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

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