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[553]	1	<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
[556]	2	<html><head>
	3
	4
	5	<meta http-equiv="CONTENT-TYPE" content="text/html; charset=utf-8"><title>PALM technical/numerical documentation</title>
	6
	7	<meta name="GENERATOR" content="OpenOffice.org 3.0 (Unix)">
	8	<meta name="AUTHOR" content="Siegfried Raasch">
	9	<meta name="CREATED" content="0;0">
	10	<meta name="CHANGED" content="20100901;15562900">
	11	<meta name="KEYWORDS" content="parallel LES model"></head><body dir="ltr" lang="en-US">
	12	<p style="margin-bottom: 0in;"><font size="7">PALM   </font>a
	13	<b>pa</b>rallelized <b>L</b>ES <b>m</b>odel
	14	</p>
	15	<hr>
	16	<p style="margin-bottom: 0in;"><br><font size="5">technical/numerical
	17	documentation</font> <br>  <br>
	18	</p>
	19	<p style="margin-bottom: 0in;" align="center">
	20	</p>
	21	<table cellpadding="0" cellspacing="0">
	22	<tbody><tr>
	23	<td>
	24	<p><b>Current fixed release:</b></p>
	25	</td>
	26	<td>
	27	<p><b>3.7a</b></p>
	28	</td>
	29	</tr>
	30	<tr>
	31	<td>
	32	<p><b>Last change of this document</b>: </p>
	33	</td>
	34	<td>
	35	<p><b>$Id: technical_documentation.html 544 2010-08-17 10:44:58Z
	36	maronga $</b></p>
	37	</td>
	38	</tr>
	39	</tbody></table>
	40	<hr>
	41	<p><font size="5">Table of contents</font> <br>  <br>
	42	</p>
	43	<ul>
	44	<p><a href="#Kapitel1.0">1.0</a>  History of changes
	45	</p>
	46	<p><a href="#Kapitel2.0">2.0</a>  How to change the source code
	47	and how to document modifications</p>
	48	<p><a href="#Kapitel3.0">3.0</a>  Description of selected model
	49	numerics<br> </p>
	50	</ul>
	51	<p><br><br>
	52	</p>
	53	<h2><a name="Kapitel1.0"></a>1.0  History of changes</h2>
	54	<p style="margin-bottom: 0in;">The following table documents all
[553]	55	changes to the PALM repository since 2009. Older changes can be found
[556]	56	<a href="tec_doc_1998-2008.html">here</a>.<br><br>Entries in the
[553]	57	fifth column specify the type of the change: change  of existing
	58	code (C), new code (N) or bugfix (B). More detailed information about
	59	the changes may sometimes be found in the header comment lines of the
[556]	60	respective routines. <br>
	61	</p>
	62	<table border="1" cellpadding="2" cellspacing="3" width="1223">
	63	<col width="37">
	64	<col width="56">
	65	<col width="68">
	66	<col width="62">
	67	<col width="36">
	68	<col width="518">
	69	<col width="393">
	70	<tbody><tr>
	71	<td style="width: 37px; vertical-align: top;">
	72	<p><font size="4"><b>date</b></font></p>
	73	</td>
	74	<td style="width: 56px; vertical-align: top;">
	75	<p><font size="4"><b>author</b></font></p>
	76	</td>
	77	<td style="width: 68px; vertical-align: top;">
	78	<p><font size="4"><b>svn revision</b></font></p>
	79	</td>
	80	<td style="width: 62px; vertical-align: top;">
	81	<p><font size="4"><b>last release</b></font></p>
	82	</td>
	83	<td style="width: 36px; vertical-align: top;">
	84	<p><font size="4"><b>type</b></font></p>
	85	</td>
	86	<td style="width: 518px; vertical-align: top;">
	87	<p><font size="4"><b>description</b></font></p>
	88	</td>
	89	<td style="width: 393px; vertical-align: top;">
	90	<p><font size="4"><b>affected routines</b></font></p>
	91	</td>
	92	</tr>
	93	<tr>
	94	<td style="vertical-align: top;">07/09/10<br>
	95	</td>
	96	<td style="vertical-align: top;">SR<br>
	97	</td>
	98	<td style="vertical-align: top;">556<br>
	99	</td>
	100	<td style="vertical-align: top;">3.7a<br>
	101	</td>
	102	<td style="vertical-align: top;">C<br>
	103	</td>
	104	<td style="vertical-align: top;">Documentation for<span style="font-family: Courier New,Courier,monospace;"> surface_heatflux </span>in case of<span style="font-family: Courier New,Courier,monospace;"> prandtl_layer </span>= <span style="font-style: italic;">.F.</span> improved.<br>
	105	<br>
	106	bugfix for wrong netcdf/3.6.3 module on lcsgi (mbuild, mrun)<br>
	107	</td>
	108	<td style="vertical-align: top;">mbuild, mrun<br>
	109	</td>
	110	</tr>
	111	<tr>
	112	<td style="vertical-align: top;"><br>
	113	</td>
	114	<td style="vertical-align: top;"><br>
	115	</td>
	116	<td style="vertical-align: top;"><br>
	117	</td>
	118	<td style="vertical-align: top;"><br>
	119	</td>
	120	<td style="vertical-align: top;">B<br>
	121	</td>
	122	<td style="vertical-align: top;">Bugfix in if statement (disturb_heatflux)<br>
	123	<br>
	124	Bugfix: in 2201 statement: closing " was missing (interpret_config)<br>
	125	<br>
	126	Bugfix: default setting of nzb_local for flat topography (init_grid)<br>
	127	<br>
	128	Bugfix: wrong dimension used for ts_value_l (user_statistics)<br>
	129	</td>
	130	<td style="vertical-align: top;">disturb_heatflux, init_grid, user_statistics<br>
	131	<br>
	132	interpret_config<br>
	133	</td>
	134	</tr>
	135	<tr>
	136	<td sdval="40187" sdnum="1033;0;MM/DD/YY" style="width: 37px; vertical-align: top;">
	137	<p style="font-weight: normal;"><font size="3">01/09/10</font></p>
	138	</td>
	139	<td style="width: 56px; vertical-align: top;">
	140	<p style="font-weight: normal;"><font size="3">CH</font></p>
	141	</td>
	142	<td sdval="553" sdnum="1033;" style="width: 68px; vertical-align: top;">
	143	<p style="font-weight: normal;"><font size="3">553</font></p>
	144	</td>
	145	<td style="width: 62px; vertical-align: top;">
	146	<p style="font-weight: normal;"><font size="3">3.7a</font></p>
	147	</td>
	148	<td style="width: 36px; vertical-align: top;">
	149	<p style="font-weight: normal;"><font size="3">C</font></p>
	150	</td>
	151	<td style="width: 518px; vertical-align: top;">
	152	<p style="font-weight: normal;"><font size="3">d3dpar-parameters for
	153	masked output <font face="Courier New, monospace">data_output_mask_*,
[553]	154	data_output_mask_user_, mask__x, mask__y, mask__z,
[556]	155	mask__x_loop, mask__y_loop </font><font face="Times New Roman, serif">and
	156	</font><font face="Courier New, monospace">mask_*_z_loop </font>have
	157	been replaced by corresponding arrays <font face="Courier New, monospace">data_output_masks,
[553]	158	data_output_masks_user, mask_x, mask_y, mask_z, mask_x_loop,
[556]	159	mask_y_loop </font><font face="Times New Roman, serif">and</font><font face="Courier New, monospace">
	160	mask_z_loop</font></font></p>
	161	<p style="font-weight: normal;"><font size="3">inipar-parameter <font face="Courier New, monospace">masks</font>
	162	has been removed. </font>
	163	</p>
	164	<p style="font-weight: normal;"><font size="3">The changes concern
	165	the masked data output, which is still not documented.</font></p>
	166	</td>
	167	<td style="width: 393px; vertical-align: top;">
	168	<p style="font-weight: normal;"><font size="3">check_parameters,
	169	init_masks, modules, parin, user_parin</font></p>
	170	</td>
	171	</tr>
	172	<tr>
	173	<td style="width: 37px; vertical-align: top;">
	174	<p>17/08/10</p>
	175	</td>
	176	<td style="width: 56px; vertical-align: top;">
	177	<p>BM</p>
	178	</td>
	179	<td style="width: 68px; vertical-align: top;">
	180	<p>544</p>
	181	</td>
	182	<td style="width: 62px; vertical-align: top;">
	183	<p>3.7a</p>
	184	</td>
	185	<td style="width: 36px; vertical-align: top;">
	186	<p>B/C/N</p>
	187	</td>
	188	<td style="width: 518px; vertical-align: top;">
	189	<p>adjustments for lcxt4; bugfix (mbuild): loading of user-defined
	190	modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway</p>
	191	</td>
	192	<td style="width: 393px; vertical-align: top;">
	193	<p>mrun, mbuild, subjob</p>
	194	</td>
	195	</tr>
	196	<tr>
	197	<td style="width: 37px; vertical-align: top;">
	198	<p>15/06/10</p>
	199	</td>
	200	<td style="width: 56px; vertical-align: top;">
	201	<p>RH</p>
	202	</td>
	203	<td style="width: 68px; vertical-align: top;">
	204	<p>540</p>
	205	</td>
	206	<td style="width: 62px; vertical-align: top;">
	207	<p>3.7a</p>
	208	</td>
	209	<td style="width: 36px; vertical-align: top;">
	210	<p>C</p>
	211	</td>
	212	<td style="width: 518px; vertical-align: top;">
	213	<p>ssh from compute nodes to login nodes on hosts lcsgih/lcsgib is
[553]	214	done using the names hicegate0/bicegate0 instead of the IP
[556]	215	addresses</p>
	216	</td>
	217	<td style="width: 393px; vertical-align: top;">
	218	<p>mrun</p>
	219	</td>
	220	</tr>
	221	<tr>
	222	<td style="width: 37px; vertical-align: top;">
	223	<p>21/04/10</p>
	224	</td>
	225	<td style="width: 56px; vertical-align: top;">
	226	<p>RH</p>
	227	</td>
	228	<td style="width: 68px; vertical-align: top;">
	229	<p>532</p>
	230	</td>
	231	<td style="width: 62px; vertical-align: top;">
	232	<p>3.7a</p>
	233	</td>
	234	<td style="width: 36px; vertical-align: top;">
	235	<p>C</p>
	236	</td>
	237	<td style="width: 518px; vertical-align: top;">
	238	<p>Large scale vertical motion (subsidence/ascent) can be added as
[553]	239	additional source to the prognostic equation for humidity/passive
[556]	240	scalar<br> <br>character length for dopr_unit
	241	enlarged<br><br>Adjustment of the NCL scripts to allow for output
[553]	242	of png files
[556]	243	</p>
	244	</td>
	245	<td style="width: 393px; vertical-align: top;">
	246	<p>modules, prognostic_equations<br><br>.ncl.config.default,
	247	cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl</p>
	248	</td>
	249	</tr>
	250	<tr>
	251	<td style="width: 37px; vertical-align: top;">
	252	<p><br>
	253	</p>
	254	</td>
	255	<td style="width: 56px; vertical-align: top;">
	256	<p><br>
	257	</p>
	258	</td>
	259	<td style="width: 68px; vertical-align: top;">
	260	<p><br>
	261	</p>
	262	</td>
	263	<td style="width: 62px; vertical-align: top;">
	264	<p><br>
	265	</p>
	266	</td>
	267	<td style="width: 36px; vertical-align: top;">
	268	<p>B</p>
	269	</td>
	270	<td style="width: 518px; vertical-align: top;">
	271	<p>Bugfix: unit of hyp changed to dbar</p>
	272	</td>
	273	<td style="width: 393px; vertical-align: top;">
	274	<p>check_parameters</p>
	275	</td>
	276	</tr>
	277	<tr>
	278	<td style="width: 37px; vertical-align: top;">
	279	<p>01/04/10</p>
	280	</td>
	281	<td style="width: 56px; vertical-align: top;">
	282	<p>RH</p>
	283	</td>
	284	<td style="width: 68px; vertical-align: top;">
	285	<p>530</p>
	286	</td>
	287	<td style="width: 62px; vertical-align: top;">
	288	<p>3.7a</p>
	289	</td>
	290	<td style="width: 36px; vertical-align: top;">
	291	<p>B</p>
	292	</td>
	293	<td style="width: 518px; vertical-align: top;">
	294	<p>Bugfix: treatment of special character * in NCL variables
	295	containing lists corrected</p>
	296	</td>
	297	<td style="width: 393px; vertical-align: top;">
	298	<p>palmplot</p>
	299	</td>
	300	</tr>
	301	<tr>
	302	<td style="width: 37px; vertical-align: top;">
	303	<p>31/03/10</p>
	304	</td>
	305	<td style="width: 56px; vertical-align: top;">
	306	<p>RH</p>
	307	</td>
	308	<td style="width: 68px; vertical-align: top;">
	309	<p>529</p>
	310	</td>
	311	<td style="width: 62px; vertical-align: top;">
	312	<p>3.7a</p>
	313	</td>
	314	<td style="width: 36px; vertical-align: top;">
	315	<p>C</p>
	316	</td>
	317	<td style="width: 518px; vertical-align: top;">
	318	<p>List of variable names have to specified using blank separated
	319	lists and single quotes</p>
	320	</td>
	321	<td style="width: 393px; vertical-align: top;">
	322	<p>palmplot</p>
	323	</td>
	324	</tr>
	325	<tr>
	326	<td style="width: 37px; vertical-align: top;">
	327	<p>30/03/10</p>
	328	</td>
	329	<td style="width: 56px; vertical-align: top;">
	330	<p>RH</p>
	331	</td>
	332	<td style="width: 68px; vertical-align: top;">
	333	<p>526</p>
	334	</td>
	335	<td style="width: 62px; vertical-align: top;">
	336	<p>3.7a</p>
	337	</td>
	338	<td style="width: 36px; vertical-align: top;">
	339	<p>C</p>
	340	</td>
	341	<td style="width: 518px; vertical-align: top;">
	342	<p>Adjustment of the NCL scripts and <font face="Courier New, Courier, monospace">palmplot
	343	</font>to allow for special characters in NetCDF variable names
	344	</p>
	345	</td>
	346	<td style="width: 393px; vertical-align: top;">
	347	<p>palmplot, .ncl.config.default, cross_sections.ncl,
	348	profiles.ncl, timeseries.ncl, spectra.ncl</p>
	349	</td>
	350	</tr>
	351	<tr>
	352	<td style="width: 37px; vertical-align: top;">
	353	<p>30/03/10</p>
	354	</td>
	355	<td style="width: 56px; vertical-align: top;">
	356	<p>SR</p>
	357	</td>
	358	<td style="width: 68px; vertical-align: top;">
	359	<p>525</p>
	360	</td>
	361	<td style="width: 62px; vertical-align: top;">
	362	<p>3.7a</p>
	363	</td>
	364	<td style="width: 36px; vertical-align: top;">
	365	<p>B</p>
	366	</td>
	367	<td style="width: 518px; vertical-align: top;">
	368	<p>Bugfix: "/" in netcdf profile variable names replaced
	369	by ":"</p>
	370	</td>
	371	<td style="width: 393px; vertical-align: top;">
	372	<p>check_parameters</p>
	373	</td>
	374	</tr>
	375	<tr>
	376	<td style="width: 37px; vertical-align: top;">
	377	<p>19/03/10</p>
	378	</td>
	379	<td style="width: 56px; vertical-align: top;">
	380	<p>SR</p>
	381	</td>
	382	<td style="width: 68px; vertical-align: top;">
	383	<p>520</p>
	384	</td>
	385	<td style="width: 62px; vertical-align: top;">
	386	<p>3.7a</p>
	387	</td>
	388	<td style="width: 36px; vertical-align: top;">
	389	<p>N</p>
	390	</td>
	391	<td style="width: 518px; vertical-align: top;">
	392	<p>NetCDF4 support for particle data. Total number of particles is
	393	allowed to increase during the run, when netcdf_data_format > <i>2</i>
	394	is used.</p>
	395	</td>
	396	<td style="width: 393px; vertical-align: top;">
	397	<p>advec_particles, check_open, netcdf</p>
	398	</td>
	399	</tr>
	400	<tr>
	401	<td style="width: 37px; vertical-align: top;">
	402	<p><br>
	403	</p>
	404	</td>
	405	<td style="width: 56px; vertical-align: top;">
	406	<p><br>
	407	</p>
	408	</td>
	409	<td style="width: 68px; vertical-align: top;">
	410	<p><br>
	411	</p>
	412	</td>
	413	<td style="width: 62px; vertical-align: top;">
	414	<p><br>
	415	</p>
	416	</td>
	417	<td style="width: 36px; vertical-align: top;">
	418	<p>C</p>
	419	</td>
	420	<td style="width: 518px; vertical-align: top;">
	421	<p>Special characters like * and " are now allowed for NetCDF
[553]	422	variable names. Replacement of these characters has been removed
[556]	423	(routine clean_netcdf_varname removed)</p>
	424	</td>
	425	<td style="width: 393px; vertical-align: top;">
	426	<p><br>
	427	</p>
	428	</td>
	429	</tr>
	430	<tr>
	431	<td style="width: 37px; vertical-align: top;">
	432	<p>18/03/10</p>
	433	</td>
	434	<td style="width: 56px; vertical-align: top;">
	435	<p>SR</p>
	436	</td>
	437	<td style="width: 68px; vertical-align: top;">
	438	<p>516</p>
	439	</td>
	440	<td style="width: 62px; vertical-align: top;">
	441	<p>3.7a</p>
	442	</td>
	443	<td style="width: 36px; vertical-align: top;">
	444	<p>N</p>
	445	</td>
	446	<td style="width: 518px; vertical-align: top;">
	447	<p>Simple installation method has been documented (see chapter
[553]	448	5.0). Respective scripts and configuration files have been
[556]	449	updated.</p>
	450	</td>
	451	<td style="width: 393px; vertical-align: top;">
	452	<p>palm_simple_install, palm_simple_run</p>
	453	</td>
	454	</tr>
	455	<tr>
	456	<td style="width: 37px; vertical-align: top;">
	457	<p><br>
	458	</p>
	459	</td>
	460	<td style="width: 56px; vertical-align: top;">
	461	<p><br>
	462	</p>
	463	</td>
	464	<td style="width: 68px; vertical-align: top;">
	465	<p><br>
	466	</p>
	467	</td>
	468	<td style="width: 62px; vertical-align: top;">
	469	<p><br>
	470	</p>
	471	</td>
	472	<td style="width: 36px; vertical-align: top;">
	473	<p>B</p>
	474	</td>
	475	<td style="width: 518px; vertical-align: top;">
	476	<p>opt=1 is forced for PGI-compiler in routine <font face="Courier New, Courier, monospace">buoyancy
	477	</font>by compiler-directive. Otherwise, program aborts with
	478	SIGFPE.</p>
	479	</td>
	480	<td style="width: 393px; vertical-align: top;">
	481	<p>buoyancy</p>
	482	</td>
	483	</tr>
	484	<tr>
	485	<td style="width: 37px; vertical-align: top;">
	486	<p>16/03/10</p>
	487	</td>
	488	<td style="width: 56px; vertical-align: top;">
	489	<p>RH</p>
	490	</td>
	491	<td style="width: 68px; vertical-align: top;">
	492	<p>513</p>
	493	</td>
	494	<td style="width: 62px; vertical-align: top;">
	495	<p>3.7a</p>
	496	</td>
	497	<td style="width: 36px; vertical-align: top;">
	498	<p>N</p>
	499	</td>
	500	<td style="width: 518px; vertical-align: top;">
	501	<p>NCL scripts can be run with the shell script <font face="Courier New, Courier, monospace">palmplot.</font></p>
	502	</td>
	503	<td style="width: 393px; vertical-align: top;">
	504	<p>palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl</p>
	505	</td>
	506	</tr>
	507	<tr>
	508	<td style="width: 37px; vertical-align: top;">
	509	<p>12/03/10</p>
	510	</td>
	511	<td style="width: 56px; vertical-align: top;">
	512	<p>SR</p>
	513	</td>
	514	<td style="width: 68px; vertical-align: top;">
	515	<p>509</p>
	516	</td>
	517	<td style="width: 62px; vertical-align: top;">
	518	<p>3.7a</p>
	519	</td>
	520	<td style="width: 36px; vertical-align: top;">
	521	<p>B</p>
	522	</td>
	523	<td style="width: 518px; vertical-align: top;">
	524	<p>bugfix for rev 504: remode_md was given a wrong value</p>
	525	</td>
	526	<td style="width: 393px; vertical-align: top;">
	527	<p>mbuild</p>
	528	</td>
	529	</tr>
	530	<tr>
	531	<td style="width: 37px; vertical-align: top;">
	532	<p>08/03/10</p>
	533	</td>
	534	<td style="width: 56px; vertical-align: top;">
	535	<p>SR</p>
	536	</td>
	537	<td style="width: 68px; vertical-align: top;">
	538	<p>506</p>
	539	</td>
	540	<td style="width: 62px; vertical-align: top;">
	541	<p>3.7a</p>
	542	</td>
	543	<td style="width: 36px; vertical-align: top;">
	544	<p>C</p>
	545	</td>
	546	<td style="width: 518px; vertical-align: top;">
	547	<p>hack for better usage of <b>mrun</b> on Kyoto computing center
	548	machine (<font face="Courier New, Courier, monospace">lckyoto</font>)</p>
	549	</td>
	550	<td style="width: 393px; vertical-align: top;">
	551	<p>mrun</p>
	552	</td>
	553	</tr>
	554	<tr>
	555	<td style="width: 37px; vertical-align: top;">
	556	<p>03/03/10</p>
	557	</td>
	558	<td style="width: 56px; vertical-align: top;">
	559	<p>SR</p>
	560	</td>
	561	<td style="width: 68px; vertical-align: top;">
	562	<p>504</p>
	563	</td>
	564	<td style="width: 62px; vertical-align: top;">
	565	<p>3.7a</p>
	566	</td>
	567	<td style="width: 36px; vertical-align: top;">
	568	<p>C</p>
	569	</td>
	570	<td style="width: 518px; vertical-align: top;">
	571	<p><font face="Courier New, Courier, monospace">combine_plot_fields</font>
	572	is now directly called within <b>mrun</b> and must not be given by
[553]	573	an output command in the configuration file any more. Please
[556]	574	remove the respective output command (<font face="Courier New, Courier, monospace">OC:combine_plot_fields.x</font>)
	575	from your configuration file!<br><br>Utility programs
	576	(<font face="Courier New, Courier, monospace">combine_plot_fields</font>,
	577	<font face="Courier New, Courier, monospace">interpret_config</font>)
	578	are created by <b>mbuild</b> separately for each block in the
	579	configuration file. Depending on option <font face="Courier New, Courier, monospace">-K</font>,
	580	<b>mrun</b> is using the utility programs for the respective
	581	block.<br><br>Utility programs are also compiled in parallel,
	582	depending on variable <font face="Courier New, Courier, monospace">%mopts</font>
	583	in the configuration file..<br><br>Default configuration files
	584	updated.</p>
	585	</td>
	586	<td style="width: 393px; vertical-align: top;">
	587	<p>mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*</p>
	588	</td>
	589	</tr>
	590	<tr>
	591	<td style="width: 37px; vertical-align: top;">
	592	<p>02/03/10</p>
	593	</td>
	594	<td style="width: 56px; vertical-align: top;">
	595	<p>SR</p>
	596	</td>
	597	<td style="width: 68px; vertical-align: top;">
	598	<p>496</p>
	599	</td>
	600	<td style="width: 62px; vertical-align: top;">
	601	<p>3.7a</p>
	602	</td>
	603	<td style="width: 36px; vertical-align: top;">
	604	<p>C</p>
	605	</td>
	606	<td style="width: 518px; vertical-align: top;">
	607	<p>Particle data for restart runs are only written if environment
	608	variable <font face="Courier New, Courier, monospace">write_binary</font>
	609	= <i>.T.</i>, i.e. particle data are now handled in the same way
	610	as the other restart data.</p>
	611	</td>
	612	<td style="width: 393px; vertical-align: top;">
	613	<p>palm</p>
	614	</td>
	615	</tr>
	616	<tr>
	617	<td style="width: 37px; vertical-align: top;">
	618	<p>01/03/10</p>
	619	</td>
	620	<td style="width: 56px; vertical-align: top;">
	621	<p>SR</p>
	622	</td>
	623	<td style="width: 68px; vertical-align: top;">
	624	<p>494</p>
	625	</td>
	626	<td style="width: 62px; vertical-align: top;">
	627	<p>3.7a</p>
	628	</td>
	629	<td style="width: 36px; vertical-align: top;">
	630	<p>N</p>
	631	</td>
	632	<td style="width: 518px; vertical-align: top;">
	633	<p>Output in NetCDF4-format.<br><br>NetCDF4 allows for parallel
[553]	634	I/O. Also, variables are not limited in size any more (i.e. arrays
	635	can be larger than 2GB). The new d3par-parameter
[556]	636	<font face="Courier New, Courier, monospace">netcdf_data_format</font>.can
	637	be used to select among the different NetCDF file formats (<i>1</i>:
	638	classic format, <i>2</i>: 64-bit-offset format (this is now the
	639	default), <i>3</i>: NetCDF4/HDF5 format, <i>4</i>: NetCDF4 format
	640	with NF90_CLASSIC_MODEL bit set). Setting <font face="Courier New, Courier, monospace">netcdf_data_format</font>
	641	> <i>2</i> only affects 2d- and 3d-output, i.e. there is no
[553]	642	parallel output for profiles, time series, spectra, and particles.
[556]	643	Parallel output of particle data may realized in the future.<br><br>In
[553]	644	case of parallel output, all PEs write into one file, which means
[556]	645	that postprocessing the data with <font face="Courier New, Courier, monospace">combine_plot_fields</font>
[553]	646	(merging data from single files - one per PE - into one file) is
	647	not neccessary. In this case, flag files are automatically set,
[556]	648	telling <font face="Courier New, Courier, monospace">combine_plot_fields</font>
	649	that nothing is to be done.<br><br>Using NetCDF4 format requires a
[553]	650	NetCDF4/HDF library. Respective settings for -I, -L, and -l
	651	compiler/loader options for the SGI-ICE at HLRN can be found in
	652	the new example configuration file
[556]	653	<font face="Courier New, Courier, monospace">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</font><br><br><b>Attention:</b><br>So
[553]	654	far, NetCDF parallel I/O has only been tested a little. Further
	655	performance optimizations may be required, especially in case of
	656	large data sets (e.g. data chunking, or lustre file system
[556]	657	settings with <font face="Courier New, Courier, monospace">lfs
	658	setstripe</font>). <b>Please report bugs and performance problems
	659	immediately!</b><br><br><font face="Courier New, Courier, monospace">combine_plot_fields</font>
	660	outputs cpu-time needed for file merging.<br><br>Modules to be
[553]	661	loaded for compilation (mbuild) or job execution (mrun) can/should
[556]	662	now be given in the configuration file (<font face="Courier New, Courier, monospace">.mrun.config</font>)
	663	using variable <font face="Courier New, Courier, monospace">modules</font>.
	664	Example:<br><br>   <font face="Courier New, Courier, monospace">%modules
[553]	665	ifort/11.0.069:netcdf       lcsgih
[556]	666	parallel</font><br><br>This method replaces the (undocumented)
	667	<font face="Courier New, Courier, monospace">mpilib</font>-variable.<br><br><b>WARNING:</b><br><b>All
[553]	668	fixed settings of modules in the scripts mbuild, mrun, and subjob
[556]	669	have been removed! Please set the </b><font face="Courier New, Courier, monospace"><b>modules</b></font><b>
[553]	670	variable appropriately and remove the mpilib variable in your
[556]	671	configuration file.<br><br></b>Compilation time can be reduced be
[553]	672	using parallel make. The number of allowed simultaneous compiler
	673	calls (threads) is set in the configuration file using variable
[556]	674	<font face="Courier New, Courier, monospace">mopt</font>, e.g.<br><br>
	675	<font face="Courier New, Courier, monospace">%mopts  -j:4
	676	lcsgih parallel</font><br><br>allows a maximum of 4 routines to be
[553]	677	compiled simultaneously (provided that the makefile does not show
[556]	678	any dependencies between these routines).</p>
	679	</td>
	680	<td style="width: 393px; vertical-align: top;">
	681	<p>check_open, check_parameters, close_file, data_output_2d,
[553]	682	data_output_3d, header, modules, netcdf,
[556]	683	parin<br><br>combine_plot_fields<br><br>mbuild, mrun, subjob</p>
	684	</td>
	685	</tr>
	686	<tr>
	687	<td style="width: 37px; vertical-align: top;">
	688	<p><br>
	689	</p>
	690	</td>
	691	<td style="width: 56px; vertical-align: top;">
	692	<p><br>
	693	</p>
	694	</td>
	695	<td style="width: 68px; vertical-align: top;">
	696	<p><br>
	697	</p>
	698	</td>
	699	<td style="width: 62px; vertical-align: top;">
	700	<p><br>
	701	</p>
	702	</td>
	703	<td style="width: 36px; vertical-align: top;">
	704	<p>C</p>
	705	</td>
	706	<td style="width: 518px; vertical-align: top;">
	707	<p>d3par-parameters <font face="Courier New, Courier, monospace">netcdf_64bit</font>
	708	and <font face="Courier New, Courier, monospace">netcdf_64bit_3d</font>
	709	have been removed. Use the new d3par-variable <font face="Courier New, Courier, monospace">netcdf_data_format</font>
	710	= <i>2</i> for choosing the NetCDF 64bit-offset format (this is
[553]	711	the default from now on). The offset-format can not be set
[556]	712	independently for the 3d-output-data any more.<br><br>d3par-parameters
	713	<font face="Courier New, Courier, monospace">netcdf_format_mask</font>,
	714	<font face="Courier New, Courier, monospace">netcdf_format_mask_av</font>,
	715	and variables <font face="Courier New, Courier, monospace">nc_format_mask</font>,
	716	<font face="Courier New, Courier, monospace">format_parallel_io</font>
[553]	717	removed. They are replaced by the new parameter
[556]	718	<font face="Courier New, Courier, monospace">netcdf_data_format</font>.
[553]	719	This change concerns the masked data output, which is still not
[556]	720	documented.</p>
	721	</td>
	722	<td style="width: 393px; vertical-align: top;">
	723	<p>check_open, close_file,<br>data_output_mask, header,
	724	init_masks, modules, parin</p>
	725	</td>
	726	</tr>
	727	<tr>
	728	<td style="width: 37px; vertical-align: top;">
	729	<p><br>
	730	</p>
	731	</td>
	732	<td style="width: 56px; vertical-align: top;">
	733	<p><br>
	734	</p>
	735	</td>
	736	<td style="width: 68px; vertical-align: top;">
	737	<p><br>
	738	</p>
	739	</td>
	740	<td style="width: 62px; vertical-align: top;">
	741	<p><br>
	742	</p>
	743	</td>
	744	<td style="width: 36px; vertical-align: top;">
	745	<p>B</p>
	746	</td>
	747	<td style="width: 518px; vertical-align: top;">
	748	<p>Bugfix in trunk/UTIL/Makefile: forgot to compile for
	749	interpret_config.<br><br>Bugfix: timeseries data have to be
	750	collected by PE0 (user_statistics).</p>
	751	</td>
	752	<td style="width: 393px; vertical-align: top;">
	753	<p>user_statistics<br><br>trunk/UTIL/Makefile</p>
	754	</td>
	755	</tr>
	756	<tr>
	757	<td style="width: 37px; vertical-align: top;">
	758	<p>05/02/10</p>
	759	</td>
	760	<td style="width: 56px; vertical-align: top;">
	761	<p>SR</p>
	762	</td>
	763	<td style="width: 68px; vertical-align: top;">
	764	<p>485</p>
	765	</td>
	766	<td style="width: 62px; vertical-align: top;">
	767	<p>3.7a</p>
	768	</td>
	769	<td style="width: 36px; vertical-align: top;">
	770	<p>B</p>
	771	</td>
	772	<td style="width: 518px; vertical-align: top;">
	773	<p><font face="Courier New, Courier, monospace">ngp_3d</font>,
	774	<font face="Courier New, Courier, monospace">ngp_3d_inner</font>
[553]	775	changed to 64 bit. Otherwise, on large grids > 210*9 grid
	776	points some global statistics (e.g. total kinetic energy) have
[556]	777	wrong values.</p>
	778	</td>
	779	<td style="width: 393px; vertical-align: top;">
	780	<p>init_3d_model, modules</p>
	781	</td>
	782	</tr>
	783	<tr>
	784	<td style="width: 37px; vertical-align: top;">
	785	<p>05/02/10</p>
	786	</td>
	787	<td style="width: 56px; vertical-align: top;">
	788	<p>SR</p>
	789	</td>
	790	<td style="width: 68px; vertical-align: top;">
	791	<p>484</p>
	792	</td>
	793	<td style="width: 62px; vertical-align: top;">
	794	<p>3.7a</p>
	795	</td>
	796	<td style="width: 36px; vertical-align: top;">
	797	<p>B</p>
	798	</td>
	799	<td style="width: 518px; vertical-align: top;">
	800	<p>Typo in file headers removed ("current" instead of
	801	"actual").</p>
	802	</td>
	803	<td style="width: 393px; vertical-align: top;">
	804	<p>many</p>
	805	</td>
	806	</tr>
	807	<tr>
	808	<td style="width: 37px; vertical-align: top;">
	809	<p>05/02/10</p>
	810	</td>
	811	<td style="width: 56px; vertical-align: top;">
	812	<p>SR</p>
	813	</td>
	814	<td style="width: 68px; vertical-align: top;">
	815	<p>483</p>
	816	</td>
	817	<td style="width: 62px; vertical-align: top;">
	818	<p>3.7a</p>
	819	</td>
	820	<td style="width: 36px; vertical-align: top;">
	821	<p>N</p>
	822	</td>
	823	<td style="width: 518px; vertical-align: top;">
	824	<p><font face="Courier New, Courier, monospace">compare_palm_logs
	825	</font>is additionally compiled with <b>mbuild</b> <font face="Courier New, Courier, monospace">-u</font>
	826	. (<font face="Courier New, Courier, monospace">Makefile</font> in
	827	<font face="Courier New, Courier, monospace">trunk/UTIL</font>)<br><br>make
	828	options (<font face="Courier New, Courier, monospace">mopts</font>)
	829	to be set by configuration file implemented. (<b>mrun</b>,
	830	<b>mbuild</b>)<br><br><font face="Courier New, Courier, monospace">humidity</font>
	831	= <i>.T.</i> can be used for runs with topography.
	832	<font face="Courier New, Courier, monospace">wall_humidityflux</font>
	833	and<br><font face="Courier New, Courier, monospace">wall_scalarflux</font>
	834	are the corresponding new inipar parameters.<br>(<font face="Courier New, Courier, monospace">check_parameters</font>,
	835	<font face="Courier New, Courier, monospace">init_3d_model</font>,
	836	<font face="Courier New, Courier, monospace">parin</font>)<br><br>Large
[553]	837	scale vertical motion (subsidence/ascent) can be added as
	838	additional source to the prognostic equation for potential
[556]	839	temperature. See new parameters <font face="Courier New, Courier, monospace">large_scale_subsidence</font>,
	840	<font face="Courier New, Courier, monospace">ws_vertical_gradient</font>,
	841	and <font face="Courier New, Courier, monospace">ws_vertical_gradient_level</font>.
	842	(<font face="Courier New, Courier, monospace">check_parameters</font>,
	843	<font face="Courier New, Courier, monospace">header</font>,
	844	<font face="Courier New, Courier, monospace">Makefile</font>,
	845	<font face="Courier New, Courier, monospace">modules</font>,
	846	<font face="Courier New, Courier, monospace">parin</font>,
	847	<font face="Courier New, Courier, monospace">prognostic_equations</font>,
	848	<font face="Courier New, Courier, monospace">read_var_list</font>,
	849	<font face="Courier New, Courier, monospace">subsidence</font>,
	850	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Scripts
[553]	851	have been updated for Cray-XT5 machine (lcxt5m) and
[556]	852	Hitachi-machine (lckyoto).<br><br>A simple method for installing
[553]	853	and running palm (with limited features) has been added.
[556]	854	(<font face="Courier New, Courier, monospace">Makefile</font>, new
	855	scripts <b>palm_simple_install</b>, <b>palm_simple_run</b>)<br><br>Masked
[553]	856	data output has been implemented but it is not documented in the
	857	user manual so far. This feature can already use NetCDF4 file
	858	format. (check_open, check_parameters, close_file, modules,
	859	netcdf, parin, time_integration, user_parin, new:
[556]	860	data_output_mask, init_masks, user_data_output_mask)</p>
	861	</td>
	862	<td style="width: 393px; vertical-align: top;">
	863	<p>check_open, check parameters, close_file, header,
[553]	864	init_3d_model, Makefile, mbuild, modules, mrun, netcdf, parin,
	865	prognostic_equations, read_var_list, time_integration, user_parin,
[556]	866	write_var_list<br><br><b>new:</b> data_output_mask,
[553]	867	init_masks, palm_simple_install, palm_simple_run, subsidence,
[556]	868	user_data_output_mask</p>
	869	</td>
	870	</tr>
	871	<tr>
	872	<td style="width: 37px; vertical-align: top;">
	873	<p><br>
	874	</p>
	875	</td>
	876	<td style="width: 56px; vertical-align: top;">
	877	<p><br>
	878	</p>
	879	</td>
	880	<td style="width: 68px; vertical-align: top;">
	881	<p><br>
	882	</p>
	883	</td>
	884	<td style="width: 62px; vertical-align: top;">
	885	<p><br>
	886	</p>
	887	</td>
	888	<td style="width: 36px; vertical-align: top;">
	889	<p>C</p>
	890	</td>
	891	<td style="width: 518px; vertical-align: top;">
	892	<p>2d-decomposition is default for Cray-XT machines.
	893	(<font face="Courier New, Courier, monospace">init_pegrid</font>)<br><br><font face="Courier New, Courier, monospace">var_ts</font>
	894	is replaced by <font face="Courier New, Courier, monospace">dots_max</font>.
	895	(<font face="Courier New, Courier, monospace">modules</font>,
	896	<font face="Courier New, Courier, monospace">init_3d_model</font>)<br><br>Every
[553]	897	cloud droplet has now an own weighting factor and can be deleted
	898	due to collisions. Condensation and collision of cloud droplets
[556]	899	are adjusted accordingly. (<font face="Courier New, Courier, monospace">advec_particles</font>)<br><br>Collision
[553]	900	efficiency for large cloud droplets has changed according to table
[556]	901	of Rogers and Yau. (<font face="Courier New, Courier, monospace">collision_efficiency</font>)</p>
	902	</td>
	903	<td style="width: 393px; vertical-align: top;">
	904	<p>advec_particles, collision_efficiency, init_3d_model,
	905	init_pegrid, modules</p>
	906	</td>
	907	</tr>
	908	<tr>
	909	<td style="width: 37px; vertical-align: top;">
	910	<p><br>
	911	</p>
	912	</td>
	913	<td style="width: 56px; vertical-align: top;">
	914	<p><br>
	915	</p>
	916	</td>
	917	<td style="width: 68px; vertical-align: top;">
	918	<p><br>
	919	</p>
	920	</td>
	921	<td style="width: 62px; vertical-align: top;">
	922	<p><br>
	923	</p>
	924	</td>
	925	<td style="width: 36px; vertical-align: top;">
	926	<p>B</p>
	927	</td>
	928	<td style="width: 518px; vertical-align: top;">
	929	<p>Bugfix for generating serial jobs. (<b>subjob</b>)<br><br>Bugfix:
[553]	930	index problem concerning gradient_level indices removed.
[556]	931	(<font face="Courier New, Courier, monospace">header</font>)<br><br>Dimension
	932	of array <font face="Courier New, Courier, monospace">stat</font>
[553]	933	in cascade change to prevent type problems with mpi2 libraries.
[556]	934	(<font face="Courier New, Courier, monospace">poisfft_hybrid</font>)<br><br>Loop
[553]	935	was split to make runs reproducible when using ifort compiler.
[556]	936	(<font face="Courier New, Courier, monospace">disturb_field</font>)<br><br>Bugfix:
	937	exchange of ghost points for <font face="Courier New, Courier, monospace">prho</font>
	938	included. (<font face="Courier New, Courier, monospace">time_integration</font>)<br><br>Bugfix
[553]	939	in calculation of time-averaged surface heatfluxes.
[556]	940	(<font face="Courier New, Courier, monospace">sum_up_3d_data</font>)<br><br>Bugfix
[553]	941	in calculation of precipitation_rate.
[556]	942	(<font face="Courier New, Courier, monospace">calc_precipitation</font>)<br><br>Bugfix:
[553]	943	initial data assignments to some dvrp arrays changed due to error
[556]	944	messages from gfortran compiler. (<font face="Courier New, Courier, monospace">modules</font>)<br><br>Bugfix
[553]	945	in calculation of cloud droplet velocity.
[556]	946	(<font face="Courier New, Courier, monospace">advec_particles</font>)<br><br>Bugfix
[553]	947	in transfer of particles at south/left edge.
[556]	948	(<font face="Courier New, Courier, monospace">advec_particles</font>)<br><br>Bugfix
	949	in calculation of collision efficiency. (<font face="Courier New, Courier, monospace">collision_efficiency</font>)</p>
	950	</td>
	951	<td style="width: 393px; vertical-align: top;">
	952	<p>advec_particles, calc_precipitation, collision_efficiency,
[553]	953	disturb_field, header, modules, poisfft_hybrid, subjob,
[556]	954	sum_up_3d_data, time_integration</p>
	955	</td>
	956	</tr>
	957	<tr>
	958	<td style="width: 37px; vertical-align: top;">
	959	<p>23/09/09</p>
	960	</td>
	961	<td style="width: 56px; vertical-align: top;">
	962	<p>SR</p>
	963	</td>
	964	<td style="width: 68px; vertical-align: top;">
	965	<p>392</p>
	966	</td>
	967	<td style="width: 62px; vertical-align: top;">
	968	<p>3.7</p>
	969	</td>
	970	<td style="width: 36px; vertical-align: top;">
	971	<p>N</p>
	972	</td>
	973	<td style="width: 518px; vertical-align: top;">
	974	<p><b>Most important changes:</b> atmosphere-ocean coupling has
[553]	975	been improved and steering of dvr-software is more user-friendly
	976	now. Beside that, the release contains a lot of optimizations,
	977	changes, and bugfixes which have accumulated over the last
[556]	978	months.<br><br>The atmosphere-ocean coupling allows to use
[553]	979	independent precursor runs in order to account for different
	980	spin-up times. The time when coupling has to be started is given
[556]	981	by new inipar parameter <font face="Courier New, Courier, monospace">coupling_start_time</font>.
	982	The precursor ocean run has to be started using new <b>mrun</b>
	983	option "<font face="Courier New, Courier, monospace">-y</font>"
	984	in order to add the appendix "<font face="Courier New, Courier, monospace">_O</font>"
	985	to all output files. (<font face="Courier New, Courier, monospace">check_for_restart</font>,
	986	<font face="Courier New, Courier, monospace">check_parameters</font>,
	987	<font face="Courier New, Courier, monospace">data_output_2d</font>,
	988	<font face="Courier New, Courier, monospace">data_output_3d</font>,
	989	<font face="Courier New, Courier, monospace">data_output_profiles</font>,
	990	<font face="Courier New, Courier, monospace">data_output_ptseries</font>,
	991	<font face="Courier New, Courier, monospace">data_output_spectra</font>,
	992	<font face="Courier New, Courier, monospace">data_output_tseries</font>,
	993	<font face="Courier New, Courier, monospace">header</font>,
	994	<font face="Courier New, Courier, monospace">init_coupling</font>,
	995	<font face="Courier New, Courier, monospace">modules</font>, <font face="Courier New, Courier, monospace">mrun</font>,
	996	<font face="Courier New, Courier, monospace">parin</font>,
	997	<font face="Courier New, Courier, monospace">read_var_list</font>,
	998	<font face="Courier New, Courier, monospace">surface_coupler</font>,
	999	<font face="Courier New, Courier, monospace">time_integration</font>,
	1000	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Clipping
[553]	1001	of dvrp output implemented. Default colourtable for particles
	1002	implemented, particle attributes (color, dvrp_size) can be set
[556]	1003	with new parameters <font face="Courier New, Courier, monospace">particle_color</font>,
	1004	<font face="Courier New, Courier, monospace">particle_dvrpsize</font>,
	1005	<font face="Courier New, Courier, monospace">color_interval</font>,
	1006	<font face="Courier New, Courier, monospace">dvrpsize_interval</font>.
[553]	1007	Slicer attributes (dvrp) are set with new routine
[556]	1008	<font face="Courier New, Courier, monospace">set_slicer_attributes_dvrp</font>
	1009	and are controlled with existing parameters <font face="Courier New, Courier, monospace">slicer_range_limits</font>.
	1010	(<font face="Courier New, Courier, monospace">init_dvrp</font>,
	1011	<font face="Courier New, Courier, monospace">data_output_dvrp</font>,
	1012	<font face="Courier New, Courier, monospace">modules</font>,
	1013	<font face="Courier New, Courier, monospace">set_slicer_attributes_dvrp</font>,
	1014	<font face="Courier New, Courier, monospace">user_data_output_dvrp</font>)<br><br>Polygon
[553]	1015	reduction for topography and ground plate isosurface. Reduction
	1016	level for buildings can be chosen with parameter cluster_size.
[556]	1017	(<font face="Courier New, Courier, monospace">init_dvrp</font>)<br><br>Variables
	1018	<font face="Courier New, Courier, monospace">bc_lr</font> / <font face="Courier New, Courier, monospace">bc_ns</font>
[553]	1019	in most subroutines replaced by LOGICAL variables
[556]	1020	<font face="Courier New, Courier, monospace">bc_lr_cyc</font>,<br><font face="Courier New, Courier, monospace">bc_ns_cyc</font>
[553]	1021	for speed optimization. This gives a significant speedup of more
[556]	1022	than 10%. (<font face="Courier New, Courier, monospace">check_parameters</font>,
	1023	<font face="Courier New, Courier, monospace">diffusion_u</font>,
	1024	<font face="Courier New, Courier, monospace">diffusion_v</font>,
	1025	<font face="Courier New, Courier, monospace">diffusion_w</font>,
	1026	<font face="Courier New, Courier, monospace">modules</font>)<br><br>Scripts
	1027	have been adapted for machine lck (Yonsei Univ.). (<font face="Courier New, Courier, monospace">mrun</font>,
	1028	<font face="Courier New, Courier, monospace">mbuild</font>,
	1029	<font face="Courier New, Courier, monospace">subjob</font>)<br><br>Additional
[553]	1030	timestep criterion in case of simulations with plant canopy.
[556]	1031	(<font face="Courier New, Courier, monospace">timestep</font>)<br><br>Check
	1032	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>
	1033	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>.
	1034	(<font face="Courier New, Courier, monospace">check_parameters</font>)<br><br>External
	1035	pressure gradient can be used as driving force. (<font face="Courier New, Courier, monospace">check_parameters</font>,
	1036	<font face="Courier New, Courier, monospace">header</font>,
	1037	<font face="Courier New, Courier, monospace">init_3d_model</font>,
	1038	<font face="Courier New, Courier, monospace">modules</font>,
	1039	<font face="Courier New, Courier, monospace">parin</font>,
	1040	<font face="Courier New, Courier, monospace">prognostic_equations</font>,
	1041	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1042	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>New
	1043	topography case '<i>single_street_canyon</i>'. (<font face="Courier New, Courier, monospace">header</font>,
	1044	<font face="Courier New, Courier, monospace">init_grid</font>,
	1045	<font face="Courier New, Courier, monospace">modules</font>,
	1046	<font face="Courier New, Courier, monospace">parin</font>,
	1047	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1048	<font face="Courier New, Courier, monospace">user_check_parameters</font>,
	1049	<font face="Courier New, Courier, monospace">user_header</font>,
	1050	<font face="Courier New, Courier, monospace">user_init_grid</font>,
	1051	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Option
	1052	to predefine a target bulk velocity for <font face="Courier New, Courier, monospace">conserve_volume_flow</font>.
	1053	(<font face="Courier New, Courier, monospace">check_parameters</font>,
	1054	<font face="Courier New, Courier, monospace">header</font>,
	1055	<font face="Courier New, Courier, monospace">init_3d_model</font>,
	1056	<font face="Courier New, Courier, monospace">modules</font>,
	1057	<font face="Courier New, Courier, monospace">parin</font>,
	1058	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1059	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Option
	1060	for user defined 2D data output in xy cross sections at z=<font face="Courier New, Courier, monospace">nzb</font>+1.
	1061	(<font face="Courier New, Courier, monospace">data_output_2d</font>,
	1062	<font face="Courier New, Courier, monospace">user_data_output_2d</font>)<br><br>xy
[553]	1063	cross section output of surface heatfluxes (sensible and latent).
[556]	1064	(<font face="Courier New, Courier, monospace">average_3d_data</font>,
	1065	<font face="Courier New, Courier, monospace">check_parameters</font>,
	1066	<font face="Courier New, Courier, monospace">data_output_2d</font>,
	1067	<font face="Courier New, Courier, monospace">modules</font>,
	1068	<font face="Courier New, Courier, monospace">read_3d_binary</font>,
	1069	<font face="Courier New, Courier, monospace">sum_up_3d_data</font>,
	1070	<font face="Courier New, Courier, monospace">write_3d_binary</font>)</p>
	1071	</td>
	1072	<td style="width: 393px; vertical-align: top;">
	1073	<p>average_3d_data, check_for_restart, check_parameters,
[553]	1074	data_output_2d, data_output_3d, data_output_dvrp,
	1075	data_output_profiles, data_output_ptseries, data_output_spectra,
	1076	data_output_tseries, diffusion_u, diffusion_v, diffusion_w,
	1077	init_coupling, init_dvrp, init_grid, init_3d_model, header,
	1078	mbuild, modules, mrun, package_parin, parin, prognostic_equations,
	1079	read_3d_binary, read_var_list, subjob, sum_up_3d_data,
	1080	surface_coupler, timestep, time_integration,
	1081	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
[556]	1082	user_header, user_init_grid, write_3d_binary, write_var_list<br><br><b>new:</b>
	1083	set_particle_attributes, set_slicer_attributes_dvrp</p>
	1084	</td>
	1085	</tr>
	1086	<tr>
	1087	<td style="width: 37px; vertical-align: top;">
	1088	<p><br>
	1089	</p>
	1090	</td>
	1091	<td style="width: 56px; vertical-align: top;">
	1092	<p><br>
	1093	</p>
	1094	</td>
	1095	<td style="width: 68px; vertical-align: top;">
	1096	<p><br>
	1097	</p>
	1098	</td>
	1099	<td style="width: 62px; vertical-align: top;">
	1100	<p><br>
	1101	</p>
	1102	</td>
	1103	<td style="width: 36px; vertical-align: top;">
	1104	<p>C</p>
	1105	</td>
	1106	<td style="width: 518px; vertical-align: top;">
	1107	<p>Output of messages replaced by message handling routine.
	1108	(<font face="Courier New, Courier, monospace">advec_particles</font>,
	1109	<font face="Courier New, Courier, monospace">advec_s_bc</font>,
	1110	<font face="Courier New, Courier, monospace">buoyancy</font>,
	1111	<font face="Courier New, Courier, monospace">calc_spectra</font>,
	1112	<font face="Courier New, Courier, monospace">check_for_restart</font>,
	1113	<font face="Courier New, Courier, monospace">check_open</font>,
	1114	<font face="Courier New, Courier, monospace">coriolis</font>,
	1115	<font face="Courier New, Courier, monospace">cpu_log</font>,
	1116	<font face="Courier New, Courier, monospace">data_output_2d</font>,
	1117	<font face="Courier New, Courier, monospace">data_output_3d</font>,
	1118	<font face="Courier New, Courier, monospace">data_output_dvrp</font>,
	1119	<font face="Courier New, Courier, monospace">data_output_profiles</font>,
	1120	<font face="Courier New, Courier, monospace">data_output_spectra</font>,
	1121	<font face="Courier New, Courier, monospace">fft_xy</font>,
	1122	<font face="Courier New, Courier, monospace">flow_statistics</font>,
	1123	<font face="Courier New, Courier, monospace">header</font>,
	1124	<font face="Courier New, Courier, monospace">init_1d_model</font>,
	1125	<font face="Courier New, Courier, monospace">init_3d_model</font>,
	1126	<font face="Courier New, Courier, monospace">init_dvrp</font>,
	1127	<font face="Courier New, Courier, monospace">init_grid</font>,
	1128	<font face="Courier New, Courier, monospace">init_particles</font>,
	1129	<font face="Courier New, Courier, monospace">init_pegrid</font>,
	1130	<font face="Courier New, Courier, monospace">netcdf</font>, <font face="Courier New, Courier, monospace">parin</font>,
	1131	<font face="Courier New, Courier, monospace">plant_canopy_model</font>,
	1132	<font face="Courier New, Courier, monospace">poisfft_hybrid</font>,
	1133	<font face="Courier New, Courier, monospace">poismg</font>,
	1134	<font face="Courier New, Courier, monospace">read_3d_binary</font>,
	1135	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1136	<font face="Courier New, Courier, monospace">surface_coupler</font>,
	1137	<font face="Courier New, Courier, monospace">temperton_fft</font>,
	1138	<font face="Courier New, Courier, monospace">timestep</font>,
	1139	<font face="Courier New, Courier, monospace">user_actions</font>,
	1140	<font face="Courier New, Courier, monospace">user_data_output_dvrp</font>,
	1141	<font face="Courier New, Courier, monospace">user_dvrp_coltab</font>,
	1142	<font face="Courier New, Courier, monospace">user_init_grid</font>,
	1143	<font face="Courier New, Courier, monospace">user_init_plant_canopy</font>,
	1144	<font face="Courier New, Courier, monospace">user_parin</font>,
	1145	<font face="Courier New, Courier, monospace">user_read_restart_data</font>,
	1146	<font face="Courier New, Courier, monospace">user_spectra</font>)<br><br>Output
[553]	1147	of NetCDF messages with aid of message handling routine.
[556]	1148	(<font face="Courier New, Courier, monospace">check_open</font>,
	1149	<font face="Courier New, Courier, monospace">close_file</font>,
	1150	<font face="Courier New, Courier, monospace">data_output_2d</font>,
	1151	<font face="Courier New, Courier, monospace">data_output_3d</font>,
	1152	<font face="Courier New, Courier, monospace">data_output_profiles</font>,
	1153	<font face="Courier New, Courier, monospace">data_output_ptseries</font>,
	1154	<font face="Courier New, Courier, monospace">data_output_spectra</font>,
	1155	<font face="Courier New, Courier, monospace">data_output_tseries</font>,
	1156	<font face="Courier New, Courier, monospace">netcdf</font>)<br><br>__lcmuk
[553]	1157	changed to __lc to avoid problems with Intel compiler on sgi-ice.
[556]	1158	(<font face="Courier New, Courier, monospace">poisfft</font>)<br><br>For
[553]	1159	extended NetCDF files, the updated title attribute includes an
[556]	1160	update of time_average_text where appropriate. (<font face="Courier New, Courier, monospace">netcdf</font>)<br><br>In
[553]	1161	case of restart runs without extension, initial profiles are not
	1162	written to NetCDF-file anymore. So far, time axis always started
[556]	1163	at t=0. (<font face="Courier New, Courier, monospace">data_output_profiles</font>,
	1164	<font face="Courier New, Courier, monospace">modules</font>,
	1165	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1166	<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>'
	1167	renamed to '<i>cyclic_fill</i>'. A cyclic fill can now <br>be used
	1168	independent of <font face="Courier New, Courier, monospace">turbulent_inflow</font>.
	1169	(<font face="Courier New, Courier, monospace">check_parameters</font>,
	1170	<font face="Courier New, Courier, monospace">header</font>,
	1171	<font face="Courier New, Courier, monospace">init_3d_model</font>)<br><br>2
	1172	NetCDF error numbers changed. (<font face="Courier New, Courier, monospace">data_output_3d</font>)<br><br>A
[553]	1173	link to the webspage appendix_a.html is printed for further
	1174	information about possible reasons of the error that appeared.
[556]	1175	(message)<br><br>Temperature gradient criterion for estimating the
[553]	1176	boundary layer height replaced by the gradient criterion of
[556]	1177	Sullivan et al. (1998). (<font face="Courier New, Courier, monospace">flow_statistics</font>)<br><br>NetCDF
[553]	1178	unit attribute in timeseries output in case of statistic regions
[556]	1179	added. (<font face="Courier New, Courier, monospace">netcdf</font>)<br><br>Maximum
[553]	1180	number of tails is calculated from maximum number of particles and
[556]	1181	<font face="Courier New, Courier, monospace">skip_particles_for_tail</font>.
	1182	(<font face="Courier New, Courier, monospace">init_particles</font>)<br><br>Value
	1183	of <font face="Courier New, Courier, monospace">vertical_particle_advection</font>
	1184	is allowed to differ for each particle group. (<font face="Courier New, Courier, monospace">advec_particles</font>,
	1185	<font face="Courier New, Courier, monospace">header</font>,
	1186	<font face="Courier New, Courier, monospace">modules</font>)
	1187	<br><br>First constant in array <font face="Courier New, Courier, monospace">den</font>
	1188	also defined as type double. (<font face="Courier New, Courier, monospace">eqn_state_seawater</font>)<br><br>Parameter
	1189	<font face="Courier New, Courier, monospace">dvrp_psize</font>
	1190	moved from <font face="Courier New, Courier, monospace">particles_par</font>
	1191	to <font face="Courier New, Courier, monospace">dvrp_graphics_par</font>.
	1192	(<font face="Courier New, Courier, monospace">package_parin</font>)<br><br><font face="Courier New, Courier, monospace">topography_grid_convention</font>
	1193	moved from <font face="Courier New, Courier, monospace">userpar</font>
	1194	to <font face="Courier New, Courier, monospace">inipar</font>
	1195	(<font face="Courier New, Courier, monospace">check_parameters</font>,
	1196	<font face="Courier New, Courier, monospace">header</font>, <font face="Courier New, Courier, monospace">parin</font>,
	1197	<font face="Courier New, Courier, monospace">read_var_list</font>,
	1198	<font face="Courier New, Courier, monospace">user_check_parameters</font>,
	1199	<font face="Courier New, Courier, monospace">user_header</font>,
	1200	<font face="Courier New, Courier, monospace">user_init_grid</font>,
	1201	<font face="Courier New, Courier, monospace">user_parin</font>,
	1202	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Default
	1203	value of <font face="Courier New, Courier, monospace">grid_matching</font>
	1204	changed to '<i>strict</i>'. (<font face="Courier New, Courier, monospace">modules</font>)<br><br>Adjustments
[553]	1205	for runs on lcxt4 (necessary due to a software update on CRAY) and
[556]	1206	for coupled runs on ibmy. (<font face="Courier New, Courier, monospace">mrun</font>,
	1207	<font face="Courier New, Courier, monospace">subjob</font>)</p>
	1208	</td>
	1209	<td style="width: 393px; vertical-align: top;">
	1210	<p>advec_particles, advec_s_bc, buoyancy, calc_spectra,
[553]	1211	check_for_restart, check_open, check_parameters, close_file,
	1212	coriolis, cpu_log, data_output_2d, data_output_3d,
	1213	data_output_dvrp, data_output_profiles, data_output_ptseries,
	1214	data_output_spectra, data_output_tseries, eqn_state_seawater,
	1215	fft_xy, flow_statistics, header, init_1d_model, init_3d_model,
	1216	init_dvrp, init_grid, init_particles, init_pegrid, message, mrun,
	1217	netcdf, package_parin, parin, plant_canopy_model, poisfft,
	1218	poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
	1219	surface_coupler, temperton_fft, timestep,
	1220	user_actions,user_check_parameters, user_data_output_dvrp,
	1221	user_dvrp_coltab, user_header, user_init_grid,
	1222	user_init_plant_canopy, user_parin, user_read_restart_data,
	1223	user_spectra, write_var_list
[556]	1224	</p>
	1225	</td>
	1226	</tr>
	1227	<tr>
	1228	<td style="width: 37px; vertical-align: top;">
	1229	<p><br>
	1230	</p>
	1231	</td>
	1232	<td style="width: 56px; vertical-align: top;">
	1233	<p><br>
	1234	</p>
	1235	</td>
	1236	<td style="width: 68px; vertical-align: top;">
	1237	<p><br>
	1238	</p>
	1239	</td>
	1240	<td style="width: 62px; vertical-align: top;">
	1241	<p><br>
	1242	</p>
	1243	</td>
	1244	<td style="width: 36px; vertical-align: top;">
	1245	<p>B</p>
	1246	</td>
	1247	<td style="width: 518px; vertical-align: top;">
	1248	<p>Bugfix: Initial hydrostatic pressure profile in case of ocean
	1249	runs is now calculated in 5 iteration steps. (<font face="Courier New, Courier, monospace">init_ocean</font>)<br><br>Bugfix:
[553]	1250	wrong sign in buoyancy production of ocean part in case of not
[556]	1251	using the reference density (only in 3D routine <font face="Courier New, Courier, monospace">production_e</font>).
	1252	(<font face="Courier New, Courier, monospace">production_e</font>)<br><br>Bugfix:
[553]	1253	output of averaged 2d/3d quantities requires that an avaraging
	1254	interval has been set, respective error message is included.
[556]	1255	(<font face="Courier New, Courier, monospace">check_parameters</font>)<br><br>Bugfix:
	1256	Output on unit 14 only if requested by <font face="Courier New, Courier, monospace">write_binary</font>.
	1257	(<font face="Courier New, Courier, monospace">user_last_actions</font>)<br><br>Bugfix
	1258	to avoid zero division by <font face="Courier New, Courier, monospace">km_neutral</font>.
	1259	(<font face="Courier New, Courier, monospace">production_e</font>)<br><br>Bugfix
[553]	1260	for extended NetCDF files: In order to avoid 'data mode' errors if
	1261	updated attributes are larger than their original size,
[556]	1262	<font face="Courier New, Courier, monospace">NF90_PUT_ATT</font>
	1263	is called in 'define mode' enclosed by <font face="Courier New, Courier, monospace">NF90_REDEF</font>
	1264	and <font face="Courier New, Courier, monospace">NF90_ENDDEF</font>
[553]	1265	calls. This implies a possible performance loss; an alternative
	1266	strategy would be to ensure equal attribute size in a job chain.
[556]	1267	(<font face="Courier New, Courier, monospace">netcdf</font>)<br><br>Bugfix:
[553]	1268	correction of initial volume flow for non-flat topography.
[556]	1269	(<font face="Courier New, Courier, monospace">init_3d_model</font>)<br><br>Bugfix:
	1270	zero initialization of arrays within buildings for '<i>cyclic_fill</i>'.
	1271	(<font face="Courier New, Courier, monospace">init_3d_model</font>)<br><br>Bugfix:
	1272	<font face="Courier New, Courier, monospace">to_be_resorted</font>
	1273	=> <font face="Courier New, Courier, monospace">s_av</font> for
	1274	time-averaged scalars. (<font face="Courier New, Courier, monospace">data_output_2d</font>,
	1275	<font face="Courier New, Courier, monospace">data_output_3d</font>)<br><br>Bugfix:
	1276	avoid that <font face="Courier New, Courier, monospace">ngp_2dh_s_inner</font>
	1277	becomes zero. (<font face="Courier New, Courier, monospace">init_3_model</font>)<br><br>Typographical
	1278	error: unit of wpt in dots_unit. (<font face="Courier New, Courier, monospace">modules</font>)<br><br>Bugfix:
[553]	1279	error in check, if particles moved further than one subdomain
	1280	length. This check must not be applied for newly released
[556]	1281	particles. (<font face="Courier New, Courier, monospace">advec_particles</font>)<br><br>Bugfix:
	1282	several tail counters are initialized, <font face="Courier New, Courier, monospace">particle_tail_coordinates</font>
[553]	1283	is only written to file if its third index is > 0, arrays for
	1284	tails are allocated with a minimum size of 10 tails if there is no
[556]	1285	tail initially. (<font face="Courier New, Courier, monospace">advec_particles</font>,
	1286	<font face="Courier New, Courier, monospace">init_particles</font>)<br><br>Bugfix:
	1287	pressure included for profile output. (<font face="Courier New, Courier, monospace">check_parameters</font>)<br><br>Bugfix:
	1288	Type of <font face="Courier New, Courier, monospace">count</font>
	1289	and <font face="Courier New, Courier, monospace">count_rate</font>
	1290	changed to default <font face="Courier New, Courier, monospace">INTEGER</font>
	1291	on NEC machines. (<font face="Courier New, Courier, monospace">cpu_log</font>)<br><br>Bugfix:
[553]	1292	output of particle time series only if particle advection is
[556]	1293	switched on. (<font face="Courier New, Courier, monospace">time_integration</font>)<br><br>Bugfix:
	1294	qsws was calculated in case of <font face="Courier New, Courier, monospace">constant
	1295	heatflux</font> = <font face="Courier New, Courier, monospace">.FALSE.</font>.
	1296	(<font face="Courier New, Courier, monospace">prandtl_fluxes</font>)<br><br>Bugfix:
[553]	1297	averaging along z is not allowed for 2d quantities (e.g. u* and
[556]	1298	z0). (<font face="Courier New, Courier, monospace">data_output_2d</font>)<br><br>Typographical
	1299	errors. (<font face="Courier New, Courier, monospace">netcdf</font>)<br><br>If
[553]	1300	the inversion height calculated by the prerun is zero,
	1301	inflow_damping_height must be explicitly specified.
[556]	1302	(<font face="Courier New, Courier, monospace">init_3d_model</font>)<br><br>Small
	1303	bugfix concerning 3d 64bit netcdf output format. (<font face="Courier New, Courier, monospace">header</font>)<br><br>Bugfix:
	1304	<font face="Courier New, Courier, monospace">dt_fixed</font>
[553]	1305	removed from the restart file, because otherwise, no change from a
	1306	fixed to a variable timestep would be possible in restart runs.
[556]	1307	(<font face="Courier New, Courier, monospace">read_var_list</font>,
	1308	<font face="Courier New, Courier, monospace">write_var_list</font>)<br><br>Bugfix:
	1309	initial setting of <font face="Courier New, Courier, monospace">time_coupling</font>
	1310	in coupled restart runs. (<font face="Courier New, Courier, monospace">time_integration</font>)</p>
	1311	</td>
	1312	<td style="width: 393px; vertical-align: top;">
	1313	<p>advec_particles, check_parameters, cpu_log, data_output_2d,
[553]	1314	data_output_3d, header, init_3d_model, init_particles, init_ocean,
	1315	modules, netcdf, prandtl_fluxes, production_e, read_var_list,
[556]	1316	time_integration, user_last_actions, write_var_list</p>
	1317	</td>
	1318	</tr>
	1319	<tr>
	1320	<td style="width: 37px; vertical-align: top;">
	1321	<p>02/02/09</p>
	1322	</td>
	1323	<td style="width: 56px; vertical-align: top;">
	1324	<p>SR</p>
	1325	</td>
	1326	<td style="width: 68px; vertical-align: top;">
	1327	<p>228</p>
	1328	</td>
	1329	<td style="width: 62px; vertical-align: top;">
	1330	<p>3.6</p>
	1331	</td>
	1332	<td style="width: 36px; vertical-align: top;">
	1333	<p>N</p>
	1334	</td>
	1335	<td style="width: 518px; vertical-align: top;">
	1336	<p>This release contains further additions, changes, and bugfixes
[553]	1337	for the SGI-ICE system, as well as important changes like the
	1338	splitting of the user-interface into single files, a complete
	1339	revision of the pre-compiling mechanism allowing to use different
	1340	make-depositories simultaneously, and a revision of the
	1341	reading-mechanism from restart files, which has no more
	1342	restrictions in case that the previous and current run have
	1343	different domain/subdomain sizes. A new handling of all kind of
	1344	output messages is introduced with this release and will be
[556]	1345	applied to all existing messages within the next releases.<br><br><b>New
	1346	features are:</b><br><br>Restart runs on SGI-ICE are working.
	1347	(mrun)<br>2d-decomposition is default on SGI-ICE systems.
	1348	(init_pegrid)<br><br>Ocean-atmosphere coupling realized with
[553]	1349	MPI-1. mrun adjusted for this case (-Y option). Check that PALM is
[556]	1350	called with <font face="Courier New, Courier, monospace">mrun</font>-option
	1351	"<i>-K parallel</i>" for coupling. Adjustments in <font face="Courier New, Courier, monospace">mrun</font>,
	1352	<font face="Courier New, Courier, monospace">mbuild</font>, and
	1353	<font face="Courier New, Courier, monospace">subjob</font> for
	1354	lcxt4.<br><br>DVRP arguments changed to single precision, mode
	1355	pathlines added.<br><br>User can add additional routines in files
	1356	<font face="Courier New, Courier, monospace">user_additional_routines</font>.<br><br>User
[553]	1357	can check user parameters and deduce further quantities in
[556]	1358	<font face="Courier New, Courier, monospace">user_check_parameters</font></p>
	1359	</td>
	1360	<td style="width: 393px; vertical-align: top;">
	1361	<p>check_for_restart, check_parameters, data_output_dvrp,
[553]	1362	init_dvrp, init_pegrid, local_stop, modules, package_parin, palm,
[556]	1363	surface_coupler, timestep<br><br>Makefile, mbuild, mrun,
	1364	subjob<br><br><b>new:</b><br>init_coupling,
	1365	user_additional_routines, user_check_parameters</p>
	1366	</td>
	1367	</tr>
	1368	<tr>
	1369	<td style="width: 37px; vertical-align: top;">
	1370	<p><br>
	1371	</p>
	1372	</td>
	1373	<td style="width: 56px; vertical-align: top;">
	1374	<p><br>
	1375	</p>
	1376	</td>
	1377	<td style="width: 68px; vertical-align: top;">
	1378	<p><br>
	1379	</p>
	1380	</td>
	1381	<td style="width: 62px; vertical-align: top;">
	1382	<p><br>
	1383	</p>
	1384	</td>
	1385	<td style="width: 36px; vertical-align: top;">
	1386	<p>C</p>
	1387	</td>
	1388	<td style="width: 518px; vertical-align: top;">
	1389	<p>User interface has been split into single files.<br><br>Type of
	1390	variables <font face="Courier New, Courier, monospace">count</font>
	1391	and <font face="Courier New, Courier, monospace">count_rate</font>
	1392	changed to INTEGER(8) in order to avoid "out of range"
[553]	1393	problems, which result in measured negative time intervals.
[556]	1394	(cpu_log, local_tremain, local_tremain_ini)<br><br>Reading
[553]	1395	mechanism from restart files completely revised. The
	1396	subdomain/total domain size is now allowed to vary arbitrarily
	1397	between the current and previous run. (read_var_list,
[556]	1398	read_3d_binary, user_read_restart_data)<br><br>Precompilation
	1399	mechanism (<font face="Courier New, Courier, monospace">mbuild</font>)
[553]	1400	completely revised: the source-tarfile remains in the source
[556]	1401	directory (<font face="Courier New, Courier, monospace">trunk/SOURCE</font>).
[553]	1402	One depository per block (given in the config-file) is created.
	1403	Always all files from the source directory are copied to the
	1404	respective depository. No additional file checks are done any more
	1405	(mrun version 2.1). The depository name used contains the
[556]	1406	conditions given by <font face="Courier New, Courier, monospace">mrun</font>-option
	1407	"<font face="Courier New, Courier, monospace">-K</font>".
	1408	(mbuild, mrun)<br><br>Output messages (including required stop of
	1409	execution) can now be handled with the new subroutine <font face="Courier New, Courier, monospace">message</font>.
[553]	1410	All output messages will be replaced by this routine step by step
[556]	1411	within the next revisions.<br><br>Neumann boundary condition at
	1412	<font face="Courier New, Courier, monospace">k=nzb</font> is
[553]	1413	explicitly set for better reading, although this has been already
[556]	1414	done in boundary_conds. (advec_s_bc)<br><br>Origin of the
[553]	1415	xy-coordinate system shifted from the center of the first grid
[556]	1416	cell (indices <font face="Courier New, Courier, monospace">i=0</font>,
	1417	<font face="Courier New, Courier, monospace">j=0</font>) to the
[553]	1418	south-left corner of this cell. (netcdf) Topography definition
[556]	1419	according to new user parameter <font face="Courier New, Courier, monospace">topography_grid_convention</font>.
	1420	(init_grid, modules, user_header, user_init_grid, user_parin)</p>
	1421	</td>
	1422	<td style="width: 393px; vertical-align: top;">
	1423	<p>advec_s_bc, check_parameters, cpu_log, init_grid, local_stop,
[553]	1424	local_tremain, local_tremain_ini, modules, netcdf, read_3d_binary,
[556]	1425	read_var_list, user_read_restart_data<br><br>Makefile, mbuild,
	1426	mrun<br><br><b>removed:</b><br>user_interface<br><br><b>new:</b><br>message,
[553]	1427	user_3d_data_averaging, user_actions, user_advec_particles,
	1428	user_check_data_output, user_check_data_output_pr,
	1429	user_data_output_2d, user_data_output_3d, user_data_output_dvrp,
	1430	user_define_netcdf_grid, user_dvrp_coltab, user_header,
	1431	user_init_3d_model, user_init, user_init_grid,
	1432	user_init_particles, user_init_plant_canopy, user_last_actions,
	1433	user_parin, user_parin, user_particle_attributes,
[556]	1434	user_read_restart_data, user_spectra, user_statistics</p>
	1435	</td>
	1436	</tr>
	1437	<tr>
	1438	<td style="width: 37px; vertical-align: top;">
	1439	<p><br>
	1440	</p>
	1441	</td>
	1442	<td style="width: 56px; vertical-align: top;">
	1443	<p><br>
	1444	</p>
	1445	</td>
	1446	<td style="width: 68px; vertical-align: top;">
	1447	<p><br>
	1448	</p>
	1449	</td>
	1450	<td style="width: 62px; vertical-align: top;">
	1451	<p><br>
	1452	</p>
	1453	</td>
	1454	<td style="width: 36px; vertical-align: top;">
	1455	<p>B</p>
	1456	</td>
	1457	<td style="width: 518px; vertical-align: top;">
	1458	<p>Bugfix: array <font face="Courier New, Courier, monospace">d</font>
[553]	1459	is reallocated in case that multigrid is used.
[556]	1460	(calc_spectra)<br><br>Bugfixes for nonparallel execution.
[553]	1461	(check_for_restart, cpu_statistics,
[556]	1462	inflow_turbulence, timestep)<br><br>Size of <font face="Courier New, Courier, monospace">pf3d
	1463	</font>adjusted to the required output size (1 gridpoint less,
[553]	1464	along all three dimensions), because output of a subset of the
[556]	1465	data (<font face="Courier New, Courier, monospace">pf3d(nxa:nxe...)</font>)
[553]	1466	in the NF90_PUT_VAR statement caused segmentation fault with the
[556]	1467	INTEL compiler. (combine_plot_fields)<br><br>Bugfix: error in <font face="Courier New, Courier, monospace">zu</font>
	1468	index in case of <font face="Courier New, Courier, monospace">section_xy=-1</font>.
	1469	(header)<br><br>Inconsistency removed: as the thermal
[553]	1470	stratification is not taken into account for the evaluation of the
[556]	1471	wall fluxes at vertical walls, the eddy viscosity <font face="Courier New, Courier, monospace">km</font>
[553]	1472	must not be used for the evaluation of the velocity gradients
[556]	1473	<font face="Courier New, Courier, monospace">dudy</font>, <font face="Courier New, Courier, monospace">dwdy</font>,
	1474	<font face="Courier New, Courier, monospace">dvdx</font> and <font face="Courier New, Courier, monospace">dwdx</font>.
	1475	(production_e)<br><br>Bugfix in calculating <font face="Courier New, Courier, monospace">k</font>
	1476	index in case of oceans runs. (sort_particles)<br><br>Bugfix: no
[553]	1477	output of particle concentration and radius unless particles have
[556]	1478	been started. (data_output_2d)<br><br>Bugfix: reading of
	1479	<font face="Courier New, Courier, monospace">spectrum_x\|y</font>
[553]	1480	from restart files ignored if total numbers of grid points do not
[556]	1481	match. (read_3d_binary)<br><br>Bugfix: abort in case that absolute
	1482	temperature is below zero. (init_cloud_physics)</p>
	1483	</td>
	1484	<td style="width: 393px; vertical-align: top;">
	1485	<p>advec_particles, calc_spectra, check_for_restart,
[553]	1486	cpu_statistics, data_output_2d, header, inflow_turbulence,
	1487	init_cloud_physics, production_e, read_3d_binary,
[556]	1488	timestep<br><br>combine_plot_fields</p>
	1489	</td>
	1490	</tr>
	1491	</tbody></table>
	1492	<p><br>  <br>
	1493	</p>
	1494	<h2><a name="Kapitel2.0"></a>2.0  How to change the source code
	1495	and how to document modifications</h2>
	1496	<p>Currently (Sep 23rd, 2009), only selected users are allowed to
[553]	1497	commit changes to the repository. Rules given below are preliminary,
[556]	1498	until we have switched to the "trac"-System.</p>
	1499	<ol>
	1500	<li><p>Change source code in your current working copy. Document
	1501	changes in the respective file headers unter "<font face="Courier New, Courier, monospace">Current
	1502	revisions:</font>". Additionally, document all changes in a
[553]	1503	local file (e.g. ~/palm/current_version/CURRENT_MODIFICATIONS),
	1504	including the files that have been changed. Classify changes in
[556]	1505	three cases, new (N), changed (C), and bugfix (B). <b>Try to be as
	1506	short and as precise as possible in describing the changes!</b></p>
	1507	</li><li><p>Test the changed version, unless it works sufficiently.</p>
	1508	</li><li><p>Commit the changes to the repository<br><br>   <font face="Courier New, Courier, monospace">svn
	1509	commit -m "message string" trunk<br></font><br>where
	1510	"<font face="Courier New, Courier, monospace">message string</font>"
	1511	is a short, <b>meaningful</b> summary of the
	1512	changes.<br><br>Alternatively, in case that you have made quite a
[553]	1513	lot of changes, you can also give the contents of your file
[556]	1514	CURRENT_MODIFICATIONS as the log message:<br><br>   <font face="Courier New, Courier, monospace">svn
	1515	commit -F CURRENT_MODIFICATIONS trunk</font></p>
	1516	</li><li><p>Enter the changes into the technical documentation (under
	1517	<font face="Courier New, Courier, monospace">.../trunk/DOC/tec/technical_documentation.html</font>).</p>
	1518	</li><li><p>Move the change comments in the file headers from "Current
	1519	revisions:" to "Former revisions:". Set the current
	1520	svn id in front of that.<br><br><b>Example:</b><br><br><b>before
	1521	move:</b><br><br><font face="Courier New, Courier, monospace">!
	1522	Current revisions:</font><br><font face="Courier New, Courier, monospace">!
	1523	-----------------</font><br><font face="Courier New, Courier, monospace">!
	1524	</font><font face="Courier New, Courier, monospace"><b>new dummy
	1525	argument abcd</b></font><br><font face="Courier New, Courier, monospace">!</font><br><font face="Courier New, Courier, monospace">!
	1526	Former revisions:</font><br><font face="Courier New, Courier, monospace">!
	1527	-----------------</font><br><font face="Courier New, Courier, monospace">! Â§Id: init_3d_model.f90 </font><font color="#3366ff"><font face="Courier New, Courier, monospace"><b>425
	1528	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">!
	1529	407 2009-12-01 15:01:15Z maronga</font><br><font face="Courier New, Courier, monospace">!
	1530	var_ts is replaced by dots_max </font><br><br><b>after move:</b><br><br><font face="Courier New, Courier, monospace">!
	1531	Current revisions:</font><br><font face="Courier New, Courier, monospace">!
	1532	-----------------</font><br><font face="Courier New, Courier, monospace">!
	1533	</font><br><font face="Courier New, Courier, monospace">!</font><br><font face="Courier New, Courier, monospace">!
	1534	Former revisions:</font><br><font face="Courier New, Courier, monospace">!
	1535	-----------------</font><br><font face="Courier New, Courier, monospace">! 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">!
	1536	</font><font color="#3366ff"><font face="Courier New, Courier, monospace"><b>425
	1537	2010-02-06 13:37:48Z raasch</b></font></font><font face="Courier New, Courier, monospace"><br>!
	1538	</font><font face="Courier New, Courier, monospace"><b>new dummy
	1539	argument abcd</b></font><br><font face="Courier New, Courier, monospace">!</font><br><font face="Courier New, Courier, monospace">!
	1540	407 2009-12-01 15:01:15Z maronga</font><br><font face="Courier New, Courier, monospace">!
	1541	var_ts is replaced by dots_max<br><br></font><font face="Times New Roman, Times, serif">Note
	1542	that the "</font><span style="font-family: Courier New,Courier,monospace;">Â§</span><font face="Times New Roman, Times, serif">"
	1543	in this example should read "$", but "$" cannot
[553]	1544	be used here, because otherwise svn would replace these entries
[556]	1545	after every change to this technical documentation.</font></p>
	1546	</li><li><p>Commit the changes in the technical documentation and the
	1547	file headers:<br><br>   <font face="Courier New, Courier, monospace">svn
	1548	commit -m "last commit documented" trunk</font><br><br><br>
	1549	</p>
	1550	</li></ol>
	1551	<h2><a name="Kapitel3.0"></a>3.0  Description of selected parts
	1552	of the model source code</h2>
	1553	<p>This section gives links to existing descriptions about special
[392]	1554	parts of the PALM code, e.g. special numerical methods that are used
	1555	(including mathematical background). Documents are stored in single
	1556	files with different formats. Some are in German (sorry for the
[556]	1557	inconvenience). <br>
	1558	</p>
	1559	<ul>
	1560	<li><p style="margin-bottom: 0in;"><a name="UPS"></a>upstream-spline
	1561	advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
[553]	1562	, only in German)
[556]	1563	</p>
	1564	</li><li><p style="margin-bottom: 0in;"><a name="Cloud_physics"></a>cloud
	1565	physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
[553]	1566	)
[556]	1567	</p>
	1568	</li><li><p style="margin-bottom: 0in;"><a name="Bitkompression"></a>data
	1569	compression with <a href="methods/bit_compression/bit_compression.html">bit
	1570	shifting method</a> (only in German)</p>
	1571	</li><li><p>Runge-Kutta time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
[553]	1572	, only in German)
[556]	1573	</p>
	1574	</li></ul>
	1575	<p><br>  <br>  <br>  <br>  <br>  <br>
	1576	<br>  <br>
	1577	</p>
	1578	</body></html>

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