><FONT FACE="Courier New, Courier, monospace"><B>modules</B></FONT>
739	<B>variable appropriately and remove the mpilib variable in your
740	configuration file.<BR><BR></B>Compilation time can be reduced be
741	using parallel make. The number of allowed simultaneous compiler
742	calls (threads) is set in the configuration file using variable
743	<FONT FACE="Courier New, Courier, monospace">mopt</FONT>, e.g.<BR><BR>
744	<FONT FACE="Courier New, Courier, monospace">%mopts  -j:4
745	lcsgih parallel</FONT><BR><BR>allows a maximum of 4 routines to be
746	compiled simultaneously (provided that the makefile does not show
747	any dependencies between these routines).</P>
748	</TD>
749	<TD WIDTH=393>
750	<P>check_open, check_parameters, close_file, data_output_2d,
751	data_output_3d, header, modules, netcdf,
752	parin<BR><BR>combine_plot_fields<BR><BR>mbuild, mrun, subjob</P>
753	</TD>
754	</TR>
755	<TR>
756	<TD WIDTH=37>
757	<P><BR>
758	</P>
759	</TD>
760	<TD WIDTH=56>
761	<P><BR>
762	</P>
763	</TD>
764	<TD WIDTH=68>
765	<P><BR>
766	</P>
767	</TD>
768	<TD WIDTH=62>
769	<P><BR>
770	</P>
771	</TD>
772	<TD WIDTH=36>
773	<P>C</P>
774	</TD>
775	<TD WIDTH=517>
776	<P>d3par-parameters <FONT FACE="Courier New, Courier, monospace">netcdf_64bit</FONT>
777	and <FONT FACE="Courier New, Courier, monospace">netcdf_64bit_3d</FONT>
778	have been removed. Use the new d3par-variable <FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>
779	= <I>2</I> for choosing the NetCDF 64bit-offset format (this is
780	the default from now on). The offset-format can not be set
781	independently for the 3d-output-data any more.<BR><BR>d3par-parameters
782	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask</FONT>,
783	<FONT FACE="Courier New, Courier, monospace">netcdf_format_mask_av</FONT>,
784	and variables <FONT FACE="Courier New, Courier, monospace">nc_format_mask</FONT>,
785	<FONT FACE="Courier New, Courier, monospace">format_parallel_io</FONT>
786	removed. They are replaced by the new parameter
787	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
788	This change concerns the masked data output, which is still not
789	documented.</P>
790	</TD>
791	<TD WIDTH=393>
792	<P>check_open, close_file,<BR>data_output_mask, header,
793	init_masks, modules, parin</P>
794	</TD>
795	</TR>
796	<TR>
797	<TD WIDTH=37>
798	<P><BR>
799	</P>
800	</TD>
801	<TD WIDTH=56>
802	<P><BR>
803	</P>
804	</TD>
805	<TD WIDTH=68>
806	<P><BR>
807	</P>
808	</TD>
809	<TD WIDTH=62>
810	<P><BR>
811	</P>
812	</TD>
813	<TD WIDTH=36>
814	<P>B</P>
815	</TD>
816	<TD WIDTH=517>
817	<P>Bugfix in trunk/UTIL/Makefile: forgot to compile for
818	interpret_config.<BR><BR>Bugfix: timeseries data have to be
819	collected by PE0 (user_statistics).</P>
820	</TD>
821	<TD WIDTH=393>
822	<P>user_statistics<BR><BR>trunk/UTIL/Makefile</P>
823	</TD>
824	</TR>
825	<TR>
826	<TD WIDTH=37>
827	<P>05/02/10</P>
828	</TD>
829	<TD WIDTH=56>
830	<P>SR</P>
831	</TD>
832	<TD WIDTH=68>
833	<P>485</P>
834	</TD>
835	<TD WIDTH=62>
836	<P>3.7a</P>
837	</TD>
838	<TD WIDTH=36>
839	<P>B</P>
840	</TD>
841	<TD WIDTH=517>
842	<P><FONT FACE="Courier New, Courier, monospace">ngp_3d</FONT>,
843	<FONT FACE="Courier New, Courier, monospace">ngp_3d_inner</FONT>
844	changed to 64 bit. Otherwise, on large grids > 210*9 grid
845	points some global statistics (e.g. total kinetic energy) have
846	wrong values.</P>
847	</TD>
848	<TD WIDTH=393>
849	<P>init_3d_model, modules</P>
850	</TD>
851	</TR>
852	<TR>
853	<TD WIDTH=37>
854	<P>05/02/10</P>
855	</TD>
856	<TD WIDTH=56>
857	<P>SR</P>
858	</TD>
859	<TD WIDTH=68>
860	<P>484</P>
861	</TD>
862	<TD WIDTH=62>
863	<P>3.7a</P>
864	</TD>
865	<TD WIDTH=36>
866	<P>B</P>
867	</TD>
868	<TD WIDTH=517>
869	<P>Typo in file headers removed ("current" instead of
870	"actual").</P>
871	</TD>
872	<TD WIDTH=393>
873	<P>many</P>
874	</TD>
875	</TR>
876	<TR>
877	<TD WIDTH=37>
878	<P>05/02/10</P>
879	</TD>
880	<TD WIDTH=56>
881	<P>SR</P>
882	</TD>
883	<TD WIDTH=68>
884	<P>483</P>
885	</TD>
886	<TD WIDTH=62>
887	<P>3.7a</P>
888	</TD>
889	<TD WIDTH=36>
890	<P>N</P>
891	</TD>
892	<TD WIDTH=517>
893	<P><FONT FACE="Courier New, Courier, monospace">compare_palm_logs
894	</FONT>is additionally compiled with <B>mbuild</B> <FONT FACE="Courier New, Courier, monospace">-u</FONT>
895	. (<FONT FACE="Courier New, Courier, monospace">Makefile</FONT> in
896	<FONT FACE="Courier New, Courier, monospace">trunk/UTIL</FONT>)<BR><BR>make
897	options (<FONT FACE="Courier New, Courier, monospace">mopts</FONT>)
898	to be set by configuration file implemented. (<B>mrun</B>,
899	<B>mbuild</B>)<BR><BR><FONT FACE="Courier New, Courier, monospace">humidity</FONT>
900	= <I>.T.</I> can be used for runs with topography.
901	<FONT FACE="Courier New, Courier, monospace">wall_humidityflux</FONT>
902	and<BR><FONT FACE="Courier New, Courier, monospace">wall_scalarflux</FONT>
903	are the corresponding new inipar parameters.<BR>(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
904	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
905	<FONT FACE="Courier New, Courier, monospace">parin</FONT>)<BR><BR>Large
906	scale vertical motion (subsidence/ascent) can be added as
907	additional source to the prognostic equation for potential
908	temperature. See new parameters <FONT FACE="Courier New, Courier, monospace">large_scale_subsidence</FONT>,
909	<FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient</FONT>,
910	and <FONT FACE="Courier New, Courier, monospace">ws_vertical_gradient_level</FONT>.
911	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
912	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
913	<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>,
914	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
915	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
916	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
917	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
918	<FONT FACE="Courier New, Courier, monospace">subsidence</FONT>,
919	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Scripts
920	have been updated for Cray-XT5 machine (lcxt5m) and
921	Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
922	and running palm (with limited features) has been added.
923	(<FONT FACE="Courier New, Courier, monospace">Makefile</FONT>, new
924	scripts <B>palm_simple_install</B>, <B>palm_simple_run</B>)<BR><BR>Masked
925	data output has been implemented but it is not documented in the
926	user manual so far. This feature can already use NetCDF4 file
927	format. (check_open, check_parameters, close_file, modules,
928	netcdf, parin, time_integration, user_parin, new:
929	data_output_mask, init_masks, user_data_output_mask)</P>
930	</TD>
931	<TD WIDTH=393>
932	<P>check_open, check parameters, close_file, header,
933	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
934	prognostic_equations, read_var_list, time_integration, user_parin,
935	write_var_list<BR><BR><B>new:</B> data_output_mask,
936	init_masks, palm_simple_install, palm_simple_run, subsidence,
937	user_data_output_mask</P>
938	</TD>
939	</TR>
940	<TR>
941	<TD WIDTH=37>
942	<P><BR>
943	</P>
944	</TD>
945	<TD WIDTH=56>
946	<P><BR>
947	</P>
948	</TD>
949	<TD WIDTH=68>
950	<P><BR>
951	</P>
952	</TD>
953	<TD WIDTH=62>
954	<P><BR>
955	</P>
956	</TD>
957	<TD WIDTH=36>
958	<P>C</P>
959	</TD>
960	<TD WIDTH=517>
961	<P>2d-decomposition is default for Cray-XT machines.
962	(<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">var_ts</FONT>
963	is replaced by <FONT FACE="Courier New, Courier, monospace">dots_max</FONT>.
964	(<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
965	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Every
966	cloud droplet has now an own weighting factor and can be deleted
967	due to collisions. Condensation and collision of cloud droplets
968	are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
969	efficiency for large cloud droplets has changed according to table
970	of Rogers and Yau. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
971	</TD>
972	<TD WIDTH=393>
973	<P>advec_particles, collision_efficiency, init_3d_model,
974	init_pegrid, modules</P>
975	</TD>
976	</TR>
977	<TR>
978	<TD WIDTH=37>
979	<P><BR>
980	</P>
981	</TD>
982	<TD WIDTH=56>
983	<P><BR>
984	</P>
985	</TD>
986	<TD WIDTH=68>
987	<P><BR>
988	</P>
989	</TD>
990	<TD WIDTH=62>
991	<P><BR>
992	</P>
993	</TD>
994	<TD WIDTH=36>
995	<P>B</P>
996	</TD>
997	<TD WIDTH=517>
998	<P>Bugfix for generating serial jobs. (<B>subjob</B>)<BR><BR>Bugfix:
999	index problem concerning gradient_level indices removed.
1000	(<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
1001	of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
1002	in cascade change to prevent type problems with mpi2 libraries.
1003	(<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
1004	was split to make runs reproducible when using ifort compiler.
1005	(<FONT FACE="Courier New, Courier, monospace">disturb_field</FONT>)<BR><BR>Bugfix:
1006	exchange of ghost points for <FONT FACE="Courier New, Courier, monospace">prho</FONT>
1007	included. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix
1008	in calculation of time-averaged surface heatfluxes.
1009	(<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
1010	in calculation of precipitation_rate.
1011	(<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
1012	initial data assignments to some dvrp arrays changed due to error
1013	messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
1014	in calculation of cloud droplet velocity.
1015	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
1016	in transfer of particles at south/left edge.
1017	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
1018	in calculation of collision efficiency. (<FONT FACE="Courier New, Courier, monospace">collision_efficiency</FONT>)</P>
1019	</TD>
1020	<TD WIDTH=393>
1021	<P>advec_particles, calc_precipitation, collision_efficiency,
1022	disturb_field, header, modules, poisfft_hybrid, subjob,
1023	sum_up_3d_data, time_integration</P>
1024	</TD>
1025	</TR>
1026	<TR>
1027	<TD WIDTH=37>
1028	<P>23/09/09</P>
1029	</TD>
1030	<TD WIDTH=56>
1031	<P>SR</P>
1032	</TD>
1033	<TD WIDTH=68>
1034	<P>392</P>
1035	</TD>
1036	<TD WIDTH=62>
1037	<P>3.7</P>
1038	</TD>
1039	<TD WIDTH=36>
1040	<P>N</P>
1041	</TD>
1042	<TD WIDTH=517>
1043	<P><B>Most important changes:</B> atmosphere-ocean coupling has
1044	been improved and steering of dvr-software is more user-friendly
1045	now. Beside that, the release contains a lot of optimizations,
1046	changes, and bugfixes which have accumulated over the last
1047	months.<BR><BR>The atmosphere-ocean coupling allows to use
1048	independent precursor runs in order to account for different
1049	spin-up times. The time when coupling has to be started is given
1050	by new inipar parameter <FONT FACE="Courier New, Courier, monospace">coupling_start_time</FONT>.
1051	The precursor ocean run has to be started using new <B>mrun</B>
1052	option "<FONT FACE="Courier New, Courier, monospace">-y</FONT>"
1053	in order to add the appendix "<FONT FACE="Courier New, Courier, monospace">_O</FONT>"
1054	to all output files. (<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
1055	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1056	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1057	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1058	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1059	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
1060	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1061	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
1062	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1063	<FONT FACE="Courier New, Courier, monospace">init_coupling</FONT>,
1064	<FONT FACE="Courier New, Courier, monospace">modules</FONT>, <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1065	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1066	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1067	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
1068	<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>,
1069	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Clipping
1070	of dvrp output implemented. Default colourtable for particles
1071	implemented, particle attributes (color, dvrp_size) can be set
1072	with new parameters <FONT FACE="Courier New, Courier, monospace">particle_color</FONT>,
1073	<FONT FACE="Courier New, Courier, monospace">particle_dvrpsize</FONT>,
1074	<FONT FACE="Courier New, Courier, monospace">color_interval</FONT>,
1075	<FONT FACE="Courier New, Courier, monospace">dvrpsize_interval</FONT>.
1076	Slicer attributes (dvrp) are set with new routine
1077	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>
1078	and are controlled with existing parameters <FONT FACE="Courier New, Courier, monospace">slicer_range_limits</FONT>.
1079	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
1080	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
1081	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1082	<FONT FACE="Courier New, Courier, monospace">set_slicer_attributes_dvrp</FONT>,
1083	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>)<BR><BR>Polygon
1084	reduction for topography and ground plate isosurface. Reduction
1085	level for buildings can be chosen with parameter cluster_size.
1086	(<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>)<BR><BR>Variables
1087	<FONT FACE="Courier New, Courier, monospace">bc_lr</FONT> / <FONT FACE="Courier New, Courier, monospace">bc_ns</FONT>
1088	in most subroutines replaced by LOGICAL variables
1089	<FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
1090	for speed optimization. This gives a significant speedup of more
1091	than 10%. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1092	<FONT FACE="Courier New, Courier, monospace">diffusion_u</FONT>,
1093	<FONT FACE="Courier New, Courier, monospace">diffusion_v</FONT>,
1094	<FONT FACE="Courier New, Courier, monospace">diffusion_w</FONT>,
1095	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Scripts
1096	have been adapted for machine lck (Yonsei Univ.). (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1097	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>,
1098	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)<BR><BR>Additional
1099	timestep criterion in case of simulations with plant canopy.
1100	(<FONT FACE="Courier New, Courier, monospace">timestep</FONT>)<BR><BR>Check
1101	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>
1102	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>.
1103	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>External
1104	pressure gradient can be used as driving force. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1105	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1106	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1107	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1108	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1109	<FONT FACE="Courier New, Courier, monospace">prognostic_equations</FONT>,
1110	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1111	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>New
1112	topography case '<I>single_street_canyon</I>'. (<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1113	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1114	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1115	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1116	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1117	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1118	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1119	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1120	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1121	to predefine a target bulk velocity for <FONT FACE="Courier New, Courier, monospace">conserve_volume_flow</FONT>.
1122	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1123	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1124	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1125	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1126	<FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1127	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1128	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Option
1129	for user defined 2D data output in xy cross sections at z=<FONT FACE="Courier New, Courier, monospace">nzb</FONT>+1.
1130	(<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1131	<FONT FACE="Courier New, Courier, monospace">user_data_output_2d</FONT>)<BR><BR>xy
1132	cross section output of surface heatfluxes (sensible and latent).
1133	(<FONT FACE="Courier New, Courier, monospace">average_3d_data</FONT>,
1134	<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1135	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1136	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1137	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1138	<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>,
1139	<FONT FACE="Courier New, Courier, monospace">write_3d_binary</FONT>)</P>
1140	</TD>
1141	<TD WIDTH=393>
1142	<P>average_3d_data, check_for_restart, check_parameters,
1143	data_output_2d, data_output_3d, data_output_dvrp,
1144	data_output_profiles, data_output_ptseries, data_output_spectra,
1145	data_output_tseries, diffusion_u, diffusion_v, diffusion_w,
1146	init_coupling, init_dvrp, init_grid, init_3d_model, header,
1147	mbuild, modules, mrun, package_parin, parin, prognostic_equations,
1148	read_3d_binary, read_var_list, subjob, sum_up_3d_data,
1149	surface_coupler, timestep, time_integration,
1150	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
1151	user_header, user_init_grid, write_3d_binary, write_var_list<BR><BR><B>new:</B>
1152	set_particle_attributes, set_slicer_attributes_dvrp</P>
1153	</TD>
1154	</TR>
1155	<TR>
1156	<TD WIDTH=37>
1157	<P><BR>
1158	</P>
1159	</TD>
1160	<TD WIDTH=56>
1161	<P><BR>
1162	</P>
1163	</TD>
1164	<TD WIDTH=68>
1165	<P><BR>
1166	</P>
1167	</TD>
1168	<TD WIDTH=62>
1169	<P><BR>
1170	</P>
1171	</TD>
1172	<TD WIDTH=36>
1173	<P>C</P>
1174	</TD>
1175	<TD WIDTH=517>
1176	<P>Output of messages replaced by message handling routine.
1177	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1178	<FONT FACE="Courier New, Courier, monospace">advec_s_bc</FONT>,
1179	<FONT FACE="Courier New, Courier, monospace">buoyancy</FONT>,
1180	<FONT FACE="Courier New, Courier, monospace">calc_spectra</FONT>,
1181	<FONT FACE="Courier New, Courier, monospace">check_for_restart</FONT>,
1182	<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1183	<FONT FACE="Courier New, Courier, monospace">coriolis</FONT>,
1184	<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>,
1185	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1186	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1187	<FONT FACE="Courier New, Courier, monospace">data_output_dvrp</FONT>,
1188	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1189	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1190	<FONT FACE="Courier New, Courier, monospace">fft_xy</FONT>,
1191	<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>,
1192	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1193	<FONT FACE="Courier New, Courier, monospace">init_1d_model</FONT>,
1194	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>,
1195	<FONT FACE="Courier New, Courier, monospace">init_dvrp</FONT>,
1196	<FONT FACE="Courier New, Courier, monospace">init_grid</FONT>,
1197	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>,
1198	<FONT FACE="Courier New, Courier, monospace">init_pegrid</FONT>,
1199	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1200	<FONT FACE="Courier New, Courier, monospace">plant_canopy_model</FONT>,
1201	<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>,
1202	<FONT FACE="Courier New, Courier, monospace">poismg</FONT>,
1203	<FONT FACE="Courier New, Courier, monospace">read_3d_binary</FONT>,
1204	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1205	<FONT FACE="Courier New, Courier, monospace">surface_coupler</FONT>,
1206	<FONT FACE="Courier New, Courier, monospace">temperton_fft</FONT>,
1207	<FONT FACE="Courier New, Courier, monospace">timestep</FONT>,
1208	<FONT FACE="Courier New, Courier, monospace">user_actions</FONT>,
1209	<FONT FACE="Courier New, Courier, monospace">user_data_output_dvrp</FONT>,
1210	<FONT FACE="Courier New, Courier, monospace">user_dvrp_coltab</FONT>,
1211	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1212	<FONT FACE="Courier New, Courier, monospace">user_init_plant_canopy</FONT>,
1213	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1214	<FONT FACE="Courier New, Courier, monospace">user_read_restart_data</FONT>,
1215	<FONT FACE="Courier New, Courier, monospace">user_spectra</FONT>)<BR><BR>Output
1216	of NetCDF messages with aid of message handling routine.
1217	(<FONT FACE="Courier New, Courier, monospace">check_open</FONT>,
1218	<FONT FACE="Courier New, Courier, monospace">close_file</FONT>,
1219	<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1220	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>,
1221	<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1222	<FONT FACE="Courier New, Courier, monospace">data_output_ptseries</FONT>,
1223	<FONT FACE="Courier New, Courier, monospace">data_output_spectra</FONT>,
1224	<FONT FACE="Courier New, Courier, monospace">data_output_tseries</FONT>,
1225	<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>__lcmuk
1226	changed to __lc to avoid problems with Intel compiler on sgi-ice.
1227	(<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
1228	extended NetCDF files, the updated title attribute includes an
1229	update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
1230	case of restart runs without extension, initial profiles are not
1231	written to NetCDF-file anymore. So far, time axis always started
1232	at t=0. (<FONT FACE="Courier New, Courier, monospace">data_output_profiles</FONT>,
1233	<FONT FACE="Courier New, Courier, monospace">modules</FONT>,
1234	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1235	<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>'
1236	renamed to '<I>cyclic_fill</I>'. A cyclic fill can now <BR>be used
1237	independent of <FONT FACE="Courier New, Courier, monospace">turbulent_inflow</FONT>.
1238	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1239	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1240	<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>2
1241	NetCDF error numbers changed. (<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>A
1242	link to the webspage appendix_a.html is printed for further
1243	information about possible reasons of the error that appeared.
1244	(message)<BR><BR>Temperature gradient criterion for estimating the
1245	boundary layer height replaced by the gradient criterion of
1246	Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
1247	unit attribute in timeseries output in case of statistic regions
1248	added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
1249	number of tails is calculated from maximum number of particles and
1250	<FONT FACE="Courier New, Courier, monospace">skip_particles_for_tail</FONT>.
1251	(<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Value
1252	of <FONT FACE="Courier New, Courier, monospace">vertical_particle_advection</FONT>
1253	is allowed to differ for each particle group. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1254	<FONT FACE="Courier New, Courier, monospace">header</FONT>,
1255	<FONT FACE="Courier New, Courier, monospace">modules</FONT>)
1256	<BR><BR>First constant in array <FONT FACE="Courier New, Courier, monospace">den</FONT>
1257	also defined as type double. (<FONT FACE="Courier New, Courier, monospace">eqn_state_seawater</FONT>)<BR><BR>Parameter
1258	<FONT FACE="Courier New, Courier, monospace">dvrp_psize</FONT>
1259	moved from <FONT FACE="Courier New, Courier, monospace">particles_par</FONT>
1260	to <FONT FACE="Courier New, Courier, monospace">dvrp_graphics_par</FONT>.
1261	(<FONT FACE="Courier New, Courier, monospace">package_parin</FONT>)<BR><BR><FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>
1262	moved from <FONT FACE="Courier New, Courier, monospace">userpar</FONT>
1263	to <FONT FACE="Courier New, Courier, monospace">inipar</FONT>
1264	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>,
1265	<FONT FACE="Courier New, Courier, monospace">header</FONT>, <FONT FACE="Courier New, Courier, monospace">parin</FONT>,
1266	<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1267	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT>,
1268	<FONT FACE="Courier New, Courier, monospace">user_header</FONT>,
1269	<FONT FACE="Courier New, Courier, monospace">user_init_grid</FONT>,
1270	<FONT FACE="Courier New, Courier, monospace">user_parin</FONT>,
1271	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Default
1272	value of <FONT FACE="Courier New, Courier, monospace">grid_matching</FONT>
1273	changed to '<I>strict</I>'. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Adjustments
1274	for runs on lcxt4 (necessary due to a software update on CRAY) and
1275	for coupled runs on ibmy. (<FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1276	<FONT FACE="Courier New, Courier, monospace">subjob</FONT>)</P>
1277	</TD>
1278	<TD WIDTH=393>
1279	<P>advec_particles, advec_s_bc, buoyancy, calc_spectra,
1280	check_for_restart, check_open, check_parameters, close_file,
1281	coriolis, cpu_log, data_output_2d, data_output_3d,
1282	data_output_dvrp, data_output_profiles, data_output_ptseries,
1283	data_output_spectra, data_output_tseries, eqn_state_seawater,
1284	fft_xy, flow_statistics, header, init_1d_model, init_3d_model,
1285	init_dvrp, init_grid, init_particles, init_pegrid, message, mrun,
1286	netcdf, package_parin, parin, plant_canopy_model, poisfft,
1287	poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
1288	surface_coupler, temperton_fft, timestep,
1289	user_actions,user_check_parameters, user_data_output_dvrp,
1290	user_dvrp_coltab, user_header, user_init_grid,
1291	user_init_plant_canopy, user_parin, user_read_restart_data,
1292	user_spectra, write_var_list
1293	</P>
1294	</TD>
1295	</TR>
1296	<TR>
1297	<TD WIDTH=37>
1298	<P><BR>
1299	</P>
1300	</TD>
1301	<TD WIDTH=56>
1302	<P><BR>
1303	</P>
1304	</TD>
1305	<TD WIDTH=68>
1306	<P><BR>
1307	</P>
1308	</TD>
1309	<TD WIDTH=62>
1310	<P><BR>
1311	</P>
1312	</TD>
1313	<TD WIDTH=36>
1314	<P>B</P>
1315	</TD>
1316	<TD WIDTH=517>
1317	<P>Bugfix: Initial hydrostatic pressure profile in case of ocean
1318	runs is now calculated in 5 iteration steps. (<FONT FACE="Courier New, Courier, monospace">init_ocean</FONT>)<BR><BR>Bugfix:
1319	wrong sign in buoyancy production of ocean part in case of not
1320	using the reference density (only in 3D routine <FONT FACE="Courier New, Courier, monospace">production_e</FONT>).
1321	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix:
1322	output of averaged 2d/3d quantities requires that an avaraging
1323	interval has been set, respective error message is included.
1324	(<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1325	Output on unit 14 only if requested by <FONT FACE="Courier New, Courier, monospace">write_binary</FONT>.
1326	(<FONT FACE="Courier New, Courier, monospace">user_last_actions</FONT>)<BR><BR>Bugfix
1327	to avoid zero division by <FONT FACE="Courier New, Courier, monospace">km_neutral</FONT>.
1328	(<FONT FACE="Courier New, Courier, monospace">production_e</FONT>)<BR><BR>Bugfix
1329	for extended NetCDF files: In order to avoid 'data mode' errors if
1330	updated attributes are larger than their original size,
1331	<FONT FACE="Courier New, Courier, monospace">NF90_PUT_ATT</FONT>
1332	is called in 'define mode' enclosed by <FONT FACE="Courier New, Courier, monospace">NF90_REDEF</FONT>
1333	and <FONT FACE="Courier New, Courier, monospace">NF90_ENDDEF</FONT>
1334	calls. This implies a possible performance loss; an alternative
1335	strategy would be to ensure equal attribute size in a job chain.
1336	(<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
1337	correction of initial volume flow for non-flat topography.
1338	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1339	zero initialization of arrays within buildings for '<I>cyclic_fill</I>'.
1340	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Bugfix:
1341	<FONT FACE="Courier New, Courier, monospace">to_be_resorted</FONT>
1342	=> <FONT FACE="Courier New, Courier, monospace">s_av</FONT> for
1343	time-averaged scalars. (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>,
1344	<FONT FACE="Courier New, Courier, monospace">data_output_3d</FONT>)<BR><BR>Bugfix:
1345	avoid that <FONT FACE="Courier New, Courier, monospace">ngp_2dh_s_inner</FONT>
1346	becomes zero. (<FONT FACE="Courier New, Courier, monospace">init_3_model</FONT>)<BR><BR>Typographical
1347	error: unit of wpt in dots_unit. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix:
1348	error in check, if particles moved further than one subdomain
1349	length. This check must not be applied for newly released
1350	particles. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix:
1351	several tail counters are initialized, <FONT FACE="Courier New, Courier, monospace">particle_tail_coordinates</FONT>
1352	is only written to file if its third index is > 0, arrays for
1353	tails are allocated with a minimum size of 10 tails if there is no
1354	tail initially. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>,
1355	<FONT FACE="Courier New, Courier, monospace">init_particles</FONT>)<BR><BR>Bugfix:
1356	pressure included for profile output. (<FONT FACE="Courier New, Courier, monospace">check_parameters</FONT>)<BR><BR>Bugfix:
1357	Type of <FONT FACE="Courier New, Courier, monospace">count</FONT>
1358	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1359	changed to default <FONT FACE="Courier New, Courier, monospace">INTEGER</FONT>
1360	on NEC machines. (<FONT FACE="Courier New, Courier, monospace">cpu_log</FONT>)<BR><BR>Bugfix:
1361	output of particle time series only if particle advection is
1362	switched on. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)<BR><BR>Bugfix:
1363	qsws was calculated in case of <FONT FACE="Courier New, Courier, monospace">constant
1364	heatflux</FONT> = <FONT FACE="Courier New, Courier, monospace">.FALSE.</FONT>.
1365	(<FONT FACE="Courier New, Courier, monospace">prandtl_fluxes</FONT>)<BR><BR>Bugfix:
1366	averaging along z is not allowed for 2d quantities (e.g. u* and
1367	z0). (<FONT FACE="Courier New, Courier, monospace">data_output_2d</FONT>)<BR><BR>Typographical
1368	errors. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>If
1369	the inversion height calculated by the prerun is zero,
1370	inflow_damping_height must be explicitly specified.
1371	(<FONT FACE="Courier New, Courier, monospace">init_3d_model</FONT>)<BR><BR>Small
1372	bugfix concerning 3d 64bit netcdf output format. (<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Bugfix:
1373	<FONT FACE="Courier New, Courier, monospace">dt_fixed</FONT>
1374	removed from the restart file, because otherwise, no change from a
1375	fixed to a variable timestep would be possible in restart runs.
1376	(<FONT FACE="Courier New, Courier, monospace">read_var_list</FONT>,
1377	<FONT FACE="Courier New, Courier, monospace">write_var_list</FONT>)<BR><BR>Bugfix:
1378	initial setting of <FONT FACE="Courier New, Courier, monospace">time_coupling</FONT>
1379	in coupled restart runs. (<FONT FACE="Courier New, Courier, monospace">time_integration</FONT>)</P>
1380	</TD>
1381	<TD WIDTH=393>
1382	<P>advec_particles, check_parameters, cpu_log, data_output_2d,
1383	data_output_3d, header, init_3d_model, init_particles, init_ocean,
1384	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
1385	time_integration, user_last_actions, write_var_list</P>
1386	</TD>
1387	</TR>
1388	<TR>
1389	<TD WIDTH=37>
1390	<P>02/02/09</P>
1391	</TD>
1392	<TD WIDTH=56>
1393	<P>SR</P>
1394	</TD>
1395	<TD WIDTH=68>
1396	<P>228</P>
1397	</TD>
1398	<TD WIDTH=62>
1399	<P>3.6</P>
1400	</TD>
1401	<TD WIDTH=36>
1402	<P>N</P>
1403	</TD>
1404	<TD WIDTH=517>
1405	<P>This release contains further additions, changes, and bugfixes
1406	for the SGI-ICE system, as well as important changes like the
1407	splitting of the user-interface into single files, a complete
1408	revision of the pre-compiling mechanism allowing to use different
1409	make-depositories simultaneously, and a revision of the
1410	reading-mechanism from restart files, which has no more
1411	restrictions in case that the previous and current run have
1412	different domain/subdomain sizes. A new handling of all kind of
1413	output messages is introduced with this release and will be
1414	applied to all existing messages within the next releases.<BR><BR><B>New
1415	features are:</B><BR><BR>Restart runs on SGI-ICE are working.
1416	(mrun)<BR>2d-decomposition is default on SGI-ICE systems.
1417	(init_pegrid)<BR><BR>Ocean-atmosphere coupling realized with
1418	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
1419	called with <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1420	"<I>-K parallel</I>" for coupling. Adjustments in <FONT FACE="Courier New, Courier, monospace">mrun</FONT>,
1421	<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>, and
1422	<FONT FACE="Courier New, Courier, monospace">subjob</FONT> for
1423	lcxt4.<BR><BR>DVRP arguments changed to single precision, mode
1424	pathlines added.<BR><BR>User can add additional routines in files
1425	<FONT FACE="Courier New, Courier, monospace">user_additional_routines</FONT>.<BR><BR>User
1426	can check user parameters and deduce further quantities in
1427	<FONT FACE="Courier New, Courier, monospace">user_check_parameters</FONT></P>
1428	</TD>
1429	<TD WIDTH=393>
1430	<P>check_for_restart, check_parameters, data_output_dvrp,
1431	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
1432	surface_coupler, timestep<BR><BR>Makefile, mbuild, mrun,
1433	subjob<BR><BR><B>new:</B><BR>init_coupling,
1434	user_additional_routines, user_check_parameters</P>
1435	</TD>
1436	</TR>
1437	<TR>
1438	<TD WIDTH=37>
1439	<P><BR>
1440	</P>
1441	</TD>
1442	<TD WIDTH=56>
1443	<P><BR>
1444	</P>
1445	</TD>
1446	<TD WIDTH=68>
1447	<P><BR>
1448	</P>
1449	</TD>
1450	<TD WIDTH=62>
1451	<P><BR>
1452	</P>
1453	</TD>
1454	<TD WIDTH=36>
1455	<P>C</P>
1456	</TD>
1457	<TD WIDTH=517>
1458	<P>User interface has been split into single files.<BR><BR>Type of
1459	variables <FONT FACE="Courier New, Courier, monospace">count</FONT>
1460	and <FONT FACE="Courier New, Courier, monospace">count_rate</FONT>
1461	changed to INTEGER(8) in order to avoid "out of range"
1462	problems, which result in measured negative time intervals.
1463	(cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
1464	mechanism from restart files completely revised. The
1465	subdomain/total domain size is now allowed to vary arbitrarily
1466	between the current and previous run. (read_var_list,
1467	read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
1468	mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
1469	completely revised: the source-tarfile remains in the source
1470	directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
1471	One depository per block (given in the config-file) is created.
1472	Always all files from the source directory are copied to the
1473	respective depository. No additional file checks are done any more
1474	(mrun version 2.1). The depository name used contains the
1475	conditions given by <FONT FACE="Courier New, Courier, monospace">mrun</FONT>-option
1476	"<FONT FACE="Courier New, Courier, monospace">-K</FONT>".
1477	(mbuild, mrun)<BR><BR>Output messages (including required stop of
1478	execution) can now be handled with the new subroutine <FONT FACE="Courier New, Courier, monospace">message</FONT>.
1479	All output messages will be replaced by this routine step by step
1480	within the next revisions.<BR><BR>Neumann boundary condition at
1481	<FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
1482	explicitly set for better reading, although this has been already
1483	done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
1484	xy-coordinate system shifted from the center of the first grid
1485	cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
1486	<FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
1487	south-left corner of this cell. (netcdf) Topography definition
1488	according to new user parameter <FONT FACE="Courier New, Courier, monospace">topography_grid_convention</FONT>.
1489	(init_grid, modules, user_header, user_init_grid, user_parin)</P>
1490	</TD>
1491	<TD WIDTH=393>
1492	<P>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop,
1493	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
1494	read_var_list, user_read_restart_data<BR><BR>Makefile, mbuild,
1495	mrun<BR><BR><B>removed:</B><BR>user_interface<BR><BR><B>new:</B><BR>message,
1496	user_3d_data_averaging, user_actions, user_advec_particles,
1497	user_check_data_output, user_check_data_output_pr,
1498	user_data_output_2d, user_data_output_3d, user_data_output_dvrp,
1499	user_define_netcdf_grid, user_dvrp_coltab, user_header,
1500	user_init_3d_model, user_init, user_init_grid,
1501	user_init_particles, user_init_plant_canopy, user_last_actions,
1502	user_parin, user_parin, user_particle_attributes,
1503	user_read_restart_data, user_spectra, user_statistics</P>
1504	</TD>
1505	</TR>
1506	<TR>
1507	<TD WIDTH=37>
1508	<P><BR>
1509	</P>
1510	</TD>
1511	<TD WIDTH=56>
1512	<P><BR>
1513	</P>
1514	</TD>
1515	<TD WIDTH=68>
1516	<P><BR>
1517	</P>
1518	</TD>
1519	<TD WIDTH=62>
1520	<P><BR>
1521	</P>
1522	</TD>
1523	<TD WIDTH=36>
1524	<P>B</P>
1525	</TD>
1526	<TD WIDTH=517>
1527	<P>Bugfix: array <FONT FACE="Courier New, Courier, monospace">d</FONT>
1528	is reallocated in case that multigrid is used.
1529	(calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
1530	(check_for_restart, cpu_statistics,
1531	inflow_turbulence, timestep)<BR><BR>Size of <FONT FACE="Courier New, Courier, monospace">pf3d
1532	</FONT>adjusted to the required output size (1 gridpoint less,
1533	along all three dimensions), because output of a subset of the
1534	data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
1535	in the NF90_PUT_VAR statement caused segmentation fault with the
1536	INTEL compiler. (combine_plot_fields)<BR><BR>Bugfix: error in <FONT FACE="Courier New, Courier, monospace">zu</FONT>
1537	index in case of <FONT FACE="Courier New, Courier, monospace">section_xy=-1</FONT>.
1538	(header)<BR><BR>Inconsistency removed: as the thermal
1539	stratification is not taken into account for the evaluation of the
1540	wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
1541	must not be used for the evaluation of the velocity gradients
1542	<FONT FACE="Courier New, Courier, monospace">dudy</FONT>, <FONT FACE="Courier New, Courier, monospace">dwdy</FONT>,
1543	<FONT FACE="Courier New, Courier, monospace">dvdx</FONT> and <FONT FACE="Courier New, Courier, monospace">dwdx</FONT>.
1544	(production_e)<BR><BR>Bugfix in calculating <FONT FACE="Courier New, Courier, monospace">k</FONT>
1545	index in case of oceans runs. (sort_particles)<BR><BR>Bugfix: no
1546	output of particle concentration and radius unless particles have
1547	been started. (data_output_2d)<BR><BR>Bugfix: reading of
1548	<FONT FACE="Courier New, Courier, monospace">spectrum_x\|y</FONT>
1549	from restart files ignored if total numbers of grid points do not
1550	match. (read_3d_binary)<BR><BR>Bugfix: abort in case that absolute
1551	temperature is below zero. (init_cloud_physics)</P>
1552	</TD>
1553	<TD WIDTH=393>
1554	<P>advec_particles, calc_spectra, check_for_restart,
1555	cpu_statistics, data_output_2d, header, inflow_turbulence,
1556	init_cloud_physics, production_e, read_3d_binary,
1557	timestep<BR><BR>combine_plot_fields</P>
1558	</TD>
1559	</TR>
1560	</TABLE>
1561	<P><BR>  <BR>
1562	</P>
1563	<H2><A NAME="Kapitel2.0"></A>2.0  How to change the source code
1564	and how to document modifications</H2>
1565	<P>Currently (Sep 23rd, 2009), only selected users are allowed to
1566	commit changes to the repository. Rules given below are preliminary,
1567	until we have switched to the "trac"-System.</P>
1568	<OL>
1569	<LI><P>Change source code in your current working copy. Document
1570	changes in the respective file headers unter "<FONT FACE="Courier New, Courier, monospace">Current
1571	revisions:</FONT>". Additionally, document all changes in a
1572	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
1573	including the files that have been changed. Classify changes in
1574	three cases, new (N), changed (C), and bugfix (B). <B>Try to be as
1575	short and as precise as possible in describing the changes!</B></P>
1576	<LI><P>Test the changed version, unless it works sufficiently.</P>
1577	<LI><P>Commit the changes to the repository<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1578	commit -m "message string" trunk<BR></FONT><BR>where
1579	"<FONT FACE="Courier New, Courier, monospace">message string</FONT>"
1580	is a short, <B>meaningful</B> summary of the
1581	changes.<BR><BR>Alternatively, in case that you have made quite a
1582	lot of changes, you can also give the contents of your file
1583	CURRENT_MODIFICATIONS as the log message:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1584	commit -F CURRENT_MODIFICATIONS trunk</FONT></P>
1585	<LI><P>Enter the changes into the technical documentation (under
1586	<FONT FACE="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</FONT>).</P>
1587	<LI><P>Move the change comments in the file headers from "Current
1588	revisions:" to "Former revisions:". Set the current
1589	svn id in front of that.<BR><BR><B>Example:</B><BR><BR><B>before
1590	move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1591	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1592	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1593	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1594	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1595	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1596	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1597	Â§Id: init_3d_model.f90 </FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1598	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">!
1599	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1600	var_ts is replaced by dots_max </FONT><BR><BR><B>after move:</B><BR><BR><FONT FACE="Courier New, Courier, monospace">!
1601	Current revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1602	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1603	</FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1604	Former revisions:</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1605	-----------------</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1606	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">!
1607	</FONT><FONT COLOR="#3366ff"><FONT FACE="Courier New, Courier, monospace"><B>425
1608	2010-02-06 13:37:48Z raasch</B></FONT></FONT><FONT FACE="Courier New, Courier, monospace"><BR>!
1609	</FONT><FONT FACE="Courier New, Courier, monospace"><B>new dummy
1610	argument abcd</B></FONT><BR><FONT FACE="Courier New, Courier, monospace">!</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1611	407 2009-12-01 15:01:15Z maronga</FONT><BR><FONT FACE="Courier New, Courier, monospace">!
1612	var_ts is replaced by dots_max<BR><BR></FONT><FONT FACE="Times New Roman, Times, serif">Note
1613	that the "</FONT><FONT FACE="Courier New, Courier, monospace">Â§</FONT><FONT FACE="Times New Roman, Times, serif">"
1614	in this example should read "$", but "$" cannot
1615	be used here, because otherwise svn would replace these entries
1616	after every change to this technical documentation.</FONT></P>
1617	<LI><P>Commit the changes in the technical documentation and the
1618	file headers:<BR><BR>   <FONT FACE="Courier New, Courier, monospace">svn
1619	commit -m "last commit documented" trunk</FONT><BR><BR><BR>
1620	</P>
1621	</OL>
1622	<H2><A NAME="Kapitel3.0"></A>3.0  Description of selected parts
1623	of the model source code</H2>
1624	<P>This section gives links to existing descriptions about special
1625	parts of the PALM code, e.g. special numerical methods that are used
1626	(including mathematical background). Documents are stored in single
1627	files with different formats. Some are in German (sorry for the
1628	inconvenience). <BR>
1629	</P>
1630	<UL>
1631	<LI><P STYLE="margin-bottom: 0in"><A NAME="UPS"></A>upstream-spline
1632	advection scheme ( <A HREF="methods/upstream_spline/ups.pdf">.pdf</A>
1633	, only in German)
1634	</P>
1635	<LI><P STYLE="margin-bottom: 0in"><A NAME="Cloud_physics"></A>cloud
1636	physics module ( <A HREF="methods/cloud_physics/cloud_physics.pdf">.pdf</A>
1637	)
1638	</P>
1639	<LI><P STYLE="margin-bottom: 0in"><A NAME="Bitkompression"></A>data
1640	compression with <A HREF="methods/bit_compression/bit_compression.html">bit
1641	shifting method</A> (only in German)</P>
1642	<LI><P>Runge-Kutta time integration scheme ( <A HREF="methods/runge_kutta/runge_kutta.pdf">.pdf</A>
1643	, only in German)
1644	</P>
1645	</UL>
1646	<P><BR>  <BR>  <BR>  <BR>  <BR>  <BR>
1647	<BR>  <BR>
1648	</P>
1649	</BODY>
1650	</HTML>

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