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

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