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Last change on this file since 2184 was 560, checked in by weinreis, 14 years ago
correction of calculating ngp_3d for 64 bit
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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">
[560]	9	<META NAME="CHANGED" CONTENT="20100909;12050600">
[557]	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>
[560]	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>
[557]	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_*,
[553]	223	data_output_mask_user_, mask__x, mask__y, mask__z,
[557]	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,
[553]	227	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
[557]	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
[553]	283	done using the names hicegate0/bicegate0 instead of the IP
[557]	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
[553]	308	additional source to the prognostic equation for humidity/passive
[557]	309	scalar<BR> <BR>character length for dopr_unit
	310	enlarged<BR><BR>Adjustment of the NCL scripts to allow for output
[553]	311	of png files
[557]	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
[553]	491	variable names. Replacement of these characters has been removed
[557]	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
[553]	517	5.0). Respective scripts and configuration files have been
[557]	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
[553]	642	an output command in the configuration file any more. Please
[557]	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
[553]	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
[557]	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
[553]	711	parallel output for profiles, time series, spectra, and particles.
[557]	712	Parallel output of particle data may realized in the future.<BR><BR>In
[553]	713	case of parallel output, all PEs write into one file, which means
[557]	714	that postprocessing the data with <FONT FACE="Courier New, Courier, monospace">combine_plot_fields</FONT>
[553]	715	(merging data from single files - one per PE - into one file) is
	716	not neccessary. In this case, flag files are automatically set,
[557]	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
[553]	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
[557]	722	<FONT FACE="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</FONT><BR><BR><B>Attention:</B><BR>So
[553]	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
[557]	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
[553]	730	loaded for compilation (mbuild) or job execution (mrun) can/should
[557]	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
[553]	734	ifort/11.0.069:netcdf       lcsgih
[557]	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
[553]	737	fixed settings of modules in the scripts mbuild, mrun, and subjob
[557]	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
[553]	741	using parallel make. The number of allowed simultaneous compiler
	742	calls (threads) is set in the configuration file using variable
[557]	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
[553]	746	compiled simultaneously (provided that the makefile does not show
[557]	747	any dependencies between these routines).</P>
	748	</TD>
	749	<TD WIDTH=393>
	750	<P>check_open, check_parameters, close_file, data_output_2d,
[553]	751	data_output_3d, header, modules, netcdf,
[557]	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
[553]	780	the default from now on). The offset-format can not be set
[557]	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>
[553]	786	removed. They are replaced by the new parameter
[557]	787	<FONT FACE="Courier New, Courier, monospace">netcdf_data_format</FONT>.
[553]	788	This change concerns the masked data output, which is still not
[557]	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>
[553]	844	changed to 64 bit. Otherwise, on large grids > 210*9 grid
	845	points some global statistics (e.g. total kinetic energy) have
[557]	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
[553]	906	scale vertical motion (subsidence/ascent) can be added as
	907	additional source to the prognostic equation for potential
[557]	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
[553]	920	have been updated for Cray-XT5 machine (lcxt5m) and
[557]	921	Hitachi-machine (lckyoto).<BR><BR>A simple method for installing
[553]	922	and running palm (with limited features) has been added.
[557]	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
[553]	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:
[557]	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,
[553]	933	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
	934	prognostic_equations, read_var_list, time_integration, user_parin,
[557]	935	write_var_list<BR><BR><B>new:</B> data_output_mask,
[553]	936	init_masks, palm_simple_install, palm_simple_run, subsidence,
[557]	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
[553]	966	cloud droplet has now an own weighting factor and can be deleted
	967	due to collisions. Condensation and collision of cloud droplets
[557]	968	are adjusted accordingly. (<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Collision
[553]	969	efficiency for large cloud droplets has changed according to table
[557]	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:
[553]	999	index problem concerning gradient_level indices removed.
[557]	1000	(<FONT FACE="Courier New, Courier, monospace">header</FONT>)<BR><BR>Dimension
	1001	of array <FONT FACE="Courier New, Courier, monospace">stat</FONT>
[553]	1002	in cascade change to prevent type problems with mpi2 libraries.
[557]	1003	(<FONT FACE="Courier New, Courier, monospace">poisfft_hybrid</FONT>)<BR><BR>Loop
[553]	1004	was split to make runs reproducible when using ifort compiler.
[557]	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
[553]	1008	in calculation of time-averaged surface heatfluxes.
[557]	1009	(<FONT FACE="Courier New, Courier, monospace">sum_up_3d_data</FONT>)<BR><BR>Bugfix
[553]	1010	in calculation of precipitation_rate.
[557]	1011	(<FONT FACE="Courier New, Courier, monospace">calc_precipitation</FONT>)<BR><BR>Bugfix:
[553]	1012	initial data assignments to some dvrp arrays changed due to error
[557]	1013	messages from gfortran compiler. (<FONT FACE="Courier New, Courier, monospace">modules</FONT>)<BR><BR>Bugfix
[553]	1014	in calculation of cloud droplet velocity.
[557]	1015	(<FONT FACE="Courier New, Courier, monospace">advec_particles</FONT>)<BR><BR>Bugfix
[553]	1016	in transfer of particles at south/left edge.
[557]	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,
[553]	1022	disturb_field, header, modules, poisfft_hybrid, subjob,
[557]	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
[553]	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
[557]	1047	months.<BR><BR>The atmosphere-ocean coupling allows to use
[553]	1048	independent precursor runs in order to account for different
	1049	spin-up times. The time when coupling has to be started is given
[557]	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
[553]	1070	of dvrp output implemented. Default colourtable for particles
	1071	implemented, particle attributes (color, dvrp_size) can be set
[557]	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>.
[553]	1076	Slicer attributes (dvrp) are set with new routine
[557]	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
[553]	1084	reduction for topography and ground plate isosurface. Reduction
	1085	level for buildings can be chosen with parameter cluster_size.
[557]	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>
[553]	1088	in most subroutines replaced by LOGICAL variables
[557]	1089	<FONT FACE="Courier New, Courier, monospace">bc_lr_cyc</FONT>,<BR><FONT FACE="Courier New, Courier, monospace">bc_ns_cyc</FONT>
[553]	1090	for speed optimization. This gives a significant speedup of more
[557]	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
[553]	1099	timestep criterion in case of simulations with plant canopy.
[557]	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
[553]	1132	cross section output of surface heatfluxes (sensible and latent).
[557]	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,
[553]	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,
[557]	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
[553]	1216	of NetCDF messages with aid of message handling routine.
[557]	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
[553]	1226	changed to __lc to avoid problems with Intel compiler on sgi-ice.
[557]	1227	(<FONT FACE="Courier New, Courier, monospace">poisfft</FONT>)<BR><BR>For
[553]	1228	extended NetCDF files, the updated title attribute includes an
[557]	1229	update of time_average_text where appropriate. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>In
[553]	1230	case of restart runs without extension, initial profiles are not
	1231	written to NetCDF-file anymore. So far, time axis always started
[557]	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
[553]	1242	link to the webspage appendix_a.html is printed for further
	1243	information about possible reasons of the error that appeared.
[557]	1244	(message)<BR><BR>Temperature gradient criterion for estimating the
[553]	1245	boundary layer height replaced by the gradient criterion of
[557]	1246	Sullivan et al. (1998). (<FONT FACE="Courier New, Courier, monospace">flow_statistics</FONT>)<BR><BR>NetCDF
[553]	1247	unit attribute in timeseries output in case of statistic regions
[557]	1248	added. (<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Maximum
[553]	1249	number of tails is calculated from maximum number of particles and
[557]	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
[553]	1274	for runs on lcxt4 (necessary due to a software update on CRAY) and
[557]	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,
[553]	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
[557]	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:
[553]	1319	wrong sign in buoyancy production of ocean part in case of not
[557]	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:
[553]	1322	output of averaged 2d/3d quantities requires that an avaraging
	1323	interval has been set, respective error message is included.
[557]	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
[553]	1329	for extended NetCDF files: In order to avoid 'data mode' errors if
	1330	updated attributes are larger than their original size,
[557]	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>
[553]	1334	calls. This implies a possible performance loss; an alternative
	1335	strategy would be to ensure equal attribute size in a job chain.
[557]	1336	(<FONT FACE="Courier New, Courier, monospace">netcdf</FONT>)<BR><BR>Bugfix:
[553]	1337	correction of initial volume flow for non-flat topography.
[557]	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:
[553]	1348	error in check, if particles moved further than one subdomain
	1349	length. This check must not be applied for newly released
[557]	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>
[553]	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
[557]	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:
[553]	1361	output of particle time series only if particle advection is
[557]	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:
[553]	1366	averaging along z is not allowed for 2d quantities (e.g. u* and
[557]	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
[553]	1369	the inversion height calculated by the prerun is zero,
	1370	inflow_damping_height must be explicitly specified.
[557]	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>
[553]	1374	removed from the restart file, because otherwise, no change from a
	1375	fixed to a variable timestep would be possible in restart runs.
[557]	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,
[553]	1383	data_output_3d, header, init_3d_model, init_particles, init_ocean,
	1384	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
[557]	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
[553]	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
[557]	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
[553]	1418	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
[557]	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
[553]	1426	can check user parameters and deduce further quantities in
[557]	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,
[553]	1431	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
[557]	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"
[553]	1462	problems, which result in measured negative time intervals.
[557]	1463	(cpu_log, local_tremain, local_tremain_ini)<BR><BR>Reading
[553]	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,
[557]	1467	read_3d_binary, user_read_restart_data)<BR><BR>Precompilation
	1468	mechanism (<FONT FACE="Courier New, Courier, monospace">mbuild</FONT>)
[553]	1469	completely revised: the source-tarfile remains in the source
[557]	1470	directory (<FONT FACE="Courier New, Courier, monospace">trunk/SOURCE</FONT>).
[553]	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
[557]	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>.
[553]	1479	All output messages will be replaced by this routine step by step
[557]	1480	within the next revisions.<BR><BR>Neumann boundary condition at
	1481	<FONT FACE="Courier New, Courier, monospace">k=nzb</FONT> is
[553]	1482	explicitly set for better reading, although this has been already
[557]	1483	done in boundary_conds. (advec_s_bc)<BR><BR>Origin of the
[553]	1484	xy-coordinate system shifted from the center of the first grid
[557]	1485	cell (indices <FONT FACE="Courier New, Courier, monospace">i=0</FONT>,
	1486	<FONT FACE="Courier New, Courier, monospace">j=0</FONT>) to the
[553]	1487	south-left corner of this cell. (netcdf) Topography definition
[557]	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,
[553]	1493	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
[557]	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,
[553]	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,
[557]	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>
[553]	1528	is reallocated in case that multigrid is used.
[557]	1529	(calc_spectra)<BR><BR>Bugfixes for nonparallel execution.
[553]	1530	(check_for_restart, cpu_statistics,
[557]	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,
[553]	1533	along all three dimensions), because output of a subset of the
[557]	1534	data (<FONT FACE="Courier New, Courier, monospace">pf3d(nxa:nxe...)</FONT>)
[553]	1535	in the NF90_PUT_VAR statement caused segmentation fault with the
[557]	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
[553]	1539	stratification is not taken into account for the evaluation of the
[557]	1540	wall fluxes at vertical walls, the eddy viscosity <FONT FACE="Courier New, Courier, monospace">km</FONT>
[553]	1541	must not be used for the evaluation of the velocity gradients
[557]	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
[553]	1546	output of particle concentration and radius unless particles have
[557]	1547	been started. (data_output_2d)<BR><BR>Bugfix: reading of
	1548	<FONT FACE="Courier New, Courier, monospace">spectrum_x\|y</FONT>
[553]	1549	from restart files ignored if total numbers of grid points do not
[557]	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,
[553]	1555	cpu_statistics, data_output_2d, header, inflow_turbulence,
	1556	init_cloud_physics, production_e, read_3d_binary,
[557]	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
[553]	1566	commit changes to the repository. Rules given below are preliminary,
[557]	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
[553]	1572	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
	1573	including the files that have been changed. Classify changes in
[557]	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
[553]	1582	lot of changes, you can also give the contents of your file
[557]	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
[553]	1615	be used here, because otherwise svn would replace these entries
[557]	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
[392]	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
[557]	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>
[553]	1633	, only in German)
[557]	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>
[553]	1637	)
[557]	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>
[553]	1643	, only in German)
[557]	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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