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	2	<html><head>
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[392]	19	<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]	20	</font>a
	21	<b>pa</b>rallelized
	22	<b>L</b>ES <b>m</b>odel
[62]	23	<br><hr width="100%">
	24	<br><font size="+2">technical/numerical documentation</font>
	25	<br>
	26	<br>
	27	<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>  <br> </caption><tbody>
[482]	28	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
[481]	29	</span></td> </tr>
[62]	30	<tr nosave=""> <td nosave=""><b>Last
	31	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 513 2010-03-16 13:37:48Z heinze $</b></td> </tr>
	32	</tbody>
	33	</table><hr width="100%">
[5]	34	<p><font size="+2">Table of contents</font>
[62]	35	<br>
	36	<br>
	37	</p><ul> <a href="#Kapitel1.0">1.0</a>
	38	History of changes <p><a href="#Kapitel2.0">2.0</a>
[493]	39	How to change the source
	40	code and how to document modifications<br>
	41	</p> <p><a href="#Kapitel3.0">3.0</a>
[481]	42	Description of selected model numerics<br>
[5]	43	</p>
[392]	44	</ul><b></b><br>
	45
[62]	46	<h2><a name="Kapitel1.0"></a>1.0
	47	History of changes</h2>
[481]	48	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>
	49	<br>
[482]	50	Entries in the fifth column specify the type of the change:
[5]	51	change
	52	of existing code (C), new code (N) or bugfix (B). More detailed
	53	information
[481]	54	about the changes may sometimes be found in the header comment lines of the
[5]	55	respective
	56	routines.
[62]	57	<br>
	58	<br>
[481]	59	<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
	60	<tbody>
	61	<tr>
[482]	62	<td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
[392]	63	</td>
[481]	64	<td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
[392]	65	</td>
[481]	66	<td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
[392]	67	</td>
[481]	68	<td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
[392]	69	</td>
[481]	70	<td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
	71	</td>
	72	<td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
	73	</td>
	74	<td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
	75	</td>
	76	</tr>
[482]	77
	78
	79
	80
	81
	82
	83
	84
	85
	86
[481]	87	<tr>
[513]	88	<td style="vertical-align: top;">16/03/10<br>
[509]	89	</td>
[513]	90	<td style="vertical-align: top;">RH<br>
	91	</td>
	92	<td style="vertical-align: top;">513<br>
	93	</td>
	94	<td style="vertical-align: top;">3.7a<br>
	95	</td>
	96	<td style="vertical-align: top;">N<br>
	97	</td>
	98	<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>
	99	</td>
	100	<td style="vertical-align: top;">palmplot .ncl.config.default cross_sections.ncl profiles.ncl<br>
	101	</td>
	102	</tr>
	103	<tr>
	104	<td style="vertical-align: top;">12/03/10<br>
	105	</td>
[509]	106	<td style="vertical-align: top;">SR<br>
	107	</td>
	108	<td style="vertical-align: top;">509<br>
	109	</td>
	110	<td style="vertical-align: top;">3.7a<br>
	111	</td>
	112	<td style="vertical-align: top;">E<br>
	113	</td>
	114	<td style="vertical-align: top;">bugfix for rev 504: remode_md was given a wrong value<br>
	115	</td>
	116	<td style="vertical-align: top;">mbuild<br>
	117	</td>
	118	</tr>
	119	<tr>
[506]	120	<td style="vertical-align: top;">08/03/10<br>
	121	</td>
	122	<td style="vertical-align: top;">SR<br>
	123	</td>
	124	<td style="vertical-align: top;">506<br>
	125	</td>
	126	<td style="vertical-align: top;">3.7a<br>
	127	</td>
	128	<td style="vertical-align: top;">C<br>
	129	</td>
	130	<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>
	131	</td>
	132	<td style="vertical-align: top;">mrun<br>
	133	</td>
	134	</tr>
	135	<tr>
[504]	136	<td style="vertical-align: top;">03/03/10<br>
	137	</td>
	138	<td style="vertical-align: top;">SR<br>
	139	</td>
	140	<td style="vertical-align: top;">504<br>
	141	</td>
	142	<td style="vertical-align: top;">3.7a<br>
	143	</td>
	144	<td style="vertical-align: top;">C<br>
	145	</td>
	146	<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>
	147	<br>
	148	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>
	149	<br>
	150	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>
	151	<br>
	152	Default configuration files updated.<br>
	153	</td>
	154	<td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
	155	</td>
	156	</tr>
	157	<tr>
[496]	158	<td style="vertical-align: top;">02/03/10<br>
	159	</td>
	160	<td style="vertical-align: top;">SR<br>
	161	</td>
	162	<td style="vertical-align: top;">496<br>
	163	</td>
	164	<td style="vertical-align: top;">3.7a<br>
	165	</td>
	166	<td style="vertical-align: top;">C<br>
	167	</td>
	168	<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>
	169	</td>
	170	<td style="vertical-align: top;">palm<br>
	171	</td>
	172	</tr>
	173	<tr>
[494]	174	<td style="vertical-align: top;">01/03/10<br>
[486]	175	</td>
	176	<td style="vertical-align: top;">SR<br>
	177	</td>
[494]	178	<td style="vertical-align: top;">494<br>
[486]	179	</td>
[494]	180	<td style="vertical-align: top;">3.7a<br>
	181	</td>
	182	<td style="vertical-align: top;">N<br>
	183	</td>
	184	<td style="vertical-align: top;">Output in NetCDF4-format.<br>
	185	<br>
	186	NetCDF4 allows for parallel I/O. Also, variables are not limited in
	187	size any more (i.e. arrays can be larger than 2GB). The new
	188	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>
	189	only affects 2d- and 3d-output, i.e. there is no parallel output for
	190	profiles, time series, spectra, and particles. Parallel output of
	191	particle data may realized in the future.<br>
	192	<br>
	193	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>
	194	(merging data from single files - one per PE - into one file) is not
	195	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>
	196	<br>
	197	Using NetCDF4 format requires a NetCDF4/HDF library. Respective
	198	settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
	199	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>
	200	<br>
	201	<span style="font-weight: bold;">Attention:</span><br>
	202	So far, NetCDF parallel I/O has only been tested a little. Further
	203	performance optimizations may be required, especially in case of large
	204	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>
	205	<br>
	206	<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
	207	<br>
	208	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>
	209	<br>
	210	<span style="font-family: Courier New,Courier,monospace;">   %modules     ifort/11.0.069:netcdf       lcsgih parallel</span><br>
	211	<br>
	212	This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
	213	<br>
	214	<span style="font-weight: bold;">WARNING:</span><br>
[497]	215	<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>
	216	<br>
	217	</span>Compilation time can be reduced be using parallel make. The
	218	number of allowed simultaneous compiler calls (threads) is set in the
	219	configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
	220	<br>
	221	<span style="font-family: Courier New,Courier,monospace;">   %mopts  -j:4   lcsgih parallel</span><br>
	222	<br>
	223	allows a maximum of 4 routines to be compiled simultaneously (provided
	224	that the makefile does not show any dependencies between these
	225	routines).<span style="font-weight: bold;"><br>
	226	</span>
[494]	227	</td>
	228	<td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
	229	<br>
	230	combine_plot_fields<br>
	231	<br>
	232	mbuild, mrun, subjob<br>
	233	</td>
	234	</tr>
	235	<tr>
[486]	236	<td style="vertical-align: top;"><br>
	237	</td>
	238	<td style="vertical-align: top;"><br>
	239	</td>
[494]	240	<td style="vertical-align: top;"><br>
	241	</td>
	242	<td style="vertical-align: top;"><br>
	243	</td>
	244	<td style="vertical-align: top;">C<br>
	245	</td>
	246	<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>
	247	for choosing the NetCDF 64bit-offset format (this is the default from
	248	now on). The offset-format can not be set independently for the
	249	3d-output-data any more.<br>
	250	<br>
	251	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>
	252	</td>
	253	<td style="vertical-align: top;">check_open, close_file,<br>
	254	data_output_mask, header, init_masks, modules, parin<br>
	255	<br>
	256	</td>
	257	</tr>
	258	<tr>
	259	<td style="vertical-align: top;"><br>
	260	</td>
	261	<td style="vertical-align: top;"><br>
	262	</td>
	263	<td style="vertical-align: top;"><br>
	264	</td>
	265	<td style="vertical-align: top;"><br>
	266	</td>
	267	<td style="vertical-align: top;">B<br>
	268	</td>
	269	<td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
	270	<br>
	271	Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
	272	</td>
	273	<td style="vertical-align: top;">user_statistics<br>
	274	<br>
	275	trunk/UTIL/Makefile<br>
	276	</td>
	277	</tr>
	278	<tr>
	279	<td style="vertical-align: top;">05/02/10<br>
	280	</td>
	281	<td style="vertical-align: top;">SR<br>
	282	</td>
	283	<td style="vertical-align: top;">485<br>
	284	</td>
	285	<td style="vertical-align: top;">3.7a<br>
	286	</td>
	287	<td style="vertical-align: top;">B<br>
	288	</td>
[486]	289	<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>
	290	changed to 64 bit. Otherwise, on large grids > 210*9 grid points
	291	some global statistics (e.g. total kinetic energy) have wrong values.<br>
	292	</td>
	293	<td style="vertical-align: top;">init_3d_model, modules<br>
	294	</td>
	295	</tr>
	296	<tr>
	297	<td style="vertical-align: top;">05/02/10<br>
	298	</td>
	299	<td style="vertical-align: top;">SR<br>
	300	</td>
	301	<td style="vertical-align: top;">484<br>
	302	</td>
[494]	303	<td style="vertical-align: top;">3.7a<br>
[486]	304	</td>
	305	<td style="vertical-align: top;">B<br>
	306	</td>
	307	<td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
	308	</td>
	309	<td style="vertical-align: top;">many<br>
	310	</td>
	311	</tr>
	312	<tr>
[482]	313	<td style="vertical-align: top; width: 27px;">05/02/10<br>
[481]	314	</td>
[482]	315	<td style="vertical-align: top; width: 38px;">SR<br>
[481]	316	</td>
[482]	317	<td style="vertical-align: top; width: 42px;">483<br>
[481]	318	</td>
[482]	319	<td style="vertical-align: top; width: 40px;">3.7a<br>
[481]	320	</td>
[482]	321	<td style="vertical-align: top; width: 27px;">N<br>
[481]	322	</td>
[482]	323	<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>
	324	<br>
	325	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>
	326	<br>
	327	<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;">
	328	wall_scalarflux</span> are the corresponding new inipar parameters.<br>
	329	(<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>
	330	<br>
	331	Large scale vertical motion (subsidence/ascent) can be added as
	332	additional source to the prognostic equation for potential temperature.
	333	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]	334	<br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
[482]	335	<br>
	336	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>
	337	<br>
	338	Masked data output has been implemented but it is not documented in the
	339	user manual so far. This feature can already use NetCDF4 file format.
	340	(check_open, check_parameters, close_file, modules, netcdf, parin,
	341	time_integration, user_parin, new: data_output_mask, init_masks,
	342	user_data_output_mask)<br>
[481]	343	</td>
[482]	344	<td style="vertical-align: top; width: 189px;">check_open, check
	345	parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
	346	netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
	347	<br><span style="font-weight: bold;">
	348	new:</span> data_output_mask,  init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
	349	<br>
[481]	350	</td>
	351	</tr>
	352	<tr>
	353	<td style="vertical-align: top; width: 27px;"><br>
	354	</td>
	355	<td style="vertical-align: top; width: 38px;"><br>
	356	</td>
	357	<td style="vertical-align: top; width: 42px;"><br>
	358	</td>
	359	<td style="vertical-align: top; width: 40px;"><br>
	360	</td>
[482]	361	<td style="vertical-align: top; width: 27px;">C<br>
[481]	362	</td>
[482]	363	<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>
	364	<br><span style="font-family: Courier New,Courier,monospace;">
	365	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>
	366	<br>
	367	Every cloud droplet has now an own weighting factor and can be deleted
	368	due to collisions. Condensation and collision of cloud droplets are
	369	adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	370	<br>
	371	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]	372	</td>
[482]	373	<td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
[481]	374	</td>
	375	</tr>
	376	<tr>
	377	<td style="vertical-align: top; width: 27px;"><br>
	378	</td>
	379	<td style="vertical-align: top; width: 38px;"><br>
	380	</td>
	381	<td style="vertical-align: top; width: 42px;"><br>
	382	</td>
	383	<td style="vertical-align: top; width: 40px;"><br>
	384	</td>
[482]	385	<td style="vertical-align: top; width: 27px;">B<br>
[481]	386	</td>
[482]	387	<td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
	388	<br>
	389	Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
	390	<br>
	391	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>
	392	<br>
	393	Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
	394	<br>
	395	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>
	396	<br>
	397	Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
	398	<br>
	399	Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
	400	<br>
	401	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>
	402	<br>
	403	Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	404	<br>
	405	Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	406	<br>
	407	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]	408	</td>
[482]	409	<td style="vertical-align: top; width: 189px;">advec_particles,
	410	calc_precipitation, collision_efficiency, disturb_field, header,
	411	modules, poisfft_hybrid, subjob, sum_up_3d_data,
	412	time_integration<br>
	413	<br>
[481]	414	</td>
	415	</tr>
	416	<tr>
	417	<td style="vertical-align: top; width: 27px;">23/09/09<br>
	418	</td>
	419	<td style="vertical-align: top; width: 38px;">SR<br>
	420	</td>
	421	<td style="vertical-align: top; width: 42px;">392<br>
	422	</td>
	423	<td style="vertical-align: top; width: 40px;">3.7<br>
	424	</td>
	425	<td style="vertical-align: top; width: 27px;">N<br>
	426	</td>
	427	<td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
	428	important changes:</span>
[392]	429	atmosphere-ocean coupling has been improved and steering of
	430	dvr-software is more user-friendly now. Beside that, the release
	431	contains a lot of optimizations, changes, and bugfixes which have
	432	accumulated over the last months.<br>
[481]	433
[392]	434	<br>
[481]	435
[392]	436	The atmosphere-ocean coupling allows to use independent precursor runs
	437	in order to account for different spin-up times. The time when coupling
[481]	438	has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
	439	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
	440	order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
	441	output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	442	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	443	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	444	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	445	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	446	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	447	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	448	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	449	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	450	<span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
	451	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	452	<span style="font-family: Courier New,Courier,monospace;">mrun</span>,
	453	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	454	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	455	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	456	<span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
	457	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
[392]	458
	459	<br>
[481]	460
[392]	461	Clipping of dvrp output implemented. Default colourtable for particles
	462	implemented, particle attributes (color, dvrp_size) can be set with new
[481]	463	parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
	464	<span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
	465	<span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
	466	<span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
	467	Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
	468	and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
	469	(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	470	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	471	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	472	<span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,
	473	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
[392]	474
	475	<br>
[481]	476
[392]	477	Polygon reduction for topography and ground plate isosurface. Reduction
	478	level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
	479
	480	<br>
	481
[481]	482	Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
	483	/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>
	484	in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
	485
	486	<span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
	487	for speed optimization. This gives a significant speedup of more than
	488	10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	489	<span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
	490	<span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
	491	<span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
	492	<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	493
[392]	494	<br>
[481]	495
[392]	496	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]	497
[392]	498	<br>
[481]	499
	500	Additional timestep criterion in case of simulations with plant canopy.
	501	(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
	502
[392]	503	<br>
[481]	504
	505	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
	506	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>
	507
[392]	508	<br>
[481]	509
	510	External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	511	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	512	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	513	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	514	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	515	<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
	516	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	517	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	518
[392]	519	<br>
[481]	520
	521	New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
	522	(<span style="font-family: Courier New,Courier,monospace;">header</span>,
	523	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	524	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	525	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	526	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	527	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	528	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	529	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	530	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	531
[392]	532	<br>
[481]	533
	534	Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
	535	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	536	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	537	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	538	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	539	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	540	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	541	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	542
[392]	543	<br>
[481]	544
	545	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>,
	546	<span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
	547
[392]	548	<br>
[481]	549
	550	xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
	551	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	552	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	553	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	554	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	555	<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
	556	<span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
	557	<td style="vertical-align: top; width: 189px;">average_3d_data,
[392]	558	check_for_restart, check_parameters, data_output_2d, data_output_3d,
	559	data_output_dvrp, data_output_profiles, data_output_ptseries,
	560	data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
	561	diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
	562	header, mbuild, modules, mrun, package_parin, parin,
	563	prognostic_equations, read_3d_binary, read_var_list, subjob,
	564	sum_up_3d_data, surface_coupler, timestep, time_integration,
	565	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
	566	user_header, user_init_grid, write_3d_binary, write_var_list<br>
[481]	567
[392]	568	<br>
[481]	569
	570	<span style="font-weight: bold;">new:</span>
	571	set_particle_attributes, set_slicer_attributes_dvrp</td>
[392]	572	</tr>
	573	<tr>
[481]	574	<td style="vertical-align: top; width: 27px;"><br>
[392]	575	</td>
[481]	576	<td style="vertical-align: top; width: 38px;"><br>
[392]	577	</td>
[481]	578	<td style="vertical-align: top; width: 42px;"><br>
[392]	579	</td>
[481]	580	<td style="vertical-align: top; width: 40px;"><br>
[392]	581	</td>
[481]	582	<td style="vertical-align: top; width: 27px;">C<br>
	583	</td>
	584	<td style="vertical-align: top; width: 497px;">Output of messages replaced by
	585	message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	586	<span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
	587	<span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
	588	<span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
	589	<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	590	<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	591	<span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
	592	<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
	593	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	594	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	595	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	596	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	597	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	598	<span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
	599	<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
	600	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	601	<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
	602	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	603	<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	604	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	605	<span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
	606	<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
	607	<span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
	608	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	609	<span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
	610	<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
	611	<span style="font-family: Courier New,Courier,monospace;">poismg</span>,
	612	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	613	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	614	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	615	<span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
	616	<span style="font-family: Courier New,Courier,monospace;">timestep</span>,
	617	<span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
	618	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
	619	<span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
	620	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	621	<span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
	622	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	623	<span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
	624	<span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
[392]	625
	626	<br>
	627
[481]	628	Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	629	<span style="font-family: Courier New,Courier,monospace;">close_file</span>,
	630	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	631	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	632	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	633	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	634	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	635	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	636	<span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	637
[392]	638	<br>
	639
[481]	640	__lcmuk changed to __lc to avoid problems with Intel compiler on
	641	sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
	642
[392]	643	<br>
[481]	644
	645	For extended NetCDF files, the updated title attribute includes an
	646	update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	647
[392]	648	<br>
[481]	649
[392]	650	In case of restart runs without extension, initial profiles are not
	651	written to NetCDF-file anymore. So far, time axis always started at
[481]	652	t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	653	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	654	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	655	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	656
[392]	657	<br>
[481]	658
	659	<span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
	660	'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
	661	can now <br>
	662
	663	be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
	664	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	665	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	666	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	667
[392]	668	<br>
[481]	669
[392]	670	2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
[481]	671
[392]	672	<br>
[481]	673
[392]	674	A link to the webspage appendix_a.html is printed for further
	675	information about possible reasons of the error that appeared. (message)<br>
[481]	676
[392]	677	<br>
[481]	678
[392]	679	Temperature gradient criterion for estimating the boundary layer height
	680	replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
[481]	681
[392]	682	<br>
[481]	683
	684	NetCDF unit attribute in timeseries output in case of statistic regions
	685	added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	686
[392]	687	<br>
[481]	688
	689	Maximum number of tails is calculated from maximum number of particles
	690	and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
	691	(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
	692
[392]	693	<br>
[481]	694
	695	Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
	696	is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	697	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	698	<span style="font-family: Courier New,Courier,monospace;">modules</span>)
[392]	699	<br>
[481]	700
[392]	701	<br>
[481]	702
	703	First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
	704	defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
	705
[392]	706	<br>
[481]	707
	708	Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
	709	moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
	710	to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
	711	(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
	712
[392]	713	<br>
[481]	714
	715	<span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
	716	moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
	717	to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
	718	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	719	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	720	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	721	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	722	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	723	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	724	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	725	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	726	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	727
[392]	728	<br>
[481]	729
	730	Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
	731	changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	732
	733	<br>
	734
	735	Adjustments for runs on lcxt4 (necessary due to a software update on
	736	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>
	737	<td style="vertical-align: top; width: 189px;">advec_particles,
	738	advec_s_bc,
[392]	739	buoyancy, calc_spectra, check_for_restart, check_open,
	740	check_parameters, close_file, coriolis, cpu_log, data_output_2d,
	741	data_output_3d, data_output_dvrp, data_output_profiles,
	742	data_output_ptseries, data_output_spectra, data_output_tseries,
	743	eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
	744	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
	745	message, mrun, netcdf, package_parin, parin, plant_canopy_model,
	746	poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
[481]	747	surface_coupler, temperton_fft, timestep,
	748	user_actions,user_check_parameters, user_data_output_dvrp,
	749	user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
	750	user_parin, user_read_restart_data, user_spectra, write_var_list </td>
[392]	751	</tr>
	752	<tr>
[481]	753	<td style="vertical-align: top; width: 27px;"><br>
[392]	754	</td>
[481]	755	<td style="vertical-align: top; width: 38px;"><br>
[392]	756	</td>
[481]	757	<td style="vertical-align: top; width: 42px;"><br>
[392]	758	</td>
[481]	759	<td style="vertical-align: top; width: 40px;"><br>
[392]	760	</td>
[482]	761	<td style="vertical-align: top; width: 27px;">B<br>
[481]	762	</td>
	763	<td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
	764	pressure profile in case of ocean runs is now calculated in 5 iteration
	765	steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
	766
[392]	767	<br>
[481]	768
	769	Bugfix: wrong sign in buoyancy production of ocean part in case of not
	770	using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
	771	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	772
[392]	773	<br>
[481]	774
[392]	775	Bugfix: output of averaged 2d/3d quantities requires that an avaraging
	776	interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	777
[392]	778	<br>
[481]	779
	780	Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
	781	(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
	782
[392]	783	<br>
[481]	784
	785	Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
	786	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	787
[392]	788	<br>
[481]	789
[392]	790	Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
[481]	791	if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
	792	is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
	793	and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
[392]	794	calls. This implies a possible performance loss; an alternative
	795	strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	796
[392]	797	<br>
[481]	798
[392]	799	Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
[481]	800
[392]	801	<br>
[481]	802
[392]	803	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]	804
[392]	805	<br>
[481]	806
	807	Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
	808	=> <span style="font-family: Courier New,Courier,monospace;">s_av</span>
	809	for time-averaged scalars. (<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>)<br>
	811
[392]	812	<br>
[481]	813
	814	Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
	815	becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
	816
[392]	817	<br>
[481]	818
[392]	819	Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
[481]	820
[392]	821	<br>
[481]	822
[392]	823	Bugfix: error in check, if particles moved further than one subdomain
	824	length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
[481]	825
[392]	826	<br>
[481]	827
[392]	828	Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
	829	is only written to file if its third index is > 0, arrays for tails
	830	are allocated with a minimum size of 10 tails if there is no tail
[481]	831	initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	832	<span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	833
[392]	834	<br>
[481]	835
[392]	836	Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	837
[392]	838	<br>
[481]	839
	840	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>
	841	changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
	842	NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
	843
[392]	844	<br>
[481]	845
	846	Bugfix: output of particle time series only if particle advection is
	847	switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
	848
[392]	849	<br>
[481]	850
	851	Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
	852	= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
	853	(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
	854
[392]	855	<br>
[481]	856
	857	Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
	858	z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
	859
[392]	860	<br>
[481]	861
[392]	862	Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	863
[392]	864	<br>
[481]	865
	866	If the inversion height calculated by the prerun is zero,
	867	inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	868
[392]	869	<br>
[481]	870
[392]	871	Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
[481]	872
[392]	873	<br>
[481]	874
[392]	875	Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
	876	removed from the restart file, because otherwise, no change from a
[481]	877	fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	878	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	879
[392]	880	<br>
[481]	881
	882	Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
	883	in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
	884	<td style="vertical-align: top; width: 189px;">advec_particles,
[392]	885	check_parameters, cpu_log, data_output_2d, data_output_3d, header,
	886	init_3d_model, init_particles, init_ocean, modules, netcdf,
	887	prandtl_fluxes, production_e, read_var_list, time_integration,
	888	user_last_actions, write_var_list<br>
[481]	889
	890	</td>
	891	</tr>
	892	<tr>
	893	<td style="vertical-align: top; width: 27px;">02/02/09<br>
	894	</td>
	895	<td style="vertical-align: top; width: 38px;">SR<br>
	896	</td>
	897	<td style="vertical-align: top; width: 42px;">228<br>
	898	</td>
	899	<td style="vertical-align: top; width: 40px;">3.6<br>
	900	</td>
	901	<td style="vertical-align: top; width: 27px;">N<br>
	902	</td>
	903	<td style="vertical-align: top; width: 497px;">This
	904	release contains further additions, changes, and bugfixes for the
	905	SGI-ICE system, as well as important changes like the splitting of the
	906	user-interface into single files, a complete revision of the
	907	pre-compiling mechanism allowing to use different make-depositories
	908	simultaneously, and a revision of the reading-mechanism from restart
	909	files, which has no more restrictions in case that the previous and
	910	current run have different domain/subdomain sizes. A new handling of
	911	all kind of output messages is introduced with this release and will be
	912	applied to all existing messages within the next releases.<br>
	913
[392]	914	<br>
[481]	915
	916	<span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
	917
	918	<br>
	919
	920	Restart runs on SGI-ICE are working. (mrun)<br>
	921
	922	2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
	923
	924	<br>
	925
	926	Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
	927	case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	928	"<span style="font-style: italic;">-K parallel</span>" for coupling.
	929	Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
	930	<span style="font-family: Courier New,Courier,monospace;">subjob</span>
	931	for lcxt4.<br>
	932
	933	<br>
	934
	935	DVRP arguments changed to single precision, mode pathlines added.<br>
	936
	937	<br>
	938
	939	User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
	940
	941	<br>
	942
	943	User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
	944	<td style="vertical-align: top; width: 189px;">check_for_restart,
	945	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
	946	modules, package_parin, palm, surface_coupler, timestep<br>
	947
	948	<br>
	949
	950	Makefile, mbuild, mrun, subjob<br>
	951
	952	<br>
	953
	954	<span style="font-weight: bold;">new:</span><br>
	955
	956	init_coupling, user_additional_routines, user_check_parameters</td>
	957	</tr>
	958	<tr>
	959	<td style="vertical-align: top; width: 27px;"><br>
[392]	960	</td>
[481]	961	<td style="vertical-align: top; width: 38px;"><br>
	962	</td>
	963	<td style="vertical-align: top; width: 42px;"><br>
	964	</td>
	965	<td style="vertical-align: top; width: 40px;"><br>
	966	</td>
	967	<td style="vertical-align: top; width: 27px;">C<br>
	968	</td>
	969	<td style="vertical-align: top; width: 497px;">User interface has been
	970	split into single files.<br>
	971
	972	<br>
	973
	974	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>
	975	changed to INTEGER(8) in order to avoid "out of range" problems, which
	976	result in measured negative time intervals. (cpu_log, local_tremain,
	977	local_tremain_ini)<br>
	978
	979	<br>
	980
	981	Reading mechanism from restart files
	982	completely revised. The subdomain/total domain size is now allowed to
	983	vary arbitrarily between the current and previous run. (read_var_list,
	984	read_3d_binary, user_read_restart_data)<br>
	985
	986	<br>
	987
	988	Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
	989	completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
	990	One depository per block (given in the config-file) is created. Always
	991	all files from the source directory are copied to the respective
	992	depository. No additional file checks are done any more (mrun version
	993	2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	994	"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
	995	(mbuild, mrun)<br>
	996
	997	<br>
	998
	999	Output messages (including required stop of execution) can now be
	1000	handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>.
	1001	All output messages will be replaced by this routine step by step
	1002	within the next revisions.<br>
	1003
	1004	<br>
	1005
	1006	Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
	1007	explicitly set for better reading, although this has been already done
	1008	in boundary_conds. (advec_s_bc)<br>
	1009
	1010	<br>
	1011
	1012	Origin of the xy-coordinate system shifted from the center of the first
	1013	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
	1014	south-left corner of this cell. (netcdf) Topography definition
	1015	according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
	1016	(init_grid, modules, user_header, user_init_grid, user_parin)</td>
	1017	<td style="vertical-align: top; width: 189px;">advec_s_bc,
	1018	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
	1019	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
	1020	user_read_restart_data<br>
	1021
	1022	<br>
	1023
	1024	Makefile, mbuild, mrun<br>
	1025
	1026	<br>
	1027
	1028	<span style="font-weight: bold;">removed:</span><br>
	1029
	1030	user_interface<br>
	1031
	1032	<br>
	1033
	1034	<span style="font-weight: bold;">new:</span><br>
	1035
	1036	message,
	1037	user_3d_data_averaging, user_actions, user_advec_particles,
	1038	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
	1039	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
	1040	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
	1041	user_init_grid, user_init_particles, user_init_plant_canopy,
	1042	user_last_actions, user_parin, user_parin, user_particle_attributes,
	1043	user_read_restart_data, user_spectra, user_statistics</td>
[392]	1044	</tr>
[481]	1045	<tr>
	1046	<td style="vertical-align: top; width: 27px;"><br>
	1047	</td>
	1048	<td style="vertical-align: top; width: 38px;"><br>
	1049	</td>
	1050	<td style="vertical-align: top; width: 42px;"><br>
	1051	</td>
	1052	<td style="vertical-align: top; width: 40px;"><br>
	1053	</td>
[482]	1054	<td style="vertical-align: top; width: 27px;">B<br>
[481]	1055	</td>
	1056	<td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
	1057	reallocated in case that multigrid is used. (calc_spectra)<br>
[392]	1058
[481]	1059	<br>
	1060
	1061	Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
	1062	inflow_turbulence, timestep)<br>
	1063
	1064	<br>
	1065
	1066	Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
	1067	</span>adjusted to the required output size (1 gridpoint less,
	1068	along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
	1069	in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
	1070	compiler. (combine_plot_fields)<br>
	1071
	1072	<br>
	1073
	1074	Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
	1075	case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
	1076	(header)<br>
	1077
	1078	<br>
	1079
	1080	Inconsistency
	1081	removed: as the thermal stratification is not taken into account for
	1082	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
	1083	<span style="font-family: Courier New,Courier,monospace;">km</span>
	1084	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>.
	1085	(production_e)<br>
	1086
	1087	<br>
	1088
	1089	Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
	1090	case of oceans runs. (sort_particles)<br>
	1091
	1092	<br>
	1093
	1094	Bugfix: no output of particle concentration and radius unless particles
	1095	have been started. (data_output_2d)<br>
	1096
	1097	<br>
	1098
	1099	Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x\|y</span>
	1100	from restart files ignored if total numbers of grid points do not
	1101	match. (read_3d_binary)<br>
	1102
	1103	<br>
	1104
	1105	Bugfix: abort in case that absolute temperature is below zero.
	1106	(init_cloud_physics)</td>
	1107	<td style="vertical-align: top; width: 189px;">advec_particles,
	1108	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
	1109	header, inflow_turbulence, init_cloud_physics, production_e,
	1110	read_3d_binary, timestep<br>
	1111
	1112	<br>
	1113
	1114	combine_plot_fields</td>
	1115	</tr>
	1116	</tbody>
	1117	</table>
	1118	<b><blink></blink></b><br>
[62]	1119	<br>
	1120	<h2><a name="Kapitel2.0"></a>2.0  How
[493]	1121	to change the source
	1122	code and how to document modifications<br>
	1123	</h2>Currently
[392]	1124	(Sep 23rd, 2009), only selected users are allowed to commit changes to
[493]	1125	the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
	1126	<br>
	1127	<ol>
	1128	<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>".
	1129	Additionally, document all changes in a local file (e.g.
	1130	~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
	1131	have been changed. Classify changes in three cases, new (N), changed
	1132	(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>
	1133	<br>
	1134	</li>
	1135	<li>Test the changed version, unless it works sufficiently.<br>
	1136	<br>
	1137	</li>
	1138
	1139	<li>Commit the changes to the repository<br>
	1140	<br>
	1141	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "message string" trunk<br>
	1142	</span><br>
	1143	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>
	1144	<br>
	1145	Alternatively, in case that you have made quite a lot of changes, you
	1146	can also give the contents of your file CURRENT_MODIFICATIONS as the
	1147	log message:<br>
	1148	<br>
	1149	<span style="font-family: Courier New,Courier,monospace;">   svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
	1150	<br>
	1151	</li>
	1152
	1153	<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>
	1154	<br>
	1155	</li>
	1156	<li>Move the change comments in the file headers from "Current
	1157	revisions:" to "Former revisions:". Set the current svn id in front of
	1158	that.<br>
	1159	<br>
	1160	<span style="font-weight: bold;">Example:</span><br>
	1161	<br>
	1162	<span style="font-weight: bold;">before move:</span><br>
	1163	<br>
	1164	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1165	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1166	<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;">
	1167	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1168	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1169	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1170	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 513 2010-03-16 13:37:48Z heinze $</span><br style="font-family: Courier New,Courier,monospace;">
	1171	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1172	<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;">
	1173	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
	1174	<br>
	1175	<span style="font-weight: bold;">after move:</span><br>
	1176	<br>
	1177	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1178
	1179	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1180
	1181	<span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
	1182
	1183	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1184
	1185	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1186
	1187	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1188
	1189	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 513 2010-03-16 13:37:48Z heinze $<br>
	1190	!</span><br style="font-family: Courier New,Courier,monospace;">
	1191	<span style="font-family: Courier New,Courier,monospace;">! </span><span style="font-family: Courier New,Courier,monospace;"><span style="font-weight: bold; color: rgb(51, 51, 255);">377 2008-08-30 11:03:41Z raasch</span><br>
	1192	! </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;">
	1193
	1194	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1195
	1196	<span style="font-family: Courier New,Courier,monospace;">! 359 2008-06-01 15:01:15Z maronga</span><br style="font-family: Courier New,Courier,monospace;">
	1197
	1198	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
	1199	</span><br>
	1200	</li>
	1201	<li>Commit the changes in the technical documentation and the file headers:<br>
	1202	<br>
	1203	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "last commit documented" trunk</span><br>
	1204	<br>
	1205	<br>
	1206	</li>
	1207	</ol>
	1208
[392]	1209	<h2>
[62]	1210	<a name="Kapitel3.0"></a>3.0  Description
	1211	of selected parts of the
[5]	1212	model source code</h2>
[392]	1213	<b></b>
	1214	<p>This section gives links to existing descriptions about special
	1215	parts of the PALM code, e.g. special numerical methods that are used
	1216	(including mathematical background). Documents are stored in single
	1217	files with different formats. Some are in German (sorry for the
	1218	inconvenience).
[62]	1219	<br>
	1220	</p><ul> <li> <a name="UPS"></a>upstream-spline
[481]	1221	advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
	1222	, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
	1223	physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
	1224	)</li>
	1225	<li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
	1226	</li>
	1227	<li>Runge-Kutta
	1228	time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
	1229	, only in German)</li>
	1230
[62]	1231	</ul><br>
[5]	1232
[62]	1233	<br>
	1234	<br>
	1235	<br>
	1236	<br>
	1237	<br>
	1238	<br>
	1239	<br>
[139]	1240	</body></html>

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