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	2	<html><head>
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[392]	29	<meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <meta content="Mozilla/4.73 [en] (X11; U; HP-UX B.10.20 9000/782) [Netscape]" name="GENERATOR"> <meta content="Siegfried Raasch" name="Author"> <meta content="parallel LES model" name="Keywords"><title>PALM technical/numerical documentation</title></head><body><font size="+4">PALM
[5]	30	</font>a
	31	<b>pa</b>rallelized
	32	<b>L</b>ES <b>m</b>odel
[62]	33	<br><hr width="100%">
	34	<br><font size="+2">technical/numerical documentation</font>
	35	<br>
	36	<br>
	37	<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>  <br> </caption><tbody>
[482]	38	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
[481]	39	</span></td> </tr>
[62]	40	<tr nosave=""> <td nosave=""><b>Last
	41	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 544 2010-08-17 10:44:58Z raasch $</b></td> </tr>
	42	</tbody>
	43	</table><hr width="100%">
[5]	44	<p><font size="+2">Table of contents</font>
[62]	45	<br>
	46	<br>
	47	</p><ul> <a href="#Kapitel1.0">1.0</a>
	48	History of changes <p><a href="#Kapitel2.0">2.0</a>
[493]	49	How to change the source
	50	code and how to document modifications<br>
	51	</p> <p><a href="#Kapitel3.0">3.0</a>
[481]	52	Description of selected model numerics<br>
[5]	53	</p>
[392]	54	</ul><b></b><br>
	55
[62]	56	<h2><a name="Kapitel1.0"></a>1.0
	57	History of changes</h2>
[481]	58	The following table documents all changes to the PALM repository since 2009. Older changes can be found <a href="tec_doc_1998-2008.html">here</a>.<br>
	59	<br>
[482]	60	Entries in the fifth column specify the type of the change:
[5]	61	change
	62	of existing code (C), new code (N) or bugfix (B). More detailed
	63	information
[481]	64	about the changes may sometimes be found in the header comment lines of the
[5]	65	respective
	66	routines.
[62]	67	<br>
	68	<br>
[481]	69	<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
	70	<tbody>
	71	<tr>
[482]	72	<td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
[392]	73	</td>
[481]	74	<td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
[392]	75	</td>
[481]	76	<td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
[392]	77	</td>
[516]	78	<td style="width: 40px;"><big><span style="font-weight: bold;">last release</span></big><br>
[392]	79	</td>
[481]	80	<td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
	81	</td>
	82	<td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
	83	</td>
	84	<td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
	85	</td>
	86	</tr>
[482]	87
	88
	89
	90
	91
	92
	93
	94
	95
[481]	96	<tr>
[544]	97	<td style="vertical-align: top;">17/08/10<br>
	98	</td>
	99	<td style="vertical-align: top;">BM<br>
	100	</td>
	101	<td style="vertical-align: top;">544<br>
	102	</td>
	103	<td style="vertical-align: top;">3.7a<br>
	104	</td>
	105	<td style="vertical-align: top;">B/C/N<br>
	106	</td>
	107	<td style="vertical-align: top;">adjustments for lcxt4; bugfix (mbuild): loading of user-defined modules; new .mrun.config.lcxt4 for Cray XT4 in Bergen/Norway<br>
	108	</td>
	109	<td style="vertical-align: top;">mrun, mbuild, subjob<br>
	110	</td>
	111	</tr>
	112
	113	<tr>
[540]	114	<td style="vertical-align: top;">15/06/10<br>
	115	</td>
	116	<td style="vertical-align: top;">RH<br>
	117	</td>
	118	<td style="vertical-align: top;">540<br>
	119	</td>
	120	<td style="vertical-align: top;">3.7a<br>
	121	</td>
	122	<td style="vertical-align: top;">C<br>
	123	</td>
	124	<td style="vertical-align: top;">ssh from compute nodes to login
	125	nodes on hosts lcsgih/lcsgib is done using the names
	126	hicegate0/bicegate0 instead of the IP addresses<br>
	127	</td>
	128	<td style="vertical-align: top;">mrun<br>
	129	</td>
	130	</tr>
	131	<tr>
[532]	132	<td style="vertical-align: top;">21/04/10<br>
	133	</td>
	134	<td style="vertical-align: top;">RH<br>
	135	</td>
	136	<td style="vertical-align: top;">532<br>
	137	</td>
[540]	138	<td style="vertical-align: top;">3.7a<br>
[532]	139	</td>
	140	<td style="vertical-align: top;">C<br>
	141	</td>
	142	<td style="vertical-align: top;">
	143	Large scale vertical motion (subsidence/ascent) can be added as
	144	additional source to the prognostic equation for humidity/passive scalar<br>
	145	<br>
	146	character length for dopr_unit enlarged<br>
	147	<br>
	148	Adjustment of the NCL scripts<span style="font-family: Courier New,Courier,monospace;"> </span>to allow for output of png files <br>
	149	</td>
	150	<td style="vertical-align: top;">modules, prognostic_equations<br>
	151	<br>
	152	.ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
	153	</td>
	154	</tr>
	155	<tr>
	156	<td style="vertical-align: top;"><br>
	157	</td>
	158	<td style="vertical-align: top;"><br>
	159	</td>
	160	<td style="vertical-align: top;"><br>
	161	</td>
	162	<td style="vertical-align: top;"><br>
	163	</td>
	164	<td style="vertical-align: top;">B<br>
	165	</td>
	166	<td style="vertical-align: top;">Bugfix: unit of hyp changed to dbar<br>
	167	</td>
	168	<td style="vertical-align: top;">check_parameters<br>
	169	</td>
	170	</tr>
	171	<tr>
[530]	172	<td style="vertical-align: top;">01/04/10<br>
	173	</td>
	174	<td style="vertical-align: top;">RH<br>
	175	</td>
	176	<td style="vertical-align: top;">530<br>
	177	</td>
	178	<td style="vertical-align: top;">3.7a<br>
	179	</td>
	180	<td style="vertical-align: top;">B<br>
	181	</td>
	182	<td style="vertical-align: top;">Bugfix: treatment of special character * in NCL variables containing lists corrected<br>
	183	</td>
	184	<td style="vertical-align: top;">palmplot<br>
	185	</td>
	186	</tr>
	187	<tr>
[529]	188	<td style="vertical-align: top;">31/03/10<br>
	189	</td>
	190	<td style="vertical-align: top;">RH<br>
	191	</td>
	192	<td style="vertical-align: top;">529<br>
	193	</td>
	194	<td style="vertical-align: top;">3.7a<br>
	195	</td>
	196	<td style="vertical-align: top;">C<br>
	197	</td>
	198	<td style="vertical-align: top;">List of variable names have to specified using blank separated lists and single quotes<br>
	199	</td>
	200	<td style="vertical-align: top;">palmplot<br>
	201	</td>
	202	</tr>
	203	<tr>
[525]	204	<td style="vertical-align: top;">30/03/10<br>
	205	</td>
[526]	206	<td style="vertical-align: top;">RH<br>
	207	</td>
	208	<td style="vertical-align: top;">526<br>
	209	</td>
	210	<td style="vertical-align: top;">3.7a<br>
	211	</td>
	212	<td style="vertical-align: top;">C<br>
	213	</td>
	214	<td style="vertical-align: top;">Adjustment of the NCL scripts and <span style="font-family: Courier New,Courier,monospace;">palmplot </span>to allow for special characters in NetCDF variable names <br>
	215	</td>
	216	<td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl, timeseries.ncl, spectra.ncl<br>
	217	</td>
	218	</tr>
	219	<tr>
	220	<td style="vertical-align: top;">30/03/10<br>
	221	</td>
[525]	222	<td style="vertical-align: top;">SR<br>
	223	</td>
	224	<td style="vertical-align: top;">525<br>
	225	</td>
	226	<td style="vertical-align: top;">3.7a<br>
	227	</td>
	228	<td style="vertical-align: top;">B<br>
	229	</td>
	230	<td style="vertical-align: top;">Bugfix: "/" in netcdf profile variable names replaced by ":"<br>
	231	</td>
	232	<td style="vertical-align: top;">check_parameters<br>
	233	</td>
	234	</tr>
	235	<tr>
[520]	236	<td style="vertical-align: top;">19/03/10<br>
	237	</td>
	238	<td style="vertical-align: top;">SR<br>
	239	</td>
	240	<td style="vertical-align: top;">520<br>
	241	</td>
	242	<td style="vertical-align: top;">3.7a<br>
	243	</td>
	244	<td style="vertical-align: top;">N<br>
	245	</td>
	246	<td style="vertical-align: top;">NetCDF4 support for particle
	247	data. Total number of particles is allowed to increase during the run,
	248	when netcdf_data_format > <span style="font-style: italic;">2</span> is used.<br>
	249	</td>
	250	<td style="vertical-align: top;">advec_particles, check_open, netcdf<br>
	251	</td>
	252	</tr>
	253	<tr>
	254	<td style="vertical-align: top;"><br>
	255	</td>
	256	<td style="vertical-align: top;"><br>
	257	</td>
	258	<td style="vertical-align: top;"><br>
	259	</td>
	260	<td style="vertical-align: top;"><br>
	261	</td>
	262	<td style="vertical-align: top;">C<br>
	263	</td>
	264	<td style="vertical-align: top;">Special characters like * and "
	265	are now allowed for NetCDF variable names. Replacement of these
	266	characters has been removed (routine clean_netcdf_varname removed)<br>
	267	</td>
	268	<td style="vertical-align: top;"><br>
	269	</td>
	270	</tr>
	271	<tr>
[516]	272	<td style="vertical-align: top;">18/03/10<br>
	273	</td>
	274	<td style="vertical-align: top;">SR<br>
	275	</td>
	276	<td style="vertical-align: top;">516<br>
	277	</td>
	278	<td style="vertical-align: top;">3.7a<br>
	279	</td>
	280	<td style="vertical-align: top;">N<br>
	281	</td>
	282	<td style="vertical-align: top;">Simple installation method has been documented (see chapter 5.0). Respective scripts and configuration files have been updated.<br>
	283	</td>
	284	<td style="vertical-align: top;">palm_simple_install, palm_simple_run<br>
	285	</td>
	286	</tr>
	287	<tr>
	288	<td style="vertical-align: top;"><br>
	289	</td>
	290	<td style="vertical-align: top;"><br>
	291	</td>
	292	<td style="vertical-align: top;"><br>
	293	</td>
	294	<td style="vertical-align: top;"><br>
	295	</td>
	296	<td style="vertical-align: top;">B<br>
	297	</td>
	298	<td style="vertical-align: top;">opt=1 is forced for PGI-compiler in routine<span style="font-family: Courier New,Courier,monospace;"> buoyancy </span>by compiler-directive. Otherwise, program aborts with SIGFPE.<br>
	299	</td>
	300	<td style="vertical-align: top;">buoyancy<br>
	301	</td>
	302	</tr>
	303	<tr>
[513]	304	<td style="vertical-align: top;">16/03/10<br>
[509]	305	</td>
[513]	306	<td style="vertical-align: top;">RH<br>
	307	</td>
	308	<td style="vertical-align: top;">513<br>
	309	</td>
	310	<td style="vertical-align: top;">3.7a<br>
	311	</td>
	312	<td style="vertical-align: top;">N<br>
	313	</td>
	314	<td style="vertical-align: top;">NCL scripts can be run with the shell script <span style="font-family: Courier New,Courier,monospace;">palmplot.</span><br>
	315	</td>
[526]	316	<td style="vertical-align: top;">palmplot, .ncl.config.default, cross_sections.ncl, profiles.ncl<br>
[513]	317	</td>
	318	</tr>
	319	<tr>
	320	<td style="vertical-align: top;">12/03/10<br>
	321	</td>
[509]	322	<td style="vertical-align: top;">SR<br>
	323	</td>
	324	<td style="vertical-align: top;">509<br>
	325	</td>
	326	<td style="vertical-align: top;">3.7a<br>
	327	</td>
[532]	328	<td style="vertical-align: top;">B<br>
[509]	329	</td>
	330	<td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
	331	</td>
	332	<td style="vertical-align: top;">mbuild<br>
	333	</td>
	334	</tr>
	335	<tr>
[506]	336	<td style="vertical-align: top;">08/03/10<br>
	337	</td>
	338	<td style="vertical-align: top;">SR<br>
	339	</td>
	340	<td style="vertical-align: top;">506<br>
	341	</td>
	342	<td style="vertical-align: top;">3.7a<br>
	343	</td>
	344	<td style="vertical-align: top;">C<br>
	345	</td>
	346	<td style="vertical-align: top;">hack for better usage of <span style="font-weight: bold;">mrun</span> on Kyoto computing center machine (<span style="font-family: Courier New,Courier,monospace;">lckyoto</span>)<br>
	347	</td>
	348	<td style="vertical-align: top;">mrun<br>
	349	</td>
	350	</tr>
	351	<tr>
[504]	352	<td style="vertical-align: top;">03/03/10<br>
	353	</td>
	354	<td style="vertical-align: top;">SR<br>
	355	</td>
	356	<td style="vertical-align: top;">504<br>
	357	</td>
	358	<td style="vertical-align: top;">3.7a<br>
	359	</td>
	360	<td style="vertical-align: top;">C<br>
	361	</td>
	362	<td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> is now directly called within <span style="font-weight: bold;">mrun</span> and must not be given by an output command in the configuration file any more. Please remove the respective output command (<span style="font-family: Courier New,Courier,monospace;">OC:combine_plot_fields.x</span>) from your configuration file!<br>
	363	<br>
	364	Utility programs (<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>, <span style="font-family: Courier New,Courier,monospace;">interpret_config</span>) are created by <span style="font-weight: bold;">mbuild</span> separately for each block in the configuration file. Depending on option <span style="font-family: Courier New,Courier,monospace;">-K</span>, <span style="font-weight: bold;">mrun</span> is using the utility programs for the respective block.<br>
	365	<br>
	366	Utility programs are also compiled in parallel, depending on variable <span style="font-family: Courier New,Courier,monospace;">%mopts</span> in the configuration file..<br>
	367	<br>
	368	Default configuration files updated.<br>
	369	</td>
	370	<td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
	371	</td>
	372	</tr>
	373	<tr>
[496]	374	<td style="vertical-align: top;">02/03/10<br>
	375	</td>
	376	<td style="vertical-align: top;">SR<br>
	377	</td>
	378	<td style="vertical-align: top;">496<br>
	379	</td>
	380	<td style="vertical-align: top;">3.7a<br>
	381	</td>
	382	<td style="vertical-align: top;">C<br>
	383	</td>
	384	<td style="vertical-align: top;">Particle data for restart runs are only written if environment variable <span style="font-family: Courier New,Courier,monospace;">write_binary</span> = <span style="font-style: italic;">.T.</span>, i.e. particle data are now handled in the same way as the other restart data.<br>
	385	</td>
	386	<td style="vertical-align: top;">palm<br>
	387	</td>
	388	</tr>
	389	<tr>
[494]	390	<td style="vertical-align: top;">01/03/10<br>
[486]	391	</td>
	392	<td style="vertical-align: top;">SR<br>
	393	</td>
[494]	394	<td style="vertical-align: top;">494<br>
[486]	395	</td>
[494]	396	<td style="vertical-align: top;">3.7a<br>
	397	</td>
	398	<td style="vertical-align: top;">N<br>
	399	</td>
	400	<td style="vertical-align: top;">Output in NetCDF4-format.<br>
	401	<br>
	402	NetCDF4 allows for parallel I/O. Also, variables are not limited in
	403	size any more (i.e. arrays can be larger than 2GB). The new
	404	d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>.can be used to select among the different NetCDF file formats (<span style="font-style: italic;">1</span>: classic format, <span style="font-style: italic;">2</span>: 64-bit-offset format (this is now the default), <span style="font-style: italic;">3</span>: NetCDF4/HDF5 format, <span style="font-style: italic;">4</span>: NetCDF4 format with NF90_CLASSIC_MODEL bit set). Setting <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> > <span style="font-style: italic;">2</span>
	405	only affects 2d- and 3d-output, i.e. there is no parallel output for
	406	profiles, time series, spectra, and particles. Parallel output of
	407	particle data may realized in the future.<br>
	408	<br>
	409	In case of parallel output, all PEs write into one file, which means that postprocessing the data with <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>
	410	(merging data from single files - one per PE - into one file) is not
	411	neccessary. In this case, flag files are automatically set, telling <span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> that nothing is to be done.<br>
	412	<br>
	413	Using NetCDF4 format requires a NetCDF4/HDF library. Respective
	414	settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
	415	HLRN can be found in the new example configuration file <span style="font-family: Courier New,Courier,monospace;">..../trunk/SCRIPTS/.mrun.config.imuk_ice2_netcdf4</span><br>
	416	<br>
	417	<span style="font-weight: bold;">Attention:</span><br>
	418	So far, NetCDF parallel I/O has only been tested a little. Further
	419	performance optimizations may be required, especially in case of large
	420	data sets (e.g. data chunking, or lustre file system settings with <span style="font-family: Courier New,Courier,monospace;">lfs setstripe</span>). <span style="font-weight: bold;">Please report bugs and performance problems immediately!</span><br>
	421	<br>
	422	<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
	423	<br>
	424	Modules to be loaded for compilation (mbuild) or job execution (mrun) can/should now be given in the configuration file (<span style="font-family: Courier New,Courier,monospace;">.mrun.config</span>) using variable <span style="font-family: Courier New,Courier,monospace;">modules</span>. Example:<br>
	425	<br>
	426	<span style="font-family: Courier New,Courier,monospace;">   %modules     ifort/11.0.069:netcdf       lcsgih parallel</span><br>
	427	<br>
	428	This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
	429	<br>
	430	<span style="font-weight: bold;">WARNING:</span><br>
[497]	431	<span style="font-weight: bold;">All fixed settings of modules in the scripts mbuild, mrun, and subjob have been removed! Please set the <span style="font-family: Courier New,Courier,monospace;">modules</span> variable appropriately and remove the mpilib variable in your configuration file.<br>
	432	<br>
	433	</span>Compilation time can be reduced be using parallel make. The
	434	number of allowed simultaneous compiler calls (threads) is set in the
	435	configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
	436	<br>
	437	<span style="font-family: Courier New,Courier,monospace;">   %mopts  -j:4   lcsgih parallel</span><br>
	438	<br>
	439	allows a maximum of 4 routines to be compiled simultaneously (provided
	440	that the makefile does not show any dependencies between these
	441	routines).<span style="font-weight: bold;"><br>
	442	</span>
[494]	443	</td>
	444	<td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
	445	<br>
	446	combine_plot_fields<br>
	447	<br>
	448	mbuild, mrun, subjob<br>
	449	</td>
	450	</tr>
	451	<tr>
[486]	452	<td style="vertical-align: top;"><br>
	453	</td>
	454	<td style="vertical-align: top;"><br>
	455	</td>
[494]	456	<td style="vertical-align: top;"><br>
	457	</td>
	458	<td style="vertical-align: top;"><br>
	459	</td>
	460	<td style="vertical-align: top;">C<br>
	461	</td>
	462	<td style="vertical-align: top;">d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit</span> and <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span> have been removed. Use the new d3par-variable <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span> = <span style="font-style: italic;">2</span>
	463	for choosing the NetCDF 64bit-offset format (this is the default from
	464	now on). The offset-format can not be set independently for the
	465	3d-output-data any more.<br>
	466	<br>
	467	d3par-parameters <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf_format_mask_av</span>, and variables <span style="font-family: Courier New,Courier,monospace;">nc_format_mask</span>, <span style="font-family: Courier New,Courier,monospace;">format_parallel_io</span> removed. They are replaced by the new parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_data_format</span>. This change concerns the masked data output, which is still not documented.<br>
	468	</td>
	469	<td style="vertical-align: top;">check_open, close_file,<br>
	470	data_output_mask, header, init_masks, modules, parin<br>
	471	<br>
	472	</td>
	473	</tr>
	474	<tr>
	475	<td style="vertical-align: top;"><br>
	476	</td>
	477	<td style="vertical-align: top;"><br>
	478	</td>
	479	<td style="vertical-align: top;"><br>
	480	</td>
	481	<td style="vertical-align: top;"><br>
	482	</td>
	483	<td style="vertical-align: top;">B<br>
	484	</td>
	485	<td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
	486	<br>
	487	Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
	488	</td>
	489	<td style="vertical-align: top;">user_statistics<br>
	490	<br>
	491	trunk/UTIL/Makefile<br>
	492	</td>
	493	</tr>
	494	<tr>
	495	<td style="vertical-align: top;">05/02/10<br>
	496	</td>
	497	<td style="vertical-align: top;">SR<br>
	498	</td>
	499	<td style="vertical-align: top;">485<br>
	500	</td>
	501	<td style="vertical-align: top;">3.7a<br>
	502	</td>
	503	<td style="vertical-align: top;">B<br>
	504	</td>
[486]	505	<td style="vertical-align: top;"><span style="font-family: Courier New,Courier,monospace;">ngp_3d</span>, <span style="font-family: Courier New,Courier,monospace;">ngp_3d_inner</span>
	506	changed to 64 bit. Otherwise, on large grids > 210*9 grid points
	507	some global statistics (e.g. total kinetic energy) have wrong values.<br>
	508	</td>
	509	<td style="vertical-align: top;">init_3d_model, modules<br>
	510	</td>
	511	</tr>
	512	<tr>
	513	<td style="vertical-align: top;">05/02/10<br>
	514	</td>
	515	<td style="vertical-align: top;">SR<br>
	516	</td>
	517	<td style="vertical-align: top;">484<br>
	518	</td>
[494]	519	<td style="vertical-align: top;">3.7a<br>
[486]	520	</td>
	521	<td style="vertical-align: top;">B<br>
	522	</td>
	523	<td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
	524	</td>
	525	<td style="vertical-align: top;">many<br>
	526	</td>
	527	</tr>
	528	<tr>
[482]	529	<td style="vertical-align: top; width: 27px;">05/02/10<br>
[481]	530	</td>
[482]	531	<td style="vertical-align: top; width: 38px;">SR<br>
[481]	532	</td>
[482]	533	<td style="vertical-align: top; width: 42px;">483<br>
[481]	534	</td>
[482]	535	<td style="vertical-align: top; width: 40px;">3.7a<br>
[481]	536	</td>
[482]	537	<td style="vertical-align: top; width: 27px;">N<br>
[481]	538	</td>
[482]	539	<td style="vertical-align: top; width: 497px;"><span style="font-family: Courier New,Courier,monospace;">compare_palm_logs </span>is additionally compiled with <span style="font-weight: bold;">mbuild</span> <span style="font-family: Courier New,Courier,monospace;">-u</span> . (<span style="font-family: Courier New,Courier,monospace;">Makefile</span> in <span style="font-family: Courier New,Courier,monospace;">trunk/UTIL</span>)<br>
	540	<br>
	541	make options (<span style="font-family: Courier New,Courier,monospace;">mopts</span>) to be set by configuration file implemented. (<span style="font-weight: bold;">mrun</span>, <span style="font-weight: bold;">mbuild</span>)<br>
	542	<br>
	543	<span style="font-family: Courier New,Courier,monospace;">humidity</span> = <span style="font-style: italic;">.T.</span> can be used for runs with topography. <span style="font-family: Courier New,Courier,monospace;">wall_humidityflux</span> and<br><span style="font-family: Courier New,Courier,monospace;">
	544	wall_scalarflux</span> are the corresponding new inipar parameters.<br>
	545	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>)<br>
	546	<br>
	547	Large scale vertical motion (subsidence/ascent) can be added as
	548	additional source to the prognostic equation for potential temperature.
	549	See new parameters <span style="font-family: Courier New,Courier,monospace;">large_scale_subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient</span>, and <span style="font-family: Courier New,Courier,monospace;">ws_vertical_gradient_level</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">Makefile</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">subsidence</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
[486]	550	<br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
[482]	551	<br>
	552	A simple method for installing and running palm (with limited features) has been added. (<span style="font-family: Courier New,Courier,monospace;">Makefile</span>, new scripts <span style="font-weight: bold;">palm_simple_install</span>, <span style="font-weight: bold;">palm_simple_run</span>)<br>
	553	<br>
	554	Masked data output has been implemented but it is not documented in the
	555	user manual so far. This feature can already use NetCDF4 file format.
	556	(check_open, check_parameters, close_file, modules, netcdf, parin,
	557	time_integration, user_parin, new: data_output_mask, init_masks,
	558	user_data_output_mask)<br>
[481]	559	</td>
[482]	560	<td style="vertical-align: top; width: 189px;">check_open, check
	561	parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
	562	netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
	563	<br><span style="font-weight: bold;">
	564	new:</span> data_output_mask,  init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
	565	<br>
[481]	566	</td>
	567	</tr>
	568	<tr>
	569	<td style="vertical-align: top; width: 27px;"><br>
	570	</td>
	571	<td style="vertical-align: top; width: 38px;"><br>
	572	</td>
	573	<td style="vertical-align: top; width: 42px;"><br>
	574	</td>
	575	<td style="vertical-align: top; width: 40px;"><br>
	576	</td>
[482]	577	<td style="vertical-align: top; width: 27px;">C<br>
[481]	578	</td>
[482]	579	<td style="vertical-align: top; width: 497px;">2d-decomposition is default for Cray-XT machines. (<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>)<br>
	580	<br><span style="font-family: Courier New,Courier,monospace;">
	581	var_ts</span> is replaced by <span style="font-family: Courier New,Courier,monospace;">dots_max</span>. (<span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	582	<br>
	583	Every cloud droplet has now an own weighting factor and can be deleted
	584	due to collisions. Condensation and collision of cloud droplets are
	585	adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	586	<br>
	587	Collision efficiency for large cloud droplets has changed according to table of Rogers and Yau. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<br>
[481]	588	</td>
[482]	589	<td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
[481]	590	</td>
	591	</tr>
	592	<tr>
	593	<td style="vertical-align: top; width: 27px;"><br>
	594	</td>
	595	<td style="vertical-align: top; width: 38px;"><br>
	596	</td>
	597	<td style="vertical-align: top; width: 42px;"><br>
	598	</td>
	599	<td style="vertical-align: top; width: 40px;"><br>
	600	</td>
[482]	601	<td style="vertical-align: top; width: 27px;">B<br>
[481]	602	</td>
[482]	603	<td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
	604	<br>
	605	Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
	606	<br>
	607	Dimension of array <span style="font-family: Courier New,Courier,monospace;">stat</span> in cascade change to prevent type problems with mpi2 libraries. (<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>)<br>
	608	<br>
	609	Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
	610	<br>
	611	Bugfix: exchange of ghost points for <span style="font-family: Courier New,Courier,monospace;">prho</span> included. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
	612	<br>
	613	Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
	614	<br>
	615	Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
	616	<br>
	617	Bugfix: initial data assignments to some dvrp arrays changed due to error messages from gfortran compiler. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	618	<br>
	619	Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	620	<br>
	621	Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	622	<br>
	623	Bugfix in calculation of collision efficiency. (<span style="font-family: Courier New,Courier,monospace;">collision_efficiency</span>)<span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><br>
[481]	624	</td>
[482]	625	<td style="vertical-align: top; width: 189px;">advec_particles,
	626	calc_precipitation, collision_efficiency, disturb_field, header,
	627	modules, poisfft_hybrid, subjob, sum_up_3d_data,
	628	time_integration<br>
	629	<br>
[481]	630	</td>
	631	</tr>
	632	<tr>
	633	<td style="vertical-align: top; width: 27px;">23/09/09<br>
	634	</td>
	635	<td style="vertical-align: top; width: 38px;">SR<br>
	636	</td>
	637	<td style="vertical-align: top; width: 42px;">392<br>
	638	</td>
	639	<td style="vertical-align: top; width: 40px;">3.7<br>
	640	</td>
	641	<td style="vertical-align: top; width: 27px;">N<br>
	642	</td>
	643	<td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
	644	important changes:</span>
[392]	645	atmosphere-ocean coupling has been improved and steering of
	646	dvr-software is more user-friendly now. Beside that, the release
	647	contains a lot of optimizations, changes, and bugfixes which have
	648	accumulated over the last months.<br>
[481]	649
[392]	650	<br>
[481]	651
[392]	652	The atmosphere-ocean coupling allows to use independent precursor runs
	653	in order to account for different spin-up times. The time when coupling
[481]	654	has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
	655	The precursor ocean run has to be started using new <span style="font-weight: bold;">mrun</span> option "<span style="font-family: Courier New,Courier,monospace;">-y</span>" in
	656	order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
	657	output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	658	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	659	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	660	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	661	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	662	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	663	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	664	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	665	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	666	<span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
	667	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	668	<span style="font-family: Courier New,Courier,monospace;">mrun</span>,
	669	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	670	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	671	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	672	<span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
	673	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
[392]	674
	675	<br>
[481]	676
[392]	677	Clipping of dvrp output implemented. Default colourtable for particles
	678	implemented, particle attributes (color, dvrp_size) can be set with new
[481]	679	parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
	680	<span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
	681	<span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
	682	<span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
	683	Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
	684	and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
	685	(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	686	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	687	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	688	<span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,
	689	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
[392]	690
	691	<br>
[481]	692
[392]	693	Polygon reduction for topography and ground plate isosurface. Reduction
	694	level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
	695
	696	<br>
	697
[481]	698	Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
	699	/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>
	700	in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
	701
	702	<span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
	703	for speed optimization. This gives a significant speedup of more than
	704	10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	705	<span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
	706	<span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
	707	<span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
	708	<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	709
[392]	710	<br>
[481]	711
[392]	712	Scripts have been adapted for machine lck (Yonsei Univ.). (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)<br>
[481]	713
[392]	714	<br>
[481]	715
	716	Additional timestep criterion in case of simulations with plant canopy.
	717	(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
	718
[392]	719	<br>
[481]	720
	721	Check for illegal entries in <span style="font-family: Courier New,Courier,monospace;">section_xy</span>\|<span style="font-family: Courier New,Courier,monospace;">xz</span>\|<span style="font-family: Courier New,Courier,monospace;">yz</span> that
	722	exceed <span style="font-family: Courier New,Courier,monospace;">nz+1</span>\|<span style="font-family: Courier New,Courier,monospace;">ny+1</span>\|<span style="font-family: Courier New,Courier,monospace;">nx+1</span>. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
	723
[392]	724	<br>
[481]	725
	726	External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	727	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	728	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	729	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	730	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	731	<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
	732	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	733	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	734
[392]	735	<br>
[481]	736
	737	New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
	738	(<span style="font-family: Courier New,Courier,monospace;">header</span>,
	739	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	740	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	741	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	742	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	743	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	744	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	745	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	746	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	747
[392]	748	<br>
[481]	749
	750	Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
	751	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	752	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	753	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	754	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	755	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	756	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	757	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	758
[392]	759	<br>
[481]	760
	761	Option for user defined 2D data output in xy cross sections at z=<span style="font-family: Courier New,Courier,monospace;">nzb</span>+1. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	762	<span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
	763
[392]	764	<br>
[481]	765
	766	xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
	767	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	768	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	769	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	770	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	771	<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
	772	<span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
	773	<td style="vertical-align: top; width: 189px;">average_3d_data,
[392]	774	check_for_restart, check_parameters, data_output_2d, data_output_3d,
	775	data_output_dvrp, data_output_profiles, data_output_ptseries,
	776	data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
	777	diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
	778	header, mbuild, modules, mrun, package_parin, parin,
	779	prognostic_equations, read_3d_binary, read_var_list, subjob,
	780	sum_up_3d_data, surface_coupler, timestep, time_integration,
	781	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
	782	user_header, user_init_grid, write_3d_binary, write_var_list<br>
[481]	783
[392]	784	<br>
[481]	785
	786	<span style="font-weight: bold;">new:</span>
	787	set_particle_attributes, set_slicer_attributes_dvrp</td>
[392]	788	</tr>
	789	<tr>
[481]	790	<td style="vertical-align: top; width: 27px;"><br>
[392]	791	</td>
[481]	792	<td style="vertical-align: top; width: 38px;"><br>
[392]	793	</td>
[481]	794	<td style="vertical-align: top; width: 42px;"><br>
[392]	795	</td>
[481]	796	<td style="vertical-align: top; width: 40px;"><br>
[392]	797	</td>
[481]	798	<td style="vertical-align: top; width: 27px;">C<br>
	799	</td>
	800	<td style="vertical-align: top; width: 497px;">Output of messages replaced by
	801	message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	802	<span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
	803	<span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
	804	<span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
	805	<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	806	<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	807	<span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
	808	<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
	809	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	810	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	811	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	812	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	813	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	814	<span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
	815	<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
	816	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	817	<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
	818	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	819	<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	820	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	821	<span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
	822	<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
	823	<span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
	824	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	825	<span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
	826	<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
	827	<span style="font-family: Courier New,Courier,monospace;">poismg</span>,
	828	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	829	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	830	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	831	<span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
	832	<span style="font-family: Courier New,Courier,monospace;">timestep</span>,
	833	<span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
	834	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
	835	<span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
	836	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	837	<span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
	838	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	839	<span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
	840	<span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
[392]	841
	842	<br>
	843
[481]	844	Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	845	<span style="font-family: Courier New,Courier,monospace;">close_file</span>,
	846	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	847	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	848	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	849	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	850	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	851	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	852	<span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	853
[392]	854	<br>
	855
[481]	856	__lcmuk changed to __lc to avoid problems with Intel compiler on
	857	sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
	858
[392]	859	<br>
[481]	860
	861	For extended NetCDF files, the updated title attribute includes an
	862	update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	863
[392]	864	<br>
[481]	865
[392]	866	In case of restart runs without extension, initial profiles are not
	867	written to NetCDF-file anymore. So far, time axis always started at
[481]	868	t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	869	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	870	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	871	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	872
[392]	873	<br>
[481]	874
	875	<span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
	876	'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
	877	can now <br>
	878
	879	be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
	880	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	881	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	882	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	883
[392]	884	<br>
[481]	885
[392]	886	2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
[481]	887
[392]	888	<br>
[481]	889
[392]	890	A link to the webspage appendix_a.html is printed for further
	891	information about possible reasons of the error that appeared. (message)<br>
[481]	892
[392]	893	<br>
[481]	894
[392]	895	Temperature gradient criterion for estimating the boundary layer height
	896	replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
[481]	897
[392]	898	<br>
[481]	899
	900	NetCDF unit attribute in timeseries output in case of statistic regions
	901	added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	902
[392]	903	<br>
[481]	904
	905	Maximum number of tails is calculated from maximum number of particles
	906	and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
	907	(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
	908
[392]	909	<br>
[481]	910
	911	Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
	912	is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	913	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	914	<span style="font-family: Courier New,Courier,monospace;">modules</span>)
[392]	915	<br>
[481]	916
[392]	917	<br>
[481]	918
	919	First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
	920	defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
	921
[392]	922	<br>
[481]	923
	924	Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
	925	moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
	926	to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
	927	(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
	928
[392]	929	<br>
[481]	930
	931	<span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
	932	moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
	933	to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
	934	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	935	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	936	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	937	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	938	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	939	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	940	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	941	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	942	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	943
[392]	944	<br>
[481]	945
	946	Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
	947	changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	948
	949	<br>
	950
	951	Adjustments for runs on lcxt4 (necessary due to a software update on
	952	CRAY) and for coupled runs on ibmy. (<span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">subjob</span>)</td>
	953	<td style="vertical-align: top; width: 189px;">advec_particles,
	954	advec_s_bc,
[392]	955	buoyancy, calc_spectra, check_for_restart, check_open,
	956	check_parameters, close_file, coriolis, cpu_log, data_output_2d,
	957	data_output_3d, data_output_dvrp, data_output_profiles,
	958	data_output_ptseries, data_output_spectra, data_output_tseries,
	959	eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
	960	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
	961	message, mrun, netcdf, package_parin, parin, plant_canopy_model,
	962	poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
[481]	963	surface_coupler, temperton_fft, timestep,
	964	user_actions,user_check_parameters, user_data_output_dvrp,
	965	user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
	966	user_parin, user_read_restart_data, user_spectra, write_var_list </td>
[392]	967	</tr>
	968	<tr>
[481]	969	<td style="vertical-align: top; width: 27px;"><br>
[392]	970	</td>
[481]	971	<td style="vertical-align: top; width: 38px;"><br>
[392]	972	</td>
[481]	973	<td style="vertical-align: top; width: 42px;"><br>
[392]	974	</td>
[481]	975	<td style="vertical-align: top; width: 40px;"><br>
[392]	976	</td>
[482]	977	<td style="vertical-align: top; width: 27px;">B<br>
[481]	978	</td>
	979	<td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
	980	pressure profile in case of ocean runs is now calculated in 5 iteration
	981	steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
	982
[392]	983	<br>
[481]	984
	985	Bugfix: wrong sign in buoyancy production of ocean part in case of not
	986	using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
	987	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	988
[392]	989	<br>
[481]	990
[392]	991	Bugfix: output of averaged 2d/3d quantities requires that an avaraging
	992	interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	993
[392]	994	<br>
[481]	995
	996	Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
	997	(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
	998
[392]	999	<br>
[481]	1000
	1001	Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
	1002	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	1003
[392]	1004	<br>
[481]	1005
[392]	1006	Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
[481]	1007	if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
	1008	is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
	1009	and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
[392]	1010	calls. This implies a possible performance loss; an alternative
	1011	strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	1012
[392]	1013	<br>
[481]	1014
[392]	1015	Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
[481]	1016
[392]	1017	<br>
[481]	1018
[392]	1019	Bugfix: zero initialization of arrays within buildings for '<span style="font-style: italic;">cyclic_fill</span>'. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
[481]	1020
[392]	1021	<br>
[481]	1022
	1023	Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
	1024	=> <span style="font-family: Courier New,Courier,monospace;">s_av</span>
	1025	for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	1026	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
	1027
[392]	1028	<br>
[481]	1029
	1030	Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
	1031	becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
	1032
[392]	1033	<br>
[481]	1034
[392]	1035	Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
[481]	1036
[392]	1037	<br>
[481]	1038
[392]	1039	Bugfix: error in check, if particles moved further than one subdomain
	1040	length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
[481]	1041
[392]	1042	<br>
[481]	1043
[392]	1044	Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
	1045	is only written to file if its third index is > 0, arrays for tails
	1046	are allocated with a minimum size of 10 tails if there is no tail
[481]	1047	initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	1048	<span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	1049
[392]	1050	<br>
[481]	1051
[392]	1052	Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	1053
[392]	1054	<br>
[481]	1055
	1056	Bugfix: Type of <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
	1057	changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
	1058	NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
	1059
[392]	1060	<br>
[481]	1061
	1062	Bugfix: output of particle time series only if particle advection is
	1063	switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
	1064
[392]	1065	<br>
[481]	1066
	1067	Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
	1068	= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
	1069	(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
	1070
[392]	1071	<br>
[481]	1072
	1073	Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
	1074	z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
	1075
[392]	1076	<br>
[481]	1077
[392]	1078	Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	1079
[392]	1080	<br>
[481]	1081
	1082	If the inversion height calculated by the prerun is zero,
	1083	inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	1084
[392]	1085	<br>
[481]	1086
[392]	1087	Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
[481]	1088
[392]	1089	<br>
[481]	1090
[392]	1091	Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
	1092	removed from the restart file, because otherwise, no change from a
[481]	1093	fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	1094	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	1095
[392]	1096	<br>
[481]	1097
	1098	Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
	1099	in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
	1100	<td style="vertical-align: top; width: 189px;">advec_particles,
[392]	1101	check_parameters, cpu_log, data_output_2d, data_output_3d, header,
	1102	init_3d_model, init_particles, init_ocean, modules, netcdf,
	1103	prandtl_fluxes, production_e, read_var_list, time_integration,
	1104	user_last_actions, write_var_list<br>
[481]	1105
	1106	</td>
	1107	</tr>
	1108	<tr>
	1109	<td style="vertical-align: top; width: 27px;">02/02/09<br>
	1110	</td>
	1111	<td style="vertical-align: top; width: 38px;">SR<br>
	1112	</td>
	1113	<td style="vertical-align: top; width: 42px;">228<br>
	1114	</td>
	1115	<td style="vertical-align: top; width: 40px;">3.6<br>
	1116	</td>
	1117	<td style="vertical-align: top; width: 27px;">N<br>
	1118	</td>
	1119	<td style="vertical-align: top; width: 497px;">This
	1120	release contains further additions, changes, and bugfixes for the
	1121	SGI-ICE system, as well as important changes like the splitting of the
	1122	user-interface into single files, a complete revision of the
	1123	pre-compiling mechanism allowing to use different make-depositories
	1124	simultaneously, and a revision of the reading-mechanism from restart
	1125	files, which has no more restrictions in case that the previous and
	1126	current run have different domain/subdomain sizes. A new handling of
	1127	all kind of output messages is introduced with this release and will be
	1128	applied to all existing messages within the next releases.<br>
	1129
[392]	1130	<br>
[481]	1131
	1132	<span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
	1133
	1134	<br>
	1135
	1136	Restart runs on SGI-ICE are working. (mrun)<br>
	1137
	1138	2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
	1139
	1140	<br>
	1141
	1142	Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
	1143	case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	1144	"<span style="font-style: italic;">-K parallel</span>" for coupling.
	1145	Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
	1146	<span style="font-family: Courier New,Courier,monospace;">subjob</span>
	1147	for lcxt4.<br>
	1148
	1149	<br>
	1150
	1151	DVRP arguments changed to single precision, mode pathlines added.<br>
	1152
	1153	<br>
	1154
	1155	User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
	1156
	1157	<br>
	1158
	1159	User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
	1160	<td style="vertical-align: top; width: 189px;">check_for_restart,
	1161	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
	1162	modules, package_parin, palm, surface_coupler, timestep<br>
	1163
	1164	<br>
	1165
	1166	Makefile, mbuild, mrun, subjob<br>
	1167
	1168	<br>
	1169
	1170	<span style="font-weight: bold;">new:</span><br>
	1171
	1172	init_coupling, user_additional_routines, user_check_parameters</td>
	1173	</tr>
	1174	<tr>
	1175	<td style="vertical-align: top; width: 27px;"><br>
[392]	1176	</td>
[481]	1177	<td style="vertical-align: top; width: 38px;"><br>
	1178	</td>
	1179	<td style="vertical-align: top; width: 42px;"><br>
	1180	</td>
	1181	<td style="vertical-align: top; width: 40px;"><br>
	1182	</td>
	1183	<td style="vertical-align: top; width: 27px;">C<br>
	1184	</td>
	1185	<td style="vertical-align: top; width: 497px;">User interface has been
	1186	split into single files.<br>
	1187
	1188	<br>
	1189
	1190	Type of variables <span style="font-family: Courier New,Courier,monospace;">count</span> and <span style="font-family: Courier New,Courier,monospace;">count_rate</span>
	1191	changed to INTEGER(8) in order to avoid "out of range" problems, which
	1192	result in measured negative time intervals. (cpu_log, local_tremain,
	1193	local_tremain_ini)<br>
	1194
	1195	<br>
	1196
	1197	Reading mechanism from restart files
	1198	completely revised. The subdomain/total domain size is now allowed to
	1199	vary arbitrarily between the current and previous run. (read_var_list,
	1200	read_3d_binary, user_read_restart_data)<br>
	1201
	1202	<br>
	1203
	1204	Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
	1205	completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
	1206	One depository per block (given in the config-file) is created. Always
	1207	all files from the source directory are copied to the respective
	1208	depository. No additional file checks are done any more (mrun version
	1209	2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	1210	"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
	1211	(mbuild, mrun)<br>
	1212
	1213	<br>
	1214
	1215	Output messages (including required stop of execution) can now be
	1216	handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>.
	1217	All output messages will be replaced by this routine step by step
	1218	within the next revisions.<br>
	1219
	1220	<br>
	1221
	1222	Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
	1223	explicitly set for better reading, although this has been already done
	1224	in boundary_conds. (advec_s_bc)<br>
	1225
	1226	<br>
	1227
	1228	Origin of the xy-coordinate system shifted from the center of the first
	1229	grid cell (indices <span style="font-family: Courier New,Courier,monospace;">i=0</span>, <span style="font-family: Courier New,Courier,monospace;">j=0</span>) to the
	1230	south-left corner of this cell. (netcdf) Topography definition
	1231	according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
	1232	(init_grid, modules, user_header, user_init_grid, user_parin)</td>
	1233	<td style="vertical-align: top; width: 189px;">advec_s_bc,
	1234	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
	1235	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
	1236	user_read_restart_data<br>
	1237
	1238	<br>
	1239
	1240	Makefile, mbuild, mrun<br>
	1241
	1242	<br>
	1243
	1244	<span style="font-weight: bold;">removed:</span><br>
	1245
	1246	user_interface<br>
	1247
	1248	<br>
	1249
	1250	<span style="font-weight: bold;">new:</span><br>
	1251
	1252	message,
	1253	user_3d_data_averaging, user_actions, user_advec_particles,
	1254	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
	1255	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
	1256	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
	1257	user_init_grid, user_init_particles, user_init_plant_canopy,
	1258	user_last_actions, user_parin, user_parin, user_particle_attributes,
	1259	user_read_restart_data, user_spectra, user_statistics</td>
[392]	1260	</tr>
[481]	1261	<tr>
	1262	<td style="vertical-align: top; width: 27px;"><br>
	1263	</td>
	1264	<td style="vertical-align: top; width: 38px;"><br>
	1265	</td>
	1266	<td style="vertical-align: top; width: 42px;"><br>
	1267	</td>
	1268	<td style="vertical-align: top; width: 40px;"><br>
	1269	</td>
[482]	1270	<td style="vertical-align: top; width: 27px;">B<br>
[481]	1271	</td>
	1272	<td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
	1273	reallocated in case that multigrid is used. (calc_spectra)<br>
[392]	1274
[481]	1275	<br>
	1276
	1277	Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
	1278	inflow_turbulence, timestep)<br>
	1279
	1280	<br>
	1281
	1282	Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
	1283	</span>adjusted to the required output size (1 gridpoint less,
	1284	along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
	1285	in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
	1286	compiler. (combine_plot_fields)<br>
	1287
	1288	<br>
	1289
	1290	Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
	1291	case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
	1292	(header)<br>
	1293
	1294	<br>
	1295
	1296	Inconsistency
	1297	removed: as the thermal stratification is not taken into account for
	1298	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
	1299	<span style="font-family: Courier New,Courier,monospace;">km</span>
	1300	must not be used for the evaluation of the velocity gradients <span style="font-family: Courier New,Courier,monospace;">dudy</span>, <span style="font-family: Courier New,Courier,monospace;">dwdy</span>, <span style="font-family: Courier New,Courier,monospace;">dvdx</span> and <span style="font-family: Courier New,Courier,monospace;">dwdx</span>.
	1301	(production_e)<br>
	1302
	1303	<br>
	1304
	1305	Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
	1306	case of oceans runs. (sort_particles)<br>
	1307
	1308	<br>
	1309
	1310	Bugfix: no output of particle concentration and radius unless particles
	1311	have been started. (data_output_2d)<br>
	1312
	1313	<br>
	1314
	1315	Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x\|y</span>
	1316	from restart files ignored if total numbers of grid points do not
	1317	match. (read_3d_binary)<br>
	1318
	1319	<br>
	1320
	1321	Bugfix: abort in case that absolute temperature is below zero.
	1322	(init_cloud_physics)</td>
	1323	<td style="vertical-align: top; width: 189px;">advec_particles,
	1324	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
	1325	header, inflow_turbulence, init_cloud_physics, production_e,
	1326	read_3d_binary, timestep<br>
	1327
	1328	<br>
	1329
	1330	combine_plot_fields</td>
	1331	</tr>
	1332	</tbody>
	1333	</table>
	1334	<b><blink></blink></b><br>
[62]	1335	<br>
	1336	<h2><a name="Kapitel2.0"></a>2.0  How
[493]	1337	to change the source
	1338	code and how to document modifications<br>
	1339	</h2>Currently
[392]	1340	(Sep 23rd, 2009), only selected users are allowed to commit changes to
[493]	1341	the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
	1342	<br>
	1343	<ol>
	1344	<li>Change source code in your current working copy. Document changes in the respective file headers unter "<span style="font-family: Courier New,Courier,monospace;">Current revisions:</span>".
	1345	Additionally, document all changes in a local file (e.g.
	1346	~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
	1347	have been changed. Classify changes in three cases, new (N), changed
	1348	(C), and bugfix (B). <span style="font-weight: bold;">Try to be as short and as precise as possible in describing the changes!</span><br>
	1349	<br>
	1350	</li>
	1351	<li>Test the changed version, unless it works sufficiently.<br>
	1352	<br>
	1353	</li>
	1354
	1355	<li>Commit the changes to the repository<br>
	1356	<br>
	1357	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "message string" trunk<br>
	1358	</span><br>
	1359	where "<span style="font-family: Courier New,Courier,monospace;">message string</span>" is a short, <span style="font-weight: bold;">meaningful</span> summary of the changes.<br>
	1360	<br>
	1361	Alternatively, in case that you have made quite a lot of changes, you
	1362	can also give the contents of your file CURRENT_MODIFICATIONS as the
	1363	log message:<br>
	1364	<br>
	1365	<span style="font-family: Courier New,Courier,monospace;">   svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
	1366	<br>
	1367	</li>
	1368
	1369	<li>Enter the changes into the technical documentation (under <span style="font-family: Courier New,Courier,monospace;">.../trunk/DOC/tec/technical_documentation.html</span>).<br>
	1370	<br>
	1371	</li>
	1372	<li>Move the change comments in the file headers from "Current
	1373	revisions:" to "Former revisions:". Set the current svn id in front of
	1374	that.<br>
	1375	<br>
	1376	<span style="font-weight: bold;">Example:</span><br>
	1377	<br>
	1378	<span style="font-weight: bold;">before move:</span><br>
	1379	<br>
	1380	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1381	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1382	<span style="font-family: Courier New,Courier,monospace;">! <span style="font-weight: bold;">new dummy argument abcd</span></span><span style="font-family: Courier New,Courier,monospace;"></span><br style="font-family: Courier New,Courier,monospace;">
	1383	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1384	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1385	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
[544]	1386	<span style="font-family: Courier New,Courier,monospace;">! ï¿œId: init_3d_model.f90 <span style="color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span> ï¿œ</span><br style="font-family: Courier New,Courier,monospace;">
[493]	1387	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1388	<span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;"></span><span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
	1389	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
	1390	<br>
	1391	<span style="font-weight: bold;">after move:</span><br>
	1392	<br>
	1393	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1394
	1395	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1396
	1397	<span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
	1398
	1399	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1400
	1401	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1402
	1403	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1404
[544]	1405	<span style="font-family: Courier New,Courier,monospace;">! ï¿œId: </span><span style="font-family: Courier New,Courier,monospace;">init_3d_model.f90 425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"> ï¿œ<br>
[493]	1406	!</span><br style="font-family: Courier New,Courier,monospace;">
[516]	1407	<span style="font-family: Courier New,Courier,monospace;">! </span><span style="font-family: Courier New,Courier,monospace; color: rgb(51, 102, 255); font-weight: bold;">425 2010-02-06 13:37:48Z raasch</span><span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold; color: rgb(51, 51, 255);"></span><br>
[493]	1408	! </span><span style="font-family: Courier New,Courier,monospace; font-weight: bold;">new dummy argument abcd</span><br style="font-family: Courier New,Courier,monospace;">
	1409
	1410	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1411
[516]	1412	<span style="font-family: Courier New,Courier,monospace;">! 407 2009-12-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
[493]	1413
	1414	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
[516]	1415	<br>
[544]	1416	<span style="font-family: Times New Roman,Times,serif;">Note that the "<span style="font-family: Courier New,Courier,monospace;">ï¿œ</span>"
[516]	1417	in this example should read "$", but "$" cannot be used here, because
	1418	otherwise svn would replace these entries after every change to this
	1419	technical documentation.</span><br>
[493]	1420	</span><br>
	1421	</li>
	1422	<li>Commit the changes in the technical documentation and the file headers:<br>
	1423	<br>
	1424	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "last commit documented" trunk</span><br>
	1425	<br>
	1426	<br>
	1427	</li>
	1428	</ol>
	1429
[392]	1430	<h2>
[62]	1431	<a name="Kapitel3.0"></a>3.0  Description
	1432	of selected parts of the
[5]	1433	model source code</h2>
[392]	1434	<b></b>
	1435	<p>This section gives links to existing descriptions about special
	1436	parts of the PALM code, e.g. special numerical methods that are used
	1437	(including mathematical background). Documents are stored in single
	1438	files with different formats. Some are in German (sorry for the
	1439	inconvenience).
[62]	1440	<br>
	1441	</p><ul> <li> <a name="UPS"></a>upstream-spline
[481]	1442	advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
	1443	, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
	1444	physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
	1445	)</li>
	1446	<li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
	1447	</li>
	1448	<li>Runge-Kutta
	1449	time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
	1450	, only in German)</li>
	1451
[62]	1452	</ul><br>
[5]	1453
[62]	1454	<br>
	1455	<br>
	1456	<br>
	1457	<br>
	1458	<br>
	1459	<br>
	1460	<br>
[139]	1461	</body></html>

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