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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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[553]	1	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
[557]	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
[553]	56	changes to the PALM repository since 2009. Older changes can be found
[557]	57	<A HREF="tec_doc_1998-2008.html">here</A>.<BR><BR>Entries in the
[553]	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
[557]	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_*,
[553]	197	data_output_mask_user_, mask__x, mask__y, mask__z,
[557]	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,
[553]	201	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
[557]	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
[553]	257	done using the names hicegate0/bicegate0 instead of the IP
[557]	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
[553]	282	additional source to the prognostic equation for humidity/passive
[557]	283	scalar<BR> <BR>character length for dopr_unit
	284	enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
[553]	285	of png files
[557]	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
[553]	465	variable names. Replacement of these characters has been removed
[557]	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
[553]	491	5.0). Respective scripts and configuration files have been
[557]	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
[553]	616	an output command in the configuration file any more. Please
[557]	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
[553]	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
[557]	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
[553]	685	parallel output for profiles, time series, spectra, and particles.
[557]	686	Parallel output of particle data may realized in the future.<BR><BR>In
[553]	687	case of parallel output, all PEs write into one file, which means
[557]	688	that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
[553]	689	(merging data from single files - one per PE - into one file) is
	690	not neccessary. In this case, flag files are automatically set,
[557]	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
[553]	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
[557]	696	<FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
[553]	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
[557]	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
[553]	704	loaded for compilation (mbuild) or job execution (mrun) can/should
[557]	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
[553]	708	ifort/11.0.069:netcdf       lcsgih
[557]	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
[553]	711	fixed settings of modules in the scripts mbuild, mrun, and subjob
[557]	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
[553]	715	using parallel make. The number of allowed simultaneous compiler
	716	calls (threads) is set in the configuration file using variable
[557]	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
[553]	720	compiled simultaneously (provided that the makefile does not show
[557]	721	any dependencies between these routines).</P>
	722	</TD>
	723	<TD WIDTH=393>
	724	<P>check_open, check_parameters, close_file, data_output_2d,
[553]	725	data_output_3d, header, modules, netcdf,
[557]	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
[553]	754	the default from now on). The offset-format can not be set
[557]	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>
[553]	760	removed. They are replaced by the new parameter
[557]	761	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
[553]	762	This change concerns the masked data output, which is still not
[557]	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>
[553]	818	changed to 64 bit. Otherwise, on large grids > 210*9 grid
	819	points some global statistics (e.g. total kinetic energy) have
[557]	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
[553]	880	scale vertical motion (subsidence/ascent) can be added as
	881	additional source to the prognostic equation for potential
[557]	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
[553]	894	have been updated for Cray-XT5 machine (lcxt5m) and
[557]	895	Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
[553]	896	and running palm (with limited features) has been added.
[557]	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
[553]	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:
[557]	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,
[553]	907	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
	908	prognostic_equations, read_var_list, time_integration, user_parin,
[557]	909	write_var_list<BR><BR><B>new:</B> data_output_mask,
[553]	910	init_masks, palm_simple_install, palm_simple_run, subsidence,
[557]	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
[553]	940	cloud droplet has now an own weighting factor and can be deleted
	941	due to collisions. Condensation and collision of cloud droplets
[557]	942	are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
[553]	943	efficiency for large cloud droplets has changed according to table
[557]	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:
[553]	973	index problem concerning gradient_level indices removed.
[557]	974	(<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
	975	of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
[553]	976	in cascade change to prevent type problems with mpi2 libraries.
[557]	977	(<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
[553]	978	was split to make runs reproducible when using ifort compiler.
[557]	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
[553]	982	in calculation of time-averaged surface heatfluxes.
[557]	983	(<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
[553]	984	in calculation of precipitation_rate.
[557]	985	(<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
[553]	986	initial data assignments to some dvrp arrays changed due to error
[557]	987	messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
[553]	988	in calculation of cloud droplet velocity.
[557]	989	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
[553]	990	in transfer of particles at south/left edge.
[557]	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,
[553]	996	disturb_field, header, modules, poisfft_hybrid, subjob,
[557]	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
[553]	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
[557]	1021	months.<BR><BR>The atmosphere-ocean coupling allows to use
[553]	1022	independent precursor runs in order to account for different
	1023	spin-up times. The time when coupling has to be started is given
[557]	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
[553]	1044	of dvrp output implemented. Default colourtable for particles
	1045	implemented, particle attributes (color, dvrp_size) can be set
[557]	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>.
[553]	1050	Slicer attributes (dvrp) are set with new routine
[557]	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
[553]	1058	reduction for topography and ground plate isosurface. Reduction
	1059	level for buildings can be chosen with parameter cluster_size.
[557]	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>
[553]	1062	in most subroutines replaced by LOGICAL variables
[557]	1063	<FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
[553]	1064	for speed optimization. This gives a significant speedup of more
[557]	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
[553]	1073	timestep criterion in case of simulations with plant canopy.
[557]	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
[553]	1106	cross section output of surface heatfluxes (sensible and latent).
[557]	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,
[553]	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,
[557]	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
[553]	1190	of NetCDF messages with aid of message handling routine.
[557]	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
[553]	1200	changed to __lc to avoid problems with Intel compiler on sgi-ice.
[557]	1201	(<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
[553]	1202	extended NetCDF files, the updated title attribute includes an
[557]	1203	update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
[553]	1204	case of restart runs without extension, initial profiles are not
	1205	written to NetCDF-file anymore. So far, time axis always started
[557]	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
[553]	1216	link to the webspage appendix_a.html is printed for further
	1217	information about possible reasons of the error that appeared.
[557]	1218	(message)<BR><BR>Temperature gradient criterion for estimating the
[553]	1219	boundary layer height replaced by the gradient criterion of
[557]	1220	Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
[553]	1221	unit attribute in timeseries output in case of statistic regions
[557]	1222	added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
[553]	1223	number of tails is calculated from maximum number of particles and
[557]	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
[553]	1248	for runs on lcxt4 (necessary due to a software update on CRAY) and
[557]	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,
[553]	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
[557]	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:
[553]	1293	wrong sign in buoyancy production of ocean part in case of not
[557]	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:
[553]	1296	output of averaged 2d/3d quantities requires that an avaraging
	1297	interval has been set, respective error message is included.
[557]	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
[553]	1303	for extended NetCDF files: In order to avoid 'data mode' errors if
	1304	updated attributes are larger than their original size,
[557]	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>
[553]	1308	calls. This implies a possible performance loss; an alternative
	1309	strategy would be to ensure equal attribute size in a job chain.
[557]	1310	(<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
[553]	1311	correction of initial volume flow for non-flat topography.
[557]	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:
[553]	1322	error in check, if particles moved further than one subdomain
	1323	length. This check must not be applied for newly released
[557]	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>
[553]	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
[557]	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:
[553]	1335	output of particle time series only if particle advection is
[557]	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:
[553]	1340	averaging along z is not allowed for 2d quantities (e.g. u* and
[557]	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
[553]	1343	the inversion height calculated by the prerun is zero,
	1344	inflow_damping_height must be explicitly specified.
[557]	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>
[553]	1348	removed from the restart file, because otherwise, no change from a
	1349	fixed to a variable timestep would be possible in restart runs.
[557]	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,
[553]	1357	data_output_3d, header, init_3d_model, init_particles, init_ocean,
	1358	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
[557]	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
[553]	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
[557]	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
[553]	1392	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
[557]	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
[553]	1400	can check user parameters and deduce further quantities in
[557]	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,
[553]	1405	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
[557]	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"
[553]	1436	problems, which result in measured negative time intervals.
[557]	1437	(cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
[553]	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,
[557]	1441	read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
	1442	mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
[553]	1443	completely revised: the source-tarfile remains in the source
[557]	1444	directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
[553]	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
[557]	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>.
[553]	1453	All output messages will be replaced by this routine step by step
[557]	1454	within the next revisions.<BR><BR>Neumann boundary condition at
	1455	<FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
[553]	1456	explicitly set for better reading, although this has been already
[557]	1457	done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
[553]	1458	xy-coordinate system shifted from the center of the first grid
[557]	1459	cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
	1460	<FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
[553]	1461	south-left corner of this cell. (netcdf) Topography definition
[557]	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,
[553]	1467	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
[557]	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,
[553]	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,
[557]	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>
[553]	1502	is reallocated in case that multigrid is used.
[557]	1503	(calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
[553]	1504	(check_for_restart, cpu_statistics,
[557]	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,
[553]	1507	along all three dimensions), because output of a subset of the
[557]	1508	data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
[553]	1509	in the NF90_PUT_VAR statement caused segmentation fault with the
[557]	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
[553]	1513	stratification is not taken into account for the evaluation of the
[557]	1514	wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
[553]	1515	must not be used for the evaluation of the velocity gradients
[557]	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
[553]	1520	output of particle concentration and radius unless particles have
[557]	1521	been started. (data_output_2d)<BR><BR>Bugfix: reading of
	1522	<FONT FACE="Courier New, Courier, monospace">spectrum_x\|y</FONT>
[553]	1523	from restart files ignored if total numbers of grid points do not
[557]	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,
[553]	1529	cpu_statistics, data_output_2d, header, inflow_turbulence,
	1530	init_cloud_physics, production_e, read_3d_binary,
[557]	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
[553]	1540	commit changes to the repository. Rules given below are preliminary,
[557]	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
[553]	1546	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
	1547	including the files that have been changed. Classify changes in
[557]	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
[553]	1556	lot of changes, you can also give the contents of your file
[557]	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
[553]	1589	be used here, because otherwise svn would replace these entries
[557]	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
[392]	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
[557]	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>
[553]	1607	, only in German)
[557]	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>
[553]	1611	)
[557]	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>
[553]	1617	, only in German)
[557]	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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