Home

Context Navigation

source: palm/trunk/DOC/tec/technical_documentation.html @ 506

Last change on this file since 506 was 506, checked in by raasch, 15 years ago
last commit documented
Property svn:keywords set to `Id`
File size: 64.1 KB

Rev	Line
[5]	1	<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
	2	<html><head>
[392]	3
[481]	4
	5
[482]	6
	7
[486]	8
[493]	9
	10
[494]	11
[496]	12
[497]	13
[504]	14
[506]	15
[392]	16	<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]	17	</font>a
	18	<b>pa</b>rallelized
	19	<b>L</b>ES <b>m</b>odel
[62]	20	<br><hr width="100%">
	21	<br><font size="+2">technical/numerical documentation</font>
	22	<br>
	23	<br>
	24	<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>  <br> </caption><tbody>
[482]	25	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current fixed release:</b></td> <td><span style="font-weight: bold;">3.7a<br>
[481]	26	</span></td> </tr>
[62]	27	<tr nosave=""> <td nosave=""><b>Last
	28	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $</b></td> </tr>
	29	</tbody>
	30	</table><hr width="100%">
[5]	31	<p><font size="+2">Table of contents</font>
[62]	32	<br>
	33	<br>
	34	</p><ul> <a href="#Kapitel1.0">1.0</a>
	35	History of changes <p><a href="#Kapitel2.0">2.0</a>
[493]	36	How to change the source
	37	code and how to document modifications<br>
	38	</p> <p><a href="#Kapitel3.0">3.0</a>
[481]	39	Description of selected model numerics<br>
[5]	40	</p>
[392]	41	</ul><b></b><br>
	42
[62]	43	<h2><a name="Kapitel1.0"></a>1.0
	44	History of changes</h2>
[481]	45	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>
	46	<br>
[482]	47	Entries in the fifth column specify the type of the change:
[5]	48	change
	49	of existing code (C), new code (N) or bugfix (B). More detailed
	50	information
[481]	51	about the changes may sometimes be found in the header comment lines of the
[5]	52	respective
	53	routines.
[62]	54	<br>
	55	<br>
[481]	56	<table style="text-align: left; width: 100%; vertical-align: top;" border="1" cellpadding="2" cellspacing="2">
	57	<tbody>
	58	<tr>
[482]	59	<td style="vertical-align: middle; width: 27px;"><big><span style="font-weight: bold;">date</span></big><br>
[392]	60	</td>
[481]	61	<td style="width: 38px;"><big><span style="font-weight: bold;">author</span></big><br>
[392]	62	</td>
[481]	63	<td style="width: 42px;"><big><span style="font-weight: bold;">svn revision</span></big><br>
[392]	64	</td>
[481]	65	<td style="width: 40px;"><big><span style="font-weight: bold;">latest release</span></big><br>
[392]	66	</td>
[481]	67	<td style="width: 27px;"><big><span style="font-weight: bold;">type</span></big><br>
	68	</td>
	69	<td style="width: 497px;"><big><span style="font-weight: bold;">description</span></big><br>
	70	</td>
	71	<td style="width: 189px;"><big><span style="font-weight: bold;">affected routines</span></big><br>
	72	</td>
	73	</tr>
[482]	74
	75
	76
	77
	78
	79
	80
	81
	82
	83
[481]	84	<tr>
[506]	85	<td style="vertical-align: top;">08/03/10<br>
	86	</td>
	87	<td style="vertical-align: top;">SR<br>
	88	</td>
	89	<td style="vertical-align: top;">506<br>
	90	</td>
	91	<td style="vertical-align: top;">3.7a<br>
	92	</td>
	93	<td style="vertical-align: top;">C<br>
	94	</td>
	95	<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>
	96	</td>
	97	<td style="vertical-align: top;">mrun<br>
	98	</td>
	99	</tr>
	100	<tr>
[504]	101	<td style="vertical-align: top;">03/03/10<br>
	102	</td>
	103	<td style="vertical-align: top;">SR<br>
	104	</td>
	105	<td style="vertical-align: top;">504<br>
	106	</td>
	107	<td style="vertical-align: top;">3.7a<br>
	108	</td>
	109	<td style="vertical-align: top;">C<br>
	110	</td>
	111	<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>
	112	<br>
	113	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>
	114	<br>
	115	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>
	116	<br>
	117	Default configuration files updated.<br>
	118	</td>
	119	<td style="vertical-align: top;">mbuild, mrun, UTIL/Makefile, SCRIPTS/.mrun.config.*<br>
	120	</td>
	121	</tr>
	122	<tr>
[496]	123	<td style="vertical-align: top;">02/03/10<br>
	124	</td>
	125	<td style="vertical-align: top;">SR<br>
	126	</td>
	127	<td style="vertical-align: top;">496<br>
	128	</td>
	129	<td style="vertical-align: top;">3.7a<br>
	130	</td>
	131	<td style="vertical-align: top;">C<br>
	132	</td>
	133	<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>
	134	</td>
	135	<td style="vertical-align: top;">palm<br>
	136	</td>
	137	</tr>
	138	<tr>
[494]	139	<td style="vertical-align: top;">01/03/10<br>
[486]	140	</td>
	141	<td style="vertical-align: top;">SR<br>
	142	</td>
[494]	143	<td style="vertical-align: top;">494<br>
[486]	144	</td>
[494]	145	<td style="vertical-align: top;">3.7a<br>
	146	</td>
	147	<td style="vertical-align: top;">N<br>
	148	</td>
	149	<td style="vertical-align: top;">Output in NetCDF4-format.<br>
	150	<br>
	151	NetCDF4 allows for parallel I/O. Also, variables are not limited in
	152	size any more (i.e. arrays can be larger than 2GB). The new
	153	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>
	154	only affects 2d- and 3d-output, i.e. there is no parallel output for
	155	profiles, time series, spectra, and particles. Parallel output of
	156	particle data may realized in the future.<br>
	157	<br>
	158	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>
	159	(merging data from single files - one per PE - into one file) is not
	160	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>
	161	<br>
	162	Using NetCDF4 format requires a NetCDF4/HDF library. Respective
	163	settings for -I, -L, and -l compiler/loader options for the SGI-ICE at
	164	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>
	165	<br>
	166	<span style="font-weight: bold;">Attention:</span><br>
	167	So far, NetCDF parallel I/O has only been tested a little. Further
	168	performance optimizations may be required, especially in case of large
	169	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>
	170	<br>
	171	<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span> outputs cpu-time needed for file merging.<br>
	172	<br>
	173	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>
	174	<br>
	175	<span style="font-family: Courier New,Courier,monospace;">   %modules     ifort/11.0.069:netcdf       lcsgih parallel</span><br>
	176	<br>
	177	This method replaces the (undocumented) <span style="font-family: Courier New,Courier,monospace;">mpilib</span>-variable.<br>
	178	<br>
	179	<span style="font-weight: bold;">WARNING:</span><br>
[497]	180	<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>
	181	<br>
	182	</span>Compilation time can be reduced be using parallel make. The
	183	number of allowed simultaneous compiler calls (threads) is set in the
	184	configuration file using variable <span style="font-family: Courier New,Courier,monospace;">mopt</span>, e.g.<br>
	185	<br>
	186	<span style="font-family: Courier New,Courier,monospace;">   %mopts  -j:4   lcsgih parallel</span><br>
	187	<br>
	188	allows a maximum of 4 routines to be compiled simultaneously (provided
	189	that the makefile does not show any dependencies between these
	190	routines).<span style="font-weight: bold;"><br>
	191	</span>
[494]	192	</td>
	193	<td style="vertical-align: top;">check_open, check_parameters, close_file, data_output_2d, data_output_3d, header, modules, netcdf, parin<br>
	194	<br>
	195	combine_plot_fields<br>
	196	<br>
	197	mbuild, mrun, subjob<br>
	198	</td>
	199	</tr>
	200	<tr>
[486]	201	<td style="vertical-align: top;"><br>
	202	</td>
	203	<td style="vertical-align: top;"><br>
	204	</td>
[494]	205	<td style="vertical-align: top;"><br>
	206	</td>
	207	<td style="vertical-align: top;"><br>
	208	</td>
	209	<td style="vertical-align: top;">C<br>
	210	</td>
	211	<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>
	212	for choosing the NetCDF 64bit-offset format (this is the default from
	213	now on). The offset-format can not be set independently for the
	214	3d-output-data any more.<br>
	215	<br>
	216	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>
	217	</td>
	218	<td style="vertical-align: top;">check_open, close_file,<br>
	219	data_output_mask, header, init_masks, modules, parin<br>
	220	<br>
	221	</td>
	222	</tr>
	223	<tr>
	224	<td style="vertical-align: top;"><br>
	225	</td>
	226	<td style="vertical-align: top;"><br>
	227	</td>
	228	<td style="vertical-align: top;"><br>
	229	</td>
	230	<td style="vertical-align: top;"><br>
	231	</td>
	232	<td style="vertical-align: top;">B<br>
	233	</td>
	234	<td style="vertical-align: top;">Bugfix in trunk/UTIL/Makefile: forgot to compile for interpret_config.<br>
	235	<br>
	236	Bugfix: timeseries data have to be collected by PE0 (user_statistics).<br>
	237	</td>
	238	<td style="vertical-align: top;">user_statistics<br>
	239	<br>
	240	trunk/UTIL/Makefile<br>
	241	</td>
	242	</tr>
	243	<tr>
	244	<td style="vertical-align: top;">05/02/10<br>
	245	</td>
	246	<td style="vertical-align: top;">SR<br>
	247	</td>
	248	<td style="vertical-align: top;">485<br>
	249	</td>
	250	<td style="vertical-align: top;">3.7a<br>
	251	</td>
	252	<td style="vertical-align: top;">B<br>
	253	</td>
[486]	254	<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>
	255	changed to 64 bit. Otherwise, on large grids > 210*9 grid points
	256	some global statistics (e.g. total kinetic energy) have wrong values.<br>
	257	</td>
	258	<td style="vertical-align: top;">init_3d_model, modules<br>
	259	</td>
	260	</tr>
	261	<tr>
	262	<td style="vertical-align: top;">05/02/10<br>
	263	</td>
	264	<td style="vertical-align: top;">SR<br>
	265	</td>
	266	<td style="vertical-align: top;">484<br>
	267	</td>
[494]	268	<td style="vertical-align: top;">3.7a<br>
[486]	269	</td>
	270	<td style="vertical-align: top;">B<br>
	271	</td>
	272	<td style="vertical-align: top;">Typo in file headers removed ("current" instead of "actual").<br>
	273	</td>
	274	<td style="vertical-align: top;">many<br>
	275	</td>
	276	</tr>
	277	<tr>
[482]	278	<td style="vertical-align: top; width: 27px;">05/02/10<br>
[481]	279	</td>
[482]	280	<td style="vertical-align: top; width: 38px;">SR<br>
[481]	281	</td>
[482]	282	<td style="vertical-align: top; width: 42px;">483<br>
[481]	283	</td>
[482]	284	<td style="vertical-align: top; width: 40px;">3.7a<br>
[481]	285	</td>
[482]	286	<td style="vertical-align: top; width: 27px;">N<br>
[481]	287	</td>
[482]	288	<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>
	289	<br>
	290	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>
	291	<br>
	292	<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;">
	293	wall_scalarflux</span> are the corresponding new inipar parameters.<br>
	294	(<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>
	295	<br>
	296	Large scale vertical motion (subsidence/ascent) can be added as
	297	additional source to the prognostic equation for potential temperature.
	298	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]	299	<br>Scripts have been updated for Cray-XT5 machine (lcxt5m) and Hitachi-machine (lckyoto).<br>
[482]	300	<br>
	301	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>
	302	<br>
	303	Masked data output has been implemented but it is not documented in the
	304	user manual so far. This feature can already use NetCDF4 file format.
	305	(check_open, check_parameters, close_file, modules, netcdf, parin,
	306	time_integration, user_parin, new: data_output_mask, init_masks,
	307	user_data_output_mask)<br>
[481]	308	</td>
[482]	309	<td style="vertical-align: top; width: 189px;">check_open, check
	310	parameters, close_file, header, init_3d_model, Makefile, mbuild, modules, mrun,
	311	netcdf, parin, prognostic_equations, read_var_list, time_integration, user_parin, write_var_list<br>
	312	<br><span style="font-weight: bold;">
	313	new:</span> data_output_mask,  init_masks, palm_simple_install, palm_simple_run, subsidence, user_data_output_mask<br>
	314	<br>
[481]	315	</td>
	316	</tr>
	317	<tr>
	318	<td style="vertical-align: top; width: 27px;"><br>
	319	</td>
	320	<td style="vertical-align: top; width: 38px;"><br>
	321	</td>
	322	<td style="vertical-align: top; width: 42px;"><br>
	323	</td>
	324	<td style="vertical-align: top; width: 40px;"><br>
	325	</td>
[482]	326	<td style="vertical-align: top; width: 27px;">C<br>
[481]	327	</td>
[482]	328	<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>
	329	<br><span style="font-family: Courier New,Courier,monospace;">
	330	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>
	331	<br>
	332	Every cloud droplet has now an own weighting factor and can be deleted
	333	due to collisions. Condensation and collision of cloud droplets are
	334	adjusted accordingly. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	335	<br>
	336	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]	337	</td>
[482]	338	<td style="vertical-align: top; width: 189px;">advec_particles, collision_efficiency, init_3d_model, init_pegrid, modules<br>
[481]	339	</td>
	340	</tr>
	341	<tr>
	342	<td style="vertical-align: top; width: 27px;"><br>
	343	</td>
	344	<td style="vertical-align: top; width: 38px;"><br>
	345	</td>
	346	<td style="vertical-align: top; width: 42px;"><br>
	347	</td>
	348	<td style="vertical-align: top; width: 40px;"><br>
	349	</td>
[482]	350	<td style="vertical-align: top; width: 27px;">B<br>
[481]	351	</td>
[482]	352	<td style="vertical-align: top; width: 497px;">Bugfix for generating serial jobs. (<span style="font-weight: bold;">subjob</span>)<br>
	353	<br>
	354	Bugfix: index problem concerning gradient_level indices removed. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
	355	<br>
	356	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>
	357	<br>
	358	Loop was split to make runs reproducible when using ifort compiler. (<span style="font-family: Courier New,Courier,monospace;">disturb_field</span>)<br>
	359	<br>
	360	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>
	361	<br>
	362	Bugfix in calculation of time-averaged surface heatfluxes. (<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>)<br>
	363	<br>
	364	Bugfix in calculation of precipitation_rate. (<span style="font-family: Courier New,Courier,monospace;">calc_precipitation</span>)<br>
	365	<br>
	366	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>
	367	<br>
	368	Bugfix in calculation of cloud droplet velocity. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	369	<br>
	370	Bugfix in transfer of particles at south/left edge. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
	371	<br>
	372	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]	373	</td>
[482]	374	<td style="vertical-align: top; width: 189px;">advec_particles,
	375	calc_precipitation, collision_efficiency, disturb_field, header,
	376	modules, poisfft_hybrid, subjob, sum_up_3d_data,
	377	time_integration<br>
	378	<br>
[481]	379	</td>
	380	</tr>
	381	<tr>
	382	<td style="vertical-align: top; width: 27px;">23/09/09<br>
	383	</td>
	384	<td style="vertical-align: top; width: 38px;">SR<br>
	385	</td>
	386	<td style="vertical-align: top; width: 42px;">392<br>
	387	</td>
	388	<td style="vertical-align: top; width: 40px;">3.7<br>
	389	</td>
	390	<td style="vertical-align: top; width: 27px;">N<br>
	391	</td>
	392	<td style="vertical-align: top; width: 497px;"><span style="font-weight: bold;">Most
	393	important changes:</span>
[392]	394	atmosphere-ocean coupling has been improved and steering of
	395	dvr-software is more user-friendly now. Beside that, the release
	396	contains a lot of optimizations, changes, and bugfixes which have
	397	accumulated over the last months.<br>
[481]	398
[392]	399	<br>
[481]	400
[392]	401	The atmosphere-ocean coupling allows to use independent precursor runs
	402	in order to account for different spin-up times. The time when coupling
[481]	403	has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>.
	404	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
	405	order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all
	406	output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	407	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	408	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	409	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	410	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	411	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	412	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	413	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	414	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	415	<span style="font-family: Courier New,Courier,monospace;">init_coupling</span>,
	416	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	417	<span style="font-family: Courier New,Courier,monospace;">mrun</span>,
	418	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	419	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	420	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	421	<span style="font-family: Courier New,Courier,monospace;">time_integration</span>,
	422	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
[392]	423
	424	<br>
[481]	425
[392]	426	Clipping of dvrp output implemented. Default colourtable for particles
	427	implemented, particle attributes (color, dvrp_size) can be set with new
[481]	428	parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>,
	429	<span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>,
	430	<span style="font-family: Courier New,Courier,monospace;">color_interval</span>,
	431	<span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>.
	432	Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>
	433	and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>.
	434	(<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	435	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	436	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	437	<span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,
	438	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
[392]	439
	440	<br>
[481]	441
[392]	442	Polygon reduction for topography and ground plate isosurface. Reduction
	443	level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
	444
	445	<br>
	446
[481]	447	Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span>
	448	/ <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>
	449	in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
	450
	451	<span style="font-family: Courier New,Courier,monospace;">bc_ns_cyc</span>
	452	for speed optimization. This gives a significant speedup of more than
	453	10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	454	<span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>,
	455	<span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>,
	456	<span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>,
	457	<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	458
[392]	459	<br>
[481]	460
[392]	461	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]	462
[392]	463	<br>
[481]	464
	465	Additional timestep criterion in case of simulations with plant canopy.
	466	(<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
	467
[392]	468	<br>
[481]	469
	470	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
	471	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>
	472
[392]	473	<br>
[481]	474
	475	External pressure gradient can be used as driving force. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	476	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	477	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	478	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	479	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	480	<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>,
	481	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	482	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	483
[392]	484	<br>
[481]	485
	486	New topography case '<span style="font-style: italic;">single_street_canyon</span>'.
	487	(<span style="font-family: Courier New,Courier,monospace;">header</span>,
	488	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	489	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	490	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	491	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	492	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	493	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	494	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	495	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	496
[392]	497	<br>
[481]	498
	499	Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</span>.
	500	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	501	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	502	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	503	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	504	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	505	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	506	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	507
[392]	508	<br>
[481]	509
	510	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>,
	511	<span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
	512
[392]	513	<br>
[481]	514
	515	xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>,
	516	<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	517	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	518	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	519	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	520	<span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>,
	521	<span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)</td>
	522	<td style="vertical-align: top; width: 189px;">average_3d_data,
[392]	523	check_for_restart, check_parameters, data_output_2d, data_output_3d,
	524	data_output_dvrp, data_output_profiles, data_output_ptseries,
	525	data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
	526	diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
	527	header, mbuild, modules, mrun, package_parin, parin,
	528	prognostic_equations, read_3d_binary, read_var_list, subjob,
	529	sum_up_3d_data, surface_coupler, timestep, time_integration,
	530	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
	531	user_header, user_init_grid, write_3d_binary, write_var_list<br>
[481]	532
[392]	533	<br>
[481]	534
	535	<span style="font-weight: bold;">new:</span>
	536	set_particle_attributes, set_slicer_attributes_dvrp</td>
[392]	537	</tr>
	538	<tr>
[481]	539	<td style="vertical-align: top; width: 27px;"><br>
[392]	540	</td>
[481]	541	<td style="vertical-align: top; width: 38px;"><br>
[392]	542	</td>
[481]	543	<td style="vertical-align: top; width: 42px;"><br>
[392]	544	</td>
[481]	545	<td style="vertical-align: top; width: 40px;"><br>
[392]	546	</td>
[481]	547	<td style="vertical-align: top; width: 27px;">C<br>
	548	</td>
	549	<td style="vertical-align: top; width: 497px;">Output of messages replaced by
	550	message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	551	<span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>,
	552	<span style="font-family: Courier New,Courier,monospace;">buoyancy</span>,
	553	<span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>,
	554	<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>,
	555	<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	556	<span style="font-family: Courier New,Courier,monospace;">coriolis</span>,
	557	<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>,
	558	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	559	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	560	<span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>,
	561	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	562	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	563	<span style="font-family: Courier New,Courier,monospace;">fft_xy</span>,
	564	<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>,
	565	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	566	<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>,
	567	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>,
	568	<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>,
	569	<span style="font-family: Courier New,Courier,monospace;">init_grid</span>,
	570	<span style="font-family: Courier New,Courier,monospace;">init_particles</span>,
	571	<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>,
	572	<span style="font-family: Courier New,Courier,monospace;">netcdf</span>,
	573	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	574	<span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>,
	575	<span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>,
	576	<span style="font-family: Courier New,Courier,monospace;">poismg</span>,
	577	<span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>,
	578	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	579	<span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>,
	580	<span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>,
	581	<span style="font-family: Courier New,Courier,monospace;">timestep</span>,
	582	<span style="font-family: Courier New,Courier,monospace;">user_actions</span>,
	583	<span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>,
	584	<span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>,
	585	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	586	<span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>,
	587	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	588	<span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>,
	589	<span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
[392]	590
	591	<br>
	592
[481]	593	Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>,
	594	<span style="font-family: Courier New,Courier,monospace;">close_file</span>,
	595	<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	596	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>,
	597	<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	598	<span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>,
	599	<span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,
	600	<span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>,
	601	<span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	602
[392]	603	<br>
	604
[481]	605	__lcmuk changed to __lc to avoid problems with Intel compiler on
	606	sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
	607
[392]	608	<br>
[481]	609
	610	For extended NetCDF files, the updated title attribute includes an
	611	update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	612
[392]	613	<br>
[481]	614
[392]	615	In case of restart runs without extension, initial profiles are not
	616	written to NetCDF-file anymore. So far, time axis always started at
[481]	617	t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>,
	618	<span style="font-family: Courier New,Courier,monospace;">modules</span>,
	619	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	620	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	621
[392]	622	<br>
[481]	623
	624	<span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to
	625	'<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill
	626	can now <br>
	627
	628	be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</span>.
	629	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	630	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	631	<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	632
[392]	633	<br>
[481]	634
[392]	635	2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
[481]	636
[392]	637	<br>
[481]	638
[392]	639	A link to the webspage appendix_a.html is printed for further
	640	information about possible reasons of the error that appeared. (message)<br>
[481]	641
[392]	642	<br>
[481]	643
[392]	644	Temperature gradient criterion for estimating the boundary layer height
	645	replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
[481]	646
[392]	647	<br>
[481]	648
	649	NetCDF unit attribute in timeseries output in case of statistic regions
	650	added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
	651
[392]	652	<br>
[481]	653
	654	Maximum number of tails is calculated from maximum number of particles
	655	and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>.
	656	(<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
	657
[392]	658	<br>
[481]	659
	660	Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span>
	661	is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	662	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	663	<span style="font-family: Courier New,Courier,monospace;">modules</span>)
[392]	664	<br>
[481]	665
[392]	666	<br>
[481]	667
	668	First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also
	669	defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
	670
[392]	671	<br>
[481]	672
	673	Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span>
	674	moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span>
	675	to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>.
	676	(<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
	677
[392]	678	<br>
[481]	679
	680	<span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>
	681	moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span>
	682	to <span style="font-family: Courier New,Courier,monospace;">inipar</span>
	683	(<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>,
	684	<span style="font-family: Courier New,Courier,monospace;">header</span>,
	685	<span style="font-family: Courier New,Courier,monospace;">parin</span>,
	686	<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	687	<span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>,
	688	<span style="font-family: Courier New,Courier,monospace;">user_header</span>,
	689	<span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>,
	690	<span style="font-family: Courier New,Courier,monospace;">user_parin</span>,
	691	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	692
[392]	693	<br>
[481]	694
	695	Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span>
	696	changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
	697
	698	<br>
	699
	700	Adjustments for runs on lcxt4 (necessary due to a software update on
	701	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>
	702	<td style="vertical-align: top; width: 189px;">advec_particles,
	703	advec_s_bc,
[392]	704	buoyancy, calc_spectra, check_for_restart, check_open,
	705	check_parameters, close_file, coriolis, cpu_log, data_output_2d,
	706	data_output_3d, data_output_dvrp, data_output_profiles,
	707	data_output_ptseries, data_output_spectra, data_output_tseries,
	708	eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
	709	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
	710	message, mrun, netcdf, package_parin, parin, plant_canopy_model,
	711	poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
[481]	712	surface_coupler, temperton_fft, timestep,
	713	user_actions,user_check_parameters, user_data_output_dvrp,
	714	user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy,
	715	user_parin, user_read_restart_data, user_spectra, write_var_list </td>
[392]	716	</tr>
	717	<tr>
[481]	718	<td style="vertical-align: top; width: 27px;"><br>
[392]	719	</td>
[481]	720	<td style="vertical-align: top; width: 38px;"><br>
[392]	721	</td>
[481]	722	<td style="vertical-align: top; width: 42px;"><br>
[392]	723	</td>
[481]	724	<td style="vertical-align: top; width: 40px;"><br>
[392]	725	</td>
[482]	726	<td style="vertical-align: top; width: 27px;">B<br>
[481]	727	</td>
	728	<td style="vertical-align: top; width: 497px;">Bugfix: Initial hydrostatic
	729	pressure profile in case of ocean runs is now calculated in 5 iteration
	730	steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
	731
[392]	732	<br>
[481]	733
	734	Bugfix: wrong sign in buoyancy production of ocean part in case of not
	735	using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>).
	736	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	737
[392]	738	<br>
[481]	739
[392]	740	Bugfix: output of averaged 2d/3d quantities requires that an avaraging
	741	interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	742
[392]	743	<br>
[481]	744
	745	Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>.
	746	(<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
	747
[392]	748	<br>
[481]	749
	750	Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>.
	751	(<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
	752
[392]	753	<br>
[481]	754
[392]	755	Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
[481]	756	if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span>
	757	is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span>
	758	and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
[392]	759	calls. This implies a possible performance loss; an alternative
	760	strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	761
[392]	762	<br>
[481]	763
[392]	764	Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
[481]	765
[392]	766	<br>
[481]	767
[392]	768	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]	769
[392]	770	<br>
[481]	771
	772	Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span>
	773	=> <span style="font-family: Courier New,Courier,monospace;">s_av</span>
	774	for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>,
	775	<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
	776
[392]	777	<br>
[481]	778
	779	Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span>
	780	becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
	781
[392]	782	<br>
[481]	783
[392]	784	Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
[481]	785
[392]	786	<br>
[481]	787
[392]	788	Bugfix: error in check, if particles moved further than one subdomain
	789	length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
[481]	790
[392]	791	<br>
[481]	792
[392]	793	Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
	794	is only written to file if its third index is > 0, arrays for tails
	795	are allocated with a minimum size of 10 tails if there is no tail
[481]	796	initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>,
	797	<span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
	798
[392]	799	<br>
[481]	800
[392]	801	Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
[481]	802
[392]	803	<br>
[481]	804
	805	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>
	806	changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on
	807	NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
	808
[392]	809	<br>
[481]	810
	811	Bugfix: output of particle time series only if particle advection is
	812	switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
	813
[392]	814	<br>
[481]	815
	816	Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span>
	817	= <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>.
	818	(<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
	819
[392]	820	<br>
[481]	821
	822	Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and
	823	z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
	824
[392]	825	<br>
[481]	826
[392]	827	Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
[481]	828
[392]	829	<br>
[481]	830
	831	If the inversion height calculated by the prerun is zero,
	832	inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
	833
[392]	834	<br>
[481]	835
[392]	836	Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
[481]	837
[392]	838	<br>
[481]	839
[392]	840	Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
	841	removed from the restart file, because otherwise, no change from a
[481]	842	fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>,
	843	<span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
	844
[392]	845	<br>
[481]	846
	847	Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span>
	848	in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)</td>
	849	<td style="vertical-align: top; width: 189px;">advec_particles,
[392]	850	check_parameters, cpu_log, data_output_2d, data_output_3d, header,
	851	init_3d_model, init_particles, init_ocean, modules, netcdf,
	852	prandtl_fluxes, production_e, read_var_list, time_integration,
	853	user_last_actions, write_var_list<br>
[481]	854
	855	</td>
	856	</tr>
	857	<tr>
	858	<td style="vertical-align: top; width: 27px;">02/02/09<br>
	859	</td>
	860	<td style="vertical-align: top; width: 38px;">SR<br>
	861	</td>
	862	<td style="vertical-align: top; width: 42px;">228<br>
	863	</td>
	864	<td style="vertical-align: top; width: 40px;">3.6<br>
	865	</td>
	866	<td style="vertical-align: top; width: 27px;">N<br>
	867	</td>
	868	<td style="vertical-align: top; width: 497px;">This
	869	release contains further additions, changes, and bugfixes for the
	870	SGI-ICE system, as well as important changes like the splitting of the
	871	user-interface into single files, a complete revision of the
	872	pre-compiling mechanism allowing to use different make-depositories
	873	simultaneously, and a revision of the reading-mechanism from restart
	874	files, which has no more restrictions in case that the previous and
	875	current run have different domain/subdomain sizes. A new handling of
	876	all kind of output messages is introduced with this release and will be
	877	applied to all existing messages within the next releases.<br>
	878
[392]	879	<br>
[481]	880
	881	<span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;">
	882
	883	<br>
	884
	885	Restart runs on SGI-ICE are working. (mrun)<br>
	886
	887	2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br>
	888
	889	<br>
	890
	891	Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this
	892	case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	893	"<span style="font-style: italic;">-K parallel</span>" for coupling.
	894	Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and
	895	<span style="font-family: Courier New,Courier,monospace;">subjob</span>
	896	for lcxt4.<br>
	897
	898	<br>
	899
	900	DVRP arguments changed to single precision, mode pathlines added.<br>
	901
	902	<br>
	903
	904	User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br>
	905
	906	<br>
	907
	908	User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span></td>
	909	<td style="vertical-align: top; width: 189px;">check_for_restart,
	910	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
	911	modules, package_parin, palm, surface_coupler, timestep<br>
	912
	913	<br>
	914
	915	Makefile, mbuild, mrun, subjob<br>
	916
	917	<br>
	918
	919	<span style="font-weight: bold;">new:</span><br>
	920
	921	init_coupling, user_additional_routines, user_check_parameters</td>
	922	</tr>
	923	<tr>
	924	<td style="vertical-align: top; width: 27px;"><br>
[392]	925	</td>
[481]	926	<td style="vertical-align: top; width: 38px;"><br>
	927	</td>
	928	<td style="vertical-align: top; width: 42px;"><br>
	929	</td>
	930	<td style="vertical-align: top; width: 40px;"><br>
	931	</td>
	932	<td style="vertical-align: top; width: 27px;">C<br>
	933	</td>
	934	<td style="vertical-align: top; width: 497px;">User interface has been
	935	split into single files.<br>
	936
	937	<br>
	938
	939	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>
	940	changed to INTEGER(8) in order to avoid "out of range" problems, which
	941	result in measured negative time intervals. (cpu_log, local_tremain,
	942	local_tremain_ini)<br>
	943
	944	<br>
	945
	946	Reading mechanism from restart files
	947	completely revised. The subdomain/total domain size is now allowed to
	948	vary arbitrarily between the current and previous run. (read_var_list,
	949	read_3d_binary, user_read_restart_data)<br>
	950
	951	<br>
	952
	953	Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>)
	954	completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
	955	One depository per block (given in the config-file) is created. Always
	956	all files from the source directory are copied to the respective
	957	depository. No additional file checks are done any more (mrun version
	958	2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option
	959	"<span style="font-family: Courier New,Courier,monospace;">-K</span>".
	960	(mbuild, mrun)<br>
	961
	962	<br>
	963
	964	Output messages (including required stop of execution) can now be
	965	handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>.
	966	All output messages will be replaced by this routine step by step
	967	within the next revisions.<br>
	968
	969	<br>
	970
	971	Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is
	972	explicitly set for better reading, although this has been already done
	973	in boundary_conds. (advec_s_bc)<br>
	974
	975	<br>
	976
	977	Origin of the xy-coordinate system shifted from the center of the first
	978	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
	979	south-left corner of this cell. (netcdf) Topography definition
	980	according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>.
	981	(init_grid, modules, user_header, user_init_grid, user_parin)</td>
	982	<td style="vertical-align: top; width: 189px;">advec_s_bc,
	983	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
	984	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
	985	user_read_restart_data<br>
	986
	987	<br>
	988
	989	Makefile, mbuild, mrun<br>
	990
	991	<br>
	992
	993	<span style="font-weight: bold;">removed:</span><br>
	994
	995	user_interface<br>
	996
	997	<br>
	998
	999	<span style="font-weight: bold;">new:</span><br>
	1000
	1001	message,
	1002	user_3d_data_averaging, user_actions, user_advec_particles,
	1003	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
	1004	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
	1005	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
	1006	user_init_grid, user_init_particles, user_init_plant_canopy,
	1007	user_last_actions, user_parin, user_parin, user_particle_attributes,
	1008	user_read_restart_data, user_spectra, user_statistics</td>
[392]	1009	</tr>
[481]	1010	<tr>
	1011	<td style="vertical-align: top; width: 27px;"><br>
	1012	</td>
	1013	<td style="vertical-align: top; width: 38px;"><br>
	1014	</td>
	1015	<td style="vertical-align: top; width: 42px;"><br>
	1016	</td>
	1017	<td style="vertical-align: top; width: 40px;"><br>
	1018	</td>
[482]	1019	<td style="vertical-align: top; width: 27px;">B<br>
[481]	1020	</td>
	1021	<td style="vertical-align: top; width: 497px;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is
	1022	reallocated in case that multigrid is used. (calc_spectra)<br>
[392]	1023
[481]	1024	<br>
	1025
	1026	Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics,
	1027	inflow_turbulence, timestep)<br>
	1028
	1029	<br>
	1030
	1031	Size of <span style="font-family: Courier New,Courier,monospace;">pf3d
	1032	</span>adjusted to the required output size (1 gridpoint less,
	1033	along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>)
	1034	in the NF90_PUT_VAR statement caused segmentation fault with the INTEL
	1035	compiler. (combine_plot_fields)<br>
	1036
	1037	<br>
	1038
	1039	Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in
	1040	case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>.
	1041	(header)<br>
	1042
	1043	<br>
	1044
	1045	Inconsistency
	1046	removed: as the thermal stratification is not taken into account for
	1047	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
	1048	<span style="font-family: Courier New,Courier,monospace;">km</span>
	1049	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>.
	1050	(production_e)<br>
	1051
	1052	<br>
	1053
	1054	Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in
	1055	case of oceans runs. (sort_particles)<br>
	1056
	1057	<br>
	1058
	1059	Bugfix: no output of particle concentration and radius unless particles
	1060	have been started. (data_output_2d)<br>
	1061
	1062	<br>
	1063
	1064	Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x\|y</span>
	1065	from restart files ignored if total numbers of grid points do not
	1066	match. (read_3d_binary)<br>
	1067
	1068	<br>
	1069
	1070	Bugfix: abort in case that absolute temperature is below zero.
	1071	(init_cloud_physics)</td>
	1072	<td style="vertical-align: top; width: 189px;">advec_particles,
	1073	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
	1074	header, inflow_turbulence, init_cloud_physics, production_e,
	1075	read_3d_binary, timestep<br>
	1076
	1077	<br>
	1078
	1079	combine_plot_fields</td>
	1080	</tr>
	1081	</tbody>
	1082	</table>
	1083	<b><blink></blink></b><br>
[62]	1084	<br>
	1085	<h2><a name="Kapitel2.0"></a>2.0  How
[493]	1086	to change the source
	1087	code and how to document modifications<br>
	1088	</h2>Currently
[392]	1089	(Sep 23rd, 2009), only selected users are allowed to commit changes to
[493]	1090	the repository. Rules given below are preliminary, until we have switched to the "trac"-System.<br>
	1091	<br>
	1092	<ol>
	1093	<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>".
	1094	Additionally, document all changes in a local file (e.g.
	1095	~/palm/current_version/CURRENT_MODIFICATIONS), including the files that
	1096	have been changed. Classify changes in three cases, new (N), changed
	1097	(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>
	1098	<br>
	1099	</li>
	1100	<li>Test the changed version, unless it works sufficiently.<br>
	1101	<br>
	1102	</li>
	1103
	1104	<li>Commit the changes to the repository<br>
	1105	<br>
	1106	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "message string" trunk<br>
	1107	</span><br>
	1108	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>
	1109	<br>
	1110	Alternatively, in case that you have made quite a lot of changes, you
	1111	can also give the contents of your file CURRENT_MODIFICATIONS as the
	1112	log message:<br>
	1113	<br>
	1114	<span style="font-family: Courier New,Courier,monospace;">   svn commit -F CURRENT_MODIFICATIONS trunk</span><br>
	1115	<br>
	1116	</li>
	1117
	1118	<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>
	1119	<br>
	1120	</li>
	1121	<li>Move the change comments in the file headers from "Current
	1122	revisions:" to "Former revisions:". Set the current svn id in front of
	1123	that.<br>
	1124	<br>
	1125	<span style="font-weight: bold;">Example:</span><br>
	1126	<br>
	1127	<span style="font-weight: bold;">before move:</span><br>
	1128	<br>
	1129	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1130	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1131	<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;">
	1132	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1133	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1134	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1135	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $</span><br style="font-family: Courier New,Courier,monospace;">
	1136	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1137	<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;">
	1138	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max </span><br>
	1139	<br>
	1140	<span style="font-weight: bold;">after move:</span><br>
	1141	<br>
	1142	<span style="font-family: Courier New,Courier,monospace;">! Current revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1143
	1144	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1145
	1146	<span style="font-family: Courier New,Courier,monospace;">! </span><br style="font-family: Courier New,Courier,monospace;">
	1147
	1148	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1149
	1150	<span style="font-family: Courier New,Courier,monospace;">! Former revisions:</span><br style="font-family: Courier New,Courier,monospace;">
	1151
	1152	<span style="font-family: Courier New,Courier,monospace;">! -----------------</span><br style="font-family: Courier New,Courier,monospace;">
	1153
	1154	<span style="font-family: Courier New,Courier,monospace;">! $Id: technical_documentation.html 506 2010-03-08 07:14:38Z raasch $<br>
	1155	!</span><br style="font-family: Courier New,Courier,monospace;">
	1156	<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>
	1157	! </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;">
	1158
	1159	<span style="font-family: Courier New,Courier,monospace;">!</span><br style="font-family: Courier New,Courier,monospace;">
	1160
	1161	<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;">
	1162
	1163	<span style="font-family: Courier New,Courier,monospace;">! var_ts is replaced by dots_max<br>
	1164	</span><br>
	1165	</li>
	1166	<li>Commit the changes in the technical documentation and the file headers:<br>
	1167	<br>
	1168	<span style="font-family: Courier New,Courier,monospace;">   svn commit -m "last commit documented" trunk</span><br>
	1169	<br>
	1170	<br>
	1171	</li>
	1172	</ol>
	1173
[392]	1174	<h2>
[62]	1175	<a name="Kapitel3.0"></a>3.0  Description
	1176	of selected parts of the
[5]	1177	model source code</h2>
[392]	1178	<b></b>
	1179	<p>This section gives links to existing descriptions about special
	1180	parts of the PALM code, e.g. special numerical methods that are used
	1181	(including mathematical background). Documents are stored in single
	1182	files with different formats. Some are in German (sorry for the
	1183	inconvenience).
[62]	1184	<br>
	1185	</p><ul> <li> <a name="UPS"></a>upstream-spline
[481]	1186	advection scheme ( <a href="methods/upstream_spline/ups.pdf">.pdf</a>
	1187	, only in German)</li> <li> <a name="Cloud_physics"></a>cloud
	1188	physics module ( <a href="methods/cloud_physics/cloud_physics.pdf">.pdf</a>
	1189	)</li>
	1190	<li> <a name="Bitkompression"></a>data compression with <a href="methods/bit_compression/bit_compression.html">bit shifting method</a> (only in German)<br>
	1191	</li>
	1192	<li>Runge-Kutta
	1193	time integration scheme ( <a href="methods/runge_kutta/runge_kutta.pdf">.pdf</a>
	1194	, only in German)</li>
	1195
[62]	1196	</ul><br>
[5]	1197
[62]	1198	<br>
	1199	<br>
	1200	<br>
	1201	<br>
	1202	<br>
	1203	<br>
	1204	<br>
[139]	1205	</body></html>

Note: See TracBrowser for help on using the repository browser.

Download in other formats:

| Impressum | ©Leibniz Universität Hannover |