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

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