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[5]	1	<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
	2	<html><head>
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[392]	15	<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]	16	</font>a
	17	<b>pa</b>rallelized
	18	<b>L</b>ES <b>m</b>odel
[62]	19	<br><hr width="100%">
	20	<br><font size="+2">technical/numerical documentation</font>
	21	<br>
	22	<br>
	23	<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>  <br> </caption><tbody>
[482]	24	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
[481]	25	</span></td> </tr>
[62]	26	<tr nosave=""> <td nosave=""><b>Last
	27	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $</b></td> </tr>
	28	</tbody>
	29	</table><hr width="100%">
[5]	30	<p><font size="+2">Table of contents</font>
[62]	31	<br>
	32	<br>
	33	</p><ul> <a href="#Kapitel1.0">1.0</a>
	34	History of changes <p><a href="#Kapitel2.0">2.0</a>
[493]	35	How to change the source
	36	code and how to document modifications<br>
	37	</p> <p><a href="#Kapitel3.0">3.0</a>
[481]	38	Description of selected model numerics<br>
[5]	39	</p>
[392]	40	</ul><b></b><br>
	41
[62]	42	<h2><a name="Kapitel1.0"></a>1.0
	43	History of changes</h2>
[481]	44	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>
	45	<br>
[482]	46	Entries in the fifth column specify the type of the change:
[5]	47	change
	48	of existing code (C), new code (N) or bugfix (B). More detailed
	49	information
[481]	50	about the changes may sometimes be found in the header comment lines of the
[5]	51	respective
	52	routines.
[62]	53	<br>
	54	<br>
[481]	55	<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
	56	<tbody>
	57	<tr>
[482]	58	<td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
[392]	59	</td>
[481]	60	<td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
[392]	61	</td>
[481]	62	<td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
[392]	63	</td>
[481]	64	<td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
[392]	65	</td>
[481]	66	<td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
	67	</td>
	68	<td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
	69	</td>
	70	<td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
	71	</td>
	72	</tr>
[482]	73
	74
	75
	76
	77
	78
	79
	80
	81
	82
[481]	83	<tr>
[504]	84	<td style="vertical-align: top;">03/03/10<br>
	85	</td>
	86	<td style="vertical-align: top;">SR<br>
	87	</td>
	88	<td style="vertical-align: top;">504<br>
	89	</td>
	90	<td style="vertical-align: top;">3.7a<br>
	91	</td>
	92	<td style="vertical-align: top;">C<br>
	93	</td>
	94	<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>
	95	<br>
	96	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>
	97	<br>
	98	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>
	99	<br>
	100	Default configuration files updated.<br>
	101	</td>
	102	<td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
	103	</td>
	104	</tr>
	105	<tr>
[496]	106	<td style="vertical-align: top;">02/03/10<br>
	107	</td>
	108	<td style="vertical-align: top;">SR<br>
	109	</td>
	110	<td style="vertical-align: top;">496<br>
	111	</td>
	112	<td style="vertical-align: top;">3.7a<br>
	113	</td>
	114	<td style="vertical-align: top;">C<br>
	115	</td>
	116	<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>
	117	</td>
	118	<td style="vertical-align: top;">palm<br>
	119	</td>
	120	</tr>
	121	<tr>
[494]	122	<td style="vertical-align: top;">01/03/10<br>
[486]	123	</td>
	124	<td style="vertical-align: top;">SR<br>
	125	</td>
[494]	126	<td style="vertical-align: top;">494<br>
[486]	127	</td>
[494]	128	<td style="vertical-align: top;">3.7a<br>
	129	</td>
	130	<td style="vertical-align: top;">N<br>
	131	</td>
	132	<td style="vertical-align: top;">Output in NetCDF4-format.<br>
	133	<br>
	134	NetCDF4 allows for parallel I/O. Also, variables are not limited in
	135	size any more (i.e. arrays can be larger than 2GB). The new
	136	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>
	137	only affects 2d- and 3d-output, i.e. there is no parallel output for
	138	profiles, time series, spectra, and particles. Parallel output of
	139	particle data may realized in the future.<br>
	140	<br>
	141	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>
	142	(merging data from single files - one per PE - into one file) is not
	143	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>
	144	<br>
	145	Using NetCDF4 format requires a NetCDF4/HDF library. Respective
	146	settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
	147	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>
	148	<br>
	149	<span style="font-weight: bold;">Attention:</span><br>
	150	So far, NetCDF parallel I/O has only been tested a little. Further
	151	performance optimizations may be required, especially in case of large
	152	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>
	153	<br>
	154	<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
	155	<br>
	156	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>
	157	<br>
	158	<span style="font-family: Courier New,Courier,monospace;">   %modules     ifort/11.0.069:netcdf       lcsgih parallel</span><br>
	159	<br>
	160	This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
	161	<br>
	162	<span style="font-weight: bold;">WARNING:</span><br>
[497]	163	<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>
	164	<br>
	165	</span>Compilation time can be reduced be using parallel make. The
	166	number of allowed simultaneous compiler calls (threads) is set in the
	167	configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
	168	<br>
	169	<span style="font-family: Courier New,Courier,monospace;">   %mopts  -j:4   lcsgih parallel</span><br>
	170	<br>
	171	allows a maximum of 4 routines to be compiled simultaneously (provided
	172	that the makefile does not show any dependencies between these
	173	routines).<span style="font-weight: bold;"><br>
	174	</span>
[494]	175	</td>
	176	<td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
	177	<br>
	178	combine_plot_fields<br>
	179	<br>
	180	mbuild, mrun, subjob<br>
	181	</td>
	182	</tr>
	183	<tr>
[486]	184	<td style="vertical-align: top;"><br>
	185	</td>
	186	<td style="vertical-align: top;"><br>
	187	</td>
[494]	188	<td style="vertical-align: top;"><br>
	189	</td>
	190	<td style="vertical-align: top;"><br>
	191	</td>
	192	<td style="vertical-align: top;">C<br>
	193	</td>
	194	<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>
	195	for choosing the NetCDF 64bit-offset format (this is the default from
	196	now on). The offset-format can not be set independently for the
	197	3d-output-data any more.<br>
	198	<br>
	199	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>
	200	</td>
	201	<td style="vertical-align: top;">check_open, close_file,<br>
	202	data_output_mask, header, init_masks, modules, parin<br>
	203	<br>
	204	</td>
	205	</tr>
	206	<tr>
	207	<td style="vertical-align: top;"><br>
	208	</td>
	209	<td style="vertical-align: top;"><br>
	210	</td>
	211	<td style="vertical-align: top;"><br>
	212	</td>
	213	<td style="vertical-align: top;"><br>
	214	</td>
	215	<td style="vertical-align: top;">B<br>
	216	</td>
	217	<td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
	218	<br>
	219	Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
	220	</td>
	221	<td style="vertical-align: top;">user_statistics<br>
	222	<br>
	223	trunk/UTIL/Makefile<br>
	224	</td>
	225	</tr>
	226	<tr>
	227	<td style="vertical-align: top;">05/02/10<br>
	228	</td>
	229	<td style="vertical-align: top;">SR<br>
	230	</td>
	231	<td style="vertical-align: top;">485<br>
	232	</td>
	233	<td style="vertical-align: top;">3.7a<br>
	234	</td>
	235	<td style="vertical-align: top;">B<br>
	236	</td>
[486]	237	<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>
	238	changed to 64 bit. Otherwise, on large grids > 210*9 grid points
	239	some global statistics (e.g. total kinetic energy) have wrong values.<br>
	240	</td>
	241	<td style="vertical-align: top;">init_3d_model, modules<br>
	242	</td>
	243	</tr>
	244	<tr>
	245	<td style="vertical-align: top;">05/02/10<br>
	246	</td>
	247	<td style="vertical-align: top;">SR<br>
	248	</td>
	249	<td style="vertical-align: top;">484<br>
	250	</td>
[494]	251	<td style="vertical-align: top;">3.7a<br>
[486]	252	</td>
	253	<td style="vertical-align: top;">B<br>
	254	</td>
	255	<td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
	256	</td>
	257	<td style="vertical-align: top;">many<br>
	258	</td>
	259	</tr>
	260	<tr>
[482]	261	<td style="vertical-align: top; width: 27px;">05/02/10<br>
[481]	262	</td>
[482]	263	<td style="vertical-align: top; width: 38px;">SR<br>
[481]	264	</td>
[482]	265	<td style="vertical-align: top; width: 42px;">483<br>
[481]	266	</td>
[482]	267	<td style="vertical-align: top; width: 40px;">3.7a<br>
[481]	268	</td>
[482]	269	<td style="vertical-align: top; width: 27px;">N<br>
[481]	270	</td>
[482]	271	<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>
	272	<br>
	273	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>
	274	<br>
	275	<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;">
	276	wall_scalarflux</span> are the corresponding new inipar parameters.<br>
	277	(<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>
	278	<br>
	279	Large scale vertical motion (subsidence/ascent) can be added as
	280	additional source to the prognostic equation for potential temperature.
	281	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]	282	<br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
[482]	283	<br>
	284	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>
	285	<br>
	286	Masked data output has been implemented but it is not documented in the
	287	user manual so far. This feature can already use NetCDF4 file format.
	288	(check_open, check_parameters, close_file, modules, netcdf, parin,
	289	time_integration, user_parin, new: data_output_mask, init_masks,
	290	user_data_output_mask)<br>
[481]	291	</td>
[482]	292	<td style="vertical-align: top; width: 189px;">check_open, check
	293	parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
	294	netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
	295	<br><span style="font-weight: bold;">
	296	new:</span> data_output_mask,  init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
	297	<br>
[481]	298	</td>
	299	</tr>
	300	<tr>
	301	<td style="vertical-align: top; width: 27px;"><br>
	302	</td>
	303	<td style="vertical-align: top; width: 38px;"><br>
	304	</td>
	305	<td style="vertical-align: top; width: 42px;"><br>
	306	</td>
	307	<td style="vertical-align: top; width: 40px;"><br>
	308	</td>
[482]	309	<td style="vertical-align: top; width: 27px;">C<br>
[481]	310	</td>
[482]	311	<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>
	312	<br><span style="font-family: Courier New,Courier,monospace;">
	313	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>
	314	<br>
	315	Every cloud droplet has now an own weighting factor and can be deleted
	316	due to collisions. Condensation and collision of cloud droplets are
	317	adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	318	<br>
	319	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]	320	</td>
[482]	321	<td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
[481]	322	</td>
	323	</tr>
	324	<tr>
	325	<td style="vertical-align: top; width: 27px;"><br>
	326	</td>
	327	<td style="vertical-align: top; width: 38px;"><br>
	328	</td>
	329	<td style="vertical-align: top; width: 42px;"><br>
	330	</td>
	331	<td style="vertical-align: top; width: 40px;"><br>
	332	</td>
[482]	333	<td style="vertical-align: top; width: 27px;">B<br>
[481]	334	</td>
[482]	335	<td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
	336	<br>
	337	Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
	338	<br>
	339	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>
	340	<br>
	341	Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
	342	<br>
	343	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>
	344	<br>
	345	Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
	346	<br>
	347	Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
	348	<br>
	349	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>
	350	<br>
	351	Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	352	<br>
	353	Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	354	<br>
	355	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]	356	</td>
[482]	357	<td style="vertical-align: top; width: 189px;">advec_particles,
	358	calc_precipitation, collision_efficiency, disturb_field, header,
	359	modules, poisfft_hybrid, subjob, sum_up_3d_data,
	360	time_integration<br>
	361	<br>
[481]	362	</td>
	363	</tr>
	364	<tr>
	365	<td style="vertical-align: top; width: 27px;">23/09/09<br>
	366	</td>
	367	<td style="vertical-align: top; width: 38px;">SR<br>
	368	</td>
	369	<td style="vertical-align: top; width: 42px;">392<br>
	370	</td>
	371	<td style="vertical-align: top; width: 40px;">3.7<br>
	372	</td>
	373	<td style="vertical-align: top; width: 27px;">N<br>
	374	</td>
	375	<td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
	376	important changes:</span>
[392]	377	atmosphere-ocean coupling has been improved and steering of
	378	dvr-software is more user-friendly now. Beside that, the release
	379	contains a lot of optimizations, changes, and bugfixes which have
	380	accumulated over the last months.<br>
[481]	381
[392]	382	<br>
[481]	383
[392]	384	The atmosphere-ocean coupling allows to use independent precursor runs
	385	in order to account for different spin-up times. The time when coupling
[481]	386	has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
	387	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
	388	order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
	389	output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	390	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	391	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	392	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	393	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	394	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	395	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	396	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	397	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	398	<span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
	399	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	400	<span style="font-family: Courier New,Courier,monospace;">mrun</span>,
	401	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	402	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	403	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	404	<span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
	405	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
[392]	406
	407	<br>
[481]	408
[392]	409	Clipping of dvrp output implemented. Default colourtable for particles
	410	implemented, particle attributes (color, dvrp_size) can be set with new
[481]	411	parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
	412	<span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
	413	<span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
	414	<span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
	415	Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
	416	and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
	417	(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	418	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	419	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	420	<span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,
	421	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
[392]	422
	423	<br>
[481]	424
[392]	425	Polygon reduction for topography and ground plate isosurface. Reduction
	426	level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
	427
	428	<br>
	429
[481]	430	Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
	431	/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>
	432	in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
	433
	434	<span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
	435	for speed optimization. This gives a significant speedup of more than
	436	10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	437	<span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
	438	<span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
	439	<span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
	440	<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	441
[392]	442	<br>
[481]	443
[392]	444	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]	445
[392]	446	<br>
[481]	447
	448	Additional timestep criterion in case of simulations with plant canopy.
	449	(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
	450
[392]	451	<br>
[481]	452
	453	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
	454	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>
	455
[392]	456	<br>
[481]	457
	458	External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	459	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	460	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	461	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	462	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	463	<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
	464	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	465	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	466
[392]	467	<br>
[481]	468
	469	New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
	470	(<span style="font-family: Courier New,Courier,monospace;">header</span>,
	471	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	472	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	473	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	474	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	475	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	476	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	477	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	478	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	479
[392]	480	<br>
[481]	481
	482	Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
	483	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	484	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	485	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	486	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	487	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	488	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	489	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	490
[392]	491	<br>
[481]	492
	493	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>,
	494	<span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
	495
[392]	496	<br>
[481]	497
	498	xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
	499	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	500	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	501	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	502	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	503	<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
	504	<span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
	505	<td style="vertical-align: top; width: 189px;">average_3d_data,
[392]	506	check_for_restart, check_parameters, data_output_2d, data_output_3d,
	507	data_output_dvrp, data_output_profiles, data_output_ptseries,
	508	data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
	509	diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
	510	header, mbuild, modules, mrun, package_parin, parin,
	511	prognostic_equations, read_3d_binary, read_var_list, subjob,
	512	sum_up_3d_data, surface_coupler, timestep, time_integration,
	513	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
	514	user_header, user_init_grid, write_3d_binary, write_var_list<br>
[481]	515
[392]	516	<br>
[481]	517
	518	<span style="font-weight: bold;">new:</span>
	519	set_particle_attributes, set_slicer_attributes_dvrp</td>
[392]	520	</tr>
	521	<tr>
[481]	522	<td style="vertical-align: top; width: 27px;"><br>
[392]	523	</td>
[481]	524	<td style="vertical-align: top; width: 38px;"><br>
[392]	525	</td>
[481]	526	<td style="vertical-align: top; width: 42px;"><br>
[392]	527	</td>
[481]	528	<td style="vertical-align: top; width: 40px;"><br>
[392]	529	</td>
[481]	530	<td style="vertical-align: top; width: 27px;">C<br>
	531	</td>
	532	<td style="vertical-align: top; width: 497px;">Output of messages replaced by
	533	message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	534	<span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
	535	<span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
	536	<span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
	537	<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	538	<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	539	<span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
	540	<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
	541	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	542	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	543	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	544	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	545	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	546	<span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
	547	<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
	548	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	549	<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
	550	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	551	<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	552	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	553	<span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
	554	<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
	555	<span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
	556	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	557	<span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
	558	<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
	559	<span style="font-family: Courier New,Courier,monospace;">poismg</span>,
	560	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	561	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	562	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	563	<span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
	564	<span style="font-family: Courier New,Courier,monospace;">timestep</span>,
	565	<span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
	566	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
	567	<span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
	568	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	569	<span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
	570	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	571	<span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
	572	<span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
[392]	573
	574	<br>
	575
[481]	576	Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	577	<span style="font-family: Courier New,Courier,monospace;">close_file</span>,
	578	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	579	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	580	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	581	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	582	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	583	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	584	<span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	585
[392]	586	<br>
	587
[481]	588	__lcmuk changed to __lc to avoid problems with Intel compiler on
	589	sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
	590
[392]	591	<br>
[481]	592
	593	For extended NetCDF files, the updated title attribute includes an
	594	update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	595
[392]	596	<br>
[481]	597
[392]	598	In case of restart runs without extension, initial profiles are not
	599	written to NetCDF-file anymore. So far, time axis always started at
[481]	600	t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	601	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	602	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	603	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	604
[392]	605	<br>
[481]	606
	607	<span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
	608	'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
	609	can now <br>
	610
	611	be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
	612	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	613	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	614	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	615
[392]	616	<br>
[481]	617
[392]	618	2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
[481]	619
[392]	620	<br>
[481]	621
[392]	622	A link to the webspage appendix_a.html is printed for further
	623	information about possible reasons of the error that appeared. (message)<br>
[481]	624
[392]	625	<br>
[481]	626
[392]	627	Temperature gradient criterion for estimating the boundary layer height
	628	replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
[481]	629
[392]	630	<br>
[481]	631
	632	NetCDF unit attribute in timeseries output in case of statistic regions
	633	added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	634
[392]	635	<br>
[481]	636
	637	Maximum number of tails is calculated from maximum number of particles
	638	and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
	639	(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
	640
[392]	641	<br>
[481]	642
	643	Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
	644	is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	645	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	646	<span style="font-family: Courier New,Courier,monospace;">modules</span>)
[392]	647	<br>
[481]	648
[392]	649	<br>
[481]	650
	651	First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
	652	defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
	653
[392]	654	<br>
[481]	655
	656	Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
	657	moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
	658	to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
	659	(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
	660
[392]	661	<br>
[481]	662
	663	<span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
	664	moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
	665	to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
	666	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	667	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	668	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	669	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	670	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	671	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	672	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	673	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	674	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	675
[392]	676	<br>
[481]	677
	678	Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
	679	changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	680
	681	<br>
	682
	683	Adjustments for runs on lcxt4 (necessary due to a software update on
	684	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>
	685	<td style="vertical-align: top; width: 189px;">advec_particles,
	686	advec_s_bc,
[392]	687	buoyancy, calc_spectra, check_for_restart, check_open,
	688	check_parameters, close_file, coriolis, cpu_log, data_output_2d,
	689	data_output_3d, data_output_dvrp, data_output_profiles,
	690	data_output_ptseries, data_output_spectra, data_output_tseries,
	691	eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
	692	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
	693	message, mrun, netcdf, package_parin, parin, plant_canopy_model,
	694	poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
[481]	695	surface_coupler, temperton_fft, timestep,
	696	user_actions,user_check_parameters, user_data_output_dvrp,
	697	user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
	698	user_parin, user_read_restart_data, user_spectra, write_var_list </td>
[392]	699	</tr>
	700	<tr>
[481]	701	<td style="vertical-align: top; width: 27px;"><br>
[392]	702	</td>
[481]	703	<td style="vertical-align: top; width: 38px;"><br>
[392]	704	</td>
[481]	705	<td style="vertical-align: top; width: 42px;"><br>
[392]	706	</td>
[481]	707	<td style="vertical-align: top; width: 40px;"><br>
[392]	708	</td>
[482]	709	<td style="vertical-align: top; width: 27px;">B<br>
[481]	710	</td>
	711	<td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
	712	pressure profile in case of ocean runs is now calculated in 5 iteration
	713	steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
	714
[392]	715	<br>
[481]	716
	717	Bugfix: wrong sign in buoyancy production of ocean part in case of not
	718	using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
	719	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	720
[392]	721	<br>
[481]	722
[392]	723	Bugfix: output of averaged 2d/3d quantities requires that an avaraging
	724	interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	725
[392]	726	<br>
[481]	727
	728	Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
	729	(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
	730
[392]	731	<br>
[481]	732
	733	Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
	734	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	735
[392]	736	<br>
[481]	737
[392]	738	Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
[481]	739	if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
	740	is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
	741	and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
[392]	742	calls. This implies a possible performance loss; an alternative
	743	strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	744
[392]	745	<br>
[481]	746
[392]	747	Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
[481]	748
[392]	749	<br>
[481]	750
[392]	751	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]	752
[392]	753	<br>
[481]	754
	755	Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
	756	=> <span style="font-family: Courier New,Courier,monospace;">s_av</span>
	757	for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	758	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
	759
[392]	760	<br>
[481]	761
	762	Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
	763	becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
	764
[392]	765	<br>
[481]	766
[392]	767	Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
[481]	768
[392]	769	<br>
[481]	770
[392]	771	Bugfix: error in check, if particles moved further than one subdomain
	772	length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
[481]	773
[392]	774	<br>
[481]	775
[392]	776	Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
	777	is only written to file if its third index is > 0, arrays for tails
	778	are allocated with a minimum size of 10 tails if there is no tail
[481]	779	initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	780	<span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	781
[392]	782	<br>
[481]	783
[392]	784	Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	785
[392]	786	<br>
[481]	787
	788	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>
	789	changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
	790	NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
	791
[392]	792	<br>
[481]	793
	794	Bugfix: output of particle time series only if particle advection is
	795	switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
	796
[392]	797	<br>
[481]	798
	799	Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
	800	= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
	801	(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
	802
[392]	803	<br>
[481]	804
	805	Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
	806	z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
	807
[392]	808	<br>
[481]	809
[392]	810	Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	811
[392]	812	<br>
[481]	813
	814	If the inversion height calculated by the prerun is zero,
	815	inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	816
[392]	817	<br>
[481]	818
[392]	819	Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
[481]	820
[392]	821	<br>
[481]	822
[392]	823	Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
	824	removed from the restart file, because otherwise, no change from a
[481]	825	fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	826	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	827
[392]	828	<br>
[481]	829
	830	Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
	831	in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
	832	<td style="vertical-align: top; width: 189px;">advec_particles,
[392]	833	check_parameters, cpu_log, data_output_2d, data_output_3d, header,
	834	init_3d_model, init_particles, init_ocean, modules, netcdf,
	835	prandtl_fluxes, production_e, read_var_list, time_integration,
	836	user_last_actions, write_var_list<br>
[481]	837
	838	</td>
	839	</tr>
	840	<tr>
	841	<td style="vertical-align: top; width: 27px;">02/02/09<br>
	842	</td>
	843	<td style="vertical-align: top; width: 38px;">SR<br>
	844	</td>
	845	<td style="vertical-align: top; width: 42px;">228<br>
	846	</td>
	847	<td style="vertical-align: top; width: 40px;">3.6<br>
	848	</td>
	849	<td style="vertical-align: top; width: 27px;">N<br>
	850	</td>
	851	<td style="vertical-align: top; width: 497px;">This
	852	release contains further additions, changes, and bugfixes for the
	853	SGI-ICE system, as well as important changes like the splitting of the
	854	user-interface into single files, a complete revision of the
	855	pre-compiling mechanism allowing to use different make-depositories
	856	simultaneously, and a revision of the reading-mechanism from restart
	857	files, which has no more restrictions in case that the previous and
	858	current run have different domain/subdomain sizes. A new handling of
	859	all kind of output messages is introduced with this release and will be
	860	applied to all existing messages within the next releases.<br>
	861
[392]	862	<br>
[481]	863
	864	<span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
	865
	866	<br>
	867
	868	Restart runs on SGI-ICE are working. (mrun)<br>
	869
	870	2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
	871
	872	<br>
	873
	874	Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
	875	case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	876	"<span style="font-style: italic;">-K parallel</span>" for coupling.
	877	Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
	878	<span style="font-family: Courier New,Courier,monospace;">subjob</span>
	879	for lcxt4.<br>
	880
	881	<br>
	882
	883	DVRP arguments changed to single precision, mode pathlines added.<br>
	884
	885	<br>
	886
	887	User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
	888
	889	<br>
	890
	891	User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
	892	<td style="vertical-align: top; width: 189px;">check_for_restart,
	893	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
	894	modules, package_parin, palm, surface_coupler, timestep<br>
	895
	896	<br>
	897
	898	Makefile, mbuild, mrun, subjob<br>
	899
	900	<br>
	901
	902	<span style="font-weight: bold;">new:</span><br>
	903
	904	init_coupling, user_additional_routines, user_check_parameters</td>
	905	</tr>
	906	<tr>
	907	<td style="vertical-align: top; width: 27px;"><br>
[392]	908	</td>
[481]	909	<td style="vertical-align: top; width: 38px;"><br>
	910	</td>
	911	<td style="vertical-align: top; width: 42px;"><br>
	912	</td>
	913	<td style="vertical-align: top; width: 40px;"><br>
	914	</td>
	915	<td style="vertical-align: top; width: 27px;">C<br>
	916	</td>
	917	<td style="vertical-align: top; width: 497px;">User interface has been
	918	split into single files.<br>
	919
	920	<br>
	921
	922	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>
	923	changed to INTEGER(8) in order to avoid "out of range" problems, which
	924	result in measured negative time intervals. (cpu_log, local_tremain,
	925	local_tremain_ini)<br>
	926
	927	<br>
	928
	929	Reading mechanism from restart files
	930	completely revised. The subdomain/total domain size is now allowed to
	931	vary arbitrarily between the current and previous run. (read_var_list,
	932	read_3d_binary, user_read_restart_data)<br>
	933
	934	<br>
	935
	936	Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
	937	completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
	938	One depository per block (given in the config-file) is created. Always
	939	all files from the source directory are copied to the respective
	940	depository. No additional file checks are done any more (mrun version
	941	2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	942	"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
	943	(mbuild, mrun)<br>
	944
	945	<br>
	946
	947	Output messages (including required stop of execution) can now be
	948	handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>.
	949	All output messages will be replaced by this routine step by step
	950	within the next revisions.<br>
	951
	952	<br>
	953
	954	Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
	955	explicitly set for better reading, although this has been already done
	956	in boundary_conds. (advec_s_bc)<br>
	957
	958	<br>
	959
	960	Origin of the xy-coordinate system shifted from the center of the first
	961	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
	962	south-left corner of this cell. (netcdf) Topography definition
	963	according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
	964	(init_grid, modules, user_header, user_init_grid, user_parin)</td>
	965	<td style="vertical-align: top; width: 189px;">advec_s_bc,
	966	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
	967	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
	968	user_read_restart_data<br>
	969
	970	<br>
	971
	972	Makefile, mbuild, mrun<br>
	973
	974	<br>
	975
	976	<span style="font-weight: bold;">removed:</span><br>
	977
	978	user_interface<br>
	979
	980	<br>
	981
	982	<span style="font-weight: bold;">new:</span><br>
	983
	984	message,
	985	user_3d_data_averaging, user_actions, user_advec_particles,
	986	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
	987	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
	988	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
	989	user_init_grid, user_init_particles, user_init_plant_canopy,
	990	user_last_actions, user_parin, user_parin, user_particle_attributes,
	991	user_read_restart_data, user_spectra, user_statistics</td>
[392]	992	</tr>
[481]	993	<tr>
	994	<td style="vertical-align: top; width: 27px;"><br>
	995	</td>
	996	<td style="vertical-align: top; width: 38px;"><br>
	997	</td>
	998	<td style="vertical-align: top; width: 42px;"><br>
	999	</td>
	1000	<td style="vertical-align: top; width: 40px;"><br>
	1001	</td>
[482]	1002	<td style="vertical-align: top; width: 27px;">B<br>
[481]	1003	</td>
	1004	<td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
	1005	reallocated in case that multigrid is used. (calc_spectra)<br>
[392]	1006
[481]	1007	<br>
	1008
	1009	Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
	1010	inflow_turbulence, timestep)<br>
	1011
	1012	<br>
	1013
	1014	Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
	1015	</span>adjusted to the required output size (1 gridpoint less,
	1016	along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
	1017	in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
	1018	compiler. (combine_plot_fields)<br>
	1019
	1020	<br>
	1021
	1022	Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
	1023	case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
	1024	(header)<br>
	1025
	1026	<br>
	1027
	1028	Inconsistency
	1029	removed: as the thermal stratification is not taken into account for
	1030	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
	1031	<span style="font-family: Courier New,Courier,monospace;">km</span>
	1032	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>.
	1033	(production_e)<br>
	1034
	1035	<br>
	1036
	1037	Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
	1038	case of oceans runs. (sort_particles)<br>
	1039
	1040	<br>
	1041
	1042	Bugfix: no output of particle concentration and radius unless particles
	1043	have been started. (data_output_2d)<br>
	1044
	1045	<br>
	1046
	1047	Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x\|y</span>
	1048	from restart files ignored if total numbers of grid points do not
	1049	match. (read_3d_binary)<br>
	1050
	1051	<br>
	1052
	1053	Bugfix: abort in case that absolute temperature is below zero.
	1054	(init_cloud_physics)</td>
	1055	<td style="vertical-align: top; width: 189px;">advec_particles,
	1056	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
	1057	header, inflow_turbulence, init_cloud_physics, production_e,
	1058	read_3d_binary, timestep<br>
	1059
	1060	<br>
	1061
	1062	combine_plot_fields</td>
	1063	</tr>
	1064	</tbody>
	1065	</table>
	1066	<b><blink></blink></b><br>
[62]	1067	<br>
	1068	<h2><a name="Kapitel2.0"></a>2.0  How
[493]	1069	to change the source
	1070	code and how to document modifications<br>
	1071	</h2>Currently
[392]	1072	(Sep 23rd, 2009), only selected users are allowed to commit changes to
[493]	1073	the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
	1074	<br>
	1075	<ol>
	1076	<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>".
	1077	Additionally, document all changes in a local file (e.g.
	1078	~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
	1079	have been changed. Classify changes in three cases, new (N), changed
	1080	(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>
	1081	<br>
	1082	</li>
	1083	<li>Test the changed version, unless it works sufficiently.<br>
	1084	<br>
	1085	</li>
	1086
	1087	<li>Commit the changes to the repository<br>
	1088	<br>
	1089	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "message string" trunk<br>
	1090	</span><br>
	1091	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>
	1092	<br>
	1093	Alternatively, in case that you have made quite a lot of changes, you
	1094	can also give the contents of your file CURRENT_MODIFICATIONS as the
	1095	log message:<br>
	1096	<br>
	1097	<span style="font-family: Courier New,Courier,monospace;">   svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
	1098	<br>
	1099	</li>
	1100
	1101	<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>
	1102	<br>
	1103	</li>
	1104	<li>Move the change comments in the file headers from "Current
	1105	revisions:" to "Former revisions:". Set the current svn id in front of
	1106	that.<br>
	1107	<br>
	1108	<span style="font-weight: bold;">Example:</span><br>
	1109	<br>
	1110	<span style="font-weight: bold;">before move:</span><br>
	1111	<br>
	1112	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1113	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1114	<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;">
	1115	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1116	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1117	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1118	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
	1119	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1120	<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;">
	1121	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
	1122	<br>
	1123	<span style="font-weight: bold;">after move:</span><br>
	1124	<br>
	1125	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1126
	1127	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1128
	1129	<span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
	1130
	1131	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1132
	1133	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1134
	1135	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1136
	1137	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 504 2010-03-03 00:34:33Z raasch $<br>
	1138	!</span><br style="font-family: Courier New,Courier,monospace;">
	1139	<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>
	1140	! </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;">
	1141
	1142	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1143
	1144	<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;">
	1145
	1146	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
	1147	</span><br>
	1148	</li>
	1149	<li>Commit the changes in the technical documentation and the file headers:<br>
	1150	<br>
	1151	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "last commit documented" trunk</span><br>
	1152	<br>
	1153	<br>
	1154	</li>
	1155	</ol>
	1156
[392]	1157	<h2>
[62]	1158	<a name="Kapitel3.0"></a>3.0  Description
	1159	of selected parts of the
[5]	1160	model source code</h2>
[392]	1161	<b></b>
	1162	<p>This section gives links to existing descriptions about special
	1163	parts of the PALM code, e.g. special numerical methods that are used
	1164	(including mathematical background). Documents are stored in single
	1165	files with different formats. Some are in German (sorry for the
	1166	inconvenience).
[62]	1167	<br>
	1168	</p><ul> <li> <a name="UPS"></a>upstream-spline
[481]	1169	advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
	1170	, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
	1171	physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
	1172	)</li>
	1173	<li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
	1174	</li>
	1175	<li>Runge-Kutta
	1176	time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
	1177	, only in German)</li>
	1178
[62]	1179	</ul><br>
[5]	1180
[62]	1181	<br>
	1182	<br>
	1183	<br>
	1184	<br>
	1185	<br>
	1186	<br>
	1187	<br>
[139]	1188	</body></html>

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