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technical_documentation.html @ 413

Last change on this file since 413 was 392, checked in by raasch, 15 years ago

New:
---

Adapted for machine lck
(mrun, mbuild, subjob)

bc_lr/bc_ns in most subroutines replaced by LOGICAL variables bc_lr_cyc,
bc_ns_cyc for speed optimization
(check_parameters, diffusion_u, diffusion_v, diffusion_w, modules)

Additional timestep criterion in case of simulations with plant canopy (timestep)

Check for illegal entries in section_xy|xz|yz that exceed nz+1|ny+1|nx+1
(check_parameters)

Clipping of dvrp output implemented. Default colourtable for particles
implemented, particle attributes (color, dvrp_size) can be set with new
parameters particle_color, particle_dvrpsize, color_interval,
dvrpsize_interval (init_dvrp, data_output_dvrp, modules, user_data_output_dvrp).
Slicer attributes (dvrp) are set with new routine set_slicer_attributes_dvrp
and are controlled with existing parameters slicer_range_limits.
(set_slicer_attributes_dvrp)

Ocean atmosphere coupling allows to use independent precursor runs in order
to account for different spin-up times. The time when coupling has to be
started is given by new inipar parameter coupling_start_time. The precursor
ocean run has to be started using new mrun option "-y" in order to add
appendix "_O" to all output files.
(check_for_restart, check_parameters, data_output_2d, data_output_3d,
data_output_profiles, data_output_ptseries, data_output_spectra,
data_output_tseries, header, init_coupling, modules, mrun,
parin, read_var_list, surface_coupler, time_integration, write_var_list)

Polygon reduction for topography and ground plate isosurface. Reduction level
for buildings can be chosen with parameter cluster_size. (init_dvrp)

External pressure gradient (check_parameters, header, init_3d_model, modules,
parin, prognostic_equations, read_var_list, write_var_list)

New topography case 'single_street_canyon' (header, init_grid, modules, parin,
read_var_list, user_check_parameters, user_header, user_init_grid, write_var_list)

Option to predefine a target bulk velocity for conserve_volume_flow
(check_parameters, header, init_3d_model, modules, parin, read_var_list,
write_var_list)

Option for user defined 2D data output in xy cross sections at z=nzb+1
(data_output_2d, user_data_output_2d)

xy cross section output of surface heatfluxes (latent, sensible)
(average_3d_data, check_parameters, data_output_2d, modules, read_3d_binary,
sum_up_3d_data, write_3d_binary)

average_3d_data, check_for_restart, check_parameters, data_output_2d, data_output_3d, data_output_dvrp, data_output_profiles, data_output_ptseries, data_output_spectra, data_output_tseries, init_coupling, init_dvrp, init_grid, init_3d_model, header, mbuild, modules, mrun, package_parin, parin, prognostic_equations, read_3d_binary, read_var_list, subjob, surface_coupler, timestep, time_integration, user_check_parameters, user_data_output_2d, user_data_output_dvrp, user_header, user_init_grid, write_3d_binary, write_var_list

New: set_particle_attributes, set_slicer_attributes_dvrp

Changed:

lcmuk changed to lc to avoid problems with Intel compiler on sgi-ice
(poisfft)

For extended NetCDF files, the updated title attribute includes an update of
time_average_text where appropriate. (netcdf)

In case of restart runs without extension, initial profiles are not written
to NetCDF-file anymore. (data_output_profiles, modules, read_var_list, write_var_list)

Small change in formatting of the message handling routine concering the output in the
job protocoll. (message)

initializing_actions='read_data_for_recycling' renamed to 'cyclic_fill', now
independent of turbulent_inflow (check_parameters, header, init_3d_model)

2 NetCDF error numbers changed. (data_output_3d)

A Link to the website appendix_a.html is printed for further information
about the possible errors. (message)

Temperature gradient criterion for estimating the boundary layer height
replaced by the gradient criterion of Sullivan et al. (1998). (flow_statistics)

NetCDF unit attribute in timeseries output in case of statistic regions added
(netcdf)

Output of NetCDF messages with aid of message handling routine.
(check_open, close_file, data_output_2d, data_output_3d,
data_output_profiles, data_output_ptseries, data_output_spectra,
data_output_tseries, netcdf, output_particles_netcdf)

Output of messages replaced by message handling routine.
(advec_particles, advec_s_bc, buoyancy, calc_spectra, check_for_restart,
check_open, coriolis, cpu_log, data_output_2d, data_output_3d, data_output_dvrp,
data_output_profiles, data_output_spectra, fft_xy, flow_statistics, header,
init_1d_model, init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
netcdf, parin, plant_canopy_model, poisfft_hybrid, poismg, read_3d_binary,
read_var_list, surface_coupler, temperton_fft, timestep, user_actions,
user_data_output_dvrp, user_dvrp_coltab, user_init_grid, user_init_plant_canopy,
user_parin, user_read_restart_data, user_spectra )

Maximum number of tails is calculated from maximum number of particles and
skip_particles_for_tail (init_particles)

Value of vertical_particle_advection may differ for each particle group
(advec_particles, header, modules)

First constant in array den also defined as type double. (eqn_state_seawater)

Parameter dvrp_psize moved from particles_par to dvrp_graphics_par. (package_parin)

topography_grid_convention moved from userpar to inipar (check_parameters,
header, parin, read_var_list, user_check_parameters, user_header,
user_init_grid, user_parin, write_var_list)

Default value of grid_matching changed to strict.

Adjustments for runs on lcxt4 (necessary due to an software update on CRAY) and
for coupled runs on ibmy (mrun, subjob)

advec_particles, advec_s_bc, buoyancy, calc_spectra, check_for_restart, check_open, check_parameters, close_file, coriolis, cpu_log, data_output_2d, data_output_3d, data_output_dvrp, data_output_profiles, data_output_ptseries, data_output_spectra, data_output_tseries, eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model, init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid, message, mrun, netcdf, output_particles_netcdf, package_parin, parin, plant_canopy_model, poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, sort_particles, subjob, user_check_parameters, user_header, user_init_grid, user_parin, surface_coupler, temperton_fft, timestep, user_actions, user_data_output_dvrp, user_dvrp_coltab, user_init_grid, user_init_plant_canopy, user_parin, user_read_restart_data, user_spectra, write_var_list

Errors:

Bugfix: Initial hydrostatic pressure profile in case of ocean runs is now
calculated in 5 iteration steps. (init_ocean)

Bugfix: wrong sign in buoyancy production of ocean part in case of not using
the reference density (only in 3D routine production_e) (production_e)

Bugfix: output of averaged 2d/3d quantities requires that an avaraging
interval has been set, respective error message is included (check_parameters)

Bugfix: Output on unit 14 only if requested by write_binary.
(user_last_actions)

Bugfix to avoid zero division by km_neutral (production_e)

Bugfix for extended NetCDF files: In order to avoid 'data mode' errors if
updated attributes are larger than their original size, NF90_PUT_ATT is called
in 'define mode' enclosed by NF90_REDEF and NF90_ENDDEF calls. This implies a
possible performance loss; an alternative strategy would be to ensure equal
attribute size in a job chain. (netcdf)

Bugfix: correction of initial volume flow for non-flat topography (init_3d_model)
Bugfix: zero initialization of arrays within buildings for 'cyclic_fill' (init_3d_model)

Bugfix: to_be_resorted => s_av for time-averaged scalars (data_output_2d, data_output_3d)

Bugfix: error in formatting the output (message)

Bugfix: avoid that ngp_2dh_s_inner becomes zero (init_3_model)

Typographical error: unit of wpt in dots_unit (modules)

Bugfix: error in check, if particles moved further than one subdomain length.
This check must not be applied for newly released particles. (advec_particles)

Bugfix: several tail counters are initialized, particle_tail_coordinates is
only written to file if its third index is > 0, arrays for tails are allocated
with a minimum size of 10 tails if there is no tail initially (init_particles,
advec_particles)

Bugfix: pressure included for profile output (check_parameters)

Bugfix: Type of count and count_rate changed to default INTEGER on NEC machines
(cpu_log)

Bugfix: output if particle time series only if particle advection is switched
on. (time_integration)

Bugfix: qsws was calculated in case of constant heatflux = .FALSE. (prandtl_fluxes)

Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0) (data_output_2d)

Typographical errors (netcdf)

If the inversion height calculated by the prerun is zero, inflow_damping_height
must be explicitly specified (init_3d_model)

Small bugfix concerning 3d 64bit netcdf output format (header)

Bugfix: dt_fixed removed from the restart file, because otherwise, no change
from a fixed to a variable timestep would be possible in restart runs.
(read_var_list, write_var_list)

Bugfix: initial setting of time_coupling in coupled restart runs (time_integration)

advec_particles, check_parameters, cpu_log, data_output_2d, data_output_3d, header, init_3d_model, init_particles, init_ocean, modules, netcdf, prandtl_fluxes, production_e, read_var_list, time_integration, user_last_actions, write_var_list

Property svn:keywords set to Id

File size: 207.4 KB

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1	<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
2	<html><head>
3
4	<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	</font>a
6	<b>pa</b>rallelized
7	<b>L</b>ES <b>m</b>odel
8	<br><hr width="100%">
9	<br><font size="+2">technical/numerical documentation</font>
10	<br>
11	<br>
12	<br><table nosave="" cellpadding="0" cellspacing="0"> <caption>  <br> </caption><tbody>
13	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Current
14	model version:</b></td> <td><span style="font-weight: bold;">3.7 (rev 392)</span></td> </tr>
15	<tr nosave=""> <td nosave=""><b>Last
16	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 392 2009-09-24 10:39:14Z heinze $</b></td> </tr>
17	</tbody>
18	</table><hr width="100%">
19	<p><font size="+2">Table of contents</font>
20	<br>
21	<br>
22	</p><ul> <a href="#Kapitel1.0">1.0</a>
23	History of changes <p><a href="#Kapitel2.0">2.0</a>
24	How to change the model source
25	code </p> <p><a href="#Kapitel3.0">3.0</a>
26	Description of selected parts
27	of
28	the model source code <br>
29	</p>
30	</ul><b></b><br>
31
32	<h2><a name="Kapitel1.0"></a>1.0
33	History of changes</h2>
34	The following table documents all changes to the model since July, 7th
35	1998. Entries in the fourth column specify the type of the change:
36	change
37	of existing code (C), new code (N) or bugfix (B). More detailed
38	information
39	about the changes may be found in the header comment lines of the
40	respective
41	routines.
42	<br>
43	<br><table nosave="" style="width: 100%;" border="1"> <caption>  <br> </caption><tbody>
44	</tbody><tbody> </tbody> <tbody> <tr> <td><b>date</b></td>
45	<td><b>author</b></td> <td><b>model</b>
46	<br> <b>version</b></td> <td><b>type</b></td>
47	<td><b>description</b></td> <td><b>affected
48	routines</b></td> </tr> <tr nosave="" valign="top"> <td>06/07/98</td> <td>SR</td>
49	<td>1.0</td> <td>C</td> <td nosave="">Änderung
50	von Default-Werten
51	(initializing_actions, end_time,
52	fcl_factor, use_prior_plot1d_parameters), zusätzliche
53	Überprüfung
54	von Parametern auf Zulässigkeit (prandtl_layer, psolver, nx,
55	ny,
56	nz,
57	fcl_factor), Höhe der Schnittebenen der Horizontalschnitte
58	wird
59	auf
60	Plots exakt ausgegeben (uv- bzw. w-Gitter).</td> <td>modules,
61	check_parameters, plot_2d</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
62	<td>1.0</td> <td>N</td> <td>Neues Modul
63	test_variables wird in (fast) allen
64	Programmteilen benutzt
65	(USE). <b>Wichtig</b>: dieses Modul steht in der Datei <tt>module_test.f90.
66	D</tt>iese Datei muß in der mrun- und add_library -
67	Konfigurationsdatei
68	bei der Variablen <tt>module_files</tt>
69	aufgeführt werden.</td> <td nosave="">(fast)
70	alle  <br>
71	Neu: module_test</td> </tr> <tr nosave="" valign="top"> <td>16/07/98</td> <td>SR</td>
72	<td>1.0</td> <td>N</td> <td nosave="">Anpassung
73	an die T3E-Rechner in Juelich (cpp -
74	Direktiven)</td> <td>advec_s_bc, check_open,
75	check_parameters, cpu_zeitmessung,
76	init_pegrid,
77	local_getenv, local_system, local_tremain, local_tremain_ini, poisfft</td>
78	</tr> <tr nosave="" valign="top"> <td>24/07/98</td>
79	<td>MS</td> <td>1.0</td> <td>C</td>
80	<td nosave="">Anpassung des Druckloesealgorithmusses an
81	Vorgehensweise von
82	Schmidt, Schumann und Volkert (DFVLR-Mitteilung 84-15, S.
83	20-26) </td> <td>poisfft</td> </tr> <tr nosave="" valign="top"> <td>27/07/98</td>
84	<td>MS</td> <td>1.0</td> <td>C</td>
85	<td nosave="">Berechnung von l in maketri geschieht nun
86	ausserhalb der k-Schleife,
87	da unabhaengig von k, dadurch Rechenzeitersparnis </td> <td>poisfft</td>
88	</tr> <tr nosave="" valign="top"> <td>05/08/98</td>
89	<td>SR</td> <td>1.0</td> <td>C</td>
90	<td>Entfernung der Sonderbehandlung der Advektionsterme
91	(Piascek-Williams)
92	bei k=1. Terme werden nun überall gleich berechnet. Evtl.
93	leichte
94	Erhöhung der Varianzen in Oberflächennähe.</td>
95	<td nosave="">advec_u_pw, advec_v_pw, advec_w_pw</td>
96	</tr> <tr nosave="" valign="top"> <td nosave="">"</td> <td>SR</td> <td>1.0</td>
97	<td>C</td> <td>Mischungsweganpassung (s.
98	adjust_mixing_length) erfolgt nur
99	noch bei
100	k=1. Unrealistische sekundäre Maxima in den Km-Profilen
101	oberhalb
102	der
103	Prandtl-Schicht werden damit vermieden. Leichte Änderungen in
104	den
105	oberflächennahen Turbulenzgrößen sind die
106	Folge.</td> <td>diffusivities</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
107	<td>1.0</td> <td>B</td> <td>Falsche
108	Berechnung der benötigten CPU-Zeit pro Sekunde
109	simulierter
110	Zeit bei Fortsetzungsläufen korrigiert.  <p>Berechnung
111	von cross_uxmin(1) und cross_uxmax(1) aus den
112	Werten von
113	ug und vg entfernt. Lieferte falsche Wertebereiche für Plots
114	von
115	Vertikalprofilen,
116	wenn im ersten Koordinatenkreuz nicht die Windgeschwindigkeiten
117	gezeichnet
118	wurden.</p> </td> <td nosave="">header,
119	check_parameters</td> </tr> <tr nosave="" valign="top"> <td nosave="">"</td> <td>SR</td>
120	<td>1.0</td> <td>N</td> <td>Das
121	erlaubte Maximum und Minimum der Rif-Zahl ist nun mittels
122	der Initialparameter
123	rif_max und rif_min einstellbar (Werte waren bisher fest auf -2.0, +1.0
124	eingestellt).</td> <td>check_parameters, header,
125	init_1d_model, modules, parin,
126	prandtl_fluxes,
127	read_var_list, write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">23/09/98</td>
128	<td>SR</td> <td>1.0</td> <td>B</td>
129	<td>Initialisierung von Feldern im Fall von initializing_action =
130	"<i>set_constant_profiles</i>"
131	und "<i>set_1d-model_profiles</i>" korrigiert.  <p>2D-Plotausgabe
132	von u* und theta* korrigiert. Hier wurden
133	bisher falsche
134	Felder herausgeschrieben.  </p> <p>Bei
135	SOR-Aufrufen war bisher dp nicht initialisiert.
136	Entsprechend geändert.</p> </td> <td>init_3d_model,
137	plot_2d, pres</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
138	<td>1.0</td> <td>C</td> <td nosave="">Ausgabeformate
139	für Statistik-Ausgaben auf
140	Datei RUN_CONTROL
141	um einige Kommastellen erweitert.  <p>Lieferung von
142	ausführlicheren Informationen bei
143	Programmabbruch
144	durch Unterschreitung des minimal erlaubten Zeitschritts.</p> </td>
145	<td>run_control, timestep</td> </tr> <tr nosave="" valign="top"> <td nosave="">"</td>
146	<td>SR</td> <td>1.0</td> <td>N</td>
147	<td>Rechnungen mit geneigter Ebene zur Simulation von
148	Kaltluftabflüssen
149	sind erlaubt. Gestartet und gesteuert werden sie mit dem
150	Intialisierungsparameter <tt>alpha_surface</tt>.
151	Realisiert wird die geneigte Ebene durch entsprechende
152	Schrägstellung
153	des Schwerkraftvektors. Dadurch erhält auch die u-Komponente
154	der
155	Windgeschwindigkeit
156	einen Anteil der Auftriebskraft.  <p>Diese
157	Implementierung ist noch nicht abgeschlossen. Die
158	Simulation von
159	Kaltluftabflüssen erfordert bisher noch Eingriffe "von Hand".</p>
160	</td> <td>buoyancy, check_parameters, header, leap_frog,
161	modules,
162	parin, prandtl_fluxes,
163	read_var_list, write_var_list</td> </tr> <tr nosave="" valign="top"> <td>15/12/98</td> <td>SR</td>
164	<td>1.0</td> <td>N</td> <td>Vereinbarung
165	einer Cache-Layer zur schnelleren binären
166	I/O auf
167	T3E-Rechnern.  <p>Ermittelung wahrer I/O-Zeiten
168	für binäre
169	Ein-/Ausgabe auf
170	T3E-Rechnern mit TIMEF.</p> </td> <td nosave="">check_open,
171	<br>cpu_zeitmessung, init_3d_model, write_3d_model</td> </tr>
172	<tr nosave="" valign="top"> <td nosave="">"</td>
173	<td>SR</td> <td>1.0</td> <td>B</td>
174	<td>Bekanntgabe von run_description_header an alle
175	PE's.  <p>Diese Programmänderung erfordert auf
176	T3E-Rechnern
177	zwingend den
178	Einsatz der MPI-Version mpt.1.2.0.1. In dieser neuen Version tritt auch
179	der alte Fehler in MPI_ALLREDUCE nicht mehr auf, so daß ab
180	jetzt
181	mpt.1.1.0.1 nicht mehr verwendet werden muß.</p> </td>
182	<td>parles</td> </tr> <tr nosave="" valign="top"> <td nosave="">05/02/99</td>
183	<td>SR</td> <td>1.1</td> <td>C/N</td>
184	<td>Implementierung des Upstream-Spline- Verfahrens zur Advektion
185	von Impuls
186	und skalaren Größen (neue UP's, s. rechts).
187	Berechnung von
188	Variablen
189	für spezielle Advektionsverfahren in eigenständiges
190	UP
191	ausgelagert
192	(<tt>init_advec</tt> + eigenes Modul <tt>advection</tt>).
193	Reines
194	Euler-/Upstream-Verfahren
195	kann gerechnet werden.  <p>Schnelle binäre I/O
196	(s. 15/12/98) wieder abgeschaltet, da
197	Dateien
198	nicht wieder einlesbar sind. Druckstörung (p) wird zu Beginn
199	auf 0
200	gesetzt, damit sie keine Tendenzen im ersten Zeitschritt hervorruft.</p>
201	</td> <td>advec_s_bc, check_open, check_parameters,
202	flow_statistics,
203	header,
204	init_3d_model, init_grid, leap_frog, modules, parin, plot_2d, plot_ts,
205	read_var_list, timestep, write_3d_binary, write_var_list  <p><b>Neu:</b>
206	<br>
207	advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, init_advec,
208	long_filter,
209	spline_x, spline_y, spline_z</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">24/02/99</td>
210	<td>SR</td> <td>1.1a</td> <td>C/N</td>
211	<td>Kleinere Ergänzungen / Änderungen
212	für Upstream
213	- Spline,  <br>
214	Diverse Verbesserungen bei Berechnung der Diffusionskoeffizienten
215	(exaktere
216	Formulierung von Scherungen, Dissipation gemaess Original - Deardorff -
217	Ansatz, Mischungswegreduktion nur, wenn Schichtung sowohl oberhalb als
218	auch unterhalb des entsprechenden Gitterpunktes stabil ist),
219	Wertebegrenzung
220	bei Spline - Berechnung zur Verhinderung von "Überschwingern"</td>
221	<td>check_parameters, diffusion_e, diffusion_pt, diffusivities,
222	header,
223	init_advec, long_filter, modules, production_e, spline_x, spline_y,
224	spline_z</td> </tr> <tr nosave="" valign="top">
225	<td>"</td> <td nosave="">SR</td> <td>1.1a</td>
226	<td>N/B</td> <td>Erweiterung des des Bott - Chlond -
227	Schemas auf Advektion der
228	TKE,
229	Korrektur der Dichteberechnung (war falsch bei Galilei-Transformation)</td>
230	<td>advec_s_bc, leap_frog</td> </tr> <tr nosave="" valign="top"> <td nosave="">01/03/99</td>
231	<td>MS</td> <td>1.1b</td> <td>N</td>
232	<td>Kleinere Ergänzungen für Upstream -
233	Spline:  <ul> <li>Gradientenkontrolle
234	für den nicht-parallelen Teil</li> <li>statistische
235	Auswertung über den prozentualen Anteil
236	des
237	Upstream-Verfahrens
238	an der Gesamtadvektion fuer nicht-parallelen Teil</li> </ul>
239	</td> <td>modules, spline_x, spline_y, spline_z</td>
240	</tr> <tr nosave="" valign="top"> <td>"</td>
241	<td>SR</td> <td>1.1b</td> <td>N</td>
242	<td>Datenkompression für 3D-Plotausgaben</td> <td nosave="">check_open, check_parameters, close_files, header,
243	modules,
244	parin, plot_3d  <p><b>Neu:</b> <br>
245	write_compressed</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">03/03/99</td>
246	<td>SR</td> <td>1.1c</td> <td>B/C</td>
247	<td>Schnelle binäre I/O auf T3E-Rechnern funktioniert
248	jetzt.
249	Beim
250	binären Einlesen dürfen Records nicht mit dem Trick "<tt>READ
251	(..) idum</tt>" überlesen werden. Zeitmessungen auf T3E
252	erfolgen
253	jetzt
254	grundsätzlich mit <tt>TIMEF.</tt></td> <td>check_open,
255	cpu_zeitmessung, init_3d_model, modules,
256	write_3d_binary</td> </tr> <tr nosave="" valign="top"> <td nosave="">25/03/99</td>
257	<td>SR</td> <td>1.1d</td> <td>N</td>
258	<td>Einbau einer Rayleigh-Dämpfungsschicht sowie
259	flexiblere
260	Wahl der
261	numerischen Begrenzer für das Upstream - Spline - Verfahren.</td>
262	<td>check_parameters, header, init_3d_model, leap_frog, modules,
263	parin,
264	read_var_list, spline_x, spline_y, spline_z, write_var_list</td> </tr>
265	<tr nosave="" valign="top"> <td nosave="">"</td>
266	<td>SR</td> <td>1.1d</td> <td>B</td>
267	<td>Korrektur des Zeitschrittkriteriums bei z=zp im 1D-Modell</td>
268	<td>init_1d_model</td> </tr> <tr nosave="" valign="top"> <td>25/11/99</td> <td>SR</td>
269	<td>1.1e</td> <td>N</td> <td nosave="">Partikelplots
270	mit vtk-Graphiksoftware sind auf t3eh
271	möglich.
272	Ausgabe erfolgt im dvr-Format. Bisher noch nicht nutzbar, da noch
273	Einstellmöglichkeiten
274	für die Partikelquelle(n) fehlen. <b>Wichtig:</b>
275	Die Benutzung
276	der
277	vtk-Software erfordert die zusätzliche mrun-Option <tt>-g</tt>.
278	Das
279	Hauptprogramm <tt>parles</tt> wird in diesem Fall zum
280	Unterprogramm
281	und
282	von einem c++-Programm aus aufgerufen.</td> <td>header,
283	init_3d_model, init_pegrid, leap_frog, modules,
284	parin, parles,
285	read_var_list, write_var_list  <p><b>Neu:</b>
286	<br>
287	advec_particles, init_particles, plot_particles</p> </td> </tr>
288	<tr nosave="" valign="top"> <td>"</td>
289	<td>SR</td> <td>1.1e</td> <td nosave="">B/C</td>
290	<td>TIMEF-Zeitmessungen von Subroutine- auf Function-Aufruf
291	umgestellt.
292	Laufindexkorrektur in <tt>spline_y</tt>. Fehler trat bei
293	nx /= ny auf.</td> <td>cpu_zeitmessung, spline_y</td>
294	</tr> <tr nosave="" valign="top"> <td nosave="">28/12/99</td> <td>SR</td> <td>1.1f</td>
295	<td>N</td> <td>Plot von Isooberflächen mit
296	vtk-Graphiksoftware sind auf
297	t3eh
298	möglich. Ausgabe erfolgt im dvr-Format. Bisher noch nicht
299	allgemein
300	nutzbar, da noch diverse manuelle Eingriffe nötig sind.</td>
301	<td>header, leap_frog, modules, parin, plot_particles,
302	read_var_list, write_var_list  <p><b>Neu:</b>
303	<br>
304	plot_isosurface</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">10/01/00</td>
305	<td>SR</td> <td>1.2</td> <td>C</td>
306	<td>Randbedingungen für w (=0) werden explizit gesetzt,
307	und
308	zwar nicht
309	nur bei  <tt>k = nzb, nzt+1</tt> sondern auch
310	bei  <tt>k =
311	nzt</tt>,
312	wo bislang der vom vorigen Zeitschritt durch den Drucklöser
313	ermittelte
314	Wert stand. Auch jetzt wird der Wert bei k = nzt anschließend
315	durch
316	den Drucklöser modifiziert. Soweit bis jetzt abzusehen, hat
317	diese
318	Änderung nur minimale Auswirkungen auf den Prognoseverlauf.
319	Evtl.
320	gibt es stärkere Auswirkungen bei exzessivem Auftreten von
321	Schwerewellen
322	am oberen Rand (die dort aber eigentlich sowieso nicht
323	hingehören).  <br>
324	Variablenübergabe an <tt>boundary_conds</tt>
325	erfolgt  <br>
326	über Modul und nicht mehr per Parameterliste.  <p>Bei
327	Galilei-Transformation wird jetzt defaultmäßig
328	der geostrophische
329	Wind als Translationsgeschwindigkeit verwendet (neuer
330	Initialisierungsparameter <tt>use_ug_for_galilei_tr</tt>).
331	Dadurch wird das verstärkte Auftreten von Schwerewellen bei
332	höheren
333	geostrophischen Windgeschwindigkeiten unterdrückt.  </p>
334	<p>3D-Feldvariablen (u, v, w, pt, e, km, kh) sowie einige
335	2D-Variablen
336	(usws, vsws, rif, shf) sind nun als Pointer deklariert, denen nach
337	jedem
338	Zeitschritt neue Targets zugeordnet werden (für die
339	benötigten
340	3 Zeitebenen existieren die Targets ..._1 (z.B. u_1), ..._2, ..._3).
341	Durch
342	die jeweilige Neuzuordnung der Targets entfällt das
343	Umspeichern
344	der
345	Zeitebenen komplett (Zeitersparung: ca. 5% der
346	Gesamtrechenzeit).  <br>
347	Die Umordnung der Zeitebenen wurde ins neue UP <tt>swap_timelevel</tt>
348	ausgelagert.  <br> <b>Wichtig:</b> Die
349	Übersetzungszeiten haben durch die
350	Einführung
351	der Pointer t.w. sehr deutlich zugenommen (<tt>leap_frog</tt>
352	benötigt
353	jetzt z.B. ca. 60 Sekunden). Außerdem benötigt der
354	Compiler
355	jetzt wesentlich mehr Speicher. Der "memory"-Parameter in den
356	Konfigurationsdateien
357	(.mrun.config, .al.config) muss nun mindestens den Wert 60 (MB) (t3eh,
358	t3ej2) bzw. 45 (t3eb) und 96 (vpp) haben.  <br> <b>Achtung:</b>
359	bislang wurde diese Änderung nur für
360	das
361	reine Leapfrog-Verfahren getestet!  </p> <p>Neue
362	Laderoption "<tt>-D preset=nan</tt>" empfohlen (s.
363	Beispiel-Konfigurationsdatei).
364	Ebenso empfehlenswert für Debug-Läufe: Compileroption
365	"<tt>-ei</tt>".
366	Diese bewirkt einen Programmabbruch, falls mit nicht initialisierten
367	Variablen
368	gearbeitet wird (ist aber zeitaufwendig in der Ausführung!).</p>
369	</td> <td>boundary_conds, check_parameters, header,
370	init_3d_model,
371	leap_frog,
372	modules, parin, read_var_list, timestep, write_var_list  <p><b>Neu:</b>
373	<br>
374	swap_timelevel</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">10/01/00</td>
375	<td>SR</td> <td>1.2</td> <td>B</td>
376	<td>Der Asselin-Filter wird vor Umordnung der Zeitebenen
377	aufgerufen. Dies
378	geschah bisher fälschlicherweise erst danach, sodass der
379	Zeitfilter
380	asymmetrisch arbeitete.  <br> <b>Achtung:</b>
381	diese Änderung hat Auswirkungen auf den
382	Prognoseverlauf.
383	Die Testergebnis-Datei wurde entsprechend geändert.</td>
384	<td>leap_frog</td> </tr> <tr nosave="">
385	<td nosave="" valign="top">14/02/00</td> <td nosave="" valign="top">MS</td> <td nosave="" valign="top">1.2</td> <td nosave="" valign="top">B/C</td> <td><b>1D-Modell:</b>
386	<br>
387	Der Asselin-Filter im 1D-Modell wird nun auch vor der Umordnung der
388	Zeitebenen aufgerufen (s.o.).  <p><b>3D-Modell:</b>
389	<br>
390	TKE wurde bisher bei <tt>scalar_advec=bc-scheme</tt> einer
391	zeitlichen
392	Filterung unterzogen. Dies wird nun unterbunden.  </p> <p>Die
393	Divergenz der Impulsflüsse an der Prandtl - Schicht -
394	Obergrenze
395	wird nun über eine ganze Gitterweite gebildet. Die bisherige
396	Methode
397	lieferte im Vergleich mit Ergebnissen anderer LES-Modelle  zu
398	große
399	Impulsflüsse.  </p> <p>Bei der
400	Berechnung der Diffusion der Temperatur werden die
401	Diffusionskoeffizienten
402	nun wieder durch Mittelung für die entsprechenden
403	Gitterpunkte
404	bereitgestllt. Das Maximumkriterium, das im Zuge der Implementierung
405	des
406	Upstream-Spline Advektionsverfahrens eingebaut wurde, bewirkte ein zu
407	rasches
408	Anwachsen der Grenzschicht mit der Zeit.  </p> <p><b>Achtung:</b>
409	diese Änderungen haben Auswirkungen auf
410	den Prognoseverlauf.
411	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
412	<td nosave="" valign="top">init_1d_model,
413	asselin_filter,
414	diffusion_u, diffusion_v,  <br>
415	diffusion_pt</td> </tr> <tr nosave="" valign="top"> <td nosave="">17/02/00</td>
416	<td>MS</td> <td>2.0</td> <td>N</td>
417	<td><b>Allgemeine Beschreibung der Änderungen:</b>
418	<br>
419	vollständige Implementierung des wolkenphysikalischen
420	Moduls  <p>Zur Implementierung der Wolkenphysik waren
421	umfangreiche
422	Änderungen
423	in zahlreichen Programmteilen notwendig (Beschreibung <a href="#Cloud_physics">siehe
424	unten</a> ). Im einzelnen wurden folgende Unprogramme
425	geändert:  <br> <b>modules</b>:
426	<br>1) Bereitstellung neuer 3D-, 2D- und 1D-Felder für
427	die Prognose
428	des Gesamtwassergehaltes  <br>
429	2) "cloud_parameters" als neues Modul mit wolkenphysikalischen
430	Variablen  <br> <b>parin: </b>Initialisierungsparameterliste
431	wurde erweitert
432	(s.u.)  <br> <font color="#000000"><b>read_var_list,
433	write_var_list,
434	write_3d_binary: </b>In/Output
435	der neuen Initialisierungsparamter und Felder für
436	Fortsetzungsläufe </font> <br> <font color="#000000"><b>check_parameters:</b>
437	Initialisierung
438	des
439	Feuchteprofils und Ausgabe von neuen Vertikalprofilen: </font>
440	<br> <font color="#ff0000">vpt</font><font color="#000000">: virtuelle
441	poteniellen
442	Temperatur,</font> <br> <font color="#ff0000">lpt</font><font color="#000000">:
443	potentielle
444	Flüssigwassertemperatur,</font> <br> <font color="#ff0000">q</font><font color="#000000">:
445	Gesamtwassergehalt,</font> <br> <font color="#ff0000">qv</font><font color="#000000">:
446	spezifische
447	Feuchte,</font> <br> <font color="#ff0000">ql</font><font color="#000000">:
448	Flüssigwassergehalt,</font> <br> <font color="#ff0000">w"vpt", wvpt, wvpt</font><font color="#000000">:
449	Auftriebsfluss (subskalig, aufgelöst, gesamt),</font> <br>
450	<font color="#ff0000">w"q", wq, wq</font><font color="#000000">:
451	Wasserfluss (subs., aufg., ges.),</font> <br> <font color="#ff0000">w"qv", wqv, wqv</font><font color="#000000">:
452	Feuchtefluss (subs, aufg., ges.)</font> <br> <b>init_3d_model</b>:
453	Initialisierung aller
454	Feuchte/Wasserfelder  <br> <b>init_1d_model</b>:
455	Anpassung an Rechnungen mit Feuchte  <br> <b>header</b>:
456	Headerausgaben für Feuchtebehandlung und
457	Wolkenphysik
458	eingefügt, außerdem Formatnummern erweitert um Platz
459	für
460	weitere Ausgaben zu schaffen  <br> <b>leap_frog:</b>
461	<br>
462	1) alle prognostischen Gleichungen wurden in prognostic_equations
463	ausgelagert  <br>
464	2) Aufrufe der neuen Unterprogramme (UP) compute_vpt,
465	calc_liquid_water_content  <br>
466	3) veraenderter Aufruf von diffusivities  <br> <b><tt>b</tt>oundary_conds,
467	asselin_filter, swap_timelevel,
468	flow_statistics: </b>Anpassung
469	an Feuchtebehandlung  <br> <b>plot2d, plot3d</b>:
470	Ausgabemöglichkeiten von q und ql <br> <b>buoyancy</b>:
471	Anpassung des Autriebstermes an
472	Feuchtebehandlung
473	durch neue Übergabeparameter: Temperatur + Nummer des
474	entsprechenden
475	mittleren Temperaturprofils  <br> <b>diffusion_e</b>:
476	Anpassung der Mischungswegberechnung an
477	Feuchtebehandlung
478	durch Variation der Übergabeparameter  <br> <b>production_e</b>:
479	TKE-Produktion durch Auftriebskräfte an
480	Feuchtebehandlung
481	angepasst  <br> <b>diffusivities</b>:
482	siehe diffusion_e  <br> <b>prandtl-fluxes</b>:
483	Prandtl-Schicht fuer den
484	Gesamtwassergehalt
485	eingefügt  </p> <p>Zusätzlich
486	wurden folgende Unterprogramme NEU
487	eingeführt:  <br> <b>inti_cloud_physics</b>:
488	Initialisierung wolkenphysikalischer
489	Parameter  <br> <b>prognostic_equations</b>:
490	Auslagerung der prognostischen
491	Gleichungen
492	aus leap_frog, zusätzliche porgnostische Gleichung
493	für den
494	Gesamtwassergehalt  <br> <b>diffusion_s</b>:
495	Berechnung der Diffusion skalarer
496	Größen
497	(Temperatur und Gesamtwassergehalt), ersetzt diffusion_pt  <br>
498	<b>calc_liquid_water_content</b>: Berechnung des
499	Flüssigwassergehalts  <br> <b>calc_radiation</b>:
500	Parametrisierung langwelliger
501	Strahlungsprozesse
502	über des Schema der effektiven Emissivität  <br>
503	<b>calc_precipitation</b>:Parametrisierung von
504	Niederschlagsprozessen
505	mit Hilfe eines vereinfachten Kesslerschemas  <br> <b>impact_of_latent_heat</b>:
506	Berücksichtigung der durch
507	Niederschlagsprozesse
508	zurückbleibenden latenten Waerme innerhalb eines
509	Gittervolumens  <br> <b>compute_vpt</b>:
510	Berechnung der virtuellen potentiellen
511	Temperatur  </p> <p><b>Liste der neuen
512	Initialisierungsparameter:</b> <br> <table nosave="" border="1"> <caption>  <br> </caption><tbody>
513	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Parameter</b></td>
514	<td nosave=""><b>Typ</b></td> <td nosave="" width="4%"><b>Default</b></td>
515	<td nosave=""><b>Beschreibung</b></td> </tr>
516	<tr nosave=""> <td nosave=""><tt>moisture</tt></td>
517	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
518	des Gesamtwassergerhaltes als neue
519	progn. Variable</td> </tr> <tr> <td><tt>cloud_physics</tt></td>
520	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
521	des Kondensationsschemas</td> </tr> <tr nosave="">
522	<td><tt>radiation</tt></td> <td>L</td>
523	<td nosave="">FALSE</td> <td>Ab-/Zuschalten
524	des Strahlungsschemas</td> </tr> <tr> <td><tt>precipitation</tt></td>
525	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
526	der Niderschlagsparametrisierung</td> </tr> <tr> <td><tt>bc_q_b</tt></td>
527	<td>C</td> <td>'dirichlet'</td> <td>untere
528	Randbedingung für q (siehe auch bc_pt_b)</td> </tr>
529	<tr> <td><tt>bc_q_t</tt></td> <td>C</td>
530	<td>'neumann'</td> <td>obere RB für q
531	(siehe auch bc_pt_t)</td> </tr> <tr> <td><tt>q_surface</tt></td>
532	<td>R</td> <td>0.0</td> <td>Feuchtewert
533	an der Erdoberfläche</td> </tr> <tr> <td><tt>q_surface_initial_change</tt></td>
534	<td>R</td> <td>0.0</td> <td>vgl.
535	pt_surface_initial_change</td> </tr> <tr> <td><tt>q_vertical_gradient</tt></td>
536	<td>R(10)</td> <td>0.0</td> <td>vgl.
537	pt_vertical_gradient</td> </tr> <tr nosave="">
538	<td nosave=""><tt>q_vertical_gradient_level</tt></td>
539	<td>R(10)</td> <td>10000.0</td> <td>vgl.
540	pt_vertical_gradient_level</td> </tr> <tr> <td><tt>surface_pressure</tt></td>
541	<td>R</td> <td>1013.25</td> <td>Luftdruck
542	an der Erdoberfläche</td> </tr> <tr> <td><tt>surface_waterflux</tt></td>
543	<td>R</td> <td>0.0</td> <td>oberflächennaher
544	Wasser/Feuchtefluss</td> </tr> </tbody> </table>
545	Fortsetzungsläufe mit Daten, die mit Modellversionen kleiner
546	2.0
547	erzeugt
548	wurden, sind aufgrund der erweiterten Initialisierungsparameterliste
549	INKOMPATIBEL
550	zu den Einleseroutinen der Version 2.0. Ein Update auf Version 2.0
551	sollte
552	deshalb nach Abschluss eines kompletten Modelllaufs erfolgen.
553	</p> <p><b>Achtung:</b> diese
554	Änderungen haben Auswirkungen auf
555	den Prognoseverlauf.
556	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
557	<td nosave="" valign="top">modules, parin,
558	read_var_list,
559	check_parameters,
560	init_3d_model, init_1d_model, header, leap_frog. buoyancy, diffusion_e,
561	production_e, diffusivities, prandtl_fluxes, boundary_conds,
562	asselin_filter,
563	swap_timelevels, flow_statistics, plot_2d, plot_3d, write_var_list,
564	write_3d_binary  <p><b>Neu:</b> <br>
565	init_cloud_physics, prognostic_equations, diffusion_s,
566	calc_liquid_water_content,
567	calc_radiation, calc_precipitation, impact_of_latent_heat, comute_vpt</p>
568	</td> </tr> <tr nosave=""> <td nosave="" valign="top">18/02/00</td> <td nosave="" valign="top">MS</td> <td nosave="" valign="top">2.0</td> <td nosave="" valign="top">B/N</td> <td>Im Zuge der
569	Umstellung auf Modellversion 2.0  wurden
570	noch kleine
571	Änderungen an den Unterprogrammen diffusion_e, production_e
572	und
573	diffusivities
574	vorgenommen. In allen genannten  <br>
575	Unterprogrammen wurde bisher ein strengeres Kriterium zur Bestimmung
576	der Schichtungsverhältnisse verwendet. Ein Modellvergleich
577	zeigte
578	jedoch, dass dadurch die Diffusion im Bereich der Inversion zu gross
579	wird.  <p>Eine weitere Ergänzung betrifft die
580	Advektionsverfahren:  <br>
581	Das Bott-Chlond Advektionsverfahren ist nun auch für
582	Rechnungen
583	mit Feuchte/Wolkenphysik verfügbar.  </p> <p><b>Achtung:</b>
584	diese Änderungen haben Auswirkungen auf
585	den Prognoseverlauf.
586	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
587	<td nosave="" valign="top">diffusion_e,
588	production_e,
589	diffusivities, check_parameters</td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
590	<td>SR</td> <td>2.0a</td> <td>C</td>
591	<td>Vollständige Umstellung von vtk-Grafik-Software auf
592	dvrp-Software.
593	Grafik-Ausgaben im dvr-Format sind mittlerweile begrenzt nutzbar
594	(Isooberflächen
595	sind darstellbar, siehe neue Laufparameter  <tt>dt_dvrp,
596	threshold</tt>),
597	es wird aber in der Anwendung in naher Zukunft noch diverse
598	Änderungen
599	geben. Partikelausgabe vorerst nicht mehr möglich (Verlagerung
600	schon).</td> <td>header, init_particles, init_3d_model,
601	leap_frog, modules,
602	parin, parles,
603	read_var_list, write_var_list  <br> <b>Gestrichen:</b>
604	<br>
605	plot_isosurface, plot_particles  <p><b>Neu:</b>
606	<br>
607	init_dvrp, plot_dvrp</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
608	<td>SR</td> <td>2.0a</td> <td>C</td>
609	<td>Durch zusätzlichen zyklischen Rand im
610	Bott-Chlond-Schema
611	sehr
612	viele SENDRECV-Aufrufe eingespart.  <br>
613	Änderung des Namens einer eingelesenen Environment-Variablen
614	in <tt>check_open</tt>
615	von <tt>remote_addres</tt> nach <tt>return_addres</tt>.
616	<br>Prozessor-Topologie kann durch Benutzer vorgegeben werden.
617	Dazu neue
618	Initialisierungsparameter <tt>npex</tt> und <tt>npey</tt>.
619	Durch
620	Änderungen
621	am Header-Format wurde Testergebnis-Datei geändert.</td>
622	<td>advec_s_bc, check_open, header, init_pegrid, modules, parin,
623	read_var_list,
624	write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
625	<td>SR</td> <td>2.0a</td> <td>N</td>
626	<td>Rechnungen mit geneigter Oberfläche erlauben jetzt
627	die
628	Vorgabe
629	eines stabil geschichteten Temperaturprofils mit konstantem Gradienten.
630	Hinzuschalten von Feuchte funktioniert für Hangrechnungen noch
631	nicht.</td> <td>advec_s_bc, buoyancy, init_3d_model,
632	modules,
633	prognostic_equations  <p><b>Neu:</b> <br>
634	init_slope</p> </td> </tr> <tr nosave="" valign="top"> <td>13/06/00</td> <td>MS</td>
635	<td>2.0a</td> <td nosave="">B</td> <td>Es
636	werden nun auch die seitlichen Ränder für ql
637	gesetzt.
638	Ein Nichtsetzen der Randbedingungen führte zu Fehlern bei der
639	Ausgabe
640	von pt</td> <td nosave="">calc_liquid_water_content</td>
641	</tr> <tr nosave="" valign="top"> <td nosave="">03/07/00</td> <td>SR</td> <td>2.0b</td>
642	<td>C</td> <td>Für eine Reihe von
643	Unterprogrammen, die innerhalb
644	von <tt>prognostic_equation</tt>
645	aufgerufen werden und an die Pointer-Variablen übergeben
646	werden,
647	sind
648	jetzt explizite Interfaces vereinbart (neues Modul <tt>pointer_interfaces</tt>).
649	Auch im Vereinbarungsteil der entsprechenden Unterprogramme sind diese
650	Übergabeparameter jetzt aus Konsistenzgründen (und
651	weil es
652	sonst
653	Laufzeitfehler gibt) als Pointer-Variablen deklariert. Mit dieser
654	Änderung
655	ist der große Speicher- und CPU-Zeit-Bedarf beim
656	Übersetzen
657	von prognostic_equations wieder auf ein erträgliches
658	Maß
659	reduziert.  <br>
660	Im Rahmen dieser Änderungen wurde auch an diffusion_e ein
661	Hilfsfeld
662	weniger übergeben.  <br>
663	Aus nicht vollständig gekärten Gründen haben
664	sich die
665	Zahlen in der Testergebnis-Datei minimal geändert (und zwar
666	die
667	Spalte
668	mit der Gesamtdivergenz nach Aufruf des Drucklösers).</td>
669	<td>advec_s_bc, buoyancy, diffusion_e, diffusion_s, diffusion_u,
670	diffusion_v,
671	diffusion_w, disturb_field, modules, production_e, prognostic_equations</td>
672	</tr> <tr nosave="" valign="top"> <td nosave="">04/07/00</td> <td>SR</td> <td>2.0b</td>
673	<td>B</td> <td>Diriclet-Randbedingungen für
674	Temperatur und
675	Flüssigwassergehalt
676	werden gesetzt. Dies wäre bereits nach Einführung der
677	Pointer
678	zwingend notwendig gewesen. Rechnungen mit vorgegebener
679	Oberflächentemperatur
680	schlugen deshalb bislang fehl.</td> <td>boundary_conds</td>
681	</tr> <tr nosave="" valign="top"> <td nosave="">07/09/00</td> <td>MS</td> <td>2.0b</td>
682	<td>B</td> <td>Die virtuelle potenielle Temperatur
683	wird nun auch für
684	k=nzb und
685	k=nzt+1 berechnet, um die Randwerte auch für Ausgabezwecke
686	bereichtzustellen. </td> <td>compute_vpt</td>
687	</tr> <tr nosave="" valign="top"> <td nosave="">28/12/00</td> <td>SR</td> <td>2.1</td>
688	<td>C/N</td> <td>PALM erlaubt jetzt den Einsatz
689	optionaler Software-Pakete,
690	die zwar
691	zum Modell gehören, standardmäßig aber
692	nicht mit
693	übersetzt
694	werden, um so unter anderem Kompilationszeit einzusparen. Siehe neues
695	Kapitel
696	3.7 in der Modelldokumentation.  <p>Einsatz der
697	dvrp-Software wurde vollständig
698	überarbeitet.
699	Sie ist nun als Software-Paket optional im Modell einsetzbar. Siehe
700	überarbeitetes
701	Kapitel 4.5.6 in der Modelldokumentation.  </p> <p>Die
702	Prognose der Partikelverlagerung ist ebenfalls in ein
703	optionales
704	Software-Paket ausgelagert.</p> </td> <td>advec_particles,
705	header, init_3d_model, init_dvrp,
706	init_particles,
707	init_pegrid, modules, parin, parles, plot_dvrp, prognostic_equations,
708	read_var_list,
709	write_var_list  <p><b>Neu:</b> <br>
710	package_parin</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">28/12/00</td>
711	<td>SR</td> <td>2.1</td> <td>B</td>
712	<td>MPI_FINALIZE ans Ende des Hauptprogramms geschoben (stand
713	vorher vor
714	cpu_auswertung, wo noch ein Barrier-Aufruf steht). comm2d war zu Beginn
715	undefiniert und wird nun erst einmal gleich MPI_COMM_WORLD gesetzt.</td>
716	<td>parles</td> </tr> <tr nosave="" valign="top"> <td nosave="">02/01/01</td>
717	<td>SR</td> <td>2.1a</td> <td>C</td>
718	<td>Offene Dateien werden sobald möglich geschlossen.
719	Wiedereröffnung
720	bestimmter Dateien mit POSITION='APPEND' möglich. In diesem
721	Zusammenhang
722	wurde das Unterprogramm close_files in close_file umbenannt und hat nun
723	1 Argument.  <br>
724	Anpassung der Diffusionsparametrisierung im 1D-Modell an das 3D-Modell.</td>
725	<td>advec_particles, check_cpu_time, check_open, cpu_auswertung,
726	init_1d_model,
727	init_3d_model, init_particles, modules.f90, parin, parles, plot_2d,
728	write_3d_binary  <p><b>Neu:</b> <br>
729	close_file  </p> <p><b>Eliminiert:</b>
730	<br>
731	close_files</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">02/01/01</td>
732	<td>SR</td> <td>2.1a</td> <td>B</td>
733	<td>Beseitigung kleiner Fehler.</td> <td>check_cpu_time,
734	diffusion_e, diffusivities, long_filter,
735	production_e</td> </tr> <tr nosave="" valign="top"> <td>05/01/01</td> <td>SR</td>
736	<td>2.1b</td> <td>N</td> <td nosave="">Neues
737	Software-Paket zur Berechnung von Spektren im
738	Ortsraum</td> <td>check_open, header, init_3d_model,
739	leap_frog, modules,
740	package_parin,
741	parles, read_var_list, write_3d_binary, write_var_list  <p><b>Neu:</b>
742	<br>
743	calc_spectra, plot_spectra</p> </td> </tr> <tr valign="top"> <td>25/01/01</td> <td>SR</td>
744	<td>2.1c</td> <td>C/N</td> <td>Drucklöser
745	kann jetzt die Singleton-FFT benutzen. Modul <tt>singleton</tt>
746	wurde deshalb von <tt>calc_spectra.f90</tt> nach <tt>modules.f90</tt>
747	geschoben
748	(neuer Initialisierungsparameter <tt>fft_method</tt>).
749	<br>Flüsse können jetzt bei k=1
750	unabhängig von der
751	Verwendung
752	einer Prandtl-Schicht vorgegeben werden (neuer
753	Initialisierungsparameter <tt>use_surface_fluxes</tt>).
754	<br>Modul <tt>test_variables</tt> wurde aus allen
755	Programmteilen entfernt.
756	Hauptprogramm wurde von parles nach <tt>palm</tt>
757	umbenannt.  <br>
758	Modell kann auf DEC-Workstations eingesetzt werden (-D <tt>dec</tt>).
759	<br>Zusätzliche Zeitmessungen mit dvrp-Software.
760	Schreiben von
761	Partikel-Informationen
762	ist optional (neuer Parameter <tt>write_particle_informations</tt>).</td>
763	<td>advec_particles, calc_spectra, check_parameters,
764	cpu_zeitmessung, diffusion_s,
765	header, init_3d_model, init_dvrp, init_particles, leap_frog, modules,
766	package_parin,
767	parin, poisfft, read_var_list, swap_timelevel, write_var_list
768	<p><b>Neu:</b> <br>
769	palm  </p> <p><b>Eliminiert:</b> <br>
770	parles, module_test</p> </td> </tr> <tr valign="top"> <td>25/01/01</td> <td>SR</td>
771	<td>2.1c</td> <td>B</td> <td>Fehler
772	beim öffnen von Unit 23 beseitigt. Modul <tt>interface</tt>
773	fehlte in disturb_field.  <br>
774	Wertebereich von theta* in Prandtl-Fluxes eingeschränkt, weil
775	sonst auf einigen Rechnern overflow droht, wenn u*=0.</td> <td>check_open,
776	disturb_field, prandtl_fluxes</td> </tr> <tr valign="top"> <td>30/01/01</td> <td>SR</td>
777	<td>2.1d</td> <td>N/C</td> <td>Prognose
778	eines passiven Skalars ist möglich (anstatt
779	Feuchte),
780	dazu neuer Initialisierungsparameter <tt>passive_scalar</tt>.
781	<p>Falls kein Pfad für ftpcopy existiert, werden in <tt>check_open</tt>
782	die Dateinamen für AVS-Koordinaten- und Datendatei auf
783	"unknown"
784	gesetzt.</p> </td> <td>asselin_filter,
785	boundary_conds, check_open, check_parameters,
786	flow_statistics,
787	header, init_1d_model, init_3d_model, modules, parin, plot_2d,
788	plot_dvrp,
789	prandtl_fluxes, prognostic_equations, read_var_list, swap_timelevel,
790	write_3d_binary,
791	write_var_list</td> </tr> <tr valign="top"> <td>30/01/01</td>
792	<td>SR</td> <td>2.1d</td> <td>B</td>
793	<td>String-Ausgabe für use_surface_fluxes korrigiert.
794	Version vom
795	25/01/01 brach deswegen bei Fortsetzungsläufen ab.  <br>
796	xy-Plotausgabe von q und ql korrigiert.</td> <td>plot_2d,
797	write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">30/03/01</td>
798	<td>SR</td> <td>2.2</td> <td>N/C</td>
799	<td>Sämtliche 3D-Felder der Zeitebene t+dt wurden
800	entfernt.
801	Ebenso
802	die Arbeitsfelder work und work1. Hilfsfelder wurden soweit
803	möglich
804	eingespart und werden grundsätzlich lokal allokiert. Dadurch
805	konnten
806	eine Reihe von Übergabeparametern gestrichen werden (z.B. beim
807	Aufruf
808	von <tt>pres, advec_s_bc, poisfft, production_e, sor </tt>sowie
809	den
810	Spline-Unterprogrammen).
811	Der Long-Filter wurde in das Upstream-Spline-Verfahren integriert. Da
812	der
813	Zeitfilter jetzt direkt in der prognostischen Gleichung angewendet wird
814	(bisher geschah dies erst nach Aufruf des Drucklösers), haben
815	sich
816	die Zahlen in der Testergebnis-Datei geändert. Die mittleren
817	Profile
818	sind aber unbeeinflusst.  <p>Eine weitere kleinere
819	Änderung der Testergebnis-Daten
820	wird dadurch
821	verursacht, dass jetzt der Parameter <tt>adjust_mixing_length</tt>
822	defaultmäßig <tt>.FALSE.</tt>
823	ist und der Mischungsweg grundsätzlich zusätzlich
824	auf  <tt>0.7
825	* zu</tt>   begrenzt wird. Falls <tt>adjust_mixing_length=T</tt>,
826	wird jetzt der Mischungsweg in <tt>diffusivities</tt>
827	analog zu <tt>diffusion_e</tt>
828	an allen Gitterpunkten modifiziert. <b>Achtung: </b>Diese
829	Änderungen
830	können bei anderen Simulationen t.w. erhebliche Auswirkungen
831	auf
832	die
833	oberflächennahen Ergebnisse haben.  </p> <p><b>Kleinere
834	Änderungen:</b> In <tt>init_cloud_physics</tt>
835	wird
836	der Wert der Variablen <tt>surface_pressure</tt> in hPa
837	belassen
838	(bisher
839	Umwandlung in Pa).  <br>
840	Die Namelist-Namen der Software-Pakete sind  t.w.
841	geändert.  <br>
842	Unit 14 (binäre Ausgabe für
843	Fortsetzungsläufe) wird
844	jetzt im Hauptprogramm geschlossen, damit auf diese Datei noch
845	benutzergesteuerte
846	Ausgaben erfolgen können.  <br>
847	Laufparameter werden in keinem Fall mehr auf Unit 14 ausgegeben bzw.
848	von Unit 13 gelesen, d.h. sie gelten jetzt tatsächlich nur
849	für
850	den jeweils aktuellen Lauf.  <br>
851	Partikeladvektion funktioniert jetzt auch zusammen mit der
852	Galilei-Transformation.  </p> <p>Restliche
853	deutsche Variablen-, Unterprogramm- und Modulnamen
854	wurden
855	ins Englische übersetzt. Davon sind fast alle Programmteile
856	betroffen
857	(nicht in rechter Spalte aufgeführt).</p> </td> <td>advec_particles,
858	advec_s_bc, advec_s_ups, advec_u_ups,
859	advec_v_ups,
860	advec_w_ups, boundary_conds, calc_spectra, check_parameters,
861	diffusion_e,
862	init_3d_model, init_cloud_physics, init_pegrid, init_rankine,
863	leap_frog,
864	modules, package_parin, palm, parin, poisfft, pres, production_e,
865	prognostic_equations,
866	read_var_list, sor, swap_timelevel, transpose_*, write_3d_binary,
867	write_var_list  <p><b>Neu:</b> <br>
868	cpu_log, cpu_statistics  </p> <p><b>Eliminiert:</b>
869	<br>
870	asselin_filter, cpu_auswertung, cpu_zeitmessung, long_filter</p> </td>
871	</tr> <tr nosave="" valign="top"> <td nosave="">12/07/01</td> <td>SR</td> <td>2.2a</td>
872	<td>N/C</td> <td>Defaultwert der unteren
873	Randbedingung für die TKE ist ab
874	sofort <tt>bc_e_b
875	= 'neumann'</tt>.  <br>
876	Partikelquelle ist über Paketparameter steuerbar.
877	Partikeleigenschaften
878	sind mittels benutzereigener Software steuerbar. Der dvrp-Ausgabeweg
879	ist
880	jetzt ebenfalls über Paketparameter steuerbar.  <br>
881	Allen Modulen (bis auf singleton) wurde eine SAVE-Anweisung
882	hinzugefügt,
883	damit die durch sie vereinbarten Variablen während der
884	Rechnung in
885	keinem Fall undefiniert werden können (diese Gefahr besteht
886	z.B.
887	auf
888	SGI-Origin-Maschinen).</td> <td>advec_particles, header,
889	init_dvrp, init_particles,
890	modules.f90, package_parin,
891	plot_dvrp, user_interface</td> </tr> <tr> <td>12/07/01</td>
892	<td>SR</td> <td>2.2a</td> <td>B</td>
893	<td>Verschiebung der OPEN-Anweisung für Unit 33
894	(AVS-FLD-Datei).</td> <td>check_open</td> </tr>
895	<tr nosave="" valign="top"> <td nosave="">20/07/01</td>
896	<td>SR</td> <td>2.3</td> <td>N</td>
897	<td>Einbau des Mehrgitterverfahrens zur Lösung der
898	Poisson-Gleichung.</td> <td>check_parameters,
899	exchange_horiz, header, init_grid,
900	init_pegrid, modules,
901	parin, pres, run_control  <p><b>Neu:</b> <br>
902	poismg</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">21/08/01</td>
903	<td>SR</td> <td>2.3a</td> <td>N/C</td>
904	<td>Ergänzung der dvrp-Software: Partikel
905	können mit
906	Schwänzen
907	versehen werden. Die Ausgabe der dvrp-Plotdaten durch einen separaten
908	PE
909	ist möglich (mrun-Option "<tt>-p dvrp_graphics+1PE</tt>").
910	Der
911	Kommunikator <tt>MPI_COMM_WORLD</tt>
912	wurde deshalb durch  <tt>comm_palm</tt>
913	ersetzt.  <p>Reduzierung des Mischungsweges im
914	Wandbereich kann wahlweise
915	abgeschaltet
916	werden. Für km und kh wird jetzt eine Neumann-Randbedingung am
917	unteren
918	Rand verwendet. Die TKE-Energieproduktionsberechnung durch Scherung des
919	Grundstroms am unteren Rand wurde verbessert.  </p> <p>Generelle
920	Verwendung der bodennahen vertikalen
921	Impulsflüsse in
922	den Diffusionstermen von u und v, immer wenn diese als Randbedingung
923	vorgegeben
924	sind (gemäß <tt>use_surface_fluxes</tt>,
925	- bisher wurde
926	dies
927	nur bei eingeschalteter Prandtl-Schicht gemacht). Schubspannungen
928	können
929	jetzt als Randbedingungen vorgegeben werden (allerdings unter
930	zuhilfenahme
931	benutzereigener Software).  </p> <p>Zusätzliche
932	Schnittstellen für benutzereigene
933	Software in
934	allen Tendenztermen, in <tt>flow_statistics,</tt> und
935	für
936	Partikel-
937	bzw. dvrp-Programmteile (Bestimmung von Partikeleigenschaften,
938	Festlegung
939	von Farbtabellen).  </p> <p><b>Achtung: </b>Diese
940	Änderungen können bei
941	Simulationen mit
942	mittlerem Wind durch die Änderungen im bereich des unteren
943	Randes
944	t.w. erhebliche Auswirkungen auf die oberflächennahen
945	Ergebnisse
946	haben.</p> </td> <td>advec_particles, diffusion_e,
947	diffusion_u, diffusion_v,
948	diffusivities,
949	flow_statistics, header, init_dvrp, init_particles, init_pegrid,
950	leap_frog,
951	modules, package_parin, palm, parin, plot_dvrp, production_e,
952	prognostic_equations,
953	read_var_list, swap_timelevel, user_interface, write_var_list</td>
954	</tr> <tr nosave="" valign="top"> <td nosave="">21/08/01</td> <td>SR</td> <td>2.3a</td>
955	<td>B</td> <td>Falsche Positionierung von
956	MPI_ALLREDUCE in check_cpu_time
957	korrigiert.</td> <td>check_cpu_time</td> </tr>
958	<tr nosave="" valign="top"> <td nosave="">04/09/01</td>
959	<td>SR</td> <td>2.3b</td> <td>N</td>
960	<td>Zusätzliche Profilausgaben für
961	Energieproduktionsterme möglich.
962	Stördruck wird bei der FFT-Methode nicht mehr durch
963	Aufsummieren
964	der
965	Werte zu den einzelnen Zeitschritten ermittelt.</td> <td>check_parameters,
966	flow_statistics, modules, pres</td> </tr> <tr nosave="" valign="top"> <td nosave="">04/09/01</td>
967	<td>SR</td> <td>2.3b</td> <td>B</td>
968	<td>Austausch der Geisterränder für die
969	zeitgefilterten
970	Felder
971	direkt nach Durchführung der Filterung (war fehlerhaft seit
972	Entfernen
973	der Zeitebene t+dt (Version 2.2) und führte zu sehr kleinen
974	Störungen
975	an den seitlichen Rändern der Teilgebiete).  <p><b>Achtung:</b>
976	Der Inhalt der Testergebnis-Datei ändert
977	sich durch
978	diese Fehlerkorrektur.</p> </td> <td>prognostic_equations</td>
979	</tr> <tr nosave="" valign="top"> <td nosave="">09/11/01</td> <td>SR</td> <td>2.3c</td>
980	<td>N</td> <td>Farbe entlang der
981	Partikelschwänze kann sich
982	ändern. Einschalten
983	der Partikeladvektion bei Fortsetzungsläufen möglich.</td>
984	<td>advec_particles, init_particles, modules, package_parin,
985	plot_dvrp</td> </tr> <tr nosave="" valign="top">
986	<td nosave="">16/04/02</td> <td>SR</td>
987	<td>2.3d</td> <td>N</td> <td>Vorgabe
988	von Randbedingungen für Partikeladvektion
989	möglich.
990	Partikeldaten können für spätere Analysen
991	auf Datei
992	geschrieben
993	werden (Unit 85). <tt>PARTICLE</tt>-Datentyp
994	enthält
995	Informationen
996	über Partikelgeschwindigkeitskomponenten und
997	Startposition.  <p>Skalartransport sowie entsprechende
998	Datenausgaben können
999	durch
1000	eigene Parameter gesteuert werden (nicht mehr über die
1001	Feuchteparameter).  </p> <p>Im Fall von
1002	pdims(1)=1 (eindimensionales virtuelles
1003	Prozessornetz in
1004	y-Richtung) werden die zyklischen Randbedingungen in x-Richtung durch
1005	direktes
1006	Umspeichern anstatt durch  <tt>sendrecv </tt>realisiert.
1007	Ebenso
1008	werden
1009	die Transponierungen xz, yz, zx  und zy eingespart (es wird
1010	aber
1011	weiter
1012	umsortiert).  </p> <p>Im Fall von
1013	3D-Plotausgaben Aufruf von ftpcopy-Script durch
1014	batch_scp-Script
1015	ersetzt (dient der Ermittelung von Dateizyklusnummern als Information
1016	für
1017	die AVS-fld-Datei).  </p> <p>Bei fehlerhafter
1018	Eröffnung einer CPU_MEASURES-Datei
1019	werden erneute
1020	Eröffnungsversuche durchgeführt.</p> </td>
1021	<td>advec_particles, check_open, check_parameters,
1022	exchange_horiz, flow_statistics,
1023	header, init_particles, modules, package_parin, parin, plot_2d,
1024	plot_3d,
1025	prognostic_equations, read_var_list, transpose_xz, transpose_yz,
1026	transpose_zx,
1027	transpose_zy, write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">02/05/02</td>
1028	<td>SR</td> <td>2.3e</td> <td>B</td>
1029	<td>Wiedereinführung der 3D-Felder für die
1030	Zeitebene
1031	t+dt, die
1032	notwendig ist, damit in den Diffusionstermen bei Leapfrog-Zeitschritten
1033	mit der korrekten Zeitebene t-dt gearbeitet wird. Seit Version 2.2
1034	wurde
1035	fälschlicherweise die Zeitebene t+dt verwendet. Asselin-Filter
1036	ist
1037	jetzt wieder eigenständiges Unterprogramm. <br>
1038	Die Wiedereinführung dieser dritten Zeitebene ist auch
1039	Voraussetzung
1040	für die in der nächsten Version geplante skalare
1041	Optimierung.  <p>Fehler bei Berechnung von
1042	Ausgabezeitpunkten eliminiert (trat
1043	auf, wenn
1044	bei Fortsetzungsläufen von Ausgabeabständen 0.0 auf
1045	von Null
1046	verschiedene Werte gewechselt werden sollte).  </p> <p><b>Achtung:</b>
1047	Der Inhalt der Testergebnis-Datei ändert
1048	sich durch
1049	diese Fehlerkorrektur.</p> </td> <td>init_3d_model,
1050	leap_frog, modules, prognostic_equations,
1051	swap_timelevel  <p><b>Neu:</b> <br>
1052	asselin_filter</p> </td> </tr> <tr nosave="" valign="top"> <td>02/05/02</td> <td>SR</td>
1053	<td>2.3e</td> <td>N/C</td> <td>Kleinere
1054	Anpassungen an IBM-Regatta-Systeme in
1055	check_parameters, cpu_log.  <p>Modul singleton in
1056	eigenständige Datei
1057	überführt.  </p> <p>Global_min_max
1058	arbeitet mit REAL*4, um Komplikationen auf
1059	32-bit-Rechnern
1060	zu vermeiden (Datentyp MPI_2REAL müsste dort sonst auf
1061	MPI_2DOUBLE_PRECISION
1062	geändert werden). <br>
1063	Horizontale Geschwindigkeitskomponenten für Partikeladvektion
1064	werden exakt zwischen den jeweils benachbarten horizontalen
1065	Gitterflächen
1066	interpoliert.</p> </td> <td nosave="">advec_particles,
1067	check_parameters, cpu_log,
1068	global_min_max,
1069	modules  <p><b>Neu:</b> <br>
1070	singleton</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">11/06/02</td>
1071	<td>SR</td> <td>2.4</td> <td>N/C</td>
1072	<td>Optimierung und Anpassungen für einzelne Knoten der
1073	IBM-Regatta-Systeme. <p><b>Skalare (Cache) Optimierung:</b>
1074	Tendenzterme werden
1075	innerhalb einer
1076	großen (i,j)-Schleife berechnet, die nun jeweils die gesamte
1077	prognostische
1078	Gleichung umfasst. Schleifenindices i und j werden an die
1079	Tendenzunterprogramme
1080	als Argumente übergeben. Die Tendenzunterprogramme sind als
1081	Module
1082	geschrieben, die mittels Technik der überladenen Funktionen
1083	auch
1084	ohne
1085	diese Indices i und j aufgerufen werden können, und dann wie
1086	in
1087	früheren
1088	Versionen funktionieren (d.h. in ihnen laufen die Schleifen
1089	über
1090	alle
1091	3 Dimensionen). Solche Teile der prognostischen Gleichungen, die
1092	globale
1093	Kommunikation beinhalten, sind vor die (i,j)-Schleife gezogen. Falls
1094	ausschließlich
1095	mit Piascek-Williams-Advektion gearbeitet wird, werden alle
1096	prognostischen
1097	Gleichungen in einer einzigen (i,j)-Schleife gerechnet. </p> <p><b>Kommunikationsoptimierung:</b>
1098	Zusätzliche
1099	Implementierung einer
1100	1D-Gebietszerlegung in x-Richtung. Mit dem neuen direkten
1101	Drucklöser
1102	(poisfft_hybrid) werden dadurch 4 von 6 notwendigen Transpositionen
1103	eingespart.
1104	Die 1D-Zerlegung wird automatisch bei Verwendung dieses neuen
1105	Lösers
1106	aktiviert. Austausch von Geisterrändern in y-Richtung wird bei
1107	dieser
1108	1D-Zerlegung durch einfache zyklische Randbedingungen ersetzt. </p>
1109	<p><b>Kleinere Anpassungen:</b> String-Vergleiche
1110	erfordern beim
1111	IBM-Compiler
1112	in der Regel den Einsatz der TRIM-Funktion, um
1113	überschüssige
1114	Blanks am Ende des Strings abzuschneiden (sonst liefert der Vergleich
1115	.F.). <br>
1116	Lokal allokierte Felder t.w. in sogenannte automatische Felder
1117	umgewandelt
1118	(günstiger, um Gefahr von eventuellen Speicherlecks zu
1119	vermeiden).
1120	Einige Feldoperationen wurden wegen schlechter Performance auf der IBM
1121	entfernt (s. pres). </p> <p><b>Achtung: </b>Die
1122	Übersetzung des Modells erfordert
1123	aufgrund
1124	der Vielzahl nunmehr eingesetzter Module die Verwendung des
1125	make-Mechanismus,
1126	um die korrekte Reihenfolge bei der Übersetzung der
1127	Programmteile
1128	zu gewährleisten. Die Beschreibung dieser
1129	Abhängigkeiten
1130	erfolgt
1131	in der Datei<tt> Makefile</tt>, die zusammen mit den
1132	Programmdateien
1133	abgelegt
1134	ist und ebenfalls unter RCS-Verwaltung steht. </p> <p>Im
1135	User-Interface ist das Unterprogramm<tt> user_actions </tt>nun
1136	ebenfalls
1137	als Modul geschrieben und bedient sich der Methode der
1138	überladenen
1139	Funktionen. Existierende benutzereigene Software muss entsprechend
1140	angepasst
1141	werden.</p> </td> <td>advec_s_pw, advec_s_up,
1142	advec_u_pw, advec_u_up, advec_v_pw,
1143	advec_v_up,
1144	advec_w_pw, advec_w_up, buoyancy, calc_precipitation, calc_radiation,
1145	calc_spectra,
1146	check_parameters, coriolis, diffusion_e, diffusion_s, diffusion_u,
1147	diffusion_v,
1148	diffusion_w, diffusivities, exchange_horiz, exchange_horiz_2d,
1149	global_min_max,
1150	header, impact_of_latent_heat, init_pegrid, leap_frog, modules,
1151	plot_2d,
1152	plot_3d, plot_spectra, poisfft, pres, production_e,
1153	prognostic_equations,
1154	user_interface, <p><b>Neu:</b> <br>
1155	fft_for_1d_decomp, Makefile, poisfft_hybrid, </p> </td>
1156	</tr> <tr nosave="" valign="top"> <td nosave="">11/06/02</td> <td>SR</td> <td>2.4</td>
1157	<td>B</td> <td>Fehlende Variablenvereinbarung in <tt>advec_particles</tt>
1158	ergänzt.</td> <td>advec_particles</td> </tr>
1159	<tr> <td valign="top">12/09/02</td> <td valign="top">SR</td> <td valign="top">2.4a</td>
1160	<td valign="top">N</td> <td valign="top">Partikel
1161	können mit Trägheit versehen
1162	werden und
1163	einen Dichteunterschied zum umgebenden Fluid haben. Zur Steuerung dient
1164	der neue Paketparameter <tt>density_ratio</tt>.</td>
1165	<td valign="top">advec_particles, header, init_particles,
1166	modules, package_parin</td> </tr> <tr> <td valign="top">12/09/02</td> <td valign="top">SR</td>
1167	<td valign="top">2.4a</td> <td valign="top">B</td>
1168	<td valign="top">Fehler in Berechnung der Anfangsprofile
1169	von pt
1170	und q entfernt
1171	(obere Feldgrenze von 10 konnte in <tt>pt_vertical_gradient_level_ind</tt>
1172	überschritten werden). Fehler führte unter
1173	Umständen zu
1174	"segmentation fault" bei Verwendung sehr großer
1175	Gitterpunktzahlen
1176	in z-Richtung. <p>Fehler in Berechnung der v-Komponente am
1177	unteren Rand
1178	entfernt, die
1179	für den Scherungsproduktionsterm der TKE verwendet wird
1180	(Variable
1181	v_0). Fälschlicherweise wurde zur Berechnung u(k=1) statt
1182	v(k=1)
1183	verwendet.</p> </td> <td valign="top">check_parameters,
1184	modules, production_e</td> </tr> <tr> <td valign="top">19/12/02</td> <td valign="top">SR</td>
1185	<td valign="top">2.5</td> <td valign="top">N</td>
1186	<td valign="top">Restart times can be set by user with new
1187	runtime (d3par)
1188	parameters <tt>restart_time</tt> and <tt>dt_restart</tt>.
1189	Run
1190	description
1191	header is written on file CONTINUE_RUN. Output of cpu statistics
1192	changed
1193	(PE results are now collected on PE0 in order to calculate mean cpu
1194	statistics).
1195	Output of warnings in the job protocol in case of negative measured
1196	cpu-times.
1197	Remaining cpu-time is also evaluated on IBM-Regatta.</td> <td valign="top">cpu_log, cpu_statistics,
1198	check_parameters,header, leap_frog,
1199	local_tremain, local_tremain_ini, modules,  palm,  <p><b>new:</b>
1200	<br>
1201	check_for_restart </p> <p><b>deleted:</b> <br>
1202	check_cpu_time</p> </td> </tr> <tr> <td valign="top"> <br> </td> <td valign="top"> <br> </td> <td valign="top"> <br> </td> <td valign="top">C</td> <td valign="top">Unit
1203	14 (BINOUT) must be opened using a special
1204	process
1205	id string, because on IBM, the PE rank differs between communicators
1206	MPI_COMM_WORLD
1207	and comm_2d. This leads to a mismatch between filename-PE-number and
1208	PE-number
1209	written on file. As the consequence, these files could not be read by
1210	restart-jobs.
1211	Reading of array <tt>hom</tt> moved from <tt>init_3d_model
1212	</tt>to <tt>read_var_list</tt>
1213	(binary version number incremented to 2.2). <p><b>Further
1214	optimization for IBM-Regatta-systems:</b> <br>
1215	Additional optimization of the hybrid-solver for multinode usage
1216	(overlapping
1217	of communication and computation). </p> <p>Further cache
1218	optimization by using strides and joining loops (<tt>hybrid_solver,
1219	pres</tt> and <tt>timestep</tt>). Joining of
1220	MPI_ALLREDUCE calls in
1221	timestep. </p> <p>In case of 1d-decomposition along x
1222	only a part of the
1223	integral divisor
1224	conditions is checked, on IBM hosts a 1d-decomposition along x is the
1225	default,
1226	a switch from Poisson-FFT-solver to the hybrid-solver is made in case
1227	of
1228	1d-decomposition along x, the hybrid-solver does not force a
1229	1d-decomposition
1230	any more. </p> <p>Array notation changed to do-loop
1231	constructs due to better
1232	performance. </p> <p>Cyclic boundary conditions along <tt>y</tt>
1233	used instead of
1234	sendrecv
1235	in case of a 1d-decomposition along <tt>x</tt>. SENDRECV
1236	replaced by
1237	nonblocking
1238	routines ISEND and IRECV in <tt>exchange_horiz.f90</tt>. </p>
1239	<p>Speed optimization by removing MINVAL/MAXVAL calls and by
1240	handling <br>
1241	the "abs" case in a different way than the min/max cases (routine <tt>global_min_max</tt>).</p>
1242	</td> <td valign="top">asselin_filter, check_open,
1243	exchange_horiz,
1244	global_min_max,
1245	init_3d_model, init_pegrid, parin, poisfft_hybrid, read_var_list,
1246	timestep,
1247	write_3d_binary, write_var_list</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1248	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">Correction
1249	of mixing length term (l(k)/ll(k)).
1250	The condition
1251	kh=3*km in the unstable case is now also exactly met in the wall
1252	adjustment
1253	region. Factor 0.7 in wall adjustment part replaced by variable <tt>wall_adjustment_factor</tt>,
1254	which is set to 1.8 in <tt>modules.f90</tt>. The factor
1255	0.7 was the
1256	possible
1257	reason for 2-delta-x-waves, which were observed since version 2.1d. <p>Calculation
1258	of deformation tensor re-designed (<tt>production_e</tt>). </p>
1259	<p>STOP statements replaced by call of new subroutine <tt>local_stop,
1260	</tt>where
1261	MPI_FINALIZE is called before STOP in case of a parallel environment. </p>
1262	<p>ISO2D parameter dp set to true for ibm hosts. </p> <p>tend=p
1263	added in <tt>pres</tt> after calling sor method.</p>
1264	</td> <td valign="top">advec_s_bc, buoyancy,
1265	check_open,
1266	check_parameters, close_file,
1267	coriolis, diffusion_e, diffusivities, fft_for_1d_decomp,
1268	flow_statistics,
1269	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
1270	parin,
1271	plot_2d, poisfft, pres, read_var_list, user_interface,  <p><b>new:</b>
1272	<br>
1273	local_stop, production_e</p> </td> </tr> <tr>
1274	<td valign="top">03/03/03</td> <td valign="top">SR</td>
1275	<td valign="top">2.5a</td> <td valign="top">N</td>
1276	<td valign="top">Particle velocities are also stored in
1277	array
1278	particles in
1279	case of zero density ratio. Steering of variables by dvrp browser
1280	included.</td> <td valign="top">advec_particles,
1281	init_dvrp, modules,</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1282	</td> <td valign="top"><br> </td> <td valign="top">C</td> <td valign="top">AVS
1283	data format changed from float to xdr_float
1284	(needed
1285	on linux machines <br>
1286	due to the little/big endian problem). Updates for new version of dvrp
1287	software (e.g. using module dvrp is now mandatory).</td> <td valign="top">close_file, init_dvrp, leap_frog, plot_dvrp</td>
1288	</tr> <tr> <td valign="top"><br> </td>
1289	<td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top">B</td>
1290	<td valign="top">Error in particle inertia part removed
1291	(exp_arg
1292	must not
1293	contain the timestep). <br>
1294	Error in calculation of the vertical flux of resolved scale energy
1295	(profile 57) removed. Displacement for integers in mpi_particle_type
1296	reduced
1297	from 16 to 8 on ibm.</td> <td valign="top">advec_particles,
1298	flow_statistics, init_particles</td> </tr> <tr> <td valign="top">12/03/03</td> <td valign="top">SR</td>
1299	<td valign="top">2.6</td> <td valign="top">N</td>
1300	<td valign="top"><b>Version optimized for NEC-SX6
1301	parallel-vector
1302	machines. </b> <p>There are two main changes. A
1303	new vectorizable routine <tt>prognostic_equations_vec</tt>
1304	is added, where cache optimizations are undone. The tendency
1305	subroutines
1306	called by <tt>prognostic_equations_vec</tt> contain the
1307	full 3d-loops
1308	(compared
1309	with the cache-optimized versions where only loops over k are carried
1310	out).
1311	Additionally, a new pressure solver <tt>poisfft_hybrid_vec</tt>
1312	is
1313	added,
1314	which requires a 1d-domain-decomposition (like poisfft_hybrid). In this
1315	solver, a very fast FFT from Clive Temperton (ECMWF) is
1316	optionally
1317	available by choosing <tt>fft_method </tt>= <i>'temperton-algorithm'</i>.
1318	</p> <p>Additional changes in <tt>flow_statistics</tt>
1319	to allow
1320	better vectorization. </p> <p>Small changes in routines <tt>diffusivities</tt>
1321	and <tt>pres</tt>
1322	which
1323	caused run time errors on IBM and NEC due to compiler problems. </p>
1324	<p>Reading of environment variable <tt>tasks_per_node</tt>
1325	moved
1326	from routine <tt>poisfft_hybrid</tt>
1327	to routine <tt>parin</tt>. </p> <p><b>Changes
1328	in makefile:</b> modules and user_interface now
1329	depend on
1330	the f90 files, dependency of singleton added, LDFLAGS moved to the end
1331	of PROG rule, temperton_fft added.</p> </td> <td valign="top">advec_s_pw, advec_s_up, advec_u_pw, advec_u_up,
1332	advec_v_pw,
1333	advec_v_up, advec_w_pw, advec_w_up, buoyancy, calc_precipitation,
1334	calc_radiation,
1335	check_parameters, coriolis, cpu_log, diffusion_e, diffusion_s,
1336	diffusion_u,
1337	diffusion_v, diffusion_w, diffusivities, fft_for_1d_decomp, header,
1338	impact_of_latent_heat,
1339	init_pegrid, leap_frog, local_tremain, modules, parin, poisfft,
1340	poisfft_hybrid,
1341	pres, production_e, prognostic_equations, user_interface <p><b>new:</b>
1342	<br>
1343	temperton_fft</p> </td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1344	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">tend=p
1345	added in routine <tt>pres</tt> after
1346	calling sor
1347	method.</td> <td valign="top">pres</td> </tr>
1348	<tr> <td valign="top">14/03/03</td> <td valign="top">SR</td> <td valign="top">2.6a</td>
1349	<td valign="top">N</td> <td valign="top">Additional
1350	vector optimization for NEC-SX6. <p>Optional system-specific
1351	random number generator available
1352	(for equal
1353	distributed numbers). </p> <p>Define strings in all
1354	relevant subroutines changed from  </p> <p><tt>
1355	#if defined( define_string )</tt> </p> <p>to </p>
1356	<p><tt>     #if
1357	defined( __define_string )</tt> </p> <p><b>Caution:
1358	</b>The relevant subroutines are NOT listed in
1359	the right
1360	column!</p> </td> <td valign="top">asselin_filter,
1361	check_parameters, diffusion_e,
1362	diffusivities,
1363	disturb_field, global_min_max, header, local_tremain, modules, parin,
1364	poisfft_hybrid,
1365	pres, read_var_list, write_var_list</td> </tr> <tr>
1366	<td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1367	</td> <td valign="top">B</td> <td valign="top">Error in particle boundary condition removed
1368	(velocity must
1369	be inverted in case of reflection)</td> <td valign="top">advec_particles</td>
1370	</tr> <tr> <td valign="top">16/04/03</td>
1371	<td valign="top">SR</td> <td valign="top">2.6b</td>
1372	<td valign="top">N</td> <td valign="top">Time
1373	series output of Monin Obukhov length. <p>Temperton fft can now
1374	be used for all hosts and every domain
1375	decomposition.
1376	Abort in case of Temperton fft, if number of gridpoints along x and/or
1377	y contain illegal factors.  </p> <p>Index values
1378	for the extrema found in global_min_max are
1379	limited to
1380	the range 0..nx, 0..ny (on IBM machines -1 and nx+1/ny+1 occured which
1381	produced different RUN_CONTROL output compared to other machines). </p>
1382	<p>Output format of iteration count in routine run_control
1383	enlarged.</p> </td> <td valign="top">check_parameters,
1384	fft_for_1d_decomp,
1385	global_min_max, init_pegrid,
1386	modules, plot_ts, poisfft, run_control, temperton_fft</td> </tr>
1387	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1388	</td> <td valign="top">B</td> <td valign="top">Additional checks of variables <tt>hybrid_solver</tt>
1389	and <tt>host</tt>
1390	(<tt>hybrid_solver</tt> must not be used for a
1391	2d-domain-decomposition, <tt>host</tt>
1392	should be set by setting environment variable <tt>localhost</tt>).
1393	<p>Header output for mixing length limitations revised.</p>
1394	</td> <td valign="top">check_parameters, header</td>
1395	</tr> <tr> <td valign="top">09/05/03</td>
1396	<td valign="top">SR</td> <td valign="top">2.7</td>
1397	<td valign="top">N</td> <td valign="top"><b>Version
1398	running on Linux Clusters using MPICH
1399	and Intel
1400	FORTRAN compiler (ifc)</b> <p>So far, only absolutely
1401	neccessary changes have been done
1402	(possible
1403	optimizations will follow in a later version): </p> <p>New
1404	time measurements for Linux (ifc) environment added. </p> <p>Some
1405	parameters in MPI calls had to be modified (arrays had to
1406	be replaced
1407	by the first element of the regarding array) in order to fulfill f90
1408	type
1409	and rank requirements, since on the MUK-cluster a FORTRAN90-version of
1410	MPI is used. This also required to replace "mpif.h" by using a special
1411	module (named <tt>mpi</tt>).  I did not find out
1412	how character
1413	strings
1414	can be send with MPI. Therefore, these strings are transformed to
1415	integers,
1416	before they are send, and transformed back to characters on the
1417	receiving
1418	PE. </p> <p>On the MUK-cluster, only PE0 is able to read
1419	the values of
1420	environment
1421	variables. Therefore, these values are communicated via broadcast to
1422	the
1423	other PEs. </p> <p>1d-decomposition is set as the default
1424	on Linux Clusters.
1425	Character
1426	strings have to be transformed to integer </p> <p>Smaller
1427	changes: </p> <p>Batch_scp paths for IBM, NEC and Linux
1428	added</p> </td> <td valign="top">check_open,
1429	cpu_log, flow_statistics,
1430	init_pegrid, local_getenv,
1431	modules, palm, poisfft_hybrid</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1432	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">Measurements
1433	on IBM are now using function <tt>irtc</tt>,
1434	which allows correct measurements for jobs running over the 24:00
1435	timeline.</td> <td valign="top">cpu_log,
1436	local_tremain, local_tremain_ini</td> </tr> <tr> <td valign="top">01/08/03</td> <td valign="top">SR</td>
1437	<td valign="top">2.7a</td> <td valign="top">B</td>
1438	<td valign="top">Check that the number processors is also
1439	an
1440	integral divisor
1441	of the number  of gridpoints along y in case of a
1442	1d-decomposition
1443	along x. <p>Error concerning the multinode-version of
1444	poisfft_hybrid
1445	removed. It
1446	was caused by the Linux changes of version 2.7 and led to program abort
1447	due to MPI errors in <tt>MPI_ALLTOALL</tt>. </p> <p>No
1448	abort on t3e-systems if system specific routines are used. </p> <p>Array<tt>
1449	sums </tt>is initialized in<tt> init_3d_model </tt>before
1450	the first call of<tt> pres</tt>. Call of<tt>
1451	init_cloud_physics </tt>moved
1452	before<tt> init_particles</tt>.</p> </td> <td valign="top">fft_1dd_init, init_3d_model, init_pegrid,
1453	poisfft_hybrid</td> </tr> <tr> <td valign="top"><br>
1454	</td> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top">N</td>
1455	<td valign="top">Interactive steering of dvrp-graphic
1456	features by
1457	dvrp-browser
1458	plugin extended (position of slicers, threshold values of isosurfaces)
1459	. New dvrp_graphics package parameter<tt> slicer_range_limits_dvrp</tt>.</td>
1460	<td valign="top">init_dvrp, modules, package_parin,
1461	plot_dvrp</td> </tr> <tr> <td valign="top">29/10/03</td>
1462	<td valign="top">SR</td> <td valign="top">2.7b</td>
1463	<td valign="top">N</td> <td valign="top">In
1464	the multigrid method, on a defined level,
1465	data are gathered
1466	on PE0 and further calculations are carried out only on this PE. New<tt>
1467	d3par </tt>parameter <tt>mg_switch_to_pe0_level</tt>.
1468	<p>Particle groups implemented. New data type<tt>
1469	particle_groups_type </tt>and data type<tt> particle_type </tt>modified.
1470	Version
1471	numbers are
1472	output on the particle files. New<tt> particles_par </tt>parameter<tt>
1473	diameter</tt>. Parameter name<tt> uniform_psize</tt>
1474	changed to<tt>
1475	dvrp_psize</tt>.
1476	Parameters<tt> density_ratio </tt>is now an array.</p>
1477	</td> <td valign="top">advec_particles, check_open,
1478	exchange_horiz,
1479	header, init_particles,
1480	init_pegrid, modules, package_parin, parin, poismg</td> </tr>
1481	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1482	</td> <td valign="top">C</td> <td valign="top">Random number generator from numerical recipes
1483	is now rewritten
1484	as a module. In restart runs the seed of this generator is set to the
1485	last
1486	values of the previous run in order to keep the sequence of the random
1487	numbers. New binary version 2.2. <p>Buffer is flushed for file
1488	RUN_CONTROL immediately after every
1489	output
1490	on IBM and Linux cluster.</p> </td> <td valign="top">advec_particles,
1491	disturb_field, init_3d_model,
1492	init_particles,
1493	random_function, random_gauss, run_control, write_3d_binary</td> </tr>
1494	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1495	</td> <td valign="top">E</td> <td valign="top">In routine buoyance, horizontal mean
1496	temperature
1497	is now
1498	taken from array hom instead of array sums (otherwise inconsistence in
1499	case of using more than one statistical region). <p>Information
1500	about the time of the last timestep change added
1501	to the
1502	restart file. </p> <p>System call of<tt> batch_scp </tt>on
1503	IBM corrected.</p> </td> <td valign="top">buoyancy,
1504	check_open, read_var_list,
1505	write_var_list</td> </tr> <tr> <td style="vertical-align: top;">28/01/04</td> <td style="vertical-align: top;">SR</td> <td style="vertical-align: top;">2.8</td> <td style="vertical-align: top;">N</td> <td style="vertical-align: top;">Runge-Kutta schemes (2nd and
1506	3rd
1507	order)
1508	for time integration implemented. The third order scheme is the new
1509	default.
1510	It allows the timestep to be 0.9*CFL, which is much larger than for the
1511	former default leapfrog scheme.  The intermediate steps, which
1512	are
1513	part of these schemes, are realized by an additional loop within routine<span style="font-family: monospace;">
1514	time_integration </span>(currently<span style="font-family: monospace;">
1515	leap_frog</span>, but this routine will be renamed soon).
1516	Steering
1517	variables<span style="font-family: monospace;">
1518	at </span>and<span style="font-family: monospace;">
1519	bt </span>have
1520	been replaced by array<span style="font-family: monospace;">
1521	sct</span>.
1522	, which is particularly used in the prognostic equations. Values of
1523	this
1524	steering array are calculated within the new routine<span style="font-family: monospace;">
1525	timestep_scheme_steering</span>. <p>When using Runge-Kutta
1526	schemes,  the timestep increment
1527	is freely
1528	allowed to adjust after each timestep (the older schemes are using some
1529	restrictions, see routine<span style="font-family: monospace;">
1530	timestep</span>).
1531	Also, routine<span style="font-family: monospace;">
1532	run_control </span>is
1533	not automatically called in case of timestep changes, when Runge-Kutta
1534	schemes are switched on. </p> <p>The old leapfrog scheme
1535	is still implemented and should
1536	produce the
1537	same results as in the previous version(s)! </p> <p>Depending
1538	on the user experience, further adjustments to the
1539	Runge-Kutta
1540	schemes may be necessary within the next minor versions.  </p>
1541	<p><span style="font-weight: bold;">Attention:</span>
1542	<br>
1543	The content of the testresult-file (run control output) has
1544	significantly
1545	changed due to the new default timestep scheme!</p> </td> <td style="vertical-align: top;">check_parameters, header,
1546	init_3d_model,
1547	init_rankine, leap_frog, modules, prognostic_equations, read_var_list,
1548	swap_timelevel, timestep, write_var_list <p><span style="font-weight: bold;">new:</span> <br>
1549	timestep_scheme_steering</p> </td> </tr> <tr>
1550	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C</td> <td style="vertical-align: top;">Output of particle infos in
1551	subroutine<span style="font-family: monospace;">
1552	allocate_prt_memory </span>on demand only. <p>Type<span style="font-family: monospace;"> log </span>(used
1553	for
1554	cpu time measurements) changed to<span style="font-family: monospace;">
1555	logpoint </span>due to name conflict with FORTRAN
1556	intrinsic<span style="font-family: monospace;">
1557	log.</span></p> </td> <td style="vertical-align: top;">advec_particles,
1558	cpu_log, </td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E</td> <td style="vertical-align: top;">In case of opening unit 80, a
1559	barrier
1560	is set only for the first call of<span style="font-family: monospace;">
1561	check_open </span>(from routine<span style="font-family: monospace;">
1562	init_particles</span>), in order to avoid the possibility of
1563	hanging
1564	jobs,
1565	which may occur if unit 80 is opened within routine<span style="font-family: monospace;">
1566	allocate_prt_memory</span>.</td> <td style="vertical-align: top;">check_open</td> </tr>
1567	<tr> <td style="vertical-align: top;">30/01/04</td>
1568	<td style="vertical-align: top;">SR</td> <td style="vertical-align: top;">2.8a</td> <td style="vertical-align: top;">N</td> <td style="vertical-align: top;">In order to prepare the code
1569	for
1570	the simulation
1571	of flow around buildings (to be realized in one of the next major
1572	versions),
1573	the lower<span style="font-family: monospace;"> k </span>index<span style="font-family: monospace;">
1574	nzb </span>has been replaced by a two-dimensional array<span style="font-family: monospace;">
1575	nzb_2d </span>in many of the three-dimensional loops. So
1576	far, all
1577	elements of this array are set to<span style="font-family: monospace;">
1578	nzb</span>. <p>This change should not effect simulation
1579	results and cpu time
1580	in any
1581	way.</p> </td> <td style="vertical-align: top;">advec_s_pw,
1582	advec_s_up,
1583	advec_u_pw, advec_u_up,
1584	advec_v_pw, advec_v_up, advec_w_pw, advec_w_up, asselin_filter,
1585	buoyancy,
1586	calc_liquid_water_content, calc_precipitation, calc_radiation,
1587	coriolis,
1588	diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w,
1589	diffusivities,
1590	impact_of_latent_heat, init_3d_model, modules, production_e,
1591	prognostic_equations, </td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C</td> <td style="vertical-align: top;">Euler step informations are
1592	removed in
1593	the run control output in case of Runge-Kutta schemes. Also, the
1594	timestep
1595	increment limitation is removed for the Runge-Kutta schemes. <p><span style="font-weight: bold;">Attention:</span> <br>
1596	The content of the testresult-file (run control output) has changed
1597	due to this modification.</p> </td> <td style="vertical-align: top;">run_control, timestep</td>
1598	</tr> <tr> <td style="vertical-align: top;"><br>
1599	</td> <td style="vertical-align: top;"><br> </td>
1600	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E</td> <td style="vertical-align: top;">Velocity gradients at the
1601	surface calculated
1602	in routine production_e are now limited. In case of inhomogeneous
1603	surface
1604	heating small diffusivities (<span style="font-family: monospace;">km</span>)
1605	sometimes caused very small timesteps due to this problem.</td> <td style="vertical-align: top;">production_e</td> </tr>
1606	<tr> <td style="vertical-align: top;">30/04/04<br>
1607	</td> <td style="vertical-align: top;">SR<br>
1608	</td> <td style="vertical-align: top;">2.8b<br>
1609	</td> <td style="vertical-align: top;">N<br> </td>
1610	<td style="vertical-align: top;">The number of processors
1611	along
1612	the respective directions of the virtual processor grid must not be
1613	integral divisors of the number of gridpoints along x, y or z any more.
1614	In case that they are not integral divisors, the subdomains on the
1615	processors at the upper borders of the virtual grid will contain less
1616	gridpoints than the other subdomains (which are all of equal size).
1617	Although this causes a load imbalance, only runs with very small
1618	numbers of processors will feel a significant decrease of performance.
1619	In order to be able to carry out the transpositions, array<span style="font-family: monospace;"> d </span>(and also
1620	working array<span style="font-family: monospace;"> tend</span>)
1621	have the same size on
1622	all processors. This new feature is switched on by setting the
1623	inipar-parameter<span style="font-family: monospace;">
1624	grid_matching </span>= <span style="font-style: italic;">'match'</span>,
1625	which is the
1626	default now.<br> <br>
1627	Routine<span style="font-family: monospace;"> poisfft </span>is
1628	now
1629	the
1630	default for solving the Poisson-equation for the case of 2d- as well as
1631	1d-domain-decompositions and has been changed from a subroutine to a
1632	module. This routine now includes most of the optimization from the
1633	(Ketelsen) routine<span style="font-family: monospace;">
1634	poisfft_hybrid </span>and additionally allows 1d-decompositions
1635	along y.<br> <span style="font-weight: bold;">ATTENTION:</span>
1636	Routine<span style="font-family: monospace;">
1637	poisfft_hybrid </span>might still be
1638	faster when running PALM on more than one node of the IBM-Regatta,
1639	although the difference is not very big. The <span style="font-family: monospace;">poisfft</span>-code
1640	for a
1641	decomposition along y has still a poor performance and needs further
1642	optimization.<br> <br>
1643	The spectra-package is now able to use all the available FFT-methods
1644	(selected by inipar-parameter<span style="font-family: monospace;">
1645	fft_method </span>).
1646	Performance of the transpositions needed for calculating the spectra
1647	has been improved by using new direct transpositions from z to y and
1648	from y to x instead of two subsequent transpositions.<br> <br>
1649	Runge-Kutta scheme implemented in the 1d-version (<span style="font-family: monospace;">init_1d_model</span>).
1650	Diffusion
1651	quantity arrays are allocated for previous timelevels only in case of
1652	leapfrog scheme.<br> <br>
1653	This version is adapted for use on COMPAQ-DECALPHA systems (main
1654	changes: calling of SHAPE function within subroutine arguments (e.g.<span style="font-family: monospace;"> singleton</span>)
1655	causes compiler errors, particle data type modified for better
1656	alignment, DATA statements from modules removed because they caused
1657	internal compiler errors).<br> </td> <td style="vertical-align: top;">advec_s_ups, advec_u_ups,
1658	advec_v_ups, advec_w_ups, calc_spectra, check_parameters, fft_xy,
1659	header, init_1d_model, init_3d_model, init_particles, init_pegrid,
1660	modules, parin, plot_2d, poisfft, prandtl_fluxes, pres, read_var_list,
1661	singleton, spline_x, spline_y, spline_z, time_integration, transpose,
1662	write_3d_binary, write_var_list<br> </td> </tr> <tr>
1663	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">FFT routines renamed. Module<span style="font-family: monospace;"> fft_for_1d_decomp </span>renamed<span style="font-family: monospace;"> fft_xy</span>.
1664	Subroutine<span style="font-family: monospace;"> leap_frog
1665	</span>renamed<span style="font-family: monospace;">
1666	time_integration</span>.<br> <br>
1667	For all transpositions, MPI_ALLTOALL is used instead of MPI_ALLTOALLV.
1668	The names of many transposition indices have been changed.<br> <br>
1669	Inipar-parameter<span style="font-family: monospace;">
1670	impulse_advec </span>renamed<span style="font-family: monospace;"> momentum_advec</span>.<br>
1671	<br>
1672	Reading of restart data is moved from<span style="font-family: monospace;"> init_3d_model </span>to
1673	new routine <span style="font-family: monospace;">read_3d_binary</span>.<br>
1674	<br>
1675	All former transpose routines collected into one file.<br> </td>
1676	<td style="vertical-align: top;">check_parameters,
1677	flow_statistics, header, init_1d_model, init_3d_model, init_advec,
1678	init_pegrid, palm, parin, poisfft, poisfft_hybrid, production_e,
1679	prognostic_equations, read_var_list, sline_x, spline_y, write_var_list<span style="font-weight: bold;"><br> <br>
1680	new:</span><br>
1681	fft_xy, read_3d_binary, time_integration, transpose<br> <br>
1682	<span style="font-weight: bold;">deleted:</span><br>
1683	fft_for_1d_decomp, leap_frog, transpose_xy, transpose_xz, transpose_yx,
1684	transpose_yz, transpose_zx, transpose_zy<br> </td> </tr>
1685	<tr> <td style="vertical-align: top;"><br> </td>
1686	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Small errors in the
1687	particle-package removed, which sometimes caused aborts of restart runs
1688	on IBM.<br> <br>
1689	Small error in calculating the time series profiles removed (array
1690	bounds of some arrays needed for profil-output had to be increased).<br>
1691	<br>
1692	Function fft (singleton method) replaced by subroutine fftn due to
1693	problems with 64-bit mode on IBM<br> </td> <td style="vertical-align: top;">advec_particles,
1694	check_parameters, <br> </td> </tr> <tr> <td style="vertical-align: top;">26/03/05<br> </td>
1695	<td style="vertical-align: top;">SR<br> </td>
1696	<td style="vertical-align: top;">2.9<br> </td>
1697	<td style="vertical-align: top;">N<br> </td> <td style="vertical-align: top;">Non-cyclic lateral boundary
1698	conditions implemented.<br>
1699	Dirichlet/Neumann conditions at the inflow/outflow can be used either
1700	along x or along y. Cyclic conditions have to be used along the
1701	remaining direction. In case of non-cyclic conditions along x (y), the
1702	upper bound nxl (nyn) of array u (v) is enlarged by one gridpoint on
1703	the rightmost (northest) processor. These array index informations are
1704	passed to routine<span style="font-family: monospace;">
1705	exchange_horiz </span>and<span style="font-family: monospace;">
1706	disturb_field </span>by two
1707	additional arguments. Boundary conditions are set with new
1708	inipar-parameters<span style="font-family: monospace;">
1709	bc_lr </span>and<span style="font-family: monospace;">
1710	bc_ns</span>. A damping layer is
1711	needed at the outflow in order to damp reflections (see new parameters<span style="font-family: monospace;"> km_damp_max </span>and<span style="font-family: monospace;"> outflow_damping_width</span>)
1712	and an
1713	additional disturbance is imposed near the inflow (see new parameters<span style="font-family: monospace;">
1714	inflow_disturbance_begin </span>and<span style="font-family: monospace;"> inflow_disturbance_end</span>).
1715	Non-cyclic conditions require the use of the multigrid-method for
1716	solving the Poisson equation. Argument<span style="font-family: monospace;"> range </span>added
1717	to routine<span style="font-family: monospace;">
1718	boundary_conds </span>(where the
1719	non-cyclic conditions are set). <br> <br>
1720	Minor changes:<br>
1721	Output of parameter<span style="font-family: monospace;">
1722	datform </span>on
1723	&GLOBAL-Namelist (iso2d). This is set to <span style="font-style: italic;">'big_endian'</span> on
1724	IBM- and
1725	NEC-machines.<br> <br>
1726	Number of particle groups are additionally calculated in<span style="font-family: monospace;"> header </span>(formerly
1727	unknown).<br> </td> <td style="vertical-align: top;">advec_u_pw,
1728	advec_u_up, advec_v_pw, advec_v_up, boundary_conds,
1729	calc_liquid_water_content, check_parameters, close_file, coriolis,
1730	diffusion_u, diffusion_v, diffusion_w, diffusivities, disturb_field,
1731	exchange_horiz, header, init_3d_model, init_pegrid, init_pt_anomaly,
1732	init_rankine, modules, parin, poismg, pres, prognostic_equations,
1733	read_var_list, sor, time_integration, timestep, write_var_list<br>
1734	</td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;"><span style="font-family: monospace;">pres </span>is called
1735	by default only
1736	at the last Runge-Kutta-substep, which spares a big amount of CPU-time
1737	(see also new parameter<span style="font-family: monospace;">
1738	call_psolver_at_all_substeps</span>). No pressure term in the
1739	momentum
1740	equations in case of Runge-Kutta-schemes.<br> <span style="font-weight: bold;">Attention:</span> <br>
1741	The content of the testresult-file (run control output) has changed
1742	due to this modification.<br> <br>
1743	Program speedup by removing the exchange of ghost points in routines <span style="font-family: monospace;">calc_liquid_water_content</span>,
1744	<span style="font-family: monospace;">diffusivities</span>,
1745	.<br> <br>
1746	Default value for residual limit increased from 1E-6 to 1E-4. Routine<span style="font-family: monospace;"> prolong </span>in<span style="font-family: monospace;"> poismg </span>simplified
1747	(one call of<span style="font-family: monospace;">
1748	exchange_horiz </span>spared).<br> </td> <td style="vertical-align: top;">calc_liquid_water_content,
1749	diffusivities, modules, poismg, pres, time_integration,
1750	timestep_scheme_steering<br> </td> </tr> <tr>
1751	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Calculation of vertical
1752	particle
1753	velocity (with inertia) corrected, exp_arg had a wrong sign.<br> <br>
1754	(e)*1.5 replaced by eSQRT(e) in init_1d_model because of wrong
1755	results on NEC machines (as a side effect, the new calculation is much
1756	faster).<br> <br>
1757	Two errors concerning switch to PE0 (multigrid method) removed from<span style="font-family: monospace;"> init_pegrid</span>.<br>
1758	<br>
1759	Two errors in<span style="font-family: monospace;">
1760	plot_2d </span>removed:
1761	local_2d is allocated with upper bound<span style="font-family: monospace;"> nzt</span> (former<span style="font-family: monospace;"> nzt+1 </span>was
1762	wrong), additional barrier in case that PE0 gathers data from the other
1763	PEs, this barrier had to be set at the end of the gathering because
1764	otherwise PE0 sometimes received wrong data on tag 0.<br> <br>
1765	Use of module indices removed from routine<span style="font-family: monospace;"> split_1dd </span>in<span style="font-family: monospace;"> poisfft </span>since
1766	it caused
1767	errors in case of<span style="font-family: monospace;"> nx
1768	/= ny </span>and
1769	a 1D-decomposition along y.<br> <br>
1770	Wrong re-definition of dx2 and dy2 in<span style="font-family: monospace;"> sor </span>removed.<br>
1771	</td> <td style="vertical-align: top;">advec_particles,
1772	init_1d_model,
1773	init_pegrid, plot_2d, poisfft, sor<br> </td> </tr> <tr>
1774	<td style="vertical-align: top;">23/04/05<br> </td>
1775	<td style="vertical-align: top;">SR<br> </td>
1776	<td style="vertical-align: top;">2.9a<br> </td>
1777	<td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">Additional check for
1778	incompatibilities between non-cyclic lateral boundary conditions and
1779	other schemes.<br> <br>
1780	fcl_factor renamed cfl_factor.<br> <br>
1781	New local array sums_ll declared in flow_statistics instead of
1782	temporarily using sums_l.<br> <br>
1783	crmax (maximum number of crosses allowed in a plot of vertical
1784	profiles) increased from 20 to 100.<br> </td> <td style="vertical-align: top;">calc_spectra, check_parameters,
1785	flow_statistics, header, modules, parin, timestep<br> </td>
1786	</tr> <tr> <td style="vertical-align: top;"><br>
1787	</td> <td style="vertical-align: top;"><br> </td>
1788	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Revised calculation of output
1789	time counters regarding a possible decrease of the output time interval
1790	in case of restart runs.<br> <br>
1791	Error removed in Dirichlet bottom boundary conditions for pt and q in
1792	case of Runge-Kutta schemes.<br> <br> <span style="font-weight: bold;">batch_scp</span> calls
1793	(needed
1794	for determining correct filenames for AVS-fld-files) is given the
1795	remote username as an additional argument.<br> <br>
1796	Default setting of outflow_damping_width corrected.<br> <br>
1797	Initial horizontal velocities at the lowest grid levels in the 1d-model
1798	are set to a very small value in order to avoid wrong results and the
1799	resulting too small timesteps.<br> <br>
1800	Implicit counters i renamed i9 in modules due to declaration conflicts
1801	with i in other subroutines (reported by Portland compiler).<br> </td>
1802	<td style="vertical-align: top;">advec_particles,
1803	boundary_conds,
1804	check_open, check_parameters, init_1d_model, modules, time_integration<br>
1805	</td> </tr> <tr> <td style="vertical-align: top;">18/05/05<br> </td>
1806	<td style="vertical-align: top;">SR<br> </td>
1807	<td style="vertical-align: top;">2.10<br> </td>
1808	<td style="vertical-align: top;">N<br> </td> <td style="vertical-align: top;">NetCDF support implemented.<br>
1809	Profiles, time series, spectra, cross-sections, 3d-volume-data and
1810	particle data can now be output in NetCDF format (file handles
1811	101-108). This output can be switched on with the new d3par-parameter <span style="font-family: monospace;">data_output_format</span>.
1812	So far, this support is available on IBM systems at HLRN and on the NEC
1813	system at DKRZ. Output in format suitable for graphic software <span style="font-weight: bold;">profil</span>, <span style="font-weight: bold;">iso2d</span> and <span style="font-weight: bold;">avs</span> is still
1814	possible.<br> <br>
1815	Output of cross sections for qv, vpt and lwp (liquid water path).<br>
1816	</td> <td style="vertical-align: top;">advec_particles,
1817	check_open,
1818	check_parameters, close_file, header, modules, parin, plot_1d, plot_2d,
1819	plot_3d, plot_spectra, plot_ts, read_var_list, write_var_list<br>
1820	<br> <span style="font-weight: bold;">new:</span><br>
1821	netcdf<br> </td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">In <span style="font-family: monospace;">calc_spectra</span>, n
1822	is assigned the
1823	number of spectra (formerly, the number of spectra was given by n-1)<br>
1824	<br>
1825	Abort if <span style="font-family: monospace;">poisfft_hybrid</span>
1826	is called in a non-parallel environment.<br> <br>
1827	Default values of spectra package parameters <span style="font-family: monospace;">pl_spectra</span> and <span style="font-family: monospace;">spectra_direction</span>
1828	changed.<br> </td> <td style="vertical-align: top;">calc_spectra,
1829	check_parameters,
1830	modules, pres, read_3d_binary, write_3d_binary<br> </td> </tr>
1831	<tr> <td style="vertical-align: top;"><br> </td>
1832	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Missing argument in ffty
1833	(non-parallel case) added.<br> <br>
1834	Error in output of particle inertia information removed.<br> </td>
1835	<td style="vertical-align: top;">poisfft, header<br>
1836	</td> </tr> <tr> <td style="vertical-align: top;">05/07/05<br> </td>
1837	<td style="vertical-align: top;">SR<br> </td>
1838	<td style="vertical-align: top;">2.11<br> </td>
1839	<td style="vertical-align: top;">N/C<br> </td>
1840	<td style="vertical-align: top;">New cloud physics code
1841	implemented, which explicitly simulates single cloud droplets,
1842	including droplet growth by condensation and collision. Using this code
1843	requires to set the new inipar-parameter <span style="font-family: monospace;">cloud_droplets</span>
1844	= .TRUE. and to use the particle package (by using the <span style="font-weight: bold;">mrun</span>-option <span style="font-family: monospace;">-p particles</span>).
1845	Coupling between droplets and the thermodynamic quantities (potential
1846	temperature and specific humidity) is regarded in the new subroutine <span style="font-family: monospace;">interaction_droplets_ptq</span>.
1847	The real number of droplets in a grid cell can steered by the new
1848	inipar-parameter <span style="font-family: monospace;">initial_weighting_factor</span>.<br>
1849	<br> <span style="font-weight: bold;">This code
1850	will be further extended and probably changed in the near future, so
1851	the current status is that of a test version!</span><br> <br>
1852	In connection with this new code implementation, several changes has
1853	been made to the existing code:<br> <br>
1854	The particle (droplet) size is now given as radius (previously
1855	diameter). E.g., the name of the respective package parameter <span style="font-family: monospace;">diameter</span> has
1856	changed to <span style="font-family: monospace;">radius</span>.<br>
1857	<br>
1858	The current weighting_factor and radius are stored as additional
1859	particle attributes in the type structure <span style="font-family: monospace;">particle_type</span>.
1860	The MPI data type <span style="font-family: monospace;">mpi_particle_type</span>,
1861	needed for exchanging particles between subdomains, has been changed
1862	correspondingly.<br> <br> <span style="font-family: monospace;">gas_constant</span> is
1863	renamed <span style="font-family: monospace;">r_d</span>,
1864	<span style="font-family: monospace;">latent_heat</span>
1865	is renamed <span style="font-family: monospace;">r_v</span>,
1866	the allowed string length of <span style="font-family: monospace;">pl2d</span>
1867	and <span style="font-family: monospace;">pl3d</span>
1868	is increased from 6 to 10.<br> <br>
1869	New 3d arrays <span style="font-family: monospace;">ql_1</span>,
1870	<span style="font-family: monospace;">ql_2</span>, <span style="font-family: monospace;">ql_v</span> and <span style="font-family: monospace;">ql_vp</span>, <span style="font-family: monospace;">ql</span> is now a
1871	pointer, new pointer <span style="font-family: monospace;">ql_c</span>.<br>
1872	<br>
1873	Data format for unit 85 (particle data output) is changed.</td> <td style="vertical-align: top;">advec_particles.f90
1874	check_open.f90, header.f90, init_3d_model.f90, init_cloud_physics.f90,
1875	init_particles.f90, modules.f90, package_parin.f90, parin.f90,
1876	plot_2d.f90, plot_3d.f90, read_var_list.f90, time_integration.f90,
1877	write_var_list.f90<br> <br> <span style="font-weight: bold;">new:</span><br>
1878	interaction_droplets_ptq.f90</td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">Default value of <span style="font-family: monospace;">call_psolver_at_all_substeps</span>
1879	is <span style="font-style: italic;">.TRUE.</span>,
1880	because small scale waves occured with <span style="font-style: italic;">.FALSE.</span></td> <td style="vertical-align: top;">modules.f90</td> </tr>
1881	<tr> <td style="vertical-align: top;"><br> </td>
1882	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">2d- and 3d-NetCDF-files are not
1883	opened if there is no output for them (<span style="font-family: monospace;">pl2d</span> = <span style="font-family: monospace;">pl3d</span> = <span style="font-style: italic;">' '</span>).<br> <br>
1884	No opening of units 101 - 108 in case of missing NetCDF support.</td>
1885	<td style="vertical-align: top;">check_open.f90, netcdf.f90<br>
1886	</td> </tr> <tr> <td style="vertical-align: top;">30/06/05<br> </td>
1887	<td style="vertical-align: top;">GS<br> </td>
1888	<td style="vertical-align: top;">2.11a<br> </td>
1889	<td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">Scalars ug and vg have been
1890	changed into
1891	arrays in order to allow the specification of a geostrophic wind that
1892	depends on height (baroclinicity). The initial profiles of the the
1893	u- and v-component of the geostrophic wind are initialized by
1894	specifying the new initialization parameters <span style="font-family: monospace;">ug_surface</span>, <span style="font-family: monospace;">ug_vertical_gradient</span>,
1895	<span style="font-family: monospace;">ug_vertical_gradient_level</span>
1896	and <span style="font-family: monospace;">vg_surface</span>,
1897	<span style="font-family: monospace;">vg_vertical_gradient</span>,
1898	<span style="font-family: monospace;">vg_vertical_gradient_level</span>,
1899	respectively. <br> <br>
1900	The former initialization parameters <span style="font-family: monospace;">ug</span> and <span style="font-family: monospace;">vg</span> have been
1901	removed. <br> </td> <td style="vertical-align: top;">boundary_conds,
1902	check_parameters, coriolis, header, init_1d_model, modules, parin,
1903	prognostic_equations, read_var_list, spline_z, write_var_list<br>
1904	</td> </tr> <tr> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Error in the calculation of u_0
1905	and
1906	v_0 in production_e.f90 removed.<br> <br> <span style="font-weight: bold;">Attention:</span> <br>
1907	The content of the testresult-file (run control output) has changed
1908	due to this modification.<br> </td> <td style="vertical-align: top;">production_e<br> </td>
1909	</tr> <tr> <td style="text-align: left; vertical-align: top;">20/10/05</td>
1910	<td style="vertical-align: top;">SR</td> <td style="vertical-align: top;">2.11b</td> <td style="vertical-align: top;">N/C</td> <td style="vertical-align: top;">Collision process for droplet
1911	growth completed.<br> <br> <span style="font-weight: bold;">The droplet code is still under
1912	development and requires further speed optimization!<br> <br>
1913	</span>Number of particles really used is additionally output on
1914	the netcdf particle data file.<span style="font-weight: bold;"></span></td>
1915	<td style="vertical-align: top;">advec_particles, modules,
1916	netcdf</td> </tr> <tr> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;">E</td> <td style="vertical-align: top;">The
1917	last PE in a row is not allowed to have more grid points than the other
1918	PES (only less). Jobs crashed in these cases that the last PE has more
1919	grid points. Therefore, the number of gridpoints along x (and y) must
1920	now meet a special condition which is checked in case that <span style="font-family: monospace;">grid_matching</span> =
1921	<span style="font-style: italic;">'match'</span> is
1922	used.<br> <br>
1923	Error removed in calculating y axis data for yz cross sections. Error
1924	in output of netcdf yz-cross-sections removed.<br> <br>
1925	2*r replaced by r in the exponential term of the particle momentum
1926	equation.<br>
1927	Error in output of yz-slice information removed.</td> <td style="vertical-align: top;">advec_particles, header,
1928	init_pegrid, netcdf, plot_2d</td> </tr> <tr> <td style="vertical-align: top;">06/12/05</td> <td style="vertical-align: top;">SR</td> <td style="vertical-align: top;">2.11c</td> <td style="vertical-align: top;">N</td> <td style="vertical-align: top;">Output of ql profile is allowed
1929	in case of using cloud droplets.</td> <td style="vertical-align: top;">check_parameters,
1930	flow_statistics, modules</td> </tr> <tr> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;"> </td> <td style="vertical-align: top;">E</td> <td style="vertical-align: top;">The horizontally averaged pt
1931	profile is calculated within<span style="font-family: monospace;">
1932	buoyancy </span>only
1933	in case of the first respective intermediate timestep. This is done in
1934	order to spare communication time and to produce identical model
1935	results with jobs which are calling<span style="font-family: monospace;"> flow_statistics </span>at
1936	different time intervals.<br> <br>
1937	Error in netcdf variable declaration for<span style="font-family: monospace;"> statistic_regions </span>/=
1938	<span style="font-style: italic;">0</span> removed.</td>
1939	<td style="vertical-align: top;">buoyancy, netcdf</td>
1940	</tr><tr><td style="vertical-align: top;">23/02/06</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.0</td><td style="vertical-align: top;">N</td><td><span style="font-weight: bold;">Version for simulating flows over
1941	topography (buildings, mountains, etc.)</span><br style="font-weight: bold;"><br>Besides
1942	the implementation of topography, this version contains several other
1943	improvements. The most important ones are listed here:<br><ul><li>The
1944	cloud droplet code has been optimized (it now runs about 100 times
1945	faster than before).</li><li>Output of time-averaged 2d/3d
1946	data (sections / volume data) is possible.</li><li>Output
1947	of 2d-section data averaged along the direction normal to this section
1948	can be done.</li><li>The user-interface has been extended
1949	in order to allow 2d-/3d-output of user-defined quantities.</li></ul>The
1950	kind of topography to be used is controlled by the new initialization
1951	parameter <span style="font-family: monospace;">topography</span>.
1952	Allowed values are <span style="font-style: italic;">'flat'</span>,
1953	<span style="font-style: italic;">'single_building'</span>,
1954	and <span style="font-style: italic;">'read_from_file'</span>.
1955	The user can define his own special topography setting within the new
1956	user-interface routine <span style="font-family: monospace;">user_init_grid</span>.
1957	For the single building case, the building (rectangular) size
1958	and position can be controlled with parameters <span style="font-family: monospace;">building_height</span>,
1959	<span style="font-family: monospace;">building_length_x</span>,
1960	<span style="font-family: monospace;">building_length_y</span>,
1961	<span style="font-family: monospace;">building_wall_left</span>,
1962	and <span style="font-family: monospace;">building_wall_south</span>.<br>
1963	<br>
1964	The topography code is already optimized (vectorized) for use on the
1965	NEC-SX6.<br><br>Output of time-averaged 2d-/3d-data can be
1966	enabled by appending the string <span style="font-style: italic;">'_av'</span>
1967	to the respective output quantities given with the new
1968	runtime-parameter <span style="font-family: monospace;">data_output</span>
1969	(see further below for the (name)changes in the parameters for data
1970	output). Example: if a time-average of the vertical cross-section of
1971	potential temperature is required, the user has to set <span style="font-family: monospace;">data_output</span> = <span style="font-style: italic;">'pt_xy_av'</span>.
1972	In case of NetCDF-output, the time-averaged data is output to
1973	additional files (seperate from the non-averaged output). The length of
1974	the averaging interval and the temporal distance of the single
1975	instantaneous sections (volumes) entering into this averaging is
1976	controlled by the new runtime-parameters <span style="font-family: monospace;">averaging_interval</span>and
1977	<span style="font-family: monospace;">dt_averaging_input</span>.
1978	<br><br>An average normal to the direction of a
1979	cross-section can be output by setting the respective cross section
1980	index to <span style="font-style: italic;">-1</span>
1981	(example: <span style="font-family: monospace;">section_xz</span>
1982	= <span style="font-style: italic;">-1</span>).<br><br>New
1983	user-interface routines allowing the output of user-defined quantities
1984	are <span style="font-family: monospace;">user_check_data_output</span>,
1985	<span style="font-family: monospace;">user_define_netcdf_grid</span>,
1986	<span style="font-family: monospace;">user_data_output_2d</span>,
1987	<span style="font-family: monospace;">user_data_output_3d</span>,
1988	and <span style="font-family: monospace;">user_3d_data_averaging</span>.
1989	These quantities can be calculated using the new <span style="font-family: monospace;">CASE</span>-Entry <span style="font-style: italic;">'after integration'</span>
1990	in the user-interface routine <span style="font-family: monospace;">user_actions</span>.<br><br>Optimization
1991	of the cloud droplet code is mainly done by re-sorting all particles
1992	after every timestep in a way that now all particles which belong to
1993	the same grid-box (k,j,i) are stored consecutively (wthout any strides)
1994	in memory.<br> <br>
1995	Code adaptation for the IBM at the department of atmospheric sciences,
1996	Yonsei university (ibmy). Affected subroutines: <span style="font-family: monospace;">fft_xy</span>, <span style="font-family: monospace;">netcdf</span>, <br><br><span style="font-weight: bold;">Further new features:</span><br><ul><li>Use
1997	of particle tails now requires setting of the new package-parameter <span style="font-family: monospace;">use_particle_tails</span>.
1998	The new parameter skip_particles_for_tail allows only every <span style="font-family: monospace;">skip_particle_for_tail</span>'th
1999	parameter having a tail.</li><li>Initialization-parameter <span style="font-family: monospace;">e_min</span> can be
2000	used to set a lower limit for the subgrid-scale TKE (i.e. to guarantee
2001	a lower limit for the flow's Reynolds-number).</li><li>A
2002	conservation of the volume flow (through the complete xz- and
2003	yz-sections  of the total domain) can be enforced by the new
2004	initialization-parameter <span style="font-family: monospace;">conserve_volume_flow</span>.</li><li>Data
2005	output can be skipped for a given time interval from simulation start
2006	(t=0) using new runtime-parameters <span style="font-family: monospace;">skip_time_dopr</span>,
2007	<span style="font-family: monospace;">skip_time_dosp</span>,
2008	<span style="font-family: monospace;">skip_time_do2d_xy</span>,
2009	<span style="font-family: monospace;">skip_time_do2d_xz</span>,
2010	<span style="font-family: monospace;">skip_time_do2d_yz</span>,
2011	and <span style="font-family: monospace;">skip_time_do3d</span>.<br>
2012	</li><li>By default, NetCDF output is now using 64-bit
2013	offset format
2014	(large file support) on most machines. The user can switch to the
2015	32-bit offset format with the new runtime-parameter <span style="font-family: monospace;">netcdf_64bit</span>.
2016	Units 111:113  and 116 are opened for NetCDF output of
2017	time-averaged 2d-3d data.<br> </li> <li>Data
2018	logging routines are added (see file data_log.f90), which can be used
2019	for debugging purposes. Output is done on unit 20 (local file
2020	name/directory name DATA_LOG).</li> <li>New routine <span style="font-family: monospace;">exchange_horiz_2d_int</span>
2021	for  ghostpoint exchange of 2d-integer arrays. Routine <span style="font-family: monospace;">exchange_horiz_2d</span>
2022	is extended for non-cyclic boundary conditions in the non-parallel case.</li>
2023	<li>Two different methods for calculating the mixing length and
2024	the dissipation can be used in the 1d-model. These are steered by the
2025	new initializing-parameters <span style="font-family: monospace;">dissipation_1d</span>
2026	and <span style="font-family: monospace;">mixing_length_1d</span>.<br>
2027	</li>
2028	</ul></td><td style="vertical-align: top;">advec_particles,
2029	advec_s_pw,
2030	advec_s_up, advec_u_pw, advec_u_up, advec_v_pw, advec_v_up, advec_w_pw,
2031	advec_w_up, boundary_conds, buoyancy, check_open, check_parameters,
2032	close_file, coriolis, diffusion_e, diffusion_s, diffusion_u,
2033	diffusion_v, diffusion_w, diffusivities, disturb_field,
2034	disturb_heatflux, exchange_horiz_2d, exchange_horiz, flow_statistics,
2035	header, init_1d_model, init_3d_model, init_grid, init_particles,
2036	init_pegrid, modules, netcdf, package_parin, parin, poisfft,
2037	prandtl_fluxes, pres, production_e, prognostic_equations,
2038	read_3d_binary, read_var_list, run_control, time_integration,
2039	user_interface, write_3d_binary, write_var_list<br> <br> <span style="font-weight: bold;">new:</span><br>
2040	average_3d_data, data_log, sum_up_3d_data<br> <br> <span style="font-weight: bold;">renamed:<br> </span>plot_dvrp
2041	-> data_output_dvrp<br>
2042	plot_spectra -> data_output_spectra<br>
2043	plot_ts -> data_output_tseries<br>
2044	plot_1d -> data_output_profiles<br> <span style="font-weight: bold;"></span>plot_2d ->
2045	data_output_2d<br>
2046	plot_3d -> data_output_3d<br>
2047	</td></tr><tr><td style="vertical-align: top;"> </td><td> </td><td> </td><td style="vertical-align: top;">C</td><td>In
2048	parallel mode, all PEs are opening the same copy of the
2049	NAMELIST-parameter file <span style="font-family: monospace;">PARIN</span>,
2050	i.e. from now on, the file attribute "<span style="font-family: monospace;">npe</span>" must be
2051	removed from the corresponding file connection statements in the <span style="font-weight: bold;">mrun</span> configuration
2052	file (.mrun.config).<br><br>A
2053	large number of parameter names and local filenames have been changed
2054	(see list below). Most of them are parameters concerning data
2055	output (do). The former denotations "plot" and "pl" have been changed
2056	to "data_output" and "do", respectively. In addition to these changes,
2057	the names of many internal PALM parameters and variables have also
2058	changed.<br><br>Restart runs now require setting of the
2059	initialization-parameter <span style="font-family: monospace;">initializing_actions</span>
2060	= <span style="font-style: italic;">'read_restart_data'</span>.<br>
2061	<br>
2062	Concerning particles, the parameters <span style="font-family: monospace;">psl</span>, <span style="font-family: monospace;">psr</span>, <span style="font-family: monospace;">pdx</span>,
2063	etc., which are controlling the position of the particle source and the
2064	number of particles within this source, are now 1d-arrays. This allows
2065	to define different particle sources for different particle groups.<br>
2066	<br>
2067	The number of particle groups has to be set by the user (no automatic
2068	calculation from the value of parameter <span style="font-family: monospace;">density_ratio</span>
2069	any more)<span style="font-style: italic;"></span>.
2070	Variable <span style="font-family: monospace;">idum</span>
2071	in type <span style="font-family: monospace;">particle_type</span>
2072	has been renamed <span style="font-family: monospace;">tail_id</span>.<br><br>Output
2073	for units 15 and 17 flushed in <span style="font-family: monospace;">init_1d_model</span>.<br><br>List
2074	of changed parameter names:<br><table style="text-align: left; width: 559px; height: 831px;" border="1" cellpadding="2" cellspacing="2"><tbody><tr><td style="font-weight: bold;" align="undefined" valign="undefined">Old name</td><td align="undefined" valign="undefined"><span style="font-weight: bold;">New name</span></td><td align="undefined" valign="undefined"><span style="font-weight: bold;">Comments</span></td></tr><tr><td align="undefined" valign="undefined">average_period_pl1d</td><td align="undefined" valign="undefined">averaging_interval_pr</td><td align="undefined" valign="undefined"><br>
2075	</td></tr><tr><td style="vertical-align: top;">average_period_pr1d</td><td style="vertical-align: top;">---</td><td style="vertical-align: top;">averaging of printed profiles
2076	is not possible any more</td></tr><tr><td align="undefined" valign="undefined">average_period_sp</td><td align="undefined" valign="undefined">averaging_interval_sp</td><td align="undefined" valign="undefined"><br>
2077	</td></tr><tr><td align="undefined" valign="undefined">dt_average</td><td align="undefined" valign="undefined">dt_averaging_input_pr</td><td align="undefined" valign="undefined"><br>
2078	</td></tr><tr><td align="undefined" valign="undefined">dt_pl1d</td><td align="undefined" valign="undefined">dt_dopr</td><td align="undefined" valign="undefined"><br>
2079	</td></tr><tr><td align="undefined" valign="undefined">dt_plsp</td><td align="undefined" valign="undefined">dt_dosp</td><td align="undefined" valign="undefined"><br>
2080	</td></tr><tr><td>dt_plts</td><td>dt_dots</td><td><br>
2081	</td></tr><tr><td align="undefined" valign="undefined">dt_pr1d</td><td align="undefined" valign="undefined">dt_dopr_listing</td><td align="undefined" valign="undefined"><br>
2082	</td></tr><tr><td align="undefined" valign="undefined">dt_pl2d_xy</td><td align="undefined" valign="undefined">dt_do2d_xy</td><td align="undefined" valign="undefined"><br>
2083	</td></tr><tr><td align="undefined" valign="undefined">dt_pl2d_xz</td><td align="undefined" valign="undefined">dt_do2d_xz</td><td align="undefined" valign="undefined"><br>
2084	</td></tr><tr><td align="undefined" valign="undefined">dt_pl2d_yz</td><td align="undefined" valign="undefined">dt_do2d_yz</td><td align="undefined" valign="undefined"><br>
2085	</td></tr><tr><td align="undefined" valign="undefined">ebene_xy</td><td align="undefined" valign="undefined">section_xy</td><td align="undefined" valign="undefined"><br>
2086	</td></tr><tr><td align="undefined" valign="undefined">ebene_xz</td><td align="undefined" valign="undefined">section_xz</td><td align="undefined" valign="undefined"><br>
2087	</td></tr><tr><td align="undefined" valign="undefined">ebene_yz</td><td align="undefined" valign="undefined">section_yz</td><td align="undefined" valign="undefined"><br>
2088	</td></tr><tr><td align="undefined" valign="undefined">nz_plot3d</td><td align="undefined" valign="undefined">nz_do3d</td><td align="undefined" valign="undefined"><br>
2089	</td></tr><tr><td align="undefined" valign="undefined">plts</td><td align="undefined" valign="undefined">data_output_ts</td><td align="undefined" valign="undefined"><br>
2090	</td></tr><tr><td align="undefined" valign="undefined">pl1d</td><td align="undefined" valign="undefined">data_output_pr</td><td align="undefined" valign="undefined"><br>
2091	</td></tr><tr><td style="vertical-align: top;">pl2d</td><td style="vertical-align: top;">data_output</td><td style="vertical-align: top;">old parameters pl2d and pl3d
2092	are joined to new parameter data_output</td></tr><tr><td align="undefined" valign="undefined">pl3d</td><td align="undefined" valign="undefined">data_output</td><td align="undefined" valign="undefined"><br>
2093	</td></tr><tr><td align="undefined" valign="undefined">pl2d_at_begin</td><td align="undefined" valign="undefined">do2d_at_begin</td><td align="undefined" valign="undefined"><br>
2094	</td></tr><tr><td align="undefined" valign="undefined">pl3d_at_begin</td><td align="undefined" valign="undefined">do3d_at_begin</td><td align="undefined" valign="undefined"><br>
2095	</td></tr><tr><td align="undefined" valign="undefined">pl3d_compress</td><td align="undefined" valign="undefined">do3d_compress</td><td align="undefined" valign="undefined"><br>
2096	</td></tr><tr><td align="undefined" valign="undefined">pl3d_precision</td><td align="undefined" valign="undefined">do3d_comp_prec</td><td align="undefined" valign="undefined"><br>
2097	</td></tr><tr><td>pl_spectra</td><td>data_output_sp</td><td><br>
2098	</td></tr><tr><td align="undefined" valign="undefined">read_fields_from_prior_run</td><td align="undefined" valign="undefined">read_restart_data</td><td align="undefined" valign="undefined"><br>
2099	</td></tr><tr><td align="undefined" valign="undefined">write_plot2d_on_each_pe</td><td align="undefined" valign="undefined">data_output_2d_on_each_pe</td><td align="undefined" valign="undefined"><br>
2100	</td></tr><tr><td align="undefined" valign="undefined">z_max_pl1d</td><td align="undefined" valign="undefined">z_max_do1d</td><td align="undefined" valign="undefined"><br>
2101	</td></tr><tr><td align="undefined" valign="undefined">z_max_pl2d</td><td align="undefined" valign="undefined">z_max_do2d</td><td align="undefined" valign="undefined"><br>
2102	</td></tr></tbody></table></td><td style="vertical-align: top;">advec_particles,
2103	advec_s_bc, check_parameters, check_open, close_file,
2104	data_output_dvrp,  data_output_profiles, data_output_tseries,
2105	data_output_2d, data_output_3d, flow_statistics, header, init_1d_model,
2106	init_3d_model, init_dvrp, init_particles, init_pegrid, init_slope,
2107	modules, netcdf, package_parin, palm, parin, print_1d, read_var_list,
2108	run_control, time_integration, timestep, write_compressed,
2109	write_var_list<br>
2110	</td></tr><tr><td> </td><td> </td><td> </td><td style="vertical-align: top;">E</td><td>Error in
2111	the particle release (defaults of <span style="font-family: monospace;">psl</span>, <span style="font-family: monospace;">psr</span>, <span style="font-family: monospace;">psn</span>, <span style="font-family: monospace;">pss</span>) at the PE
2112	boundary has been fixed.<br> <br>
2113	Error removed getting the variable ids for <span style="font-family: monospace;">_ext</span> for
2114	profiles and time series.<br><br>NetCDF calls in <span style="font-family: monospace;">data_output_tseries</span>
2115	only if NetCDF output is switched on.<br><br>Output of the
2116	initial geostrophic wind profile corrected.<br><br>Maximum
2117	possibel timestep for Runge-Kutta-schemes reduced, error concerning
2118	initialization of  <span style="font-family: monospace;">l_black</span>
2119	removed (both in <span style="font-family: monospace;">init_1d_model</span>).<br>
2120	</td><td style="vertical-align: top;">advec_particles,
2121	data_output_tseries, header, init_particles, init_1d_model, netcdf<br>
2122	</td></tr><tr><td align="left" valign="top">26/04/06</td><td align="left" valign="top">SR</td><td align="left" valign="top">3.0a</td><td align="left" valign="top">N</td><td align="left" valign="top">OpenMP parallelization for
2123	the cache-optimized PALM code.<br><br>OpenMP
2124	directives have been added where necessary. Still further tuning will
2125	be necessary to get optimum performance. Other parts of the code than
2126	the cache-optimized code still need to be (OpenMP-) parallelized. <br><br>So
2127	far, threads are activated by setting the <span style="font-weight: bold;">mrun</span>-options <span style="font-family: monospace;">-T</span> <span style="font-style: italic;"><number_of_threads></span>
2128	and <span style="font-family: monospace;">-O</span>,
2129	i.e. when the Option <span style="font-family: monospace;">-O</span>
2130	is given, the <span style="font-family: monospace;">-T</span>
2131	argument is interpreted as the number of threads to be used. When <span style="font-family: monospace;">-O</span> is given,
2132	the number of MPI tasks per node is automatically set to <span style="font-style: italic;">1</span>.<br><br>Beside
2133	the additional compiler directives, the main code change required by
2134	the OpenMP parallelization is that global sums are now calculated by
2135	first calculating local sums on each thread. As the next step, local
2136	sums are calculated from these thread sums for each MPI task before the
2137	global sum is computed via MPI_ALLREDUCE.  For storing the
2138	thread
2139	sums, arrays sums_l and sums_l_l now have three dimensions where the
2140	number of elements of the third dimension is equal to the number of
2141	OpenMP threads.</td><td align="left" valign="top">buoyancy,
2142	cpu_statistics, diffusivities, flow_statistics, header, init_pegrid,
2143	init_3d_model, modules, prandtl_fluxes, pres, production_e</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top">ML</td><td align="left" valign="top"> </td><td align="left" valign="top">C</td><td align="left" valign="top">Provisional
2144	correction for Piacsek & Williams advection scheme: keep u and
2145	v
2146	zero one layer below the topography (in case of set_1d-model_profiles).</td><td align="left" valign="top">init_3d_model</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top">SR/ML</td><td align="left" valign="top"> </td><td align="left" valign="top">E</td><td align="left" valign="top">In <span style="font-family: monospace;">flow_statistics.f90</span>
2147	nzb_s_inner(j,i) replaced by nzb in determination of z_i.<br><br>Errors
2148	removed in the computation of the diabatic mixing length (<span style="font-family: monospace;">init_1d_model.f90</span>).<br><br>Error
2149	removed in extend mode when checking whether the selected cross
2150	sections match those in the already existing NetCDF file (<span style="font-family: monospace;">netcdf.f90</span>).</td><td align="left" valign="top">flow_statistics,
2151	init_1d_model, netcdf</td></tr><tr><td align="left" valign="top">02/06/06</td><td align="left" valign="top">SR</td><td align="left" valign="top">3.0b</td><td align="left" valign="top">N</td><td align="left" valign="top">This version is adapted to the Sun Fire X4600
2152	system at TIT (to be used by setting the <span style="font-weight: bold;">mrun</span> option <span style="font-family: monospace;">-h lctit</span>).</td><td align="left" valign="top">cpu_log, init_1d_model,
2153	local_tremain, locaö_tremain_ini, run_control</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top">C</td><td align="left" valign="top">NetCDF 2d-
2154	and 3d-datasets now contain the exact coordinates of the variables
2155	along x and y with respect to the positions where they are defined on
2156	the staggered grid.<br><br>NetCDF datasets of cross
2157	sections (e.g. <span style="font-family: monospace;">DATA_2D_XY_NETCDF</span>)
2158	are only opened if the respective cross sections are really requested
2159	by the settings of parameter <span style="font-family: monospace;">data_output</span>.</td><td align="left" valign="top">check_parameters,
2160	data_output_2d, data_output_3d, modules, netcdf, user_interface</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top">E</td><td align="left" valign="top">p is assigned to <span style="font-family: monospace;">to_be_resorted</span>
2161	instead of w</td><td align="left" valign="top">data_output_2d</td></tr><tr><td align="left" valign="top">04/08/06</td><td align="left" valign="top">SR</td><td align="left" valign="top">3.1</td><td align="left" valign="top">N</td><td align="left" valign="top">Subgrid
2162	scale velocities can (optionally) be included for calculating the
2163	particle advection, using the method of Weil et al. (2004, JAS, 61,
2164	2877-2887). This method is switched on by the new particle package
2165	parameter <span style="font-family: monospace;">use_sgs_for_particles</span>.
2166	This also forces the Euler/upstream method to be used for time
2167	advancement of the TKE (see new parameter <span style="font-family: monospace;">use_upstream_for_tke</span>).
2168	The minimum timestep during the sub-timesteps is controlled by
2169	parameter <span style="font-family: monospace;">dt_min_part</span>.
2170	The data type <span style="font-family: monospace;">particle_type</span>
2171	has additional new attributes <span style="font-family: monospace;">e_m</span>,
2172	<span style="font-family: monospace;">dt_sum</span>,
2173	and <span style="font-family: monospace;">speed_x/y/z_sgs</span>.<br><br>Other
2174	new particle features: output of particle quantities as timeseries in
2175	NetCDF format (on local file <span style="font-family: monospace;">DATA_1D_PTS_NETCDF</span>).
2176	The output time interval is controlled by parameter <span style="font-family: monospace;">dt_dopts</span>.
2177	Particle advection can be switched off after some time using parameter <span style="font-family: monospace;">end_time_prel</span>.
2178	More than one particle per point can be started with parameter <span style="font-family: monospace;">particles_per_point</span>.<br><br>Additional
2179	parameter in function <span style="font-family: monospace;">random_gauss</span>
2180	which limits the range of the created random numbers to five times the
2181	standard deviation (=1). Seeds <span style="font-family: monospace;">iran</span>
2182	and <span style="font-family: monospace;">iran_part</span>
2183	are stored for restart runs.</td><td align="left" valign="top">advec_particles,
2184	check_open, check_parameters, close_file, diffusion_e,
2185	disturb_heatflux, header, init_3d_model, init_particles, modules,
2186	netcdf, package_parin, parin, prognostic_equations, random_gauss,
2187	read_3d_binary, read_var_list, time_integration, write_3d_binary,
2188	write_var_list<br><br><span style="font-weight: bold;">new:</span><br>data_output_ptseries</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top">C</td><td align="left" valign="top">Call of subroutine <span style="font-family: monospace;">header</span> is moved
2189	after call of subroutine <span style="font-family: monospace;">init_3d_model</span>.
2190	Generation of <span style="font-family: monospace;">run_description_header</span>
2191	is moved from routines <span style="font-family: monospace;">palm</span>
2192	and <span style="font-family: monospace;">header</span>
2193	to <span style="font-family: monospace;">check_parameters</span>.
2194	Determination of the number of particle groups is moved from <span style="font-family: monospace;">header</span> to <span style="font-family: monospace;">init_particles</span>.<br><br><span style="font-family: monospace;">izuf</span> renamed <span style="font-family: monospace;">iran</span>.</td><td align="left" valign="top">check_parameters,
2195	disturb_field, disturb_heatflux, header, init_particles, modules, palm</td></tr><tr><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top"> </td><td align="left" valign="top">E</td><td align="left" valign="top">Variables
2196	do2d_unit and do3d_unit now defined as 2d-arrays. Before, in some
2197	cases, the units of variables in the 2d- and 3d-NetCDF-files have been
2198	wrong.<br><br>In routine <span style="font-family: monospace;">poisfft</span> default
2199	setting of the thread number tn in case of not using OpenMP.<br><br>Error
2200	removed in the non-parallel part of routine <span style="font-family: monospace;">flow_statistics</span>
2201	(number of arguments of array <span style="font-family: monospace;">sums_l</span>).<br><br>Error
2202	removed which appeared if the user had decreased the value of <span style="font-family: monospace;">dt_dopr</span> within
2203	a job chain and if simulataneous time averaging of profiles was
2204	switched on.</td><td align="left" valign="top">check_parameters,
2205	data_output_profiles, flow_statistics, modules, netcdf, poisfft</td></tr><tr><td style="vertical-align: top;">22/08/06</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.1a</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">In case of more than one
2206	particle group, seperate output of timeseries for each of the groups.<br><br>New
2207	initial parameter <span style="font-family: monospace;">dz_max</span>,
2208	which limits the vertical gridspacing in case of a vertically stretched
2209	grid.</td><td style="vertical-align: top;">data_output_ptseries,
2210	header, init_grid, modules, netcdf, parin, read_var_list, write_var_list</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Disturbances are imposed only
2211	for the last Runge-Kutta-substep. <br><span style="font-weight: bold;">Attention:</span> <br>
2212	The content of the testresult-file (run control output) has changed
2213	due to this modification.<br><br>Output of xz and yz cross
2214	sections now up to gridpoint nzt+1.<br><br>Default settings
2215	of particle start positions changed.</td><td style="vertical-align: top;">check_open, close_file,
2216	data_output_2d, init_particles, netcdf, time_integration</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Initialisation of all tendency
2217	arrays (t.._m) needed for the Runge-Kutta schemes.<br><br>Bugfix
2218	in index array initialization for line- or point-like topography
2219	structures.<br><br>Bugfix: yv coordinates are now used for
2220	yz cross sections, where neccessary.</td><td style="vertical-align: top;">init_3d_model, init_grid, netcdf</td></tr><tr><td style="vertical-align: top;">12/02/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.1b</td><td style="vertical-align: top;"> N</td><td style="vertical-align: top;"><span style="font-weight: bold;">Attention:</span><br>This
2221	is the last revision before switching to the subversion revison control
2222	system!<br><br>Informative output to the job protocoll in
2223	case of restarts.</td><td style="vertical-align: top;">check_for_restart</td></tr><tr><td>  </td><td>  </td><td>  </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Values of environment variables
2224	are now read from local file <span style="font-family: monospace;">ENVPAR</span>
2225	instead of getting them by a system call.<br><br>For
2226	interpolation in <span style="font-family: monospace;">advec_particles</span>,
2227	allways level k is used.</td><td style="vertical-align: top;">advec_particles,
2228	local_tremain_ini, parin</td></tr><tr><td> </td><td> </td><td> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Several bugfixes in <span style="font-family: monospace;">advec_particles</span>:
2229	new particles are released only if <span style="font-family: monospace;">end_time_prel</span>
2230	> <span style="font-family: monospace;">simulated_time</span>, transfer
2231	of particles when x < -0.5*dx (0.0 before), etc., index i,j used
2232	instead of cartesian (x,y) coordinate to check for transfer because
2233	this failed under very rare conditions, calculation of number of
2234	particles with same radius as the current particle (cloud droplet code).<br><br>Allocation
2235	of <span style="font-family: monospace;">tail_mask</span>
2236	and <span style="font-family: monospace;">new_tail_id</span>
2237	in case of restart-runs. "__" added in a cpp-directive. (both <span style="font-family: monospace;">init_particles</span>)</td><td style="vertical-align: top;">advec_particles, init_particles</td></tr><tr><td style="vertical-align: top;">02/03/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.1c</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">A heatflux can be prescribed at
2238	the top with new inipar parameters <span style="font-family: monospace;">top_heatflux</span>
2239	and <span style="font-family: monospace;">use_top_fluxes</span>.
2240	New 2d-arrays <span style="font-family: monospace;">qswst</span>,
2241	<span style="font-family: monospace;">qswst_m</span>,
2242	<span style="font-family: monospace;">tswst</span>
2243	and <span style="font-family: monospace;">tswst_m</span>
2244	are used to store this flux. Use of fluxes are controlled with new
2245	index variable <span style="font-family: monospace;">nzt_diff</span>.
2246	A Neumann boundary condition for temperature can be applied under these
2247	conditions.<br><br>Additionally, a Dirichlet condition for
2248	temperature can be used at the top.<br><br><span style="font-weight: bold;">Attention:</span> <br>
2249	The content of the testresult-file (run control output) has changed
2250	due to this modification.</td><td style="vertical-align: top;">check_parameters,
2251	diffusion_s, flow_statistics, header, init_grid, init_3d_model,
2252	modules, parin, production_e, prognostic_equations, read_var_list,
2253	read_3d_binary, swap_timelevel, write_var_list, write_3d_binary</td></tr><tr><td> </td><td> </td><td> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Prognostic equations for all
2254	scalars are now solved up to gridpoint nzt (formerly nzt-1).
2255	Boundary conditions for scalars at top adjusted respectively (now
2256	applied only at nzt+1).<br><br>The
2257	default top boundary condition for temperature has been renamed to <span style="font-style: italic;">'initial_gradient'</span>.<br><br>Calls
2258	of dvrp_output_local,
2259	which were commented out for a long time, are now activated for all
2260	streams.</td><td style="vertical-align: top;">advec_s_pw,
2261	boundary_conds, calc_precipitation, check_parameters, diffusion_e,
2262	diffusion_s, impact_of_latent_heat, init_dvrp, init_pt_anomaly,
2263	modules, production_e, prognostic_equations, spline_z</td></tr><tr><td> </td><td> </td><td> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: 3d-array p is not a
2264	pointer any more.<br><br>Bugfix in init_particles:
2265	MPI_REAL
2266	argument in MPI_ALLREDUCE
2267	replaced by<br>MPI_INTEGER
2268	(caused error on NEC only).<br><br>Bugfix:  ddzw now
2269	dimensioned 1:nzt"+1".</td><td style="vertical-align: top;">diffusion_e, diffusion_s,
2270	diffusion_u, diffusion_v, diffusion_w, init_particles, modules</td></tr><tr><td style="vertical-align: top;">29/03/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.2</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">The code, including scripts, utility programs and documentation is now under full control of <span style="font-family: Courier New,Courier,monospace;">subversion</span>. This revision includes a quite large number of new features, changes and bugfixes.<br> <br>Particle reflection from vertical walls implemented. The particle SGS model is also adjusted to these vertical walls.<br><br>Wall functions for vertical walls now include diabatic conditions. New subroutines <span style="font-family: Courier New,Courier,monospace;">wall_fluxes</span>, <span style="font-family: Courier New,Courier,monospace;">wall_fluxes_e</span>. New 4D-array <span style="font-family: Courier New,Courier,monospace;">rif_wall</span>.<br><br>Calculation/output of precipitation amount, precipitation rate and z0 (by setting "<span style="font-style: italic;">pra</span>", "<span style="font-style: italic;">prr</span>", "<span style="font-style: italic;">z0*</span>" with <span style="font-family: Courier New,Courier,monospace;">data_output</span>). The time interval on which the precipitation amount is defined is set by new d3par-parameter <span style="font-family: Courier New,Courier,monospace;">precipitation_amount_interval</span>.<br><br>New inipar-parameter <span style="font-family: Courier New,Courier,monospace;">loop_optimization</span> to control the loop optimization method.<br><br>New
2271	inipar-parameter <span style="font-family: Courier New,Courier,monospace;">pt_reference</span>. If given, this value is used as the
2272	reference that is used in the buoyancy terms (otherwise, the instantaneous
2273	horizontally averaged temperature is used).<br><br>New d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span>
2274	to switch on and especially to switch off 64bit offset for 3D
2275	files only (because still some pd-software is unable to handle 64bit
2276	offset).<br><br>New d3par-parameter <span style="font-family: Courier New,Courier,monospace;">dt_max</span> to set the maximum value allowed for the timestep. <br><br>New user interfaces <span style="font-family: Courier New,Courier,monospace;">user_advec_particles</span> and <span style="font-family: Courier New,Courier,monospace;">user_init_3d_model</span>. The new initializing action "<span style="font-style: italic;">by_user</span>" calls <span style="font-family: Courier New,Courier,monospace;">user_init_3d_model</span> and allows the initial setting of all 3d arrays under complete user control.<br><br>Samples added to the user interface which show how to add user-define time series quantities.<br><br>Topography height informations are stored on arrays <span style="font-family: Courier New,Courier,monospace;">zu_s_inner</span> and <span style="font-family: Courier New,Courier,monospace;">zw_w_inner</span> and output to the 2d/3d NetCDF files.<br><br>Unit 9 is generally opened for output of debug informations (file <span style="font-family: Courier New,Courier,monospace;">DEBUG_<pe#></span>).</td><td style="vertical-align: top;">Makefile<br><br>advec_particles,
2277	average_3d_data, buoyancy, calc_precipitation, check_open,
2278	check_parameters, data_output_2d, diffusion_e, diffusion_u,
2279	diffusion_v, diffusion_w, diffusivities, header, impact_of_latent_heat,
2280	init_particles, init_3d_model, modules, netcdf, parin, production_e,
2281	read_var_list, read_3d_binary, sum_up_3d_data, user_interface,
2282	write_var_list, write_3d_binary<br><br><span style="font-weight: bold;">new:</span><br>wall_fluxes<br></td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">General revision of non-cyclic horizontal boundary conditions:<br>Radiation boundary conditions are now used instead of Neumann conditions at the outflow (calculation needs velocity values for <span style="font-family: Courier New,Courier,monospace;">t-dt</span>, which are stored on new arrays <span style="font-family: Courier New,Courier,monospace;">u_m_l</span>, <span style="font-family: Courier New,Courier,monospace;">u_m_r</span>, etc.). The calculation of a mean outflow is not needed any more. Volume flow control is added for the outflow boundary (<span style="font-weight: bold;">currently only for the north boundary!!</span>). Additional gridpoints along x and y (<span style="font-family: Courier New,Courier,monospace;">uxrp</span>, <span style="font-family: Courier New,Courier,monospace;">vynp</span>) are not needed any more and removed from the code. Routine "<span style="font-family: Courier New,Courier,monospace;">boundary_conds</span>" now operates on timelevel <span style="font-family: Courier New,Courier,monospace;">t+dt</span> and is not split in two parts (<span style="font-style: italic;">main</span>, <span style="font-style: italic;">uvw_outflow</span>) any more. Neumann boundary conditions are used at inflow/outflow in case of non-cyclic boundary conditions <span style="font-weight: bold;">for all 2d-arrays</span> that are handled by <span style="font-family: Courier New,Courier,monospace;">exchange_horiz_2d</span>.<br><span style="font-weight: bold;">Attention: the
2283	non-cyclic boundary conditions of this revision still contain some bugs
2284	which will be removed within the next revisions!</span><br><br>The Bott-Chlond-scheme can now be used in the vectorization-optimized part (NEC, etc.). Equations are solved up to gridpoint <span style="font-family: Courier New,Courier,monospace;">nzt</span>.<br><br>The
2285	FFT-method for solving the Poisson-equation is now working with Neumann
2286	boundary conditions both at the bottom and the top. This requires
2287	adjustments of the tridiagonal coefficients and subtracting the
2288	horizontally averaged mean from the vertical velocity field.<br><br>Particles-package is now part of the default code ("<span style="font-family: Courier New,Courier,monospace;">-p particles</span>" is not needed as an <span style="font-weight: bold;">mrun</span>-option any more). New attribute <span style="font-family: Courier New,Courier,monospace;">age_m</span> in <span style="font-family: Courier New,Courier,monospace;">particle_type</span>.<br><br>Move call of <span style="font-family: Courier New,Courier,monospace;">user_actions</span>( '<span style="font-style: italic;">after_integration</span>' ) below the increments of times<br>and counters. <span style="font-family: Courier New,Courier,monospace;">user_actions</span> is now called for each statistic region and has as an argument the number of the respective region (<span style="font-family: Courier New,Courier,monospace;">sr</span>).<br><br>d3par-parameter <span style="font-family: Courier New,Courier,monospace;">data_output_ts</span> is removed. Timeseries output for <span style="font-weight: bold;">profil</span>-software removed. Timeseries are now switched on by setting <span style="font-family: Courier New,Courier,monospace;">dt_dots</span>. Timeseries data is collected in <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>.<br><br>Initial velocities at <span style="font-family: Courier New,Courier,monospace;">nzb+1</span>
2289	are regarded for volume flow control in case they have been set zero
2290	before (to avoid small timesteps); see new internal parameters <span style="font-family: Courier New,Courier,monospace;">u/v_nzb_p1_for_vfc</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">q</span> is not allowed any more to become negative (<span style="font-family: Courier New,Courier,monospace;">prognostic_equations</span>).<br><br><span style="font-family: Courier New,Courier,monospace;">poisfft_init</span> is only called if the fft-solver is switched on (<span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>).<br><br>d3par-parameter <span style="font-family: Courier New,Courier,monospace;">moisture</span> renamed to <span style="font-family: Courier New,Courier,monospace;">humidity</span>.<br><br>Subversion global revision number is read from <span style="font-weight: bold;">mrun</span> and added to the run description header and to the run control (<span style="font-family: Courier New,Courier,monospace;">_rc</span>) file.<br><br><span style="font-family: Courier New,Courier,monospace;">__vtk</span> directives removed from main program.<br><br>The uitility routine <span style="font-family: Courier New,Courier,monospace;">interpret_config</span> now reads PALM environment variables from <span style="font-family: Courier New,Courier,monospace;">NAMELIST</span> instead using the system call <span style="font-family: Courier New,Courier,monospace;">GETENV</span>.</td><td style="vertical-align: top;">advec_s_bc, advec_u_pw,
2291	advec_u_up, advec_v_pw, advec_v_up, asselin_filter, boundary_conds, check_parameters,
2292	coriolis, data_output_dvrp, data_output_ptseries, data_output_ts,
2293	data_output_2d, data_output_3d, diffusion_u, diffusion_v,
2294	disturb_field, exchange_horiz, exchange_horiz_2d, flow_statistics, header, init_grid,
2295	init_particles, init_pegrid, init_rankine, init_pt_anomaly,
2296	init_1d_model, init_3d_model, modules, palm, package_parin, parin,
2297	poisfft, poismg, prandtl_fluxes, pres, production_e,
2298	prognostic_equations, read_var_list, read_3d_binary, sor,
2299	swap_timelevel, time_integration, write_var_list, write_3d_binary</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: preset of tendencies <span style="font-family: Courier New,Courier,monospace;">te_em</span>, <span style="font-family: Courier New,Courier,monospace;">te_um</span>, and <span style="font-family: Courier New,Courier,monospace;">te_vm</span> (<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>).<br><br>Bugfix in sample for reading user defined data from restart file (<span style="font-family: Courier New,Courier,monospace;">user_init</span>).<br><br>Bugfix in setting diffusivities for cases with the outflow damping layer extending over more than one subdomain (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>).<br><br>Check for possible negative humidities in the initial humidity profile.<br><br>In <span style="font-family: Courier New,Courier,monospace;">Makefile</span>, default suffixes are removed from the suffix list to avoid calling of <span style="font-family: Courier New,Courier,monospace;">m2c</span> in cases of existing <span style="font-family: Courier New,Courier,monospace;">.mod</span> files (problem on Linux systems).</td><td style="vertical-align: top;">Makefile<br><br>check_parameters, init_1d_model, init_3d_model, user_interface</td></tr><tr><td style="vertical-align: top;">19/04/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.2a</td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">All system relevant compile and link options (e.g. cpp-directives,
2300	library paths, etc.) as well as the host identifier (local_host) are
2301	now specified in the configuration file. This generally allows to install
2302	PALM on any kind of Linux-, IBM-AIX-, or NEC-SX-system by adding
2303	appropriate
2304	settings to the configuration file. A description is added to chapter
2305	5.0 of the online documentation.<br><br>Scripts are also running under the public domain ksh.<br><br>Filetransfer by ftp removed (options<span style="font-family: Courier New,Courier,monospace;"> -f </span>removed from <span style="font-weight: bold;">mrun</span> and <span style="font-weight: bold;">mbuild</span>).<br><br>Call of (system-)FLUSH routine moved to new routine<span style="font-family: Courier New,Courier,monospace;"> local_flush</span>.<br><br><span style="font-family: Courier New,Courier,monospace;">return_addres </span>and<span style="font-family: Courier New,Courier,monospace;"> return_username </span>are read from ENVPAR-NAMELIST-file instead of using<span style="font-family: Courier New,Courier,monospace;"> local_getenv</span>.<br><br>Preprocessor strings for different linux clusters changed to "<span style="font-family: Courier New,Courier,monospace;">lc</span>", some preprocessor directives renamed (new:<span style="font-family: Courier New,Courier,monospace;"> __intel_openmp_bug</span> which is used for the bug in<span style="font-family: Courier New,Courier,monospace;"> tridia_1dd </span>and the OpenMP directives). Preprocessor directives for old systems have been removed.<br><br></td><td style="vertical-align: top;">advec_particles,
2306	check_open, cpu_log, cpu_statistics, data_output_dvrp, flow_statistics,
2307	header, init_dvrp, init_particles, init_1d_model, init_dvrp,
2308	init_pegrid, local_getenv, local_system, local_tremain,
2309	local_tremain_ini, modules, palm, parin, run_control<br><br><span style="font-weight: bold;">new:</span><br>local_flush<br><br><span style="font-weight: bold;">changed scripts:</span><br>mbuild, mrun, .mrun.config.default<br></td></tr><tr><td style="vertical-align: top;">30/05/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.2b</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">Calculation and output of user-defined profiles: New userpar-parameter <span style="font-family: Courier New,Courier,monospace;">data_output_pr_user</span>. In the user-interface, routine <span style="font-family: Courier New,Courier,monospace;">user_check_data_output_pr</span> has been added and <span style="font-family: Courier New,Courier,monospace;">user_statistics</span> has been extended.<br></td><td style="vertical-align: top;">check_parameters, flow_statistics, modules, parin, read_var_list, user_interface, write_var_list</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">In <span style="font-family: Courier New,Courier,monospace;">pres.f90</span>, division through <span style="font-family: Courier New,Courier,monospace;">dt_3d</span>
2310	replaced by multiplication of the inverse. For performance
2311	optimisation, this is done in the loop calculating the divergence
2312	instead of using a seperate loop.<br><br>Variables <span style="font-family: Courier New,Courier,monospace;">var_hom</span> and <span style="font-family: Courier New,Courier,monospace;">var_sum</span> are both renamed <span style="font-family: Courier New,Courier,monospace;">pr_palm</span>.</td><td style="vertical-align: top;">data_output_profiles, flow_statistics, init_3d_model, modules, parin, pres, read_var_list, run_control, time_integration</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: <span style="font-family: Courier New,Courier,monospace;">work_fft*_vec</span> removed from some PRIVATE-declarations (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>).<br><br>Bugfix: <span style="font-family: Courier New,Courier,monospace;">field_chr</span> renamed <span style="font-family: Courier New,Courier,monospace;">field_char</span> (<span style="font-family: Courier New,Courier,monospace;">user_interface</span>).<br><br>Bugfix: output of <span style="font-family: Courier New,Courier,monospace;">use_upstream_for_tke</span> (<span style="font-family: Courier New,Courier,monospace;">header</span>).</td><td style="vertical-align: top;">header, poisfft, user_interface</td></tr><tr><td style="vertical-align: top;">21/06/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.3</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">This version allows runs for the ocean. These runs can be switched on with the new inipar-parameter <span style="font-family: Courier New,Courier,monospace;">ocean</span>.<br><br>Setting this switch has several effects:<br><ul><li>An additional prognostic equation for salinity is solved.</li><li>Potential temperature in buoyancy and stability-related terms is replaced by potential density.</li><li>Potential
2313	density is calculated from the equation of state for seawater after
2314	each timestep, using the algorithm proposed by Jackett et al. (2006, J.
2315	Atmos. Oceanic Technol., <span style="font-weight: bold;">23</span>, 1709-1728).<br>So far, only the initial hydrostatic pressure is entered into this equation.</li><li>z=0 (sea surface) is assumed at the model top (vertical grid index <span style="font-family: Courier New,Courier,monospace;">k=nzt</span> on the w-grid), with negative values of z indicating the depth.</li><li>Initial profiles are constructed (e.g. from <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_vertical_gradient">pt_vertical_gradient</a> / <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_vertical_gradient_level">pt_vertical_gradient_level</a>) starting from the sea surface, using surface values given by <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#pt_surface">pt_surface</a>, <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#sa_surface">sa_surface</a>, <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#ug_surface">ug_surface</a>, and <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/doc/app/chapter_4.1.html#vg_surface">vg_surface</a>.</li><li>Zero salinity flux is used as default boundary condition at the bottom of the sea.</li><li>If switched on, random perturbations are by default imposed to the upper model domain from zu(nzt2/3) to zu(nzt-3).</li></ul>Relevant new inipar-parameters to be exclusively used for steering ocean runs are <span style="font-family: Courier New,Courier,monospace;">bc_sa_t</span>, <span style="font-family: Courier New,Courier,monospace;">bottom_salinityflux</span>, <span style="font-family: Courier New,Courier,monospace;">sa_surface</span>, <span style="font-family: Courier New,Courier,monospace;">sa_vertical_gradient</span>, <span style="font-family: Courier New,Courier,monospace;">sa_vertical_gradient_level</span>, and <span style="font-family: Courier New,Courier,monospace;">top_salinityflux</span>.<br><br>Salinity (<span style="font-family: Courier New,Courier,monospace;">sa</span>) and potential density (<span style="font-family: Courier New,Courier,monospace;">rho</span>) are included as new 2d/3d output quantities. Vertical profiles of salinity (<span style="font-family: Courier New,Courier,monospace;">sa</span>), salinity fluxes (<span style="font-family: Courier New,Courier,monospace;">w"sa"</span>, <span style="font-family: Courier New,Courier,monospace;">wsa*</span>, <span style="font-family: Courier New,Courier,monospace;">wsa</span>), and potential density (<span style="font-family: Courier New,Courier,monospace;">rho</span>) can also be output.<span style="font-family: Courier New,Courier,monospace;"></span></td><td style="vertical-align: top;">advec_s_bc, average_3d_data,<br>boundary_conds, buoyancy,<br>check_parameters, data_output_2d,<br>data_output_3d, diffusion_e,<br>diffusivities, flow_statistics, header,<br>init_grid, init_3d_model, modules,<br>netcdf, parin, production_e,<br>prognostic_equations,<br>read_3d_binary,  read_var_list,<br>sum_up_3d_data, swap_timelevel,<br>time_integration, user_interface,<br>write_var_list, write_3d_binary<br><br><span style="font-weight: bold;">new:</span><br>eqn_state_seawater, init_ocean</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Inipar-parameter <span style="font-family: Courier New,Courier,monospace;">use_pt_reference</span> renamed <span style="font-family: Courier New,Courier,monospace;">use_reference.</span><br>Internal variable <span style="font-family: Courier New,Courier,monospace;">hydro_press</span> renamed <span style="font-family: Courier New,Courier,monospace;">hyp</span>, routine <span style="font-family: Courier New,Courier,monospace;">calc_mean_pt_profile</span> renamed <span style="font-family: Courier New,Courier,monospace;">calc_mean_profile</span>.<br><br>The format of the <span style="font-family: Courier New,Courier,monospace;">RUN_CONTROL</span> file has been adjusted for ocean runs.<br><br>Defaults of <span style="font-family: Courier New,Courier,monospace;">.._vertical_gradient_levels</span> changed from <span style="font-style: italic;">-1.0</span> to <span style="font-style: italic;">-9999999.9</span>.</td><td style="vertical-align: top;">advec_particles, buoyancy, <br>calc_liquid_water_content, <br>check_parameters, diffusion_e,<br>diffusivities, header,<br>init_cloud_physics, modules,<br>production_e, prognostic_equations,<br>run_control</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: height above topography instead of height above level k=0 is used for calculating the mixing length (<span style="font-family: Courier New,Courier,monospace;">diffusion_e</span> and <span style="font-family: Courier New,Courier,monospace;">diffusivities</span>).<br><br>Bugfix: error in boundary condition for TKE removed (<span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>).</td><td style="vertical-align: top;">advec_s_bc, diffusion_e, diffusivities</td></tr><tr><td style="vertical-align: top;">05/10/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.4</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">This version allows runs for a coupled atmosphere-ocean LES.<br><br>Coupling frequency is controlled by new d3par-parameter <span style="font-family: Courier New,Courier,monospace;">dt_coupling</span>, the coupling mode ('<span style="font-style: italic;">atmosphere_to_ocean</span>' or '<span style="font-style: italic;">ocean_to_atmosphere</span>') for the respective processes is read from environment variable <span style="font-family: Courier New,Courier,monospace;">coupling_mode</span>, which is set by the mpiexec-command in <span style="font-weight: bold;">mrun</span>. Communication between the two models is handled by the intercommunicator <span style="font-family: Courier New,Courier,monospace;">comm_inter</span>. Local files opened by the ocean model get the additional suffic "<span style="font-family: Courier New,Courier,monospace;">_O</span>".
2316	Saturation at k=nzb is assumed for the atmosphere coupled to ocean.
2317	Usage of the coupled model is described in the new section 3.8.<br><br>A momentum flux can be set as top boundary condition using the new inipar parameters <span style="font-family: Courier New,Courier,monospace;">top_momentumflux_u\|v</span>.<br><br>Non-cyclic boundary conditions can be used along all horizontal directions.<br><br>Quantities wp and w"e can be output as vertical profiles.<br><br>Initial profiles are reset to constant profiles in case that <span style="font-family: Courier New,Courier,monospace;">initializing_actions</span> /= '<span style="font-style: italic;">set_constant_profiles</span>'. (init_rankine)<br><br>Optionally calculate km and kh from initial TKE e_init.<br>
2318	</td><td style="vertical-align: top;">boundary_conds,
2319	check_open, check_parameters, diffusion_u, diffusion_v,
2320	flow_statistics, header, init_pegrid, init_rankine, init_3d_model,
2321	local_stop, modules, palm, parin, prandtl_fluxes, pres,
2322	prognostic_equations, read_var_list, read_3d_binary, swap_timelevel,
2323	timestep, time_integration, write_var_list, write_3d_binary<br><br><span style="font-weight: bold;">new:</span><br>surface_coupler</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Remaining variables <span style="font-family: Courier New,Courier,monospace;">iran</span> changed to <span style="font-family: Courier New,Courier,monospace;">iran_part</span> (advec_particles, init_particles).<br><br>In case that the presure solver is not called for every Runge-Kutta substep (<span style="font-family: Courier New,Courier,monospace;">call_psolver_at_all_substeps</span> = <span style="font-style: italic;">.F.</span>),
2324	it is called after the first substep instead of the last. In that case,
2325	random perturbations are also added to the velocity field after the
2326	first substep.<br><br>Initialization of <span style="font-family: Courier New,Courier,monospace;">km</span>, <span style="font-family: Courier New,Courier,monospace;">kh</span> = 0.00001 for <span style="font-family: Courier New,Courier,monospace;">ocean</span> = <span style="font-style: italic;">.T.</span> (for <span style="font-family: Courier New,Courier,monospace;">ocean</span> = <span style="font-style: italic;">.F.</span> it remains 0.01).<br><br>Allow <span style="font-family: Courier New,Courier,monospace;">data_output_pr</span> = '<span style="font-style: italic;">q</span>', '<span style="font-style: italic;">wq</span>', '<span style="font-style: italic;">w"q"</span>', '<span style="font-style: italic;">wq</span>' for <span style="font-family: Courier New,Courier,monospace;">humidity</span> = <span style="font-style: italic;">.T.</span> (instead of <span style="font-family: Courier New,Courier,monospace;">cloud_physics</span> = <span style="font-style: italic;">.T.</span>).</td><td style="vertical-align: top;">advec_particles, check_for_restart, check_parameters, init_particles, init_3d_model, time_integration<br></td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugs from code parts for non-cyclic boundary conditions are removed:<br>loops for u and v are starting from index <span style="font-family: Courier New,Courier,monospace;">nxlu</span>, <span style="font-family: Courier New,Courier,monospace;">nysv</span>,
2327	respectively. The radiation boundary condition is used for every
2328	Runge-Kutta substep. Velocity phase speeds for the radiation boundary
2329	conditions are calculated for the first Runge-Kutta substep only and
2330	reused for the further substeps. New arrays <span style="font-family: Courier New,Courier,monospace;">c_u</span>, <span style="font-family: Courier New,Courier,monospace;">c_v</span>, and <span style="font-family: Courier New,Courier,monospace;">c_w</span>
2331	are defined for this purpose. Several index errors are removed from the
2332	radiation boundary condition code parts. Upper bounds for calculating <span style="font-family: Courier New,Courier,monospace;">u_0</span> and <span style="font-family: Courier New,Courier,monospace;">v_0</span> (in production_e) are <span style="font-style: italic;">nxr+1</span> and <span style="font-style: italic;">nyn+1</span> because otherwise these values are not available in case of non-cyclic boundary conditions.<br><br>+<span style="font-family: Courier New,Courier,monospace;">dots_num_palm</span> in module user, +module netcdf_control in user_init (both in user_interface)<br><br>Bugfix: wrong sign removed from the buoyancy production term in the case <span style="font-family: Courier New,Courier,monospace;">use_reference</span> = <span style="font-style: italic;">.T.</span> (production_e)<br><br>Bugfix: Error message concerning output of particle concentration (pc) modified (check_parameters).<br><br>Bugfix: Rayleigh damping for ocean fixed.</td><td style="vertical-align: top;">advec_u_pw,
2333	advec_u_up, advec_v_pw, advec_v_up, boundary_conds, buoyancy,
2334	check_parameters, coriolis, diffusion_u, diffusion_v, header,
2335	init_pegrid, init_3d_model, modules, poismg, production_e,
2336	prognostic_equations, user_interface<br></td></tr><tr><td style="vertical-align: top;">29/11/07</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.4a</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">Pressure boundary conditions for vertical walls added to the multigrid solver. They are applied using new wall flag arrays (<span style="font-family: Courier New,Courier,monospace;">wall_flags_..</span>) which are defined for each grid level. New argument<span style="font-family: Courier New,Courier,monospace;"> gls </span>added to routine<span style="font-family: Courier New,Courier,monospace;"> user_init_grid </span>(<span style="font-family: Courier New,Courier,monospace;">user_interface</span>).<br><br>Plant canopy model of Watanabe (2004,BLM 112,307-341) added.  It can be switched on by the new inipar parameter <span style="font-family: Courier New,Courier,monospace;">plant_canopy</span>. The inipar parameter<span style="font-family: Courier New,Courier,monospace;"> canopy_mode </span>can
2337	be used to prescribe a plant canopy type. The default case is a
2338	homogeneous plant canopy. Heterogeneous distributions of the leaf area
2339	density and the canopy drag coefficient can be defined in the new
2340	routine<span style="font-family: Courier New,Courier,monospace;"> user_init_plant_canopy </span>(<span style="font-family: Courier New,Courier,monospace;">user_interface</span>). The inipar parameters <span style="font-family: Courier New,Courier,monospace;">lad_surface</span>,<span style="font-family: Courier New,Courier,monospace;"> lad_vertical_gradient </span>and<span style="font-family: Courier New,Courier,monospace;"> lad_vertical_gradient_level </span>can be used to prescribe the vertical profile of leaf area density. The inipar parameter<span style="font-family: Courier New,Courier,monospace;"> drag_coefficient </span>determines the canopy drag coefficient. Finally, the inipar parameter<span style="font-family: Courier New,Courier,monospace;"> pch_index </span>determines the index of the upper boundary of the plant canopy.  <br><br>Allow new case<span style="font-family: Courier New,Courier,monospace;"> bc_uv_t </span>= <span style="font-style: italic;">'dirichlet_0'</span> for channel flow.<br><br>For unknown variables (CASE DEFAULT) call new subroutine<span style="font-family: Courier New,Courier,monospace;"> user_data_output_dvrp</span>.<br><br>Frequence of sorting particles can be controlled with new particles_par parameter<span style="font-family: Courier New,Courier,monospace;"> dt_sort_particles</span>. Sorting is moved from the SGS timestep loop in<span style="font-family: Courier New,Courier,monospace;"> advec_particles </span>after the end of this loop.</td><td style="vertical-align: top;">advec_particles,
2341	check_parameters, data_output_dvrp, header, init_3d_model, init_grid,
2342	init_particles, init_pegrid, modules, package_parin,
2343	parin, read_var_list, user_interface, write_var_list<br><br><span style="font-weight: bold;">new:</span><br>plant_canopy_model</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Redefine initial<span style="font-family: Courier New,Courier,monospace;"> nzb_local </span>as the actual total size of topography (later the extent of topography in<span style="font-family: Courier New,Courier,monospace;"> nzb_local </span>is reduced by 1dx at the E topography walls and by 1dy at the N topography walls to form the basis for<span style="font-family: Courier New,Courier,monospace;"> nzb_s_inner</span>); for consistency redefine 'single_building' case.<br><br>Vertical profiles now based on<span style="font-family: Courier New,Courier,monospace;"> nzb_s_inner</span>; they are divided by<span style="font-family: Courier New,Courier,monospace;"> ngp_2dh_s_inner </span>(scalars, procucts of scalars) and<span style="font-family: Courier New,Courier,monospace;"> ngp_2dh </span>(staggered velocity components and their products, procucts of scalars and velocity components), respectively.<br><br>Allow two instead of one digit to specify isosurface and slicer variables.<br><br>Status of 3D-volume NetCDF data file only depends on switch<span style="font-family: Courier New,Courier,monospace;"> netcdf_64bit_3d </span>(check_open).<br><br><span style="font-family: Courier New,Courier,monospace;">prognostic_equations </span>include the respective<span style="font-family: Courier New,Courier,monospace;"> wall_flux </span>in the parameter list of calls of<span style="font-family: Courier New,Courier,monospace;"> diffusion_s</span>. Same as before, only the values<span style="font-family: Courier New,Courier,monospace;"> of wall_heatflux(0:4) </span>can be assigned. At present,<span style="font-family: Courier New,Courier,monospace;">  wall_humidityflux</span>,<span style="font-family: Courier New,Courier,monospace;"> wall_qflux</span>,<span style="font-family: Courier New,Courier,monospace;"> wall_salinityflux</span>, and<span style="font-family: Courier New,Courier,monospace;"> wall_scalarflux </span>are kept zero.<span style="font-family: Courier New,Courier,monospace;"> diffusion_s </span>uses the respective<span style="font-family: Courier New,Courier,monospace;"> wall_flux </span>instead of<span style="font-family: Courier New,Courier,monospace;"> wall_heatflux</span>.
2344	This update serves two purposes: - it avoids errors in calculations
2345	with humidity/scalar/salinity and prescribed non-zero wall heatflux, -
2346	it prepares PALM for a possible assignment of wall fluxes of
2347	humidity/scalar/salinity in a future releases.</td><td style="vertical-align: top;">buoyancy,
2348	check_open, data_output_dvrp, diffusion_s, diffusivities,
2349	flow_statistics, header, init_3d_model, init_dvrp, init_grid, modules,
2350	prognostic_equations</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: summation of<span style="font-family: Courier New,Courier,monospace;"> sums_l_l </span>(<span style="font-family: Courier New,Courier,monospace;">diffusivities</span>).<br><br>Several bugfixes in the ocean part: Initial density<span style="font-family: Courier New,Courier,monospace;"> rho </span>is calculated (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>). Error in initializing<span style="font-family: Courier New,Courier,monospace;"> u_init </span>and<span style="font-family: Courier New,Courier,monospace;"> v_init </span>removed (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>). Calculation of density flux now starts from<span style="font-family: Courier New,Courier,monospace;"> nzb+1 </span>(<span style="font-family: Courier New,Courier,monospace;">production_e</span>).<br><br>Bugfix: <span style="font-family: Courier New,Courier,monospace;">pleft</span>/<span style="font-family: Courier New,Courier,monospace;">pright</span> changed to <span style="font-family: Courier New,Courier,monospace;">pnorth</span>/<span style="font-family: Courier New,Courier,monospace;">psouth</span> in sendrecv of particle tail numbers along y, small bugfixes in the SGS part (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>).<br><br>Bugfix:<span style="font-family: Courier New,Courier,monospace;"> model_string </span>needed a default value (<span style="font-family: Courier New,Courier,monospace;">combine_plot_fields</span>).<br><br>Bugfix: wavenumber calculation for even<span style="font-family: Courier New,Courier,monospace;"> nx </span>in routines<span style="font-family: Courier New,Courier,monospace;"> maketri </span>(<span style="font-family: Courier New,Courier,monospace;">poisfft</span>).<br><br>Bugfix: assignment of fluxes at walls.<br><br>Bugfix: absolute value of<span style="font-family: Courier New,Courier,monospace;"> f </span>must be used when calculating the Blackadar mixing length (<span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>).</td><td style="vertical-align: top;">advec_particles,
2351	check_parameters, combine_plot_fields, diffusion_s, diffusivities,
2352	init_ocean, init_1d_model, poisfft, production_e</td></tr><tr><td style="vertical-align: top;">16/09/08</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.5</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">The
2353	turbulence recycling method of Kataoka and Mizuno (2002) has been
2354	implemented. A precursor run must be used to initialize the main run
2355	with a quasi-stationary turbulence state (see <span style="font-family: monospace;">initializing_actions</span> = <span style="font-style: italic;">'read_data_for_recycling'</span>).
2356	The precursor run may have a smaller domain than the main run, which
2357	helps to spare CPU time. New parameters for steering the recycling
2358	method are <span style="font-family: monospace;">turbulent_inflow</span>, <span style="font-family: monospace;">recycling_width</span>, <span style="font-family: monospace;">inflow_damping_height</span>, and <span style="font-family: monospace;">inflow_damping_width</span>.<br><br>One
2359	new feature related with the recycling method is that within a job
2360	chain, the number of processors or the virtual processor grid is now
2361	allowed to change. Such a change modifies the domain decomposition
2362	and requires that the PEs within a restart job have to know from which
2363	file(s) they have to read their restart data (up to now there has been
2364	a one to one relation between the restart files and the PEs, i.e.
2365	processor 4 only reads data from file "_0004"). Informations about the
2366	subdomain index limits of all restart files are now written by PE0 (to
2367	file "_0000"). Also, all variables containing global values which do
2368	not depend on the subdomain are written to file "_0000" only. In a
2369	restart run, this file is opened by all PEs to read these global values
2370	and the informations about the subdomain index limits. Depending on
2371	these index limit information it is decided which restart file(s)
2372	has/have to be opened in order to read the complete data necessary for
2373	the current subdomain.<br><br>The plant canopy model has been extended
2374	to the prognostic equation for the potential temperature
2375	and passive scalar, as proposed by Watanabe (2004) and Shaw and
2376	Schumann (1992).<br><br>Particle advection adjusted for ocean runs.<br><br>Grid
2377	coarsening (multigrid method) is limited to subdomains (i.e. no
2378	collection of data on PE0 for further coarsening beyond subdomains) if <span style="font-family: monospace;">mg_switch_to_pe0_level</span> = <span style="font-style: italic;">-1</span>.<br><br>User-defined spectra are allowed.<br><br>Output of <span style="font-family: monospace;">q*2</span> profile and <span style="font-family: monospace;">w"u"0</span>, <span style="font-family: monospace;">w"v"0</span>, <span style="font-family: monospace;">w"q"0</span> timeseries are added.<br><br>Argument<span style="font-family: monospace;"> -c </span>introduced to most of the subjob calls, which allows the user to choose his own job catalog by setting the environment variable<span style="font-family: monospace;"> job_catalog </span>in the configuration file (default is <span style="font-family: monospace;">~/job_queue</span>).<br><br>This release contains first adjustments for the SGI-ICE system at HLRN.<br><br><span style="font-weight: bold;">Attention: On the SGI-ICE, runs are still aborted or are hanging for unknown reasons from time to time.</span></td><td style="vertical-align: top;">advec_particles, calc_spectra, check_open, check_parameters, data_output_spectra,
2379	header, init_3d_model, init_particles, init_pegrid, modules, netcdf, parin, particle_boundary_conds, plant_canopy_model,
2380
2381	prognostic_equations, read_3d_binary, read_var_list, time_integration,
2382	user_interface, write_3d_binary, write_var_list<br><br><span style="font-weight: bold;">new:</span><br>inflow_turbulence<br></td></tr><tr><td align="undefined" valign="undefined"> </td><td align="undefined" valign="undefined"> </td><td align="undefined" valign="undefined"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;">Allow 100 spectra levels instead of 10 for consistency with define_netcdf_header. (<span style="font-family: monospace;">calc_spectra</span>, <span style="font-family: monospace;">data_output_spectra</span>, <span style="font-family: monospace;">header</span>, <span style="font-family: monospace;">modules</span>, <span style="font-family: monospace;">netcdf</span>)<br><br>Modification
2383	of the integrated version of the profile function for momentum for
2384	unstable stratification; more consistent flux definitions. (<span style="font-family: monospace;">wall_fluxes</span>, <span style="font-family: monospace;">production_e</span>)<br><br>Strict grid matching along z is not needed for mg-solver. (<span style="font-family: monospace;">check_parameters</span>)<br><br>Sharp
2385	lateral edges of the plant canopy introduced. Before, smaller values of
2386	the leaf area density than those applied in the prognostic equation for
2387	the vertical velocity were used in the prognostic equations for u and v
2388	at the boundaries of the plant_canopy. (<span style="font-family: monospace;">init_3d_model</span>)<br><br>-<span style="font-family: monospace;">cross_ts_</span> (<span style="font-family: monospace;">read_var_list</span>, <span style="font-family: monospace;">write_var_list</span>), -<span style="font-family: monospace;">dopr_time_count</span>, old profil parameters (<span style="font-family: monospace;">cross_...</span>, <span style="font-family: monospace;">dopr_crossindex</span>, <span style="font-family: monospace;">profile_**</span>) removed. (<span style="font-family: monospace;">read_3d_binary</span>, <span style="font-family: monospace;">write_3d_binary</span>)<br><br>Reading/writing of <span style="font-family: monospace;">hom_sum</span>, <span style="font-family: monospace;">volume_flow_area</span>, <span style="font-family: monospace;">volume_flow_initial</span> is moved from <span style="font-family: monospace;">..._3d_binary</span> to <span style="font-family: monospace;">..._var_list</span>, <span style="font-family: monospace;">hom_sum</span> is now allocated in <span style="font-family: monospace;">parin</span> instead of <span style="font-family: monospace;">init_3d_model</span>.<br><br><span style="font-family: monospace;">npex</span>, <span style="font-family: monospace;">npey</span> moved from inipar- to d3par-namelist. (<span style="font-family: monospace;">parin</span>)<br><br><span style="font-family: monospace;">myid_char14</span>
2389	removed. This was used, since on IBM machines the process rank could be
2390	changed when the final communicator was defined, in order to save the
2391	preliminary processor-id for opening the binary output file for
2392	restarts (unit 14), because otherwise a mismatch occured when reading
2393	this file in a restart job. This mechanism is not needed any more since
2394	the subdomain informations are now contained in file _0000. (<span style="font-family: monospace;">parin</span>, <span style="font-family: monospace;">check_open</span>)<br><br>Transpositions for the 2D domain decomposition have been optimized by using <span style="font-family: monospace;">f_inv</span>
2395	as an automatic array instead of providing the memory by a dummy
2396	argument. This spares one copy loop per transposition. Order of indices
2397	in the 3D loops in some of the transpose routines have been rearranged
2398	for better cache utilization. Both have been suggested by Roland
2399	Richter (SGI) as part of the HLRN-II benchmark process. (<span style="font-family: monospace;">transpose</span>)<br><br>Workaround for getting information about the coupling mode, because the<span style="font-family: monospace;"> -env </span>Option (mpiexec) is not available on many systems (SGI, lcxt4 at  Bergen Center for Computational Science). (<span style="font-family: monospace;">palm</span>, <span style="font-family: monospace;">mrun</span>)<br><br>Format adjustments in order to allow CPU# > 999. (<span style="font-family: monospace;">cpu_statistics</span>)<br><br>Provisional solution for run_control_1d output: add 'CALL check_open( 15 )'. (<span style="font-family: monospace;">init_1d_model</span>)<br><br>Subdomain data are read into temporary arrays <span style="font-family: monospace;">pf_tmp</span> / <span style="font-family: monospace;">pf3d_tmp</span> in order to avoid INTEL compiler warnings about (automatic) creation of temporary arrays. (<span style="font-family: monospace;">combine_plot_fields</span>)<br><br>Time coordinate t=0 stored on netcdf-file only if an output is required for this time for at least one of the profiles.<br><br>Output of spline timeseries <span style="font-family: monospace;">splptx</span> etc. removed. (<span style="font-family: monospace;">flow_statistics</span>)</td><td style="vertical-align: top;">advec_s_ups,
2400	advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open,
2401	check_parameters, cpu_statistics, data_output_profiles,
2402	data_output_spectra, flow_statistics, header, init_1d_model,
2403	init_3d_model, modules, netcdf, palm, parin, poisfft, production_e,
2404	read_3d_binary, read_var_list, transpose, wall_fluxes, write_3d_binary, write_var_list<br></td></tr><tr><td align="undefined" valign="undefined"> </td><td align="undefined" valign="undefined"> </td><td align="undefined" valign="undefined"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix:
2405	modification of the calculation of the vertical turbulent momentum
2406	fluxes u'w' and v'w'; the first usws that is computed corresponds to
2407	-u'w'/u* and not as priorily assumed to (-u'w')**0.5, the first vsws
2408	that is computed corresponds to -v'w'/u* and not as priorily assumed to
2409	(-v'w')**0.5. Therefore, the intermediate result for usws has to be
2410	multiplied by -u* instead by itself in order to get u'w'. Accordingly,
2411	the intermediate result for vsws has to be multiplied by -u* instead by
2412	itself in order to get v'w'. As u* is calculated for the position of a
2413	scalar an additional interpolation of u* to the position of u and v,
2414	respectively, is necessary. As u* is not determined for the ghost
2415	points on each PE, an additional exchange of information from
2416	neighbouring PEs is necessary. Tests showed that this
2417	decreases u* by some 10% and increases TKE and momentum fluxes by some
2418	10% because friction was underestimated and momentum fluxes were
2419	wrongly calculated due to the bug. (<span style="font-family: monospace;">prandtl_fluxes</span>, <span style="font-family: monospace;">wall_fluxes</span>)<br><br><span style="font-weight: bold;">Attention:</span> <br><span style="font-weight: bold;">
2420	The content of the testresult-file (run control output) has changed
2421	due to the above bugfix.</span><br><br>Bugfix:
2422	change definition of us_wall from 1D to 2D. <br><br>Bugfix: exponent = 1.0 / ( ny + 1.0 ) in calc_spectra_x. (<span style="font-family: monospace;">calc_spectra</span>)<br><br>Bugfix: calculation of horizontal fluxes at vertical walls. (<span style="font-family: monospace;">diffusion_s</span>)<br><br>Bugfix: zero assignments to tendency arrays in case of restarts. (<span style="font-family: monospace;">init_3d_model</span>)<br><br>Bugfix: wrong grid level used in multigrid solver, routine <span style="font-family: monospace;">restrict</span>. (<span style="font-family: monospace;">poismg</span>)<br><br>Bugfix:
2423	Construction of vertical profiles when 10 gradients have been specified
2424	in the parameter list (ug, vg, pt, q, sa, lad). (<span style="font-family: monospace;">check_parameters</span>)<br><br>Bugfix: Determination of the number of vertical levels for which spectra shall be output - 100 replaced by 10. (<span style="font-family: monospace;">netcdf</span>)<br><br>Bugfix:
2425	Lengths of those characters that are needed for the output of the
2426	characteristic levels of potential temperature, the geostrophic wind,
2427	scalar concentration, humidity and leaf area density to the header file
2428	has been increased. (<span style="font-family: monospace;">header</span>)<br><br>Bugfix: add ')' in <span style="font-family: monospace;">user_read_restart_data</span>.<br><br>The leaf area density is explicitly set to its surface value at k=0. (<span style="font-family: monospace;">check_parameters</span>)<br><br>Introduce<span style="font-family: monospace;"> prefix_chr</span> to ensure unique dvrp_file path.<br><br>small bugfixes for <span style="font-family: monospace;">user_interface</span> sample code (comments):<br>- initialize ustvst with 0.0 as it is now computed only until <span style="font-family: monospace;">nxr</span> and <span style="font-family: monospace;">nyn</span><br>- two ALLOCATE statements moved from <span style="font-family: monospace;">user_read_restart_data</span> back to <span style="font-family: monospace;">user_init</span><br>- remove 'READ (13) u2_av' statement in <span style="font-family: monospace;">user_read_restart_data</span><br><br>Bugfix: remove IF statement in <span style="font-family: monospace;">plant_canopy_model_ij</span>.<br><br>Bugfix: divide sums(k,8) (e) and sums(k,34) (e*) by ngp_2dh_s_inner(k,sr) (like other scalars). (<span style="font-family: monospace;">flow_statistics</span>)<br><br>Bugfix: <span style="font-family: monospace;">dopr_time_count</span>
2429	was written on the binary file, which caused that NetCDF files newly
2430	created by restart files (no append of existing files!) contained
2431	uneccessary time levels. (<span style="font-family: monospace;">read_3d_binary</span>, <span style="font-family: monospace;">write_3d_binary</span>)<br><br>Bugfix: extra '*' removed in user_statistics sample code. (<span style="font-family: monospace;">user_interface</span>)<br><br>Bugfix: a stop command was missing in some cases of the parallel branch. (<span style="font-family: monospace;">local_stop</span>)<br><br>Bugfix in volume flow control for non-cyclic boundary conditions. (<span style="font-family: monospace;">pres</span>)<br><br>Bugfix: misplaced #endif directives. (<span style="font-family: monospace;">combine_plot_fields</span>)<br><br>Data are collected from PE0 in an ordered sequence which seems to avoid hanging of processes on SGI-ICE. (<span style="font-family: monospace;">cpu_statistics</span>)</td><td style="vertical-align: top;">calc_spectra,
2432	check_parameters, cpu_statistics, diffusion_s, flow_statistics,
2433	init_3d_model, init_dvrp, local_stop, plant_canopy_model, poismg,
2434	prandtl_fluxes, pres, read_3d_binary, user_interface, wall_fluxes,
2435	write_3d_binary<br></td></tr><tr><td style="vertical-align: top;">02/02/09</td><td style="vertical-align: top;">SR</td><td style="vertical-align: top;">3.6<br>(r228)</td><td style="vertical-align: top;">N</td><td style="vertical-align: top;">This
2436	release contains further additions, changes, and bugfixes for the
2437	SGI-ICE system, as well as important changes like the splitting of the
2438	user-interface into single files, a complete revision of the
2439	pre-compiling mechanism allowing to use different make-depositories
2440	simultaneously, and a revision of the reading-mechanism from restart
2441	files, which has no more restrictions in case that the previous and
2442	current run have different domain/subdomain sizes. A new handling of
2443	all kind of output messages is introduced with this release and will be
2444	applied to all existing messages within the next releases.<br><br><span style="font-weight: bold;">New features are:</span><br style="font-weight: bold;"><br>Restart runs on SGI-ICE are working. (mrun)<br>2d-decomposition is default on SGI-ICE systems. (init_pegrid)<br><br>Ocean-atmosphere coupling realized with MPI-1. mrun adjusted for this case (-Y option). Check that PALM is called with <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option "<span style="font-style: italic;">-K parallel</span>" for coupling. Adjustments in <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">mbuild</span>, and <span style="font-family: Courier New,Courier,monospace;">subjob</span> for lcxt4.<br><br>DVRP arguments changed to single precision, mode pathlines added.<br><br>User can add additional routines in files <span style="font-family: Courier New,Courier,monospace;">user_additional_routines</span>.<br><br>User can check user parameters and deduce further quantities in <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>.</td><td style="vertical-align: top;">check_for_restart,
2445	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
2446	modules, package_parin, palm, surface_coupler, timestep<br><br>Makefile, mbuild, mrun, subjob<br><br><span style="font-weight: bold;">new:</span><br>init_coupling, user_additional_routines, user_check_parameters</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">C</td><td style="vertical-align: top;"> User interface has been split into single files.<br><br>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>
2447	changed to INTEGER(8) in order to avoid "out of range" problems, which
2448	result in measured negative time intervals. (cpu_log, local_tremain,
2449	local_tremain_ini)<br><br>Reading mechanism from restart files
2450	completely revised. The subdomain/total domain size is now allowed to
2451	vary arbitrarily between the current and previous run. (read_var_list,
2452	read_3d_binary, user_read_restart_data)<br><br>Precompilation mechanism (<span style="font-family: Courier New,Courier,monospace;">mbuild</span>) completely revised: the source-tarfile remains in the source directory (<span style="font-family: Courier New,Courier,monospace;">trunk/SOURCE</span>).
2453	One depository per block (given in the config-file) is created. Always
2454	all files from the source directory are copied to the respective
2455	depository. No additional file checks are done any more (mrun version
2456	2.1). The depository name used contains the conditions given by <span style="font-family: Courier New,Courier,monospace;">mrun</span>-option "<span style="font-family: Courier New,Courier,monospace;">-K</span>". (mbuild, mrun)<br><br>Output messages (including required stop of execution) can now be handled with the new subroutine <span style="font-family: Courier New,Courier,monospace;">message</span>. All output messages will be replaced by this routine step by step within the next revisions.<br><br>Neumann boundary condition at <span style="font-family: Courier New,Courier,monospace;">k=nzb</span> is explicitly set for better reading, although this has been already done in boundary_conds. (advec_s_bc)<br><br>Origin of the xy-coordinate system shifted from the center of the first 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 south-left corner of this cell. (netcdf) Topography definition according to new user parameter <span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span>. (init_grid, modules, user_header, user_init_grid, user_parin)</td><td style="vertical-align: top;">advec_s_bc,
2457	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
2458	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
2459	user_read_restart_data<br><br>Makefile, mbuild, mrun<br><br><span style="font-weight: bold;">removed:</span><br>user_interface<br><br><span style="font-weight: bold;">new:</span><br>message,
2460	user_3d_data_averaging, user_actions, user_advec_particles,
2461	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
2462	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
2463	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
2464	user_init_grid, user_init_particles, user_init_plant_canopy,
2465	user_last_actions, user_parin, user_parin, user_particle_attributes,
2466	user_read_restart_data, user_spectra, user_statistics</td></tr><tr><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;"> </td><td style="vertical-align: top;">E</td><td style="vertical-align: top;">Bugfix: array <span style="font-family: Courier New,Courier,monospace;">d</span> is reallocated in case that multigrid is used. (calc_spectra)<br><br>Bugfixes for nonparallel execution. (check_for_restart, cpu_statistics, inflow_turbulence, timestep)<br><br>Size of <span style="font-family: Courier New,Courier,monospace;">pf3d </span>adjusted to the required output size (1 gridpoint less, along all three dimensions), because output of a subset of the data (<span style="font-family: Courier New,Courier,monospace;">pf3d(nxa:nxe...)</span>) in the NF90_PUT_VAR statement caused segmentation fault with the INTEL compiler. (combine_plot_fields)<br><br>Bugfix: error in <span style="font-family: Courier New,Courier,monospace;">zu</span> index in case of <span style="font-family: Courier New,Courier,monospace;">section_xy=-1</span>. (header)<br><br>Inconsistency
2467	removed: as the thermal stratification is not taken into account for
2468	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
2469	<span style="font-family: Courier New,Courier,monospace;">km</span> 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>. (production_e)<br><br>Bugfix in calculating <span style="font-family: Courier New,Courier,monospace;">k</span> index in case of oceans runs. (sort_particles)<br><br>Bugfix: no output of particle concentration and radius unless particles have been started. (data_output_2d)<br><br>Bugfix: reading of <span style="font-family: Courier New,Courier,monospace;">spectrum_x\|y</span> from restart files ignored if total numbers of grid points do not match. (read_3d_binary)<br><br>Bugfix: abort in case that absolute temperature is below zero. (init_cloud_physics)</td><td style="vertical-align: top;">advec_particles,
2470	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
2471	header, inflow_turbulence, init_cloud_physics, production_e,
2472	read_3d_binary, timestep<br><br>combine_plot_fields</td></tr><tr>
2473	<td style="vertical-align: top;">23/09/09<br>
2474	</td>
2475	<td style="vertical-align: top;">SR<br>
2476	</td>
2477	<td style="vertical-align: top;">3.7 (r392)<br>
2478	</td>
2479	<td style="vertical-align: top;">N<br>
2480	</td>
2481	<td style="vertical-align: top;"><span style="font-weight: bold;">Most important changes:</span>
2482	atmosphere-ocean coupling has been improved and steering of
2483	dvr-software is more user-friendly now. Beside that, the release
2484	contains a lot of optimizations, changes, and bugfixes which have
2485	accumulated over the last months.<br>
2486	<br>
2487	The atmosphere-ocean coupling allows to use independent precursor runs
2488	in order to account for different spin-up times. The time when coupling
2489	has to be started is given by new inipar parameter <span style="font-family: Courier New,Courier,monospace;">coupling_start_time</span>. 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 order to add the appendix "<span style="font-family: Courier New,Courier,monospace;">_O</span>" to all output files. (<span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>, <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">init_coupling</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">mrun</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>, <span style="font-family: Courier New,Courier,monospace;">time_integration</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2490
2491	<br>
2492	Clipping of dvrp output implemented. Default colourtable for particles
2493	implemented, particle attributes (color, dvrp_size) can be set with new
2494	parameters <span style="font-family: Courier New,Courier,monospace;">particle_color</span>, <span style="font-family: Courier New,Courier,monospace;">particle_dvrpsize</span>, <span style="font-family: Courier New,Courier,monospace;">color_interval</span>, <span style="font-family: Courier New,Courier,monospace;">dvrpsize_interval</span>. Slicer attributes (dvrp) are set with new routine <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span> and are controlled with existing parameters <span style="font-family: Courier New,Courier,monospace;">slicer_range_limits</span>. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">set_slicer_attributes_dvrp</span>,  <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>)<br>
2495
2496	<br>
2497	Polygon reduction for topography and ground plate isosurface. Reduction
2498	level for buildings can be chosen with parameter cluster_size. (<span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>)<br>
2499
2500	<br>
2501	Variables <span style="font-family: Courier New,Courier,monospace;">bc_lr</span> / <span style="font-family: Courier New,Courier,monospace;">bc_ns</span>  in most subroutines replaced by LOGICAL variables <span style="font-family: Courier New,Courier,monospace;">bc_lr_cyc</span>,<br>
2502	<span style="font-family: Courier New,Courier,monospace;">
2503	bc_ns_cyc</span> for speed optimization. This gives a significant speedup of more than 10%. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">diffusion_u</span>, <span style="font-family: Courier New,Courier,monospace;">diffusion_v</span>, <span style="font-family: Courier New,Courier,monospace;">diffusion_w</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
2504
2505	<br>
2506	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>
2507	<br>
2508	Additional timestep criterion in case of simulations with plant canopy. (<span style="font-family: Courier New,Courier,monospace;">timestep</span>)<br>
2509	<br>
2510	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 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>
2511	<br>
2512	External pressure gradient can be used as driving force. (<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;">init_3d_model</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;">write_var_list</span>)<br>
2513	<br>
2514	New topography case '<span style="font-style: italic;">single_street_canyon</span>'. (<span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">init_grid</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;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">user_header</span>, <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2515	<br>
2516	Option to predefine a target bulk velocity for <span style="font-family: Courier New,Courier,monospace;">conserve_volume_flow</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;">init_3d_model</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;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2517	<br>
2518	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>, <span style="font-family: Courier New,Courier,monospace;">user_data_output_2d</span>)<br>
2519	<br>
2520	xy cross section output of surface heatfluxes (sensible and latent). (<span style="font-family: Courier New,Courier,monospace;">average_3d_data</span>, <span style="font-family: Courier New,Courier,monospace;">check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>, <span style="font-family: Courier New,Courier,monospace;">sum_up_3d_data</span>, <span style="font-family: Courier New,Courier,monospace;">write_3d_binary</span>)<br>
2521	</td>
2522	<td style="vertical-align: top;">average_3d_data,
2523	check_for_restart, check_parameters, data_output_2d, data_output_3d,
2524	data_output_dvrp, data_output_profiles, data_output_ptseries,
2525	data_output_spectra, data_output_tseries, diffusion_u, diffusion_v,
2526	diffusion_w, init_coupling, init_dvrp, init_grid, init_3d_model,
2527	header, mbuild, modules, mrun, package_parin, parin,
2528	prognostic_equations, read_3d_binary, read_var_list, subjob,
2529	sum_up_3d_data, surface_coupler, timestep, time_integration,
2530	user_check_parameters, user_data_output_2d, user_data_output_dvrp,
2531	user_header, user_init_grid, write_3d_binary, write_var_list<br>
2532	<br>
2533	<span style="font-weight: bold;">new:</span> set_particle_attributes, set_slicer_attributes_dvrp<br>
2534	<br>
2535	</td>
2536	</tr>
2537	<tr>
2538	<td style="vertical-align: top;"><br>
2539	</td>
2540	<td style="vertical-align: top;"><br>
2541	</td>
2542	<td style="vertical-align: top;"><br>
2543	</td>
2544	<td style="vertical-align: top;">C<br>
2545	</td>
2546	<td style="vertical-align: top;">Output of messages replaced by message handling routine. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, <span style="font-family: Courier New,Courier,monospace;">advec_s_bc</span>, <span style="font-family: Courier New,Courier,monospace;">buoyancy</span>, <span style="font-family: Courier New,Courier,monospace;">calc_spectra</span>, <span style="font-family: Courier New,Courier,monospace;">check_for_restart</span>, <span style="font-family: Courier New,Courier,monospace;">check_open</span>, <span style="font-family: Courier New,Courier,monospace;">coriolis</span>, <span style="font-family: Courier New,Courier,monospace;">cpu_log</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_dvrp</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>, <span style="font-family: Courier New,Courier,monospace;">fft_xy</span>, <span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>,  <span style="font-family: Courier New,Courier,monospace;">init_1d_model</span>, <span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>, <span style="font-family: Courier New,Courier,monospace;">init_dvrp</span>, <span style="font-family: Courier New,Courier,monospace;">init_grid</span>, <span style="font-family: Courier New,Courier,monospace;">init_particles</span>, <span style="font-family: Courier New,Courier,monospace;">init_pegrid</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf</span>, <span style="font-family: Courier New,Courier,monospace;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">plant_canopy_model</span>, <span style="font-family: Courier New,Courier,monospace;">poisfft_hybrid</span>, <span style="font-family: Courier New,Courier,monospace;">poismg</span>, <span style="font-family: Courier New,Courier,monospace;">read_3d_binary</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">surface_coupler</span>, <span style="font-family: Courier New,Courier,monospace;">temperton_fft</span>, <span style="font-family: Courier New,Courier,monospace;">timestep</span>, <span style="font-family: Courier New,Courier,monospace;">user_actions</span>, <span style="font-family: Courier New,Courier,monospace;">user_data_output_dvrp</span>, <span style="font-family: Courier New,Courier,monospace;">user_dvrp_coltab</span>, <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, <span style="font-family: Courier New,Courier,monospace;">user_init_plant_canopy</span>, <span style="font-family: Courier New,Courier,monospace;">user_parin</span>, <span style="font-family: Courier New,Courier,monospace;">user_read_restart_data</span>, <span style="font-family: Courier New,Courier,monospace;">user_spectra</span>)<br>
2547
2548	<br>
2549	Output of NetCDF messages with aid of message handling routine. (<span style="font-family: Courier New,Courier,monospace;">check_open</span>, <span style="font-family: Courier New,Courier,monospace;">close_file</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_ptseries</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_spectra</span>,  <span style="font-family: Courier New,Courier,monospace;">data_output_tseries</span>, <span style="font-family: Courier New,Courier,monospace;">netcdf</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
2550
2551	<br>
2552
2553	__lcmuk changed to __lc to avoid problems with Intel compiler on sgi-ice. (<span style="font-family: Courier New,Courier,monospace;">poisfft</span>)<br>
2554	<br>
2555	For extended NetCDF files, the updated title attribute includes an update of time_average_text where appropriate. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
2556	<br>
2557	In case of restart runs without extension, initial profiles are not
2558	written to NetCDF-file anymore. So far, time axis always started at
2559	t=0. (<span style="font-family: Courier New,Courier,monospace;">data_output_profiles</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2560	<br>
2561	<span style="font-family: Courier New,Courier,monospace;">initializing_actions</span>='<span style="font-style: italic;">read_data_for_recycling</span>' renamed to '<span style="font-style: italic;">cyclic_fill</span>'. A cyclic fill can now <br>
2562	be used independent of <span style="font-family: Courier New,Courier,monospace;">turbulent_inflow</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;">init_3d_model</span>)<br>
2563	<br>
2564	2 NetCDF error numbers changed. (<span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
2565	<br>
2566	A link to the webspage appendix_a.html is printed for further
2567	information about possible reasons of the error that appeared. (message)<br>
2568	<br>
2569	Temperature gradient criterion for estimating the boundary layer height
2570	replaced by the gradient criterion of Sullivan et al. (1998). (<span style="font-family: Courier New,Courier,monospace;">flow_statistics</span>)<br>
2571	<br>
2572	NetCDF unit attribute in timeseries output in case of statistic regions added. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
2573	<br>
2574	Maximum number of tails is calculated from maximum number of particles and <span style="font-family: Courier New,Courier,monospace;">skip_particles_for_tail</span>. (<span style="font-family: Courier New,Courier,monospace;">init_particles</span>)<br>
2575	<br>
2576	Value of <span style="font-family: Courier New,Courier,monospace;">vertical_particle_advection</span> is allowed to differ for each particle group. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, <span style="font-family: Courier New,Courier,monospace;">header</span>, <span style="font-family: Courier New,Courier,monospace;">modules</span>) <br>
2577	<br>
2578	First constant in array <span style="font-family: Courier New,Courier,monospace;">den</span> also defined as type double. (<span style="font-family: Courier New,Courier,monospace;">eqn_state_seawater</span>)<br>
2579	<br>
2580	Parameter <span style="font-family: Courier New,Courier,monospace;">dvrp_psize</span> moved from <span style="font-family: Courier New,Courier,monospace;">particles_par</span> to <span style="font-family: Courier New,Courier,monospace;">dvrp_graphics_par</span>. (<span style="font-family: Courier New,Courier,monospace;">package_parin</span>)<br>
2581	<br>
2582	<span style="font-family: Courier New,Courier,monospace;">topography_grid_convention</span> moved from <span style="font-family: Courier New,Courier,monospace;">userpar</span> to <span style="font-family: Courier New,Courier,monospace;">inipar</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;">parin</span>, <span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">user_check_parameters</span>, <span style="font-family: Courier New,Courier,monospace;">user_header</span>, <span style="font-family: Courier New,Courier,monospace;">user_init_grid</span>, <span style="font-family: Courier New,Courier,monospace;">user_parin</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2583	<br>
2584	Default value of <span style="font-family: Courier New,Courier,monospace;">grid_matching</span> changed to '<span style="font-style: italic;">strict</span>'. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
2585	<br>
2586	Adjustments for runs on lcxt4 (necessary due to a software update on 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>)<br>
2587	</td>
2588	<td style="vertical-align: top;">advec_particles, advec_s_bc,
2589	buoyancy, calc_spectra, check_for_restart, check_open,
2590	check_parameters, close_file, coriolis, cpu_log, data_output_2d,
2591	data_output_3d, data_output_dvrp, data_output_profiles,
2592	data_output_ptseries, data_output_spectra, data_output_tseries,
2593	eqn_state_seawater, fft_xy, flow_statistics, header, init_1d_model,
2594	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
2595	message, mrun, netcdf, package_parin, parin, plant_canopy_model,
2596	poisfft, poisfft_hybrid, poismg, read_3d_binary, read_var_list, subjob,
2597	surface_coupler, temperton_fft, timestep, user_actions,user_check_parameters, user_data_output_dvrp, user_dvrp_coltab, user_header, user_init_grid, user_init_plant_canopy, user_parin, user_read_restart_data, user_spectra, write_var_list <br>
2598	</td>
2599	</tr>
2600	<tr>
2601	<td style="vertical-align: top;"><br>
2602	</td>
2603	<td style="vertical-align: top;"><br>
2604	</td>
2605	<td style="vertical-align: top;"><br>
2606	</td>
2607	<td style="vertical-align: top;">E<br>
2608	</td>
2609	<td style="vertical-align: top;">Bugfix: Initial hydrostatic pressure profile in case of ocean runs is now calculated in 5 iteration steps. (<span style="font-family: Courier New,Courier,monospace;">init_ocean</span>)<br>
2610	<br>
2611	Bugfix: wrong sign in buoyancy production of ocean part in case of not using the reference density (only in 3D routine <span style="font-family: Courier New,Courier,monospace;">production_e</span>). (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
2612	<br>
2613	Bugfix: output of averaged 2d/3d quantities requires that an avaraging
2614	interval has been set, respective error message is included. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
2615	<br>
2616	Bugfix: Output on unit 14 only if requested by <span style="font-family: Courier New,Courier,monospace;">write_binary</span>. (<span style="font-family: Courier New,Courier,monospace;">user_last_actions</span>)<br>
2617	<br>
2618	Bugfix to avoid zero division by <span style="font-family: Courier New,Courier,monospace;">km_neutral</span>. (<span style="font-family: Courier New,Courier,monospace;">production_e</span>)<br>
2619	<br>
2620	Bugfix for extended NetCDF files: In order to avoid 'data mode' errors
2621	if updated attributes are larger than their original size, <span style="font-family: Courier New,Courier,monospace;">NF90_PUT_ATT</span> is called in 'define mode' enclosed by <span style="font-family: Courier New,Courier,monospace;">NF90_REDEF</span> and <span style="font-family: Courier New,Courier,monospace;">NF90_ENDDEF</span>
2622	calls. This implies a possible performance loss; an alternative
2623	strategy would be to ensure equal attribute size in a job chain. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
2624	<br>
2625	Bugfix: correction of initial volume flow for non-flat topography. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
2626	<br>
2627	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>
2628	<br>
2629	Bugfix: <span style="font-family: Courier New,Courier,monospace;">to_be_resorted</span> => <span style="font-family: Courier New,Courier,monospace;">s_av</span> for time-averaged scalars. (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>, <span style="font-family: Courier New,Courier,monospace;">data_output_3d</span>)<br>
2630	<br>
2631	Bugfix: avoid that <span style="font-family: Courier New,Courier,monospace;">ngp_2dh_s_inner</span> becomes zero. (<span style="font-family: Courier New,Courier,monospace;">init_3_model</span>)<br>
2632	<br>
2633	Typographical error: unit of wpt in dots_unit. (<span style="font-family: Courier New,Courier,monospace;">modules</span>)<br>
2634	<br>
2635	Bugfix: error in check, if particles moved further than one subdomain
2636	length. This check must not be applied for newly released particles. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>)<br>
2637	<br>
2638	Bugfix: several tail counters are initialized, <span style="font-family: Courier New,Courier,monospace;">particle_tail_coordinates</span>
2639	is only written to file if its third index is > 0, arrays for tails
2640	are allocated with a minimum size of 10 tails if there is no tail
2641	initially. (<span style="font-family: Courier New,Courier,monospace;">advec_particles</span>, <span style="font-family: Courier New,Courier,monospace;">init_particles</span><span style="font-family: Courier New,Courier,monospace;"></span>)<br>
2642	<br>
2643	Bugfix: pressure included for profile output. (<span style="font-family: Courier New,Courier,monospace;">check_parameters</span>)<br>
2644	<br>
2645	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> changed to default <span style="font-family: Courier New,Courier,monospace;">INTEGER</span> on NEC machines. (<span style="font-family: Courier New,Courier,monospace;">cpu_log</span>)<br>
2646	<br>
2647	Bugfix: output of particle time series only if particle advection is switched on. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
2648	<br>
2649	Bugfix: qsws was calculated in case of <span style="font-family: Courier New,Courier,monospace;">constant heatflux</span> = <span style="font-family: Courier New,Courier,monospace;">.FALSE.</span>. (<span style="font-family: Courier New,Courier,monospace;">prandtl_fluxes</span>)<br>
2650	<br>
2651	Bugfix: averaging along z is not allowed for 2d quantities (e.g. u* and z0). (<span style="font-family: Courier New,Courier,monospace;">data_output_2d</span>)<br>
2652	<br>
2653	Typographical errors. (<span style="font-family: Courier New,Courier,monospace;">netcdf</span>)<br>
2654	<br>
2655	If the inversion height calculated by the prerun is zero, inflow_damping_height must be explicitly specified. (<span style="font-family: Courier New,Courier,monospace;">init_3d_model</span>)<br>
2656	<br>
2657	Small bugfix concerning 3d 64bit netcdf output format. (<span style="font-family: Courier New,Courier,monospace;">header</span>)<br>
2658	<br>
2659	Bugfix: <span style="font-family: Courier New,Courier,monospace;">dt_fixed</span>
2660	removed from the restart file, because otherwise, no change from a
2661	fixed to a variable timestep would be possible in restart runs. (<span style="font-family: Courier New,Courier,monospace;">read_var_list</span>, <span style="font-family: Courier New,Courier,monospace;">write_var_list</span>)<br>
2662	<br>
2663	Bugfix: initial setting of <span style="font-family: Courier New,Courier,monospace;">time_coupling</span> in coupled restart runs. (<span style="font-family: Courier New,Courier,monospace;">time_integration</span>)<br>
2664	</td>
2665	<td style="vertical-align: top;">advec_particles,
2666	check_parameters, cpu_log, data_output_2d, data_output_3d, header,
2667	init_3d_model, init_particles, init_ocean, modules, netcdf,
2668	prandtl_fluxes, production_e, read_var_list, time_integration,
2669	user_last_actions, write_var_list<br>
2670	<br>
2671	</td>
2672	</tr>
2673
2674	</tbody>
2675	</table> <b><blink>Attention:</blink></b>
2676	If<tt> make </tt>is not used
2677	for
2678	compiling,
2679	<b>all routines</b> have to be re-compiled after every
2680	change
2681	to <b>modules.f90!</b>
2682	<br>
2683	<br>
2684	<h2><a name="Kapitel2.0"></a>2.0  How
2685	to change the model source
2686	code</h2>Currently
2687	(Sep 23rd, 2009), only selected users are allowed to commit changes to
2688	the repository. Some rules about how to check in modified code will be
2689	added later.<br>
2690	<h2>
2691	<a name="Kapitel3.0"></a>3.0  Description
2692	of selected parts of the
2693	model source code</h2>
2694	<b></b>
2695	<p>This section gives links to existing descriptions about special
2696	parts of the PALM code, e.g. special numerical methods that are used
2697	(including mathematical background). Documents are stored in single
2698	files with different formats. Some are in German (sorry for the
2699	inconvenience).
2700	<br>
2701	</p><ul> <li> <a name="UPS"></a>upstream-spline
2702	advection scheme ( <a href="Upstream_Spline/ups.ps">.ps</a>
2703	)</li> <li> <a name="Cloud_physics"></a>cloud
2704	physics module ( <a href="Cloud_physics/wolken.pdf">.pdf</a>
2705	)</li> <li> <a name="Bitkompression"></a>Datenkompression
2706	mit dem Verfahren
2707	der <a href="Bitkompression/kompression.html">Bitverschiebung</a></li>
2708	<li> <a name="Runge-kutta"></a>Runge-Kutta
2709	time integration scheme ( <a href="numerik.heiko/zeitschrittverfahren.pdf">.pdf</a>
2710	)</li>
2711	</ul><br>
2712
2713	<br>
2714	<br>
2715	<br>
2716	<br>
2717	<br>
2718	<br>
2719	<br>
2720	</body></html>

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