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1	<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
2	<html><head>
3	<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>
4	<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;">3.6 (rev 235)</span></td> </tr>
15	<tr nosave=""> <td nosave=""><b>Last
16	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 238 2009-02-16 10:00:46Z 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>Please note: Parts of this document are still in
31	German. We
32	apologize
33	for any inconvenience.</b>
34	<br>
35	<h2><a name="Kapitel1.0"></a>1.0
36	History of changes</h2>
37	The following table documents all changes to the model since July, 7th
38	1998. Entries in the fourth column specify the type of the change:
39	change
40	of existing code (C), new code (N) or bugfix (B). More detailed
41	information
42	about the changes may be found in the header comment lines of the
43	respective
44	routines.
45	<br>
46	<br><table nosave="" style="width: 100%;" border="1"> <caption>  <br> </caption><tbody>
47	</tbody><tbody> </tbody> <tbody> <tr> <td><b>date</b></td>
48	<td><b>author</b></td> <td><b>model</b>
49	<br> <b>version</b></td> <td><b>type</b></td>
50	<td><b>description</b></td> <td><b>affected
51	routines</b></td> </tr> <tr nosave="" valign="top"> <td>06/07/98</td> <td>SR</td>
52	<td>1.0</td> <td>C</td> <td nosave="">Änderung
53	von Default-Werten
54	(initializing_actions, end_time,
55	fcl_factor, use_prior_plot1d_parameters), zusätzliche
56	Überprüfung
57	von Parametern auf Zulässigkeit (prandtl_layer, psolver, nx,
58	ny,
59	nz,
60	fcl_factor), Höhe der Schnittebenen der Horizontalschnitte
61	wird
62	auf
63	Plots exakt ausgegeben (uv- bzw. w-Gitter).</td> <td>modules,
64	check_parameters, plot_2d</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
65	<td>1.0</td> <td>N</td> <td>Neues Modul
66	test_variables wird in (fast) allen
67	Programmteilen benutzt
68	(USE). <b>Wichtig</b>: dieses Modul steht in der Datei <tt>module_test.f90.
69	D</tt>iese Datei muß in der mrun- und add_library -
70	Konfigurationsdatei
71	bei der Variablen <tt>module_files</tt>
72	aufgeführt werden.</td> <td nosave="">(fast)
73	alle  <br>
74	Neu: module_test</td> </tr> <tr nosave="" valign="top"> <td>16/07/98</td> <td>SR</td>
75	<td>1.0</td> <td>N</td> <td nosave="">Anpassung
76	an die T3E-Rechner in Juelich (cpp -
77	Direktiven)</td> <td>advec_s_bc, check_open,
78	check_parameters, cpu_zeitmessung,
79	init_pegrid,
80	local_getenv, local_system, local_tremain, local_tremain_ini, poisfft</td>
81	</tr> <tr nosave="" valign="top"> <td>24/07/98</td>
82	<td>MS</td> <td>1.0</td> <td>C</td>
83	<td nosave="">Anpassung des Druckloesealgorithmusses an
84	Vorgehensweise von
85	Schmidt, Schumann und Volkert (DFVLR-Mitteilung 84-15, S.
86	20-26) </td> <td>poisfft</td> </tr> <tr nosave="" valign="top"> <td>27/07/98</td>
87	<td>MS</td> <td>1.0</td> <td>C</td>
88	<td nosave="">Berechnung von l in maketri geschieht nun
89	ausserhalb der k-Schleife,
90	da unabhaengig von k, dadurch Rechenzeitersparnis </td> <td>poisfft</td>
91	</tr> <tr nosave="" valign="top"> <td>05/08/98</td>
92	<td>SR</td> <td>1.0</td> <td>C</td>
93	<td>Entfernung der Sonderbehandlung der Advektionsterme
94	(Piascek-Williams)
95	bei k=1. Terme werden nun überall gleich berechnet. Evtl.
96	leichte
97	Erhöhung der Varianzen in Oberflächennähe.</td>
98	<td nosave="">advec_u_pw, advec_v_pw, advec_w_pw</td>
99	</tr> <tr nosave="" valign="top"> <td nosave="">"</td> <td>SR</td> <td>1.0</td>
100	<td>C</td> <td>Mischungsweganpassung (s.
101	adjust_mixing_length) erfolgt nur
102	noch bei
103	k=1. Unrealistische sekundäre Maxima in den Km-Profilen
104	oberhalb
105	der
106	Prandtl-Schicht werden damit vermieden. Leichte Änderungen in
107	den
108	oberflächennahen Turbulenzgrößen sind die
109	Folge.</td> <td>diffusivities</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
110	<td>1.0</td> <td>B</td> <td>Falsche
111	Berechnung der benötigten CPU-Zeit pro Sekunde
112	simulierter
113	Zeit bei Fortsetzungsläufen korrigiert.  <p>Berechnung
114	von cross_uxmin(1) und cross_uxmax(1) aus den
115	Werten von
116	ug und vg entfernt. Lieferte falsche Wertebereiche für Plots
117	von
118	Vertikalprofilen,
119	wenn im ersten Koordinatenkreuz nicht die Windgeschwindigkeiten
120	gezeichnet
121	wurden.</p> </td> <td nosave="">header,
122	check_parameters</td> </tr> <tr nosave="" valign="top"> <td nosave="">"</td> <td>SR</td>
123	<td>1.0</td> <td>N</td> <td>Das
124	erlaubte Maximum und Minimum der Rif-Zahl ist nun mittels
125	der Initialparameter
126	rif_max und rif_min einstellbar (Werte waren bisher fest auf -2.0, +1.0
127	eingestellt).</td> <td>check_parameters, header,
128	init_1d_model, modules, parin,
129	prandtl_fluxes,
130	read_var_list, write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">23/09/98</td>
131	<td>SR</td> <td>1.0</td> <td>B</td>
132	<td>Initialisierung von Feldern im Fall von initializing_action =
133	"<i>set_constant_profiles</i>"
134	und "<i>set_1d-model_profiles</i>" korrigiert.  <p>2D-Plotausgabe
135	von u* und theta* korrigiert. Hier wurden
136	bisher falsche
137	Felder herausgeschrieben.  </p> <p>Bei
138	SOR-Aufrufen war bisher dp nicht initialisiert.
139	Entsprechend geändert.</p> </td> <td>init_3d_model,
140	plot_2d, pres</td> </tr> <tr nosave="" valign="top"> <td>"</td> <td>SR</td>
141	<td>1.0</td> <td>C</td> <td nosave="">Ausgabeformate
142	für Statistik-Ausgaben auf
143	Datei RUN_CONTROL
144	um einige Kommastellen erweitert.  <p>Lieferung von
145	ausführlicheren Informationen bei
146	Programmabbruch
147	durch Unterschreitung des minimal erlaubten Zeitschritts.</p> </td>
148	<td>run_control, timestep</td> </tr> <tr nosave="" valign="top"> <td nosave="">"</td>
149	<td>SR</td> <td>1.0</td> <td>N</td>
150	<td>Rechnungen mit geneigter Ebene zur Simulation von
151	Kaltluftabflüssen
152	sind erlaubt. Gestartet und gesteuert werden sie mit dem
153	Intialisierungsparameter <tt>alpha_surface</tt>.
154	Realisiert wird die geneigte Ebene durch entsprechende
155	Schrägstellung
156	des Schwerkraftvektors. Dadurch erhält auch die u-Komponente
157	der
158	Windgeschwindigkeit
159	einen Anteil der Auftriebskraft.  <p>Diese
160	Implementierung ist noch nicht abgeschlossen. Die
161	Simulation von
162	Kaltluftabflüssen erfordert bisher noch Eingriffe "von Hand".</p>
163	</td> <td>buoyancy, check_parameters, header, leap_frog,
164	modules,
165	parin, prandtl_fluxes,
166	read_var_list, write_var_list</td> </tr> <tr nosave="" valign="top"> <td>15/12/98</td> <td>SR</td>
167	<td>1.0</td> <td>N</td> <td>Vereinbarung
168	einer Cache-Layer zur schnelleren binären
169	I/O auf
170	T3E-Rechnern.  <p>Ermittelung wahrer I/O-Zeiten
171	für binäre
172	Ein-/Ausgabe auf
173	T3E-Rechnern mit TIMEF.</p> </td> <td nosave="">check_open,
174	<br>cpu_zeitmessung, init_3d_model, write_3d_model</td> </tr>
175	<tr nosave="" valign="top"> <td nosave="">"</td>
176	<td>SR</td> <td>1.0</td> <td>B</td>
177	<td>Bekanntgabe von run_description_header an alle
178	PE's.  <p>Diese Programmänderung erfordert auf
179	T3E-Rechnern
180	zwingend den
181	Einsatz der MPI-Version mpt.1.2.0.1. In dieser neuen Version tritt auch
182	der alte Fehler in MPI_ALLREDUCE nicht mehr auf, so daß ab
183	jetzt
184	mpt.1.1.0.1 nicht mehr verwendet werden muß.</p> </td>
185	<td>parles</td> </tr> <tr nosave="" valign="top"> <td nosave="">05/02/99</td>
186	<td>SR</td> <td>1.1</td> <td>C/N</td>
187	<td>Implementierung des Upstream-Spline- Verfahrens zur Advektion
188	von Impuls
189	und skalaren Größen (neue UP's, s. rechts).
190	Berechnung von
191	Variablen
192	für spezielle Advektionsverfahren in eigenständiges
193	UP
194	ausgelagert
195	(<tt>init_advec</tt> + eigenes Modul <tt>advection</tt>).
196	Reines
197	Euler-/Upstream-Verfahren
198	kann gerechnet werden.  <p>Schnelle binäre I/O
199	(s. 15/12/98) wieder abgeschaltet, da
200	Dateien
201	nicht wieder einlesbar sind. Druckstörung (p) wird zu Beginn
202	auf 0
203	gesetzt, damit sie keine Tendenzen im ersten Zeitschritt hervorruft.</p>
204	</td> <td>advec_s_bc, check_open, check_parameters,
205	flow_statistics,
206	header,
207	init_3d_model, init_grid, leap_frog, modules, parin, plot_2d, plot_ts,
208	read_var_list, timestep, write_3d_binary, write_var_list  <p><b>Neu:</b>
209	<br>
210	advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, init_advec,
211	long_filter,
212	spline_x, spline_y, spline_z</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">24/02/99</td>
213	<td>SR</td> <td>1.1a</td> <td>C/N</td>
214	<td>Kleinere Ergänzungen / Änderungen
215	für Upstream
216	- Spline,  <br>
217	Diverse Verbesserungen bei Berechnung der Diffusionskoeffizienten
218	(exaktere
219	Formulierung von Scherungen, Dissipation gemaess Original - Deardorff -
220	Ansatz, Mischungswegreduktion nur, wenn Schichtung sowohl oberhalb als
221	auch unterhalb des entsprechenden Gitterpunktes stabil ist),
222	Wertebegrenzung
223	bei Spline - Berechnung zur Verhinderung von "Überschwingern"</td>
224	<td>check_parameters, diffusion_e, diffusion_pt, diffusivities,
225	header,
226	init_advec, long_filter, modules, production_e, spline_x, spline_y,
227	spline_z</td> </tr> <tr nosave="" valign="top">
228	<td>"</td> <td nosave="">SR</td> <td>1.1a</td>
229	<td>N/B</td> <td>Erweiterung des des Bott - Chlond -
230	Schemas auf Advektion der
231	TKE,
232	Korrektur der Dichteberechnung (war falsch bei Galilei-Transformation)</td>
233	<td>advec_s_bc, leap_frog</td> </tr> <tr nosave="" valign="top"> <td nosave="">01/03/99</td>
234	<td>MS</td> <td>1.1b</td> <td>N</td>
235	<td>Kleinere Ergänzungen für Upstream -
236	Spline:  <ul> <li>Gradientenkontrolle
237	für den nicht-parallelen Teil</li> <li>statistische
238	Auswertung über den prozentualen Anteil
239	des
240	Upstream-Verfahrens
241	an der Gesamtadvektion fuer nicht-parallelen Teil</li> </ul>
242	</td> <td>modules, spline_x, spline_y, spline_z</td>
243	</tr> <tr nosave="" valign="top"> <td>"</td>
244	<td>SR</td> <td>1.1b</td> <td>N</td>
245	<td>Datenkompression für 3D-Plotausgaben</td> <td nosave="">check_open, check_parameters, close_files, header,
246	modules,
247	parin, plot_3d  <p><b>Neu:</b> <br>
248	write_compressed</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">03/03/99</td>
249	<td>SR</td> <td>1.1c</td> <td>B/C</td>
250	<td>Schnelle binäre I/O auf T3E-Rechnern funktioniert
251	jetzt.
252	Beim
253	binären Einlesen dürfen Records nicht mit dem Trick "<tt>READ
254	(..) idum</tt>" überlesen werden. Zeitmessungen auf T3E
255	erfolgen
256	jetzt
257	grundsätzlich mit <tt>TIMEF.</tt></td> <td>check_open,
258	cpu_zeitmessung, init_3d_model, modules,
259	write_3d_binary</td> </tr> <tr nosave="" valign="top"> <td nosave="">25/03/99</td>
260	<td>SR</td> <td>1.1d</td> <td>N</td>
261	<td>Einbau einer Rayleigh-Dämpfungsschicht sowie
262	flexiblere
263	Wahl der
264	numerischen Begrenzer für das Upstream - Spline - Verfahren.</td>
265	<td>check_parameters, header, init_3d_model, leap_frog, modules,
266	parin,
267	read_var_list, spline_x, spline_y, spline_z, write_var_list</td> </tr>
268	<tr nosave="" valign="top"> <td nosave="">"</td>
269	<td>SR</td> <td>1.1d</td> <td>B</td>
270	<td>Korrektur des Zeitschrittkriteriums bei z=zp im 1D-Modell</td>
271	<td>init_1d_model</td> </tr> <tr nosave="" valign="top"> <td>25/11/99</td> <td>SR</td>
272	<td>1.1e</td> <td>N</td> <td nosave="">Partikelplots
273	mit vtk-Graphiksoftware sind auf t3eh
274	möglich.
275	Ausgabe erfolgt im dvr-Format. Bisher noch nicht nutzbar, da noch
276	Einstellmöglichkeiten
277	für die Partikelquelle(n) fehlen. <b>Wichtig:</b>
278	Die Benutzung
279	der
280	vtk-Software erfordert die zusätzliche mrun-Option <tt>-g</tt>.
281	Das
282	Hauptprogramm <tt>parles</tt> wird in diesem Fall zum
283	Unterprogramm
284	und
285	von einem c++-Programm aus aufgerufen.</td> <td>header,
286	init_3d_model, init_pegrid, leap_frog, modules,
287	parin, parles,
288	read_var_list, write_var_list  <p><b>Neu:</b>
289	<br>
290	advec_particles, init_particles, plot_particles</p> </td> </tr>
291	<tr nosave="" valign="top"> <td>"</td>
292	<td>SR</td> <td>1.1e</td> <td nosave="">B/C</td>
293	<td>TIMEF-Zeitmessungen von Subroutine- auf Function-Aufruf
294	umgestellt.
295	Laufindexkorrektur in <tt>spline_y</tt>. Fehler trat bei
296	nx /= ny auf.</td> <td>cpu_zeitmessung, spline_y</td>
297	</tr> <tr nosave="" valign="top"> <td nosave="">28/12/99</td> <td>SR</td> <td>1.1f</td>
298	<td>N</td> <td>Plot von Isooberflächen mit
299	vtk-Graphiksoftware sind auf
300	t3eh
301	möglich. Ausgabe erfolgt im dvr-Format. Bisher noch nicht
302	allgemein
303	nutzbar, da noch diverse manuelle Eingriffe nötig sind.</td>
304	<td>header, leap_frog, modules, parin, plot_particles,
305	read_var_list, write_var_list  <p><b>Neu:</b>
306	<br>
307	plot_isosurface</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">10/01/00</td>
308	<td>SR</td> <td>1.2</td> <td>C</td>
309	<td>Randbedingungen für w (=0) werden explizit gesetzt,
310	und
311	zwar nicht
312	nur bei  <tt>k = nzb, nzt+1</tt> sondern auch
313	bei  <tt>k =
314	nzt</tt>,
315	wo bislang der vom vorigen Zeitschritt durch den Drucklöser
316	ermittelte
317	Wert stand. Auch jetzt wird der Wert bei k = nzt anschließend
318	durch
319	den Drucklöser modifiziert. Soweit bis jetzt abzusehen, hat
320	diese
321	Änderung nur minimale Auswirkungen auf den Prognoseverlauf.
322	Evtl.
323	gibt es stärkere Auswirkungen bei exzessivem Auftreten von
324	Schwerewellen
325	am oberen Rand (die dort aber eigentlich sowieso nicht
326	hingehören).  <br>
327	Variablenübergabe an <tt>boundary_conds</tt>
328	erfolgt  <br>
329	über Modul und nicht mehr per Parameterliste.  <p>Bei
330	Galilei-Transformation wird jetzt defaultmäßig
331	der geostrophische
332	Wind als Translationsgeschwindigkeit verwendet (neuer
333	Initialisierungsparameter <tt>use_ug_for_galilei_tr</tt>).
334	Dadurch wird das verstärkte Auftreten von Schwerewellen bei
335	höheren
336	geostrophischen Windgeschwindigkeiten unterdrückt.  </p>
337	<p>3D-Feldvariablen (u, v, w, pt, e, km, kh) sowie einige
338	2D-Variablen
339	(usws, vsws, rif, shf) sind nun als Pointer deklariert, denen nach
340	jedem
341	Zeitschritt neue Targets zugeordnet werden (für die
342	benötigten
343	3 Zeitebenen existieren die Targets ..._1 (z.B. u_1), ..._2, ..._3).
344	Durch
345	die jeweilige Neuzuordnung der Targets entfällt das
346	Umspeichern
347	der
348	Zeitebenen komplett (Zeitersparung: ca. 5% der
349	Gesamtrechenzeit).  <br>
350	Die Umordnung der Zeitebenen wurde ins neue UP <tt>swap_timelevel</tt>
351	ausgelagert.  <br> <b>Wichtig:</b> Die
352	Übersetzungszeiten haben durch die
353	Einführung
354	der Pointer t.w. sehr deutlich zugenommen (<tt>leap_frog</tt>
355	benötigt
356	jetzt z.B. ca. 60 Sekunden). Außerdem benötigt der
357	Compiler
358	jetzt wesentlich mehr Speicher. Der "memory"-Parameter in den
359	Konfigurationsdateien
360	(.mrun.config, .al.config) muss nun mindestens den Wert 60 (MB) (t3eh,
361	t3ej2) bzw. 45 (t3eb) und 96 (vpp) haben.  <br> <b>Achtung:</b>
362	bislang wurde diese Änderung nur für
363	das
364	reine Leapfrog-Verfahren getestet!  </p> <p>Neue
365	Laderoption "<tt>-D preset=nan</tt>" empfohlen (s.
366	Beispiel-Konfigurationsdatei).
367	Ebenso empfehlenswert für Debug-Läufe: Compileroption
368	"<tt>-ei</tt>".
369	Diese bewirkt einen Programmabbruch, falls mit nicht initialisierten
370	Variablen
371	gearbeitet wird (ist aber zeitaufwendig in der Ausführung!).</p>
372	</td> <td>boundary_conds, check_parameters, header,
373	init_3d_model,
374	leap_frog,
375	modules, parin, read_var_list, timestep, write_var_list  <p><b>Neu:</b>
376	<br>
377	swap_timelevel</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">10/01/00</td>
378	<td>SR</td> <td>1.2</td> <td>B</td>
379	<td>Der Asselin-Filter wird vor Umordnung der Zeitebenen
380	aufgerufen. Dies
381	geschah bisher fälschlicherweise erst danach, sodass der
382	Zeitfilter
383	asymmetrisch arbeitete.  <br> <b>Achtung:</b>
384	diese Änderung hat Auswirkungen auf den
385	Prognoseverlauf.
386	Die Testergebnis-Datei wurde entsprechend geändert.</td>
387	<td>leap_frog</td> </tr> <tr nosave="">
388	<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>
389	<br>
390	Der Asselin-Filter im 1D-Modell wird nun auch vor der Umordnung der
391	Zeitebenen aufgerufen (s.o.).  <p><b>3D-Modell:</b>
392	<br>
393	TKE wurde bisher bei <tt>scalar_advec=bc-scheme</tt> einer
394	zeitlichen
395	Filterung unterzogen. Dies wird nun unterbunden.  </p> <p>Die
396	Divergenz der Impulsflüsse an der Prandtl - Schicht -
397	Obergrenze
398	wird nun über eine ganze Gitterweite gebildet. Die bisherige
399	Methode
400	lieferte im Vergleich mit Ergebnissen anderer LES-Modelle  zu
401	große
402	Impulsflüsse.  </p> <p>Bei der
403	Berechnung der Diffusion der Temperatur werden die
404	Diffusionskoeffizienten
405	nun wieder durch Mittelung für die entsprechenden
406	Gitterpunkte
407	bereitgestllt. Das Maximumkriterium, das im Zuge der Implementierung
408	des
409	Upstream-Spline Advektionsverfahrens eingebaut wurde, bewirkte ein zu
410	rasches
411	Anwachsen der Grenzschicht mit der Zeit.  </p> <p><b>Achtung:</b>
412	diese Änderungen haben Auswirkungen auf
413	den Prognoseverlauf.
414	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
415	<td nosave="" valign="top">init_1d_model,
416	asselin_filter,
417	diffusion_u, diffusion_v,  <br>
418	diffusion_pt</td> </tr> <tr nosave="" valign="top"> <td nosave="">17/02/00</td>
419	<td>MS</td> <td>2.0</td> <td>N</td>
420	<td><b>Allgemeine Beschreibung der Änderungen:</b>
421	<br>
422	vollständige Implementierung des wolkenphysikalischen
423	Moduls  <p>Zur Implementierung der Wolkenphysik waren
424	umfangreiche
425	Änderungen
426	in zahlreichen Programmteilen notwendig (Beschreibung <a href="#Cloud_physics">siehe
427	unten</a> ). Im einzelnen wurden folgende Unprogramme
428	geändert:  <br> <b>modules</b>:
429	<br>1) Bereitstellung neuer 3D-, 2D- und 1D-Felder für
430	die Prognose
431	des Gesamtwassergehaltes  <br>
432	2) "cloud_parameters" als neues Modul mit wolkenphysikalischen
433	Variablen  <br> <b>parin: </b>Initialisierungsparameterliste
434	wurde erweitert
435	(s.u.)  <br> <font color="#000000"><b>read_var_list,
436	write_var_list,
437	write_3d_binary: </b>In/Output
438	der neuen Initialisierungsparamter und Felder für
439	Fortsetzungsläufe </font> <br> <font color="#000000"><b>check_parameters:</b>
440	Initialisierung
441	des
442	Feuchteprofils und Ausgabe von neuen Vertikalprofilen: </font>
443	<br> <font color="#ff0000">vpt</font><font color="#000000">: virtuelle
444	poteniellen
445	Temperatur,</font> <br> <font color="#ff0000">lpt</font><font color="#000000">:
446	potentielle
447	Flüssigwassertemperatur,</font> <br> <font color="#ff0000">q</font><font color="#000000">:
448	Gesamtwassergehalt,</font> <br> <font color="#ff0000">qv</font><font color="#000000">:
449	spezifische
450	Feuchte,</font> <br> <font color="#ff0000">ql</font><font color="#000000">:
451	Flüssigwassergehalt,</font> <br> <font color="#ff0000">w"vpt", wvpt, wvpt</font><font color="#000000">:
452	Auftriebsfluss (subskalig, aufgelöst, gesamt),</font> <br>
453	<font color="#ff0000">w"q", wq, wq</font><font color="#000000">:
454	Wasserfluss (subs., aufg., ges.),</font> <br> <font color="#ff0000">w"qv", wqv, wqv</font><font color="#000000">:
455	Feuchtefluss (subs, aufg., ges.)</font> <br> <b>init_3d_model</b>:
456	Initialisierung aller
457	Feuchte/Wasserfelder  <br> <b>init_1d_model</b>:
458	Anpassung an Rechnungen mit Feuchte  <br> <b>header</b>:
459	Headerausgaben für Feuchtebehandlung und
460	Wolkenphysik
461	eingefügt, außerdem Formatnummern erweitert um Platz
462	für
463	weitere Ausgaben zu schaffen  <br> <b>leap_frog:</b>
464	<br>
465	1) alle prognostischen Gleichungen wurden in prognostic_equations
466	ausgelagert  <br>
467	2) Aufrufe der neuen Unterprogramme (UP) compute_vpt,
468	calc_liquid_water_content  <br>
469	3) veraenderter Aufruf von diffusivities  <br> <b><tt>b</tt>oundary_conds,
470	asselin_filter, swap_timelevel,
471	flow_statistics: </b>Anpassung
472	an Feuchtebehandlung  <br> <b>plot2d, plot3d</b>:
473	Ausgabemöglichkeiten von q und ql <br> <b>buoyancy</b>:
474	Anpassung des Autriebstermes an
475	Feuchtebehandlung
476	durch neue Übergabeparameter: Temperatur + Nummer des
477	entsprechenden
478	mittleren Temperaturprofils  <br> <b>diffusion_e</b>:
479	Anpassung der Mischungswegberechnung an
480	Feuchtebehandlung
481	durch Variation der Übergabeparameter  <br> <b>production_e</b>:
482	TKE-Produktion durch Auftriebskräfte an
483	Feuchtebehandlung
484	angepasst  <br> <b>diffusivities</b>:
485	siehe diffusion_e  <br> <b>prandtl-fluxes</b>:
486	Prandtl-Schicht fuer den
487	Gesamtwassergehalt
488	eingefügt  </p> <p>Zusätzlich
489	wurden folgende Unterprogramme NEU
490	eingeführt:  <br> <b>inti_cloud_physics</b>:
491	Initialisierung wolkenphysikalischer
492	Parameter  <br> <b>prognostic_equations</b>:
493	Auslagerung der prognostischen
494	Gleichungen
495	aus leap_frog, zusätzliche porgnostische Gleichung
496	für den
497	Gesamtwassergehalt  <br> <b>diffusion_s</b>:
498	Berechnung der Diffusion skalarer
499	Größen
500	(Temperatur und Gesamtwassergehalt), ersetzt diffusion_pt  <br>
501	<b>calc_liquid_water_content</b>: Berechnung des
502	Flüssigwassergehalts  <br> <b>calc_radiation</b>:
503	Parametrisierung langwelliger
504	Strahlungsprozesse
505	über des Schema der effektiven Emissivität  <br>
506	<b>calc_precipitation</b>:Parametrisierung von
507	Niederschlagsprozessen
508	mit Hilfe eines vereinfachten Kesslerschemas  <br> <b>impact_of_latent_heat</b>:
509	Berücksichtigung der durch
510	Niederschlagsprozesse
511	zurückbleibenden latenten Waerme innerhalb eines
512	Gittervolumens  <br> <b>compute_vpt</b>:
513	Berechnung der virtuellen potentiellen
514	Temperatur  </p> <p><b>Liste der neuen
515	Initialisierungsparameter:</b> <br> <table nosave="" border="1"> <caption>  <br> </caption><tbody>
516	</tbody><tbody> </tbody> <tbody> <tr nosave=""> <td nosave=""><b>Parameter</b></td>
517	<td nosave=""><b>Typ</b></td> <td nosave="" width="4%"><b>Default</b></td>
518	<td nosave=""><b>Beschreibung</b></td> </tr>
519	<tr nosave=""> <td nosave=""><tt>moisture</tt></td>
520	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
521	des Gesamtwassergerhaltes als neue
522	progn. Variable</td> </tr> <tr> <td><tt>cloud_physics</tt></td>
523	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
524	des Kondensationsschemas</td> </tr> <tr nosave="">
525	<td><tt>radiation</tt></td> <td>L</td>
526	<td nosave="">FALSE</td> <td>Ab-/Zuschalten
527	des Strahlungsschemas</td> </tr> <tr> <td><tt>precipitation</tt></td>
528	<td>L</td> <td>FALSE</td> <td>Ab-/Zuschalten
529	der Niderschlagsparametrisierung</td> </tr> <tr> <td><tt>bc_q_b</tt></td>
530	<td>C</td> <td>'dirichlet'</td> <td>untere
531	Randbedingung für q (siehe auch bc_pt_b)</td> </tr>
532	<tr> <td><tt>bc_q_t</tt></td> <td>C</td>
533	<td>'neumann'</td> <td>obere RB für q
534	(siehe auch bc_pt_t)</td> </tr> <tr> <td><tt>q_surface</tt></td>
535	<td>R</td> <td>0.0</td> <td>Feuchtewert
536	an der Erdoberfläche</td> </tr> <tr> <td><tt>q_surface_initial_change</tt></td>
537	<td>R</td> <td>0.0</td> <td>vgl.
538	pt_surface_initial_change</td> </tr> <tr> <td><tt>q_vertical_gradient</tt></td>
539	<td>R(10)</td> <td>0.0</td> <td>vgl.
540	pt_vertical_gradient</td> </tr> <tr nosave="">
541	<td nosave=""><tt>q_vertical_gradient_level</tt></td>
542	<td>R(10)</td> <td>10000.0</td> <td>vgl.
543	pt_vertical_gradient_level</td> </tr> <tr> <td><tt>surface_pressure</tt></td>
544	<td>R</td> <td>1013.25</td> <td>Luftdruck
545	an der Erdoberfläche</td> </tr> <tr> <td><tt>surface_waterflux</tt></td>
546	<td>R</td> <td>0.0</td> <td>oberflächennaher
547	Wasser/Feuchtefluss</td> </tr> </tbody> </table>
548	Fortsetzungsläufe mit Daten, die mit Modellversionen kleiner
549	2.0
550	erzeugt
551	wurden, sind aufgrund der erweiterten Initialisierungsparameterliste
552	INKOMPATIBEL
553	zu den Einleseroutinen der Version 2.0. Ein Update auf Version 2.0
554	sollte
555	deshalb nach Abschluss eines kompletten Modelllaufs erfolgen.
556	</p> <p><b>Achtung:</b> diese
557	Änderungen haben Auswirkungen auf
558	den Prognoseverlauf.
559	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
560	<td nosave="" valign="top">modules, parin,
561	read_var_list,
562	check_parameters,
563	init_3d_model, init_1d_model, header, leap_frog. buoyancy, diffusion_e,
564	production_e, diffusivities, prandtl_fluxes, boundary_conds,
565	asselin_filter,
566	swap_timelevels, flow_statistics, plot_2d, plot_3d, write_var_list,
567	write_3d_binary  <p><b>Neu:</b> <br>
568	init_cloud_physics, prognostic_equations, diffusion_s,
569	calc_liquid_water_content,
570	calc_radiation, calc_precipitation, impact_of_latent_heat, comute_vpt</p>
571	</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
572	Umstellung auf Modellversion 2.0  wurden
573	noch kleine
574	Änderungen an den Unterprogrammen diffusion_e, production_e
575	und
576	diffusivities
577	vorgenommen. In allen genannten  <br>
578	Unterprogrammen wurde bisher ein strengeres Kriterium zur Bestimmung
579	der Schichtungsverhältnisse verwendet. Ein Modellvergleich
580	zeigte
581	jedoch, dass dadurch die Diffusion im Bereich der Inversion zu gross
582	wird.  <p>Eine weitere Ergänzung betrifft die
583	Advektionsverfahren:  <br>
584	Das Bott-Chlond Advektionsverfahren ist nun auch für
585	Rechnungen
586	mit Feuchte/Wolkenphysik verfügbar.  </p> <p><b>Achtung:</b>
587	diese Änderungen haben Auswirkungen auf
588	den Prognoseverlauf.
589	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
590	<td nosave="" valign="top">diffusion_e,
591	production_e,
592	diffusivities, check_parameters</td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
593	<td>SR</td> <td>2.0a</td> <td>C</td>
594	<td>Vollständige Umstellung von vtk-Grafik-Software auf
595	dvrp-Software.
596	Grafik-Ausgaben im dvr-Format sind mittlerweile begrenzt nutzbar
597	(Isooberflächen
598	sind darstellbar, siehe neue Laufparameter  <tt>dt_dvrp,
599	threshold</tt>),
600	es wird aber in der Anwendung in naher Zukunft noch diverse
601	Änderungen
602	geben. Partikelausgabe vorerst nicht mehr möglich (Verlagerung
603	schon).</td> <td>header, init_particles, init_3d_model,
604	leap_frog, modules,
605	parin, parles,
606	read_var_list, write_var_list  <br> <b>Gestrichen:</b>
607	<br>
608	plot_isosurface, plot_particles  <p><b>Neu:</b>
609	<br>
610	init_dvrp, plot_dvrp</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
611	<td>SR</td> <td>2.0a</td> <td>C</td>
612	<td>Durch zusätzlichen zyklischen Rand im
613	Bott-Chlond-Schema
614	sehr
615	viele SENDRECV-Aufrufe eingespart.  <br>
616	Änderung des Namens einer eingelesenen Environment-Variablen
617	in <tt>check_open</tt>
618	von <tt>remote_addres</tt> nach <tt>return_addres</tt>.
619	<br>Prozessor-Topologie kann durch Benutzer vorgegeben werden.
620	Dazu neue
621	Initialisierungsparameter <tt>npex</tt> und <tt>npey</tt>.
622	Durch
623	Änderungen
624	am Header-Format wurde Testergebnis-Datei geändert.</td>
625	<td>advec_s_bc, check_open, header, init_pegrid, modules, parin,
626	read_var_list,
627	write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">26/04/00</td>
628	<td>SR</td> <td>2.0a</td> <td>N</td>
629	<td>Rechnungen mit geneigter Oberfläche erlauben jetzt
630	die
631	Vorgabe
632	eines stabil geschichteten Temperaturprofils mit konstantem Gradienten.
633	Hinzuschalten von Feuchte funktioniert für Hangrechnungen noch
634	nicht.</td> <td>advec_s_bc, buoyancy, init_3d_model,
635	modules,
636	prognostic_equations  <p><b>Neu:</b> <br>
637	init_slope</p> </td> </tr> <tr nosave="" valign="top"> <td>13/06/00</td> <td>MS</td>
638	<td>2.0a</td> <td nosave="">B</td> <td>Es
639	werden nun auch die seitlichen Ränder für ql
640	gesetzt.
641	Ein Nichtsetzen der Randbedingungen führte zu Fehlern bei der
642	Ausgabe
643	von pt</td> <td nosave="">calc_liquid_water_content</td>
644	</tr> <tr nosave="" valign="top"> <td nosave="">03/07/00</td> <td>SR</td> <td>2.0b</td>
645	<td>C</td> <td>Für eine Reihe von
646	Unterprogrammen, die innerhalb
647	von <tt>prognostic_equation</tt>
648	aufgerufen werden und an die Pointer-Variablen übergeben
649	werden,
650	sind
651	jetzt explizite Interfaces vereinbart (neues Modul <tt>pointer_interfaces</tt>).
652	Auch im Vereinbarungsteil der entsprechenden Unterprogramme sind diese
653	Übergabeparameter jetzt aus Konsistenzgründen (und
654	weil es
655	sonst
656	Laufzeitfehler gibt) als Pointer-Variablen deklariert. Mit dieser
657	Änderung
658	ist der große Speicher- und CPU-Zeit-Bedarf beim
659	Übersetzen
660	von prognostic_equations wieder auf ein erträgliches
661	Maß
662	reduziert.  <br>
663	Im Rahmen dieser Änderungen wurde auch an diffusion_e ein
664	Hilfsfeld
665	weniger übergeben.  <br>
666	Aus nicht vollständig gekärten Gründen haben
667	sich die
668	Zahlen in der Testergebnis-Datei minimal geändert (und zwar
669	die
670	Spalte
671	mit der Gesamtdivergenz nach Aufruf des Drucklösers).</td>
672	<td>advec_s_bc, buoyancy, diffusion_e, diffusion_s, diffusion_u,
673	diffusion_v,
674	diffusion_w, disturb_field, modules, production_e, prognostic_equations</td>
675	</tr> <tr nosave="" valign="top"> <td nosave="">04/07/00</td> <td>SR</td> <td>2.0b</td>
676	<td>B</td> <td>Diriclet-Randbedingungen für
677	Temperatur und
678	Flüssigwassergehalt
679	werden gesetzt. Dies wäre bereits nach Einführung der
680	Pointer
681	zwingend notwendig gewesen. Rechnungen mit vorgegebener
682	Oberflächentemperatur
683	schlugen deshalb bislang fehl.</td> <td>boundary_conds</td>
684	</tr> <tr nosave="" valign="top"> <td nosave="">07/09/00</td> <td>MS</td> <td>2.0b</td>
685	<td>B</td> <td>Die virtuelle potenielle Temperatur
686	wird nun auch für
687	k=nzb und
688	k=nzt+1 berechnet, um die Randwerte auch für Ausgabezwecke
689	bereichtzustellen. </td> <td>compute_vpt</td>
690	</tr> <tr nosave="" valign="top"> <td nosave="">28/12/00</td> <td>SR</td> <td>2.1</td>
691	<td>C/N</td> <td>PALM erlaubt jetzt den Einsatz
692	optionaler Software-Pakete,
693	die zwar
694	zum Modell gehören, standardmäßig aber
695	nicht mit
696	übersetzt
697	werden, um so unter anderem Kompilationszeit einzusparen. Siehe neues
698	Kapitel
699	3.7 in der Modelldokumentation.  <p>Einsatz der
700	dvrp-Software wurde vollständig
701	überarbeitet.
702	Sie ist nun als Software-Paket optional im Modell einsetzbar. Siehe
703	überarbeitetes
704	Kapitel 4.5.6 in der Modelldokumentation.  </p> <p>Die
705	Prognose der Partikelverlagerung ist ebenfalls in ein
706	optionales
707	Software-Paket ausgelagert.</p> </td> <td>advec_particles,
708	header, init_3d_model, init_dvrp,
709	init_particles,
710	init_pegrid, modules, parin, parles, plot_dvrp, prognostic_equations,
711	read_var_list,
712	write_var_list  <p><b>Neu:</b> <br>
713	package_parin</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">28/12/00</td>
714	<td>SR</td> <td>2.1</td> <td>B</td>
715	<td>MPI_FINALIZE ans Ende des Hauptprogramms geschoben (stand
716	vorher vor
717	cpu_auswertung, wo noch ein Barrier-Aufruf steht). comm2d war zu Beginn
718	undefiniert und wird nun erst einmal gleich MPI_COMM_WORLD gesetzt.</td>
719	<td>parles</td> </tr> <tr nosave="" valign="top"> <td nosave="">02/01/01</td>
720	<td>SR</td> <td>2.1a</td> <td>C</td>
721	<td>Offene Dateien werden sobald möglich geschlossen.
722	Wiedereröffnung
723	bestimmter Dateien mit POSITION='APPEND' möglich. In diesem
724	Zusammenhang
725	wurde das Unterprogramm close_files in close_file umbenannt und hat nun
726	1 Argument.  <br>
727	Anpassung der Diffusionsparametrisierung im 1D-Modell an das 3D-Modell.</td>
728	<td>advec_particles, check_cpu_time, check_open, cpu_auswertung,
729	init_1d_model,
730	init_3d_model, init_particles, modules.f90, parin, parles, plot_2d,
731	write_3d_binary  <p><b>Neu:</b> <br>
732	close_file  </p> <p><b>Eliminiert:</b>
733	<br>
734	close_files</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">02/01/01</td>
735	<td>SR</td> <td>2.1a</td> <td>B</td>
736	<td>Beseitigung kleiner Fehler.</td> <td>check_cpu_time,
737	diffusion_e, diffusivities, long_filter,
738	production_e</td> </tr> <tr nosave="" valign="top"> <td>05/01/01</td> <td>SR</td>
739	<td>2.1b</td> <td>N</td> <td nosave="">Neues
740	Software-Paket zur Berechnung von Spektren im
741	Ortsraum</td> <td>check_open, header, init_3d_model,
742	leap_frog, modules,
743	package_parin,
744	parles, read_var_list, write_3d_binary, write_var_list  <p><b>Neu:</b>
745	<br>
746	calc_spectra, plot_spectra</p> </td> </tr> <tr valign="top"> <td>25/01/01</td> <td>SR</td>
747	<td>2.1c</td> <td>C/N</td> <td>Drucklöser
748	kann jetzt die Singleton-FFT benutzen. Modul <tt>singleton</tt>
749	wurde deshalb von <tt>calc_spectra.f90</tt> nach <tt>modules.f90</tt>
750	geschoben
751	(neuer Initialisierungsparameter <tt>fft_method</tt>).
752	<br>Flüsse können jetzt bei k=1
753	unabhängig von der
754	Verwendung
755	einer Prandtl-Schicht vorgegeben werden (neuer
756	Initialisierungsparameter <tt>use_surface_fluxes</tt>).
757	<br>Modul <tt>test_variables</tt> wurde aus allen
758	Programmteilen entfernt.
759	Hauptprogramm wurde von parles nach <tt>palm</tt>
760	umbenannt.  <br>
761	Modell kann auf DEC-Workstations eingesetzt werden (-D <tt>dec</tt>).
762	<br>Zusätzliche Zeitmessungen mit dvrp-Software.
763	Schreiben von
764	Partikel-Informationen
765	ist optional (neuer Parameter <tt>write_particle_informations</tt>).</td>
766	<td>advec_particles, calc_spectra, check_parameters,
767	cpu_zeitmessung, diffusion_s,
768	header, init_3d_model, init_dvrp, init_particles, leap_frog, modules,
769	package_parin,
770	parin, poisfft, read_var_list, swap_timelevel, write_var_list
771	<p><b>Neu:</b> <br>
772	palm  </p> <p><b>Eliminiert:</b> <br>
773	parles, module_test</p> </td> </tr> <tr valign="top"> <td>25/01/01</td> <td>SR</td>
774	<td>2.1c</td> <td>B</td> <td>Fehler
775	beim öffnen von Unit 23 beseitigt. Modul <tt>interface</tt>
776	fehlte in disturb_field.  <br>
777	Wertebereich von theta* in Prandtl-Fluxes eingeschränkt, weil
778	sonst auf einigen Rechnern overflow droht, wenn u*=0.</td> <td>check_open,
779	disturb_field, prandtl_fluxes</td> </tr> <tr valign="top"> <td>30/01/01</td> <td>SR</td>
780	<td>2.1d</td> <td>N/C</td> <td>Prognose
781	eines passiven Skalars ist möglich (anstatt
782	Feuchte),
783	dazu neuer Initialisierungsparameter <tt>passive_scalar</tt>.
784	<p>Falls kein Pfad für ftpcopy existiert, werden in <tt>check_open</tt>
785	die Dateinamen für AVS-Koordinaten- und Datendatei auf
786	"unknown"
787	gesetzt.</p> </td> <td>asselin_filter,
788	boundary_conds, check_open, check_parameters,
789	flow_statistics,
790	header, init_1d_model, init_3d_model, modules, parin, plot_2d,
791	plot_dvrp,
792	prandtl_fluxes, prognostic_equations, read_var_list, swap_timelevel,
793	write_3d_binary,
794	write_var_list</td> </tr> <tr valign="top"> <td>30/01/01</td>
795	<td>SR</td> <td>2.1d</td> <td>B</td>
796	<td>String-Ausgabe für use_surface_fluxes korrigiert.
797	Version vom
798	25/01/01 brach deswegen bei Fortsetzungsläufen ab.  <br>
799	xy-Plotausgabe von q und ql korrigiert.</td> <td>plot_2d,
800	write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">30/03/01</td>
801	<td>SR</td> <td>2.2</td> <td>N/C</td>
802	<td>Sämtliche 3D-Felder der Zeitebene t+dt wurden
803	entfernt.
804	Ebenso
805	die Arbeitsfelder work und work1. Hilfsfelder wurden soweit
806	möglich
807	eingespart und werden grundsätzlich lokal allokiert. Dadurch
808	konnten
809	eine Reihe von Übergabeparametern gestrichen werden (z.B. beim
810	Aufruf
811	von <tt>pres, advec_s_bc, poisfft, production_e, sor </tt>sowie
812	den
813	Spline-Unterprogrammen).
814	Der Long-Filter wurde in das Upstream-Spline-Verfahren integriert. Da
815	der
816	Zeitfilter jetzt direkt in der prognostischen Gleichung angewendet wird
817	(bisher geschah dies erst nach Aufruf des Drucklösers), haben
818	sich
819	die Zahlen in der Testergebnis-Datei geändert. Die mittleren
820	Profile
821	sind aber unbeeinflusst.  <p>Eine weitere kleinere
822	Änderung der Testergebnis-Daten
823	wird dadurch
824	verursacht, dass jetzt der Parameter <tt>adjust_mixing_length</tt>
825	defaultmäßig <tt>.FALSE.</tt>
826	ist und der Mischungsweg grundsätzlich zusätzlich
827	auf  <tt>0.7
828	* zu</tt>   begrenzt wird. Falls <tt>adjust_mixing_length=T</tt>,
829	wird jetzt der Mischungsweg in <tt>diffusivities</tt>
830	analog zu <tt>diffusion_e</tt>
831	an allen Gitterpunkten modifiziert. <b>Achtung: </b>Diese
832	Änderungen
833	können bei anderen Simulationen t.w. erhebliche Auswirkungen
834	auf
835	die
836	oberflächennahen Ergebnisse haben.  </p> <p><b>Kleinere
837	Änderungen:</b> In <tt>init_cloud_physics</tt>
838	wird
839	der Wert der Variablen <tt>surface_pressure</tt> in hPa
840	belassen
841	(bisher
842	Umwandlung in Pa).  <br>
843	Die Namelist-Namen der Software-Pakete sind  t.w.
844	geändert.  <br>
845	Unit 14 (binäre Ausgabe für
846	Fortsetzungsläufe) wird
847	jetzt im Hauptprogramm geschlossen, damit auf diese Datei noch
848	benutzergesteuerte
849	Ausgaben erfolgen können.  <br>
850	Laufparameter werden in keinem Fall mehr auf Unit 14 ausgegeben bzw.
851	von Unit 13 gelesen, d.h. sie gelten jetzt tatsächlich nur
852	für
853	den jeweils aktuellen Lauf.  <br>
854	Partikeladvektion funktioniert jetzt auch zusammen mit der
855	Galilei-Transformation.  </p> <p>Restliche
856	deutsche Variablen-, Unterprogramm- und Modulnamen
857	wurden
858	ins Englische übersetzt. Davon sind fast alle Programmteile
859	betroffen
860	(nicht in rechter Spalte aufgeführt).</p> </td> <td>advec_particles,
861	advec_s_bc, advec_s_ups, advec_u_ups,
862	advec_v_ups,
863	advec_w_ups, boundary_conds, calc_spectra, check_parameters,
864	diffusion_e,
865	init_3d_model, init_cloud_physics, init_pegrid, init_rankine,
866	leap_frog,
867	modules, package_parin, palm, parin, poisfft, pres, production_e,
868	prognostic_equations,
869	read_var_list, sor, swap_timelevel, transpose_*, write_3d_binary,
870	write_var_list  <p><b>Neu:</b> <br>
871	cpu_log, cpu_statistics  </p> <p><b>Eliminiert:</b>
872	<br>
873	asselin_filter, cpu_auswertung, cpu_zeitmessung, long_filter</p> </td>
874	</tr> <tr nosave="" valign="top"> <td nosave="">12/07/01</td> <td>SR</td> <td>2.2a</td>
875	<td>N/C</td> <td>Defaultwert der unteren
876	Randbedingung für die TKE ist ab
877	sofort <tt>bc_e_b
878	= 'neumann'</tt>.  <br>
879	Partikelquelle ist über Paketparameter steuerbar.
880	Partikeleigenschaften
881	sind mittels benutzereigener Software steuerbar. Der dvrp-Ausgabeweg
882	ist
883	jetzt ebenfalls über Paketparameter steuerbar.  <br>
884	Allen Modulen (bis auf singleton) wurde eine SAVE-Anweisung
885	hinzugefügt,
886	damit die durch sie vereinbarten Variablen während der
887	Rechnung in
888	keinem Fall undefiniert werden können (diese Gefahr besteht
889	z.B.
890	auf
891	SGI-Origin-Maschinen).</td> <td>advec_particles, header,
892	init_dvrp, init_particles,
893	modules.f90, package_parin,
894	plot_dvrp, user_interface</td> </tr> <tr> <td>12/07/01</td>
895	<td>SR</td> <td>2.2a</td> <td>B</td>
896	<td>Verschiebung der OPEN-Anweisung für Unit 33
897	(AVS-FLD-Datei).</td> <td>check_open</td> </tr>
898	<tr nosave="" valign="top"> <td nosave="">20/07/01</td>
899	<td>SR</td> <td>2.3</td> <td>N</td>
900	<td>Einbau des Mehrgitterverfahrens zur Lösung der
901	Poisson-Gleichung.</td> <td>check_parameters,
902	exchange_horiz, header, init_grid,
903	init_pegrid, modules,
904	parin, pres, run_control  <p><b>Neu:</b> <br>
905	poismg</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">21/08/01</td>
906	<td>SR</td> <td>2.3a</td> <td>N/C</td>
907	<td>Ergänzung der dvrp-Software: Partikel
908	können mit
909	Schwänzen
910	versehen werden. Die Ausgabe der dvrp-Plotdaten durch einen separaten
911	PE
912	ist möglich (mrun-Option "<tt>-p dvrp_graphics+1PE</tt>").
913	Der
914	Kommunikator <tt>MPI_COMM_WORLD</tt>
915	wurde deshalb durch  <tt>comm_palm</tt>
916	ersetzt.  <p>Reduzierung des Mischungsweges im
917	Wandbereich kann wahlweise
918	abgeschaltet
919	werden. Für km und kh wird jetzt eine Neumann-Randbedingung am
920	unteren
921	Rand verwendet. Die TKE-Energieproduktionsberechnung durch Scherung des
922	Grundstroms am unteren Rand wurde verbessert.  </p> <p>Generelle
923	Verwendung der bodennahen vertikalen
924	Impulsflüsse in
925	den Diffusionstermen von u und v, immer wenn diese als Randbedingung
926	vorgegeben
927	sind (gemäß <tt>use_surface_fluxes</tt>,
928	- bisher wurde
929	dies
930	nur bei eingeschalteter Prandtl-Schicht gemacht). Schubspannungen
931	können
932	jetzt als Randbedingungen vorgegeben werden (allerdings unter
933	zuhilfenahme
934	benutzereigener Software).  </p> <p>Zusätzliche
935	Schnittstellen für benutzereigene
936	Software in
937	allen Tendenztermen, in <tt>flow_statistics,</tt> und
938	für
939	Partikel-
940	bzw. dvrp-Programmteile (Bestimmung von Partikeleigenschaften,
941	Festlegung
942	von Farbtabellen).  </p> <p><b>Achtung: </b>Diese
943	Änderungen können bei
944	Simulationen mit
945	mittlerem Wind durch die Änderungen im bereich des unteren
946	Randes
947	t.w. erhebliche Auswirkungen auf die oberflächennahen
948	Ergebnisse
949	haben.</p> </td> <td>advec_particles, diffusion_e,
950	diffusion_u, diffusion_v,
951	diffusivities,
952	flow_statistics, header, init_dvrp, init_particles, init_pegrid,
953	leap_frog,
954	modules, package_parin, palm, parin, plot_dvrp, production_e,
955	prognostic_equations,
956	read_var_list, swap_timelevel, user_interface, write_var_list</td>
957	</tr> <tr nosave="" valign="top"> <td nosave="">21/08/01</td> <td>SR</td> <td>2.3a</td>
958	<td>B</td> <td>Falsche Positionierung von
959	MPI_ALLREDUCE in check_cpu_time
960	korrigiert.</td> <td>check_cpu_time</td> </tr>
961	<tr nosave="" valign="top"> <td nosave="">04/09/01</td>
962	<td>SR</td> <td>2.3b</td> <td>N</td>
963	<td>Zusätzliche Profilausgaben für
964	Energieproduktionsterme möglich.
965	Stördruck wird bei der FFT-Methode nicht mehr durch
966	Aufsummieren
967	der
968	Werte zu den einzelnen Zeitschritten ermittelt.</td> <td>check_parameters,
969	flow_statistics, modules, pres</td> </tr> <tr nosave="" valign="top"> <td nosave="">04/09/01</td>
970	<td>SR</td> <td>2.3b</td> <td>B</td>
971	<td>Austausch der Geisterränder für die
972	zeitgefilterten
973	Felder
974	direkt nach Durchführung der Filterung (war fehlerhaft seit
975	Entfernen
976	der Zeitebene t+dt (Version 2.2) und führte zu sehr kleinen
977	Störungen
978	an den seitlichen Rändern der Teilgebiete).  <p><b>Achtung:</b>
979	Der Inhalt der Testergebnis-Datei ändert
980	sich durch
981	diese Fehlerkorrektur.</p> </td> <td>prognostic_equations</td>
982	</tr> <tr nosave="" valign="top"> <td nosave="">09/11/01</td> <td>SR</td> <td>2.3c</td>
983	<td>N</td> <td>Farbe entlang der
984	Partikelschwänze kann sich
985	ändern. Einschalten
986	der Partikeladvektion bei Fortsetzungsläufen möglich.</td>
987	<td>advec_particles, init_particles, modules, package_parin,
988	plot_dvrp</td> </tr> <tr nosave="" valign="top">
989	<td nosave="">16/04/02</td> <td>SR</td>
990	<td>2.3d</td> <td>N</td> <td>Vorgabe
991	von Randbedingungen für Partikeladvektion
992	möglich.
993	Partikeldaten können für spätere Analysen
994	auf Datei
995	geschrieben
996	werden (Unit 85). <tt>PARTICLE</tt>-Datentyp
997	enthält
998	Informationen
999	über Partikelgeschwindigkeitskomponenten und
1000	Startposition.  <p>Skalartransport sowie entsprechende
1001	Datenausgaben können
1002	durch
1003	eigene Parameter gesteuert werden (nicht mehr über die
1004	Feuchteparameter).  </p> <p>Im Fall von
1005	pdims(1)=1 (eindimensionales virtuelles
1006	Prozessornetz in
1007	y-Richtung) werden die zyklischen Randbedingungen in x-Richtung durch
1008	direktes
1009	Umspeichern anstatt durch  <tt>sendrecv </tt>realisiert.
1010	Ebenso
1011	werden
1012	die Transponierungen xz, yz, zx  und zy eingespart (es wird
1013	aber
1014	weiter
1015	umsortiert).  </p> <p>Im Fall von
1016	3D-Plotausgaben Aufruf von ftpcopy-Script durch
1017	batch_scp-Script
1018	ersetzt (dient der Ermittelung von Dateizyklusnummern als Information
1019	für
1020	die AVS-fld-Datei).  </p> <p>Bei fehlerhafter
1021	Eröffnung einer CPU_MEASURES-Datei
1022	werden erneute
1023	Eröffnungsversuche durchgeführt.</p> </td>
1024	<td>advec_particles, check_open, check_parameters,
1025	exchange_horiz, flow_statistics,
1026	header, init_particles, modules, package_parin, parin, plot_2d,
1027	plot_3d,
1028	prognostic_equations, read_var_list, transpose_xz, transpose_yz,
1029	transpose_zx,
1030	transpose_zy, write_var_list</td> </tr> <tr nosave="" valign="top"> <td nosave="">02/05/02</td>
1031	<td>SR</td> <td>2.3e</td> <td>B</td>
1032	<td>Wiedereinführung der 3D-Felder für die
1033	Zeitebene
1034	t+dt, die
1035	notwendig ist, damit in den Diffusionstermen bei Leapfrog-Zeitschritten
1036	mit der korrekten Zeitebene t-dt gearbeitet wird. Seit Version 2.2
1037	wurde
1038	fälschlicherweise die Zeitebene t+dt verwendet. Asselin-Filter
1039	ist
1040	jetzt wieder eigenständiges Unterprogramm. <br>
1041	Die Wiedereinführung dieser dritten Zeitebene ist auch
1042	Voraussetzung
1043	für die in der nächsten Version geplante skalare
1044	Optimierung.  <p>Fehler bei Berechnung von
1045	Ausgabezeitpunkten eliminiert (trat
1046	auf, wenn
1047	bei Fortsetzungsläufen von Ausgabeabständen 0.0 auf
1048	von Null
1049	verschiedene Werte gewechselt werden sollte).  </p> <p><b>Achtung:</b>
1050	Der Inhalt der Testergebnis-Datei ändert
1051	sich durch
1052	diese Fehlerkorrektur.</p> </td> <td>init_3d_model,
1053	leap_frog, modules, prognostic_equations,
1054	swap_timelevel  <p><b>Neu:</b> <br>
1055	asselin_filter</p> </td> </tr> <tr nosave="" valign="top"> <td>02/05/02</td> <td>SR</td>
1056	<td>2.3e</td> <td>N/C</td> <td>Kleinere
1057	Anpassungen an IBM-Regatta-Systeme in
1058	check_parameters, cpu_log.  <p>Modul singleton in
1059	eigenständige Datei
1060	überführt.  </p> <p>Global_min_max
1061	arbeitet mit REAL*4, um Komplikationen auf
1062	32-bit-Rechnern
1063	zu vermeiden (Datentyp MPI_2REAL müsste dort sonst auf
1064	MPI_2DOUBLE_PRECISION
1065	geändert werden). <br>
1066	Horizontale Geschwindigkeitskomponenten für Partikeladvektion
1067	werden exakt zwischen den jeweils benachbarten horizontalen
1068	Gitterflächen
1069	interpoliert.</p> </td> <td nosave="">advec_particles,
1070	check_parameters, cpu_log,
1071	global_min_max,
1072	modules  <p><b>Neu:</b> <br>
1073	singleton</p> </td> </tr> <tr nosave="" valign="top"> <td nosave="">11/06/02</td>
1074	<td>SR</td> <td>2.4</td> <td>N/C</td>
1075	<td>Optimierung und Anpassungen für einzelne Knoten der
1076	IBM-Regatta-Systeme. <p><b>Skalare (Cache) Optimierung:</b>
1077	Tendenzterme werden
1078	innerhalb einer
1079	großen (i,j)-Schleife berechnet, die nun jeweils die gesamte
1080	prognostische
1081	Gleichung umfasst. Schleifenindices i und j werden an die
1082	Tendenzunterprogramme
1083	als Argumente übergeben. Die Tendenzunterprogramme sind als
1084	Module
1085	geschrieben, die mittels Technik der überladenen Funktionen
1086	auch
1087	ohne
1088	diese Indices i und j aufgerufen werden können, und dann wie
1089	in
1090	früheren
1091	Versionen funktionieren (d.h. in ihnen laufen die Schleifen
1092	über
1093	alle
1094	3 Dimensionen). Solche Teile der prognostischen Gleichungen, die
1095	globale
1096	Kommunikation beinhalten, sind vor die (i,j)-Schleife gezogen. Falls
1097	ausschließlich
1098	mit Piascek-Williams-Advektion gearbeitet wird, werden alle
1099	prognostischen
1100	Gleichungen in einer einzigen (i,j)-Schleife gerechnet. </p> <p><b>Kommunikationsoptimierung:</b>
1101	Zusätzliche
1102	Implementierung einer
1103	1D-Gebietszerlegung in x-Richtung. Mit dem neuen direkten
1104	Drucklöser
1105	(poisfft_hybrid) werden dadurch 4 von 6 notwendigen Transpositionen
1106	eingespart.
1107	Die 1D-Zerlegung wird automatisch bei Verwendung dieses neuen
1108	Lösers
1109	aktiviert. Austausch von Geisterrändern in y-Richtung wird bei
1110	dieser
1111	1D-Zerlegung durch einfache zyklische Randbedingungen ersetzt. </p>
1112	<p><b>Kleinere Anpassungen:</b> String-Vergleiche
1113	erfordern beim
1114	IBM-Compiler
1115	in der Regel den Einsatz der TRIM-Funktion, um
1116	überschüssige
1117	Blanks am Ende des Strings abzuschneiden (sonst liefert der Vergleich
1118	.F.). <br>
1119	Lokal allokierte Felder t.w. in sogenannte automatische Felder
1120	umgewandelt
1121	(günstiger, um Gefahr von eventuellen Speicherlecks zu
1122	vermeiden).
1123	Einige Feldoperationen wurden wegen schlechter Performance auf der IBM
1124	entfernt (s. pres). </p> <p><b>Achtung: </b>Die
1125	Übersetzung des Modells erfordert
1126	aufgrund
1127	der Vielzahl nunmehr eingesetzter Module die Verwendung des
1128	make-Mechanismus,
1129	um die korrekte Reihenfolge bei der Übersetzung der
1130	Programmteile
1131	zu gewährleisten. Die Beschreibung dieser
1132	Abhängigkeiten
1133	erfolgt
1134	in der Datei<tt> Makefile</tt>, die zusammen mit den
1135	Programmdateien
1136	abgelegt
1137	ist und ebenfalls unter RCS-Verwaltung steht. </p> <p>Im
1138	User-Interface ist das Unterprogramm<tt> user_actions </tt>nun
1139	ebenfalls
1140	als Modul geschrieben und bedient sich der Methode der
1141	überladenen
1142	Funktionen. Existierende benutzereigene Software muss entsprechend
1143	angepasst
1144	werden.</p> </td> <td>advec_s_pw, advec_s_up,
1145	advec_u_pw, advec_u_up, advec_v_pw,
1146	advec_v_up,
1147	advec_w_pw, advec_w_up, buoyancy, calc_precipitation, calc_radiation,
1148	calc_spectra,
1149	check_parameters, coriolis, diffusion_e, diffusion_s, diffusion_u,
1150	diffusion_v,
1151	diffusion_w, diffusivities, exchange_horiz, exchange_horiz_2d,
1152	global_min_max,
1153	header, impact_of_latent_heat, init_pegrid, leap_frog, modules,
1154	plot_2d,
1155	plot_3d, plot_spectra, poisfft, pres, production_e,
1156	prognostic_equations,
1157	user_interface, <p><b>Neu:</b> <br>
1158	fft_for_1d_decomp, Makefile, poisfft_hybrid, </p> </td>
1159	</tr> <tr nosave="" valign="top"> <td nosave="">11/06/02</td> <td>SR</td> <td>2.4</td>
1160	<td>B</td> <td>Fehlende Variablenvereinbarung in <tt>advec_particles</tt>
1161	ergänzt.</td> <td>advec_particles</td> </tr>
1162	<tr> <td valign="top">12/09/02</td> <td valign="top">SR</td> <td valign="top">2.4a</td>
1163	<td valign="top">N</td> <td valign="top">Partikel
1164	können mit Trägheit versehen
1165	werden und
1166	einen Dichteunterschied zum umgebenden Fluid haben. Zur Steuerung dient
1167	der neue Paketparameter <tt>density_ratio</tt>.</td>
1168	<td valign="top">advec_particles, header, init_particles,
1169	modules, package_parin</td> </tr> <tr> <td valign="top">12/09/02</td> <td valign="top">SR</td>
1170	<td valign="top">2.4a</td> <td valign="top">B</td>
1171	<td valign="top">Fehler in Berechnung der Anfangsprofile
1172	von pt
1173	und q entfernt
1174	(obere Feldgrenze von 10 konnte in <tt>pt_vertical_gradient_level_ind</tt>
1175	überschritten werden). Fehler führte unter
1176	Umständen zu
1177	"segmentation fault" bei Verwendung sehr großer
1178	Gitterpunktzahlen
1179	in z-Richtung. <p>Fehler in Berechnung der v-Komponente am
1180	unteren Rand
1181	entfernt, die
1182	für den Scherungsproduktionsterm der TKE verwendet wird
1183	(Variable
1184	v_0). Fälschlicherweise wurde zur Berechnung u(k=1) statt
1185	v(k=1)
1186	verwendet.</p> </td> <td valign="top">check_parameters,
1187	modules, production_e</td> </tr> <tr> <td valign="top">19/12/02</td> <td valign="top">SR</td>
1188	<td valign="top">2.5</td> <td valign="top">N</td>
1189	<td valign="top">Restart times can be set by user with new
1190	runtime (d3par)
1191	parameters <tt>restart_time</tt> and <tt>dt_restart</tt>.
1192	Run
1193	description
1194	header is written on file CONTINUE_RUN. Output of cpu statistics
1195	changed
1196	(PE results are now collected on PE0 in order to calculate mean cpu
1197	statistics).
1198	Output of warnings in the job protocol in case of negative measured
1199	cpu-times.
1200	Remaining cpu-time is also evaluated on IBM-Regatta.</td> <td valign="top">cpu_log, cpu_statistics,
1201	check_parameters,header, leap_frog,
1202	local_tremain, local_tremain_ini, modules,  palm,  <p><b>new:</b>
1203	<br>
1204	check_for_restart </p> <p><b>deleted:</b> <br>
1205	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
1206	14 (BINOUT) must be opened using a special
1207	process
1208	id string, because on IBM, the PE rank differs between communicators
1209	MPI_COMM_WORLD
1210	and comm_2d. This leads to a mismatch between filename-PE-number and
1211	PE-number
1212	written on file. As the consequence, these files could not be read by
1213	restart-jobs.
1214	Reading of array <tt>hom</tt> moved from <tt>init_3d_model
1215	</tt>to <tt>read_var_list</tt>
1216	(binary version number incremented to 2.2). <p><b>Further
1217	optimization for IBM-Regatta-systems:</b> <br>
1218	Additional optimization of the hybrid-solver for multinode usage
1219	(overlapping
1220	of communication and computation). </p> <p>Further cache
1221	optimization by using strides and joining loops (<tt>hybrid_solver,
1222	pres</tt> and <tt>timestep</tt>). Joining of
1223	MPI_ALLREDUCE calls in
1224	timestep. </p> <p>In case of 1d-decomposition along x
1225	only a part of the
1226	integral divisor
1227	conditions is checked, on IBM hosts a 1d-decomposition along x is the
1228	default,
1229	a switch from Poisson-FFT-solver to the hybrid-solver is made in case
1230	of
1231	1d-decomposition along x, the hybrid-solver does not force a
1232	1d-decomposition
1233	any more. </p> <p>Array notation changed to do-loop
1234	constructs due to better
1235	performance. </p> <p>Cyclic boundary conditions along <tt>y</tt>
1236	used instead of
1237	sendrecv
1238	in case of a 1d-decomposition along <tt>x</tt>. SENDRECV
1239	replaced by
1240	nonblocking
1241	routines ISEND and IRECV in <tt>exchange_horiz.f90</tt>. </p>
1242	<p>Speed optimization by removing MINVAL/MAXVAL calls and by
1243	handling <br>
1244	the "abs" case in a different way than the min/max cases (routine <tt>global_min_max</tt>).</p>
1245	</td> <td valign="top">asselin_filter, check_open,
1246	exchange_horiz,
1247	global_min_max,
1248	init_3d_model, init_pegrid, parin, poisfft_hybrid, read_var_list,
1249	timestep,
1250	write_3d_binary, write_var_list</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1251	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">Correction
1252	of mixing length term (l(k)/ll(k)).
1253	The condition
1254	kh=3*km in the unstable case is now also exactly met in the wall
1255	adjustment
1256	region. Factor 0.7 in wall adjustment part replaced by variable <tt>wall_adjustment_factor</tt>,
1257	which is set to 1.8 in <tt>modules.f90</tt>. The factor
1258	0.7 was the
1259	possible
1260	reason for 2-delta-x-waves, which were observed since version 2.1d. <p>Calculation
1261	of deformation tensor re-designed (<tt>production_e</tt>). </p>
1262	<p>STOP statements replaced by call of new subroutine <tt>local_stop,
1263	</tt>where
1264	MPI_FINALIZE is called before STOP in case of a parallel environment. </p>
1265	<p>ISO2D parameter dp set to true for ibm hosts. </p> <p>tend=p
1266	added in <tt>pres</tt> after calling sor method.</p>
1267	</td> <td valign="top">advec_s_bc, buoyancy,
1268	check_open,
1269	check_parameters, close_file,
1270	coriolis, diffusion_e, diffusivities, fft_for_1d_decomp,
1271	flow_statistics,
1272	init_3d_model, init_dvrp, init_grid, init_particles, init_pegrid,
1273	parin,
1274	plot_2d, poisfft, pres, read_var_list, user_interface,  <p><b>new:</b>
1275	<br>
1276	local_stop, production_e</p> </td> </tr> <tr>
1277	<td valign="top">03/03/03</td> <td valign="top">SR</td>
1278	<td valign="top">2.5a</td> <td valign="top">N</td>
1279	<td valign="top">Particle velocities are also stored in
1280	array
1281	particles in
1282	case of zero density ratio. Steering of variables by dvrp browser
1283	included.</td> <td valign="top">advec_particles,
1284	init_dvrp, modules,</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1285	</td> <td valign="top"><br> </td> <td valign="top">C</td> <td valign="top">AVS
1286	data format changed from float to xdr_float
1287	(needed
1288	on linux machines <br>
1289	due to the little/big endian problem). Updates for new version of dvrp
1290	software (e.g. using module dvrp is now mandatory).</td> <td valign="top">close_file, init_dvrp, leap_frog, plot_dvrp</td>
1291	</tr> <tr> <td valign="top"><br> </td>
1292	<td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top">B</td>
1293	<td valign="top">Error in particle inertia part removed
1294	(exp_arg
1295	must not
1296	contain the timestep). <br>
1297	Error in calculation of the vertical flux of resolved scale energy
1298	(profile 57) removed. Displacement for integers in mpi_particle_type
1299	reduced
1300	from 16 to 8 on ibm.</td> <td valign="top">advec_particles,
1301	flow_statistics, init_particles</td> </tr> <tr> <td valign="top">12/03/03</td> <td valign="top">SR</td>
1302	<td valign="top">2.6</td> <td valign="top">N</td>
1303	<td valign="top"><b>Version optimized for NEC-SX6
1304	parallel-vector
1305	machines. </b> <p>There are two main changes. A
1306	new vectorizable routine <tt>prognostic_equations_vec</tt>
1307	is added, where cache optimizations are undone. The tendency
1308	subroutines
1309	called by <tt>prognostic_equations_vec</tt> contain the
1310	full 3d-loops
1311	(compared
1312	with the cache-optimized versions where only loops over k are carried
1313	out).
1314	Additionally, a new pressure solver <tt>poisfft_hybrid_vec</tt>
1315	is
1316	added,
1317	which requires a 1d-domain-decomposition (like poisfft_hybrid). In this
1318	solver, a very fast FFT from Clive Temperton (ECMWF) is
1319	optionally
1320	available by choosing <tt>fft_method </tt>= <i>'temperton-algorithm'</i>.
1321	</p> <p>Additional changes in <tt>flow_statistics</tt>
1322	to allow
1323	better vectorization. </p> <p>Small changes in routines <tt>diffusivities</tt>
1324	and <tt>pres</tt>
1325	which
1326	caused run time errors on IBM and NEC due to compiler problems. </p>
1327	<p>Reading of environment variable <tt>tasks_per_node</tt>
1328	moved
1329	from routine <tt>poisfft_hybrid</tt>
1330	to routine <tt>parin</tt>. </p> <p><b>Changes
1331	in makefile:</b> modules and user_interface now
1332	depend on
1333	the f90 files, dependency of singleton added, LDFLAGS moved to the end
1334	of PROG rule, temperton_fft added.</p> </td> <td valign="top">advec_s_pw, advec_s_up, advec_u_pw, advec_u_up,
1335	advec_v_pw,
1336	advec_v_up, advec_w_pw, advec_w_up, buoyancy, calc_precipitation,
1337	calc_radiation,
1338	check_parameters, coriolis, cpu_log, diffusion_e, diffusion_s,
1339	diffusion_u,
1340	diffusion_v, diffusion_w, diffusivities, fft_for_1d_decomp, header,
1341	impact_of_latent_heat,
1342	init_pegrid, leap_frog, local_tremain, modules, parin, poisfft,
1343	poisfft_hybrid,
1344	pres, production_e, prognostic_equations, user_interface <p><b>new:</b>
1345	<br>
1346	temperton_fft</p> </td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1347	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">tend=p
1348	added in routine <tt>pres</tt> after
1349	calling sor
1350	method.</td> <td valign="top">pres</td> </tr>
1351	<tr> <td valign="top">14/03/03</td> <td valign="top">SR</td> <td valign="top">2.6a</td>
1352	<td valign="top">N</td> <td valign="top">Additional
1353	vector optimization for NEC-SX6. <p>Optional system-specific
1354	random number generator available
1355	(for equal
1356	distributed numbers). </p> <p>Define strings in all
1357	relevant subroutines changed from  </p> <p><tt>
1358	#if defined( define_string )</tt> </p> <p>to </p>
1359	<p><tt>     #if
1360	defined( __define_string )</tt> </p> <p><b>Caution:
1361	</b>The relevant subroutines are NOT listed in
1362	the right
1363	column!</p> </td> <td valign="top">asselin_filter,
1364	check_parameters, diffusion_e,
1365	diffusivities,
1366	disturb_field, global_min_max, header, local_tremain, modules, parin,
1367	poisfft_hybrid,
1368	pres, read_var_list, write_var_list</td> </tr> <tr>
1369	<td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1370	</td> <td valign="top">B</td> <td valign="top">Error in particle boundary condition removed
1371	(velocity must
1372	be inverted in case of reflection)</td> <td valign="top">advec_particles</td>
1373	</tr> <tr> <td valign="top">16/04/03</td>
1374	<td valign="top">SR</td> <td valign="top">2.6b</td>
1375	<td valign="top">N</td> <td valign="top">Time
1376	series output of Monin Obukhov length. <p>Temperton fft can now
1377	be used for all hosts and every domain
1378	decomposition.
1379	Abort in case of Temperton fft, if number of gridpoints along x and/or
1380	y contain illegal factors.  </p> <p>Index values
1381	for the extrema found in global_min_max are
1382	limited to
1383	the range 0..nx, 0..ny (on IBM machines -1 and nx+1/ny+1 occured which
1384	produced different RUN_CONTROL output compared to other machines). </p>
1385	<p>Output format of iteration count in routine run_control
1386	enlarged.</p> </td> <td valign="top">check_parameters,
1387	fft_for_1d_decomp,
1388	global_min_max, init_pegrid,
1389	modules, plot_ts, poisfft, run_control, temperton_fft</td> </tr>
1390	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1391	</td> <td valign="top">B</td> <td valign="top">Additional checks of variables <tt>hybrid_solver</tt>
1392	and <tt>host</tt>
1393	(<tt>hybrid_solver</tt> must not be used for a
1394	2d-domain-decomposition, <tt>host</tt>
1395	should be set by setting environment variable <tt>localhost</tt>).
1396	<p>Header output for mixing length limitations revised.</p>
1397	</td> <td valign="top">check_parameters, header</td>
1398	</tr> <tr> <td valign="top">09/05/03</td>
1399	<td valign="top">SR</td> <td valign="top">2.7</td>
1400	<td valign="top">N</td> <td valign="top"><b>Version
1401	running on Linux Clusters using MPICH
1402	and Intel
1403	FORTRAN compiler (ifc)</b> <p>So far, only absolutely
1404	neccessary changes have been done
1405	(possible
1406	optimizations will follow in a later version): </p> <p>New
1407	time measurements for Linux (ifc) environment added. </p> <p>Some
1408	parameters in MPI calls had to be modified (arrays had to
1409	be replaced
1410	by the first element of the regarding array) in order to fulfill f90
1411	type
1412	and rank requirements, since on the MUK-cluster a FORTRAN90-version of
1413	MPI is used. This also required to replace "mpif.h" by using a special
1414	module (named <tt>mpi</tt>).  I did not find out
1415	how character
1416	strings
1417	can be send with MPI. Therefore, these strings are transformed to
1418	integers,
1419	before they are send, and transformed back to characters on the
1420	receiving
1421	PE. </p> <p>On the MUK-cluster, only PE0 is able to read
1422	the values of
1423	environment
1424	variables. Therefore, these values are communicated via broadcast to
1425	the
1426	other PEs. </p> <p>1d-decomposition is set as the default
1427	on Linux Clusters.
1428	Character
1429	strings have to be transformed to integer </p> <p>Smaller
1430	changes: </p> <p>Batch_scp paths for IBM, NEC and Linux
1431	added</p> </td> <td valign="top">check_open,
1432	cpu_log, flow_statistics,
1433	init_pegrid, local_getenv,
1434	modules, palm, poisfft_hybrid</td> </tr> <tr> <td valign="top"><br> </td> <td valign="top"><br>
1435	</td> <td valign="top"><br> </td> <td valign="top">B</td> <td valign="top">Measurements
1436	on IBM are now using function <tt>irtc</tt>,
1437	which allows correct measurements for jobs running over the 24:00
1438	timeline.</td> <td valign="top">cpu_log,
1439	local_tremain, local_tremain_ini</td> </tr> <tr> <td valign="top">01/08/03</td> <td valign="top">SR</td>
1440	<td valign="top">2.7a</td> <td valign="top">B</td>
1441	<td valign="top">Check that the number processors is also
1442	an
1443	integral divisor
1444	of the number  of gridpoints along y in case of a
1445	1d-decomposition
1446	along x. <p>Error concerning the multinode-version of
1447	poisfft_hybrid
1448	removed. It
1449	was caused by the Linux changes of version 2.7 and led to program abort
1450	due to MPI errors in <tt>MPI_ALLTOALL</tt>. </p> <p>No
1451	abort on t3e-systems if system specific routines are used. </p> <p>Array<tt>
1452	sums </tt>is initialized in<tt> init_3d_model </tt>before
1453	the first call of<tt> pres</tt>. Call of<tt>
1454	init_cloud_physics </tt>moved
1455	before<tt> init_particles</tt>.</p> </td> <td valign="top">fft_1dd_init, init_3d_model, init_pegrid,
1456	poisfft_hybrid</td> </tr> <tr> <td valign="top"><br>
1457	</td> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top">N</td>
1458	<td valign="top">Interactive steering of dvrp-graphic
1459	features by
1460	dvrp-browser
1461	plugin extended (position of slicers, threshold values of isosurfaces)
1462	. New dvrp_graphics package parameter<tt> slicer_range_limits_dvrp</tt>.</td>
1463	<td valign="top">init_dvrp, modules, package_parin,
1464	plot_dvrp</td> </tr> <tr> <td valign="top">29/10/03</td>
1465	<td valign="top">SR</td> <td valign="top">2.7b</td>
1466	<td valign="top">N</td> <td valign="top">In
1467	the multigrid method, on a defined level,
1468	data are gathered
1469	on PE0 and further calculations are carried out only on this PE. New<tt>
1470	d3par </tt>parameter <tt>mg_switch_to_pe0_level</tt>.
1471	<p>Particle groups implemented. New data type<tt>
1472	particle_groups_type </tt>and data type<tt> particle_type </tt>modified.
1473	Version
1474	numbers are
1475	output on the particle files. New<tt> particles_par </tt>parameter<tt>
1476	diameter</tt>. Parameter name<tt> uniform_psize</tt>
1477	changed to<tt>
1478	dvrp_psize</tt>.
1479	Parameters<tt> density_ratio </tt>is now an array.</p>
1480	</td> <td valign="top">advec_particles, check_open,
1481	exchange_horiz,
1482	header, init_particles,
1483	init_pegrid, modules, package_parin, parin, poismg</td> </tr>
1484	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1485	</td> <td valign="top">C</td> <td valign="top">Random number generator from numerical recipes
1486	is now rewritten
1487	as a module. In restart runs the seed of this generator is set to the
1488	last
1489	values of the previous run in order to keep the sequence of the random
1490	numbers. New binary version 2.2. <p>Buffer is flushed for file
1491	RUN_CONTROL immediately after every
1492	output
1493	on IBM and Linux cluster.</p> </td> <td valign="top">advec_particles,
1494	disturb_field, init_3d_model,
1495	init_particles,
1496	random_function, random_gauss, run_control, write_3d_binary</td> </tr>
1497	<tr> <td valign="top"><br> </td> <td valign="top"><br> </td> <td valign="top"><br>
1498	</td> <td valign="top">E</td> <td valign="top">In routine buoyance, horizontal mean
1499	temperature
1500	is now
1501	taken from array hom instead of array sums (otherwise inconsistence in
1502	case of using more than one statistical region). <p>Information
1503	about the time of the last timestep change added
1504	to the
1505	restart file. </p> <p>System call of<tt> batch_scp </tt>on
1506	IBM corrected.</p> </td> <td valign="top">buoyancy,
1507	check_open, read_var_list,
1508	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
1509	3rd
1510	order)
1511	for time integration implemented. The third order scheme is the new
1512	default.
1513	It allows the timestep to be 0.9*CFL, which is much larger than for the
1514	former default leapfrog scheme.  The intermediate steps, which
1515	are
1516	part of these schemes, are realized by an additional loop within routine<span style="font-family: monospace;">
1517	time_integration </span>(currently<span style="font-family: monospace;">
1518	leap_frog</span>, but this routine will be renamed soon).
1519	Steering
1520	variables<span style="font-family: monospace;">
1521	at </span>and<span style="font-family: monospace;">
1522	bt </span>have
1523	been replaced by array<span style="font-family: monospace;">
1524	sct</span>.
1525	, which is particularly used in the prognostic equations. Values of
1526	this
1527	steering array are calculated within the new routine<span style="font-family: monospace;">
1528	timestep_scheme_steering</span>. <p>When using Runge-Kutta
1529	schemes,  the timestep increment
1530	is freely
1531	allowed to adjust after each timestep (the older schemes are using some
1532	restrictions, see routine<span style="font-family: monospace;">
1533	timestep</span>).
1534	Also, routine<span style="font-family: monospace;">
1535	run_control </span>is
1536	not automatically called in case of timestep changes, when Runge-Kutta
1537	schemes are switched on. </p> <p>The old leapfrog scheme
1538	is still implemented and should
1539	produce the
1540	same results as in the previous version(s)! </p> <p>Depending
1541	on the user experience, further adjustments to the
1542	Runge-Kutta
1543	schemes may be necessary within the next minor versions.  </p>
1544	<p><span style="font-weight: bold;">Attention:</span>
1545	<br>
1546	The content of the testresult-file (run control output) has
1547	significantly
1548	changed due to the new default timestep scheme!</p> </td> <td style="vertical-align: top;">check_parameters, header,
1549	init_3d_model,
1550	init_rankine, leap_frog, modules, prognostic_equations, read_var_list,
1551	swap_timelevel, timestep, write_var_list <p><span style="font-weight: bold;">new:</span> <br>
1552	timestep_scheme_steering</p> </td> </tr> <tr>
1553	<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
1554	subroutine<span style="font-family: monospace;">
1555	allocate_prt_memory </span>on demand only. <p>Type<span style="font-family: monospace;"> log </span>(used
1556	for
1557	cpu time measurements) changed to<span style="font-family: monospace;">
1558	logpoint </span>due to name conflict with FORTRAN
1559	intrinsic<span style="font-family: monospace;">
1560	log.</span></p> </td> <td style="vertical-align: top;">advec_particles,
1561	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
1562	barrier
1563	is set only for the first call of<span style="font-family: monospace;">
1564	check_open </span>(from routine<span style="font-family: monospace;">
1565	init_particles</span>), in order to avoid the possibility of
1566	hanging
1567	jobs,
1568	which may occur if unit 80 is opened within routine<span style="font-family: monospace;">
1569	allocate_prt_memory</span>.</td> <td style="vertical-align: top;">check_open</td> </tr>
1570	<tr> <td style="vertical-align: top;">30/01/04</td>
1571	<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
1572	for
1573	the simulation
1574	of flow around buildings (to be realized in one of the next major
1575	versions),
1576	the lower<span style="font-family: monospace;"> k </span>index<span style="font-family: monospace;">
1577	nzb </span>has been replaced by a two-dimensional array<span style="font-family: monospace;">
1578	nzb_2d </span>in many of the three-dimensional loops. So
1579	far, all
1580	elements of this array are set to<span style="font-family: monospace;">
1581	nzb</span>. <p>This change should not effect simulation
1582	results and cpu time
1583	in any
1584	way.</p> </td> <td style="vertical-align: top;">advec_s_pw,
1585	advec_s_up,
1586	advec_u_pw, advec_u_up,
1587	advec_v_pw, advec_v_up, advec_w_pw, advec_w_up, asselin_filter,
1588	buoyancy,
1589	calc_liquid_water_content, calc_precipitation, calc_radiation,
1590	coriolis,
1591	diffusion_e, diffusion_s, diffusion_u, diffusion_v, diffusion_w,
1592	diffusivities,
1593	impact_of_latent_heat, init_3d_model, modules, production_e,
1594	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
1595	removed in
1596	the run control output in case of Runge-Kutta schemes. Also, the
1597	timestep
1598	increment limitation is removed for the Runge-Kutta schemes. <p><span style="font-weight: bold;">Attention:</span> <br>
1599	The content of the testresult-file (run control output) has changed
1600	due to this modification.</p> </td> <td style="vertical-align: top;">run_control, timestep</td>
1601	</tr> <tr> <td style="vertical-align: top;"><br>
1602	</td> <td style="vertical-align: top;"><br> </td>
1603	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E</td> <td style="vertical-align: top;">Velocity gradients at the
1604	surface calculated
1605	in routine production_e are now limited. In case of inhomogeneous
1606	surface
1607	heating small diffusivities (<span style="font-family: monospace;">km</span>)
1608	sometimes caused very small timesteps due to this problem.</td> <td style="vertical-align: top;">production_e</td> </tr>
1609	<tr> <td style="vertical-align: top;">30/04/04<br>
1610	</td> <td style="vertical-align: top;">SR<br>
1611	</td> <td style="vertical-align: top;">2.8b<br>
1612	</td> <td style="vertical-align: top;">N<br> </td>
1613	<td style="vertical-align: top;">The number of processors
1614	along
1615	the respective directions of the virtual processor grid must not be
1616	integral divisors of the number of gridpoints along x, y or z any more.
1617	In case that they are not integral divisors, the subdomains on the
1618	processors at the upper borders of the virtual grid will contain less
1619	gridpoints than the other subdomains (which are all of equal size).
1620	Although this causes a load imbalance, only runs with very small
1621	numbers of processors will feel a significant decrease of performance.
1622	In order to be able to carry out the transpositions, array<span style="font-family: monospace;"> d </span>(and also
1623	working array<span style="font-family: monospace;"> tend</span>)
1624	have the same size on
1625	all processors. This new feature is switched on by setting the
1626	inipar-parameter<span style="font-family: monospace;">
1627	grid_matching </span>= <span style="font-style: italic;">'match'</span>,
1628	which is the
1629	default now.<br> <br>
1630	Routine<span style="font-family: monospace;"> poisfft </span>is
1631	now
1632	the
1633	default for solving the Poisson-equation for the case of 2d- as well as
1634	1d-domain-decompositions and has been changed from a subroutine to a
1635	module. This routine now includes most of the optimization from the
1636	(Ketelsen) routine<span style="font-family: monospace;">
1637	poisfft_hybrid </span>and additionally allows 1d-decompositions
1638	along y.<br> <span style="font-weight: bold;">ATTENTION:</span>
1639	Routine<span style="font-family: monospace;">
1640	poisfft_hybrid </span>might still be
1641	faster when running PALM on more than one node of the IBM-Regatta,
1642	although the difference is not very big. The <span style="font-family: monospace;">poisfft</span>-code
1643	for a
1644	decomposition along y has still a poor performance and needs further
1645	optimization.<br> <br>
1646	The spectra-package is now able to use all the available FFT-methods
1647	(selected by inipar-parameter<span style="font-family: monospace;">
1648	fft_method </span>).
1649	Performance of the transpositions needed for calculating the spectra
1650	has been improved by using new direct transpositions from z to y and
1651	from y to x instead of two subsequent transpositions.<br> <br>
1652	Runge-Kutta scheme implemented in the 1d-version (<span style="font-family: monospace;">init_1d_model</span>).
1653	Diffusion
1654	quantity arrays are allocated for previous timelevels only in case of
1655	leapfrog scheme.<br> <br>
1656	This version is adapted for use on COMPAQ-DECALPHA systems (main
1657	changes: calling of SHAPE function within subroutine arguments (e.g.<span style="font-family: monospace;"> singleton</span>)
1658	causes compiler errors, particle data type modified for better
1659	alignment, DATA statements from modules removed because they caused
1660	internal compiler errors).<br> </td> <td style="vertical-align: top;">advec_s_ups, advec_u_ups,
1661	advec_v_ups, advec_w_ups, calc_spectra, check_parameters, fft_xy,
1662	header, init_1d_model, init_3d_model, init_particles, init_pegrid,
1663	modules, parin, plot_2d, poisfft, prandtl_fluxes, pres, read_var_list,
1664	singleton, spline_x, spline_y, spline_z, time_integration, transpose,
1665	write_3d_binary, write_var_list<br> </td> </tr> <tr>
1666	<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>.
1667	Subroutine<span style="font-family: monospace;"> leap_frog
1668	</span>renamed<span style="font-family: monospace;">
1669	time_integration</span>.<br> <br>
1670	For all transpositions, MPI_ALLTOALL is used instead of MPI_ALLTOALLV.
1671	The names of many transposition indices have been changed.<br> <br>
1672	Inipar-parameter<span style="font-family: monospace;">
1673	impulse_advec </span>renamed<span style="font-family: monospace;"> momentum_advec</span>.<br>
1674	<br>
1675	Reading of restart data is moved from<span style="font-family: monospace;"> init_3d_model </span>to
1676	new routine <span style="font-family: monospace;">read_3d_binary</span>.<br>
1677	<br>
1678	All former transpose routines collected into one file.<br> </td>
1679	<td style="vertical-align: top;">check_parameters,
1680	flow_statistics, header, init_1d_model, init_3d_model, init_advec,
1681	init_pegrid, palm, parin, poisfft, poisfft_hybrid, production_e,
1682	prognostic_equations, read_var_list, sline_x, spline_y, write_var_list<span style="font-weight: bold;"><br> <br>
1683	new:</span><br>
1684	fft_xy, read_3d_binary, time_integration, transpose<br> <br>
1685	<span style="font-weight: bold;">deleted:</span><br>
1686	fft_for_1d_decomp, leap_frog, transpose_xy, transpose_xz, transpose_yx,
1687	transpose_yz, transpose_zx, transpose_zy<br> </td> </tr>
1688	<tr> <td style="vertical-align: top;"><br> </td>
1689	<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
1690	particle-package removed, which sometimes caused aborts of restart runs
1691	on IBM.<br> <br>
1692	Small error in calculating the time series profiles removed (array
1693	bounds of some arrays needed for profil-output had to be increased).<br>
1694	<br>
1695	Function fft (singleton method) replaced by subroutine fftn due to
1696	problems with 64-bit mode on IBM<br> </td> <td style="vertical-align: top;">advec_particles,
1697	check_parameters, <br> </td> </tr> <tr> <td style="vertical-align: top;">26/03/05<br> </td>
1698	<td style="vertical-align: top;">SR<br> </td>
1699	<td style="vertical-align: top;">2.9<br> </td>
1700	<td style="vertical-align: top;">N<br> </td> <td style="vertical-align: top;">Non-cyclic lateral boundary
1701	conditions implemented.<br>
1702	Dirichlet/Neumann conditions at the inflow/outflow can be used either
1703	along x or along y. Cyclic conditions have to be used along the
1704	remaining direction. In case of non-cyclic conditions along x (y), the
1705	upper bound nxl (nyn) of array u (v) is enlarged by one gridpoint on
1706	the rightmost (northest) processor. These array index informations are
1707	passed to routine<span style="font-family: monospace;">
1708	exchange_horiz </span>and<span style="font-family: monospace;">
1709	disturb_field </span>by two
1710	additional arguments. Boundary conditions are set with new
1711	inipar-parameters<span style="font-family: monospace;">
1712	bc_lr </span>and<span style="font-family: monospace;">
1713	bc_ns</span>. A damping layer is
1714	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>)
1715	and an
1716	additional disturbance is imposed near the inflow (see new parameters<span style="font-family: monospace;">
1717	inflow_disturbance_begin </span>and<span style="font-family: monospace;"> inflow_disturbance_end</span>).
1718	Non-cyclic conditions require the use of the multigrid-method for
1719	solving the Poisson equation. Argument<span style="font-family: monospace;"> range </span>added
1720	to routine<span style="font-family: monospace;">
1721	boundary_conds </span>(where the
1722	non-cyclic conditions are set). <br> <br>
1723	Minor changes:<br>
1724	Output of parameter<span style="font-family: monospace;">
1725	datform </span>on
1726	&GLOBAL-Namelist (iso2d). This is set to <span style="font-style: italic;">'big_endian'</span> on
1727	IBM- and
1728	NEC-machines.<br> <br>
1729	Number of particle groups are additionally calculated in<span style="font-family: monospace;"> header </span>(formerly
1730	unknown).<br> </td> <td style="vertical-align: top;">advec_u_pw,
1731	advec_u_up, advec_v_pw, advec_v_up, boundary_conds,
1732	calc_liquid_water_content, check_parameters, close_file, coriolis,
1733	diffusion_u, diffusion_v, diffusion_w, diffusivities, disturb_field,
1734	exchange_horiz, header, init_3d_model, init_pegrid, init_pt_anomaly,
1735	init_rankine, modules, parin, poismg, pres, prognostic_equations,
1736	read_var_list, sor, time_integration, timestep, write_var_list<br>
1737	</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
1738	by default only
1739	at the last Runge-Kutta-substep, which spares a big amount of CPU-time
1740	(see also new parameter<span style="font-family: monospace;">
1741	call_psolver_at_all_substeps</span>). No pressure term in the
1742	momentum
1743	equations in case of Runge-Kutta-schemes.<br> <span style="font-weight: bold;">Attention:</span> <br>
1744	The content of the testresult-file (run control output) has changed
1745	due to this modification.<br> <br>
1746	Program speedup by removing the exchange of ghost points in routines <span style="font-family: monospace;">calc_liquid_water_content</span>,
1747	<span style="font-family: monospace;">diffusivities</span>,
1748	.<br> <br>
1749	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
1750	(one call of<span style="font-family: monospace;">
1751	exchange_horiz </span>spared).<br> </td> <td style="vertical-align: top;">calc_liquid_water_content,
1752	diffusivities, modules, poismg, pres, time_integration,
1753	timestep_scheme_steering<br> </td> </tr> <tr>
1754	<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
1755	particle
1756	velocity (with inertia) corrected, exp_arg had a wrong sign.<br> <br>
1757	(e)*1.5 replaced by eSQRT(e) in init_1d_model because of wrong
1758	results on NEC machines (as a side effect, the new calculation is much
1759	faster).<br> <br>
1760	Two errors concerning switch to PE0 (multigrid method) removed from<span style="font-family: monospace;"> init_pegrid</span>.<br>
1761	<br>
1762	Two errors in<span style="font-family: monospace;">
1763	plot_2d </span>removed:
1764	local_2d is allocated with upper bound<span style="font-family: monospace;"> nzt</span> (former<span style="font-family: monospace;"> nzt+1 </span>was
1765	wrong), additional barrier in case that PE0 gathers data from the other
1766	PEs, this barrier had to be set at the end of the gathering because
1767	otherwise PE0 sometimes received wrong data on tag 0.<br> <br>
1768	Use of module indices removed from routine<span style="font-family: monospace;"> split_1dd </span>in<span style="font-family: monospace;"> poisfft </span>since
1769	it caused
1770	errors in case of<span style="font-family: monospace;"> nx
1771	/= ny </span>and
1772	a 1D-decomposition along y.<br> <br>
1773	Wrong re-definition of dx2 and dy2 in<span style="font-family: monospace;"> sor </span>removed.<br>
1774	</td> <td style="vertical-align: top;">advec_particles,
1775	init_1d_model,
1776	init_pegrid, plot_2d, poisfft, sor<br> </td> </tr> <tr>
1777	<td style="vertical-align: top;">23/04/05<br> </td>
1778	<td style="vertical-align: top;">SR<br> </td>
1779	<td style="vertical-align: top;">2.9a<br> </td>
1780	<td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">Additional check for
1781	incompatibilities between non-cyclic lateral boundary conditions and
1782	other schemes.<br> <br>
1783	fcl_factor renamed cfl_factor.<br> <br>
1784	New local array sums_ll declared in flow_statistics instead of
1785	temporarily using sums_l.<br> <br>
1786	crmax (maximum number of crosses allowed in a plot of vertical
1787	profiles) increased from 20 to 100.<br> </td> <td style="vertical-align: top;">calc_spectra, check_parameters,
1788	flow_statistics, header, modules, parin, timestep<br> </td>
1789	</tr> <tr> <td style="vertical-align: top;"><br>
1790	</td> <td style="vertical-align: top;"><br> </td>
1791	<td style="vertical-align: top;"><br> </td> <td style="vertical-align: top;">E<br> </td> <td style="vertical-align: top;">Revised calculation of output
1792	time counters regarding a possible decrease of the output time interval
1793	in case of restart runs.<br> <br>
1794	Error removed in Dirichlet bottom boundary conditions for pt and q in
1795	case of Runge-Kutta schemes.<br> <br> <span style="font-weight: bold;">batch_scp</span> calls
1796	(needed
1797	for determining correct filenames for AVS-fld-files) is given the
1798	remote username as an additional argument.<br> <br>
1799	Default setting of outflow_damping_width corrected.<br> <br>
1800	Initial horizontal velocities at the lowest grid levels in the 1d-model
1801	are set to a very small value in order to avoid wrong results and the
1802	resulting too small timesteps.<br> <br>
1803	Implicit counters i renamed i9 in modules due to declaration conflicts
1804	with i in other subroutines (reported by Portland compiler).<br> </td>
1805	<td style="vertical-align: top;">advec_particles,
1806	boundary_conds,
1807	check_open, check_parameters, init_1d_model, modules, time_integration<br>
1808	</td> </tr> <tr> <td style="vertical-align: top;">18/05/05<br> </td>
1809	<td style="vertical-align: top;">SR<br> </td>
1810	<td style="vertical-align: top;">2.10<br> </td>
1811	<td style="vertical-align: top;">N<br> </td> <td style="vertical-align: top;">NetCDF support implemented.<br>
1812	Profiles, time series, spectra, cross-sections, 3d-volume-data and
1813	particle data can now be output in NetCDF format (file handles
1814	101-108). This output can be switched on with the new d3par-parameter <span style="font-family: monospace;">data_output_format</span>.
1815	So far, this support is available on IBM systems at HLRN and on the NEC
1816	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
1817	possible.<br> <br>
1818	Output of cross sections for qv, vpt and lwp (liquid water path).<br>
1819	</td> <td style="vertical-align: top;">advec_particles,
1820	check_open,
1821	check_parameters, close_file, header, modules, parin, plot_1d, plot_2d,
1822	plot_3d, plot_spectra, plot_ts, read_var_list, write_var_list<br>
1823	<br> <span style="font-weight: bold;">new:</span><br>
1824	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
1825	is assigned the
1826	number of spectra (formerly, the number of spectra was given by n-1)<br>
1827	<br>
1828	Abort if <span style="font-family: monospace;">poisfft_hybrid</span>
1829	is called in a non-parallel environment.<br> <br>
1830	Default values of spectra package parameters <span style="font-family: monospace;">pl_spectra</span> and <span style="font-family: monospace;">spectra_direction</span>
1831	changed.<br> </td> <td style="vertical-align: top;">calc_spectra,
1832	check_parameters,
1833	modules, pres, read_3d_binary, write_3d_binary<br> </td> </tr>
1834	<tr> <td style="vertical-align: top;"><br> </td>
1835	<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
1836	(non-parallel case) added.<br> <br>
1837	Error in output of particle inertia information removed.<br> </td>
1838	<td style="vertical-align: top;">poisfft, header<br>
1839	</td> </tr> <tr> <td style="vertical-align: top;">05/07/05<br> </td>
1840	<td style="vertical-align: top;">SR<br> </td>
1841	<td style="vertical-align: top;">2.11<br> </td>
1842	<td style="vertical-align: top;">N/C<br> </td>
1843	<td style="vertical-align: top;">New cloud physics code
1844	implemented, which explicitly simulates single cloud droplets,
1845	including droplet growth by condensation and collision. Using this code
1846	requires to set the new inipar-parameter <span style="font-family: monospace;">cloud_droplets</span>
1847	= .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>).
1848	Coupling between droplets and the thermodynamic quantities (potential
1849	temperature and specific humidity) is regarded in the new subroutine <span style="font-family: monospace;">interaction_droplets_ptq</span>.
1850	The real number of droplets in a grid cell can steered by the new
1851	inipar-parameter <span style="font-family: monospace;">initial_weighting_factor</span>.<br>
1852	<br> <span style="font-weight: bold;">This code
1853	will be further extended and probably changed in the near future, so
1854	the current status is that of a test version!</span><br> <br>
1855	In connection with this new code implementation, several changes has
1856	been made to the existing code:<br> <br>
1857	The particle (droplet) size is now given as radius (previously
1858	diameter). E.g., the name of the respective package parameter <span style="font-family: monospace;">diameter</span> has
1859	changed to <span style="font-family: monospace;">radius</span>.<br>
1860	<br>
1861	The current weighting_factor and radius are stored as additional
1862	particle attributes in the type structure <span style="font-family: monospace;">particle_type</span>.
1863	The MPI data type <span style="font-family: monospace;">mpi_particle_type</span>,
1864	needed for exchanging particles between subdomains, has been changed
1865	correspondingly.<br> <br> <span style="font-family: monospace;">gas_constant</span> is
1866	renamed <span style="font-family: monospace;">r_d</span>,
1867	<span style="font-family: monospace;">latent_heat</span>
1868	is renamed <span style="font-family: monospace;">r_v</span>,
1869	the allowed string length of <span style="font-family: monospace;">pl2d</span>
1870	and <span style="font-family: monospace;">pl3d</span>
1871	is increased from 6 to 10.<br> <br>
1872	New 3d arrays <span style="font-family: monospace;">ql_1</span>,
1873	<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
1874	pointer, new pointer <span style="font-family: monospace;">ql_c</span>.<br>
1875	<br>
1876	Data format for unit 85 (particle data output) is changed.</td> <td style="vertical-align: top;">advec_particles.f90
1877	check_open.f90, header.f90, init_3d_model.f90, init_cloud_physics.f90,
1878	init_particles.f90, modules.f90, package_parin.f90, parin.f90,
1879	plot_2d.f90, plot_3d.f90, read_var_list.f90, time_integration.f90,
1880	write_var_list.f90<br> <br> <span style="font-weight: bold;">new:</span><br>
1881	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>
1882	is <span style="font-style: italic;">.TRUE.</span>,
1883	because small scale waves occured with <span style="font-style: italic;">.FALSE.</span></td> <td style="vertical-align: top;">modules.f90</td> </tr>
1884	<tr> <td style="vertical-align: top;"><br> </td>
1885	<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
1886	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>
1887	No opening of units 101 - 108 in case of missing NetCDF support.</td>
1888	<td style="vertical-align: top;">check_open.f90, netcdf.f90<br>
1889	</td> </tr> <tr> <td style="vertical-align: top;">30/06/05<br> </td>
1890	<td style="vertical-align: top;">GS<br> </td>
1891	<td style="vertical-align: top;">2.11a<br> </td>
1892	<td style="vertical-align: top;">C<br> </td> <td style="vertical-align: top;">Scalars ug and vg have been
1893	changed into
1894	arrays in order to allow the specification of a geostrophic wind that
1895	depends on height (baroclinicity). The initial profiles of the the
1896	u- and v-component of the geostrophic wind are initialized by
1897	specifying the new initialization parameters <span style="font-family: monospace;">ug_surface</span>, <span style="font-family: monospace;">ug_vertical_gradient</span>,
1898	<span style="font-family: monospace;">ug_vertical_gradient_level</span>
1899	and <span style="font-family: monospace;">vg_surface</span>,
1900	<span style="font-family: monospace;">vg_vertical_gradient</span>,
1901	<span style="font-family: monospace;">vg_vertical_gradient_level</span>,
1902	respectively. <br> <br>
1903	The former initialization parameters <span style="font-family: monospace;">ug</span> and <span style="font-family: monospace;">vg</span> have been
1904	removed. <br> </td> <td style="vertical-align: top;">boundary_conds,
1905	check_parameters, coriolis, header, init_1d_model, modules, parin,
1906	prognostic_equations, read_var_list, spline_z, write_var_list<br>
1907	</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
1908	and
1909	v_0 in production_e.f90 removed.<br> <br> <span style="font-weight: bold;">Attention:</span> <br>
1910	The content of the testresult-file (run control output) has changed
1911	due to this modification.<br> </td> <td style="vertical-align: top;">production_e<br> </td>
1912	</tr> <tr> <td style="text-align: left; vertical-align: top;">20/10/05</td>
1913	<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
1914	growth completed.<br> <br> <span style="font-weight: bold;">The droplet code is still under
1915	development and requires further speed optimization!<br> <br>
1916	</span>Number of particles really used is additionally output on
1917	the netcdf particle data file.<span style="font-weight: bold;"></span></td>
1918	<td style="vertical-align: top;">advec_particles, modules,
1919	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
1920	last PE in a row is not allowed to have more grid points than the other
1921	PES (only less). Jobs crashed in these cases that the last PE has more
1922	grid points. Therefore, the number of gridpoints along x (and y) must
1923	now meet a special condition which is checked in case that <span style="font-family: monospace;">grid_matching</span> =
1924	<span style="font-style: italic;">'match'</span> is
1925	used.<br> <br>
1926	Error removed in calculating y axis data for yz cross sections. Error
1927	in output of netcdf yz-cross-sections removed.<br> <br>
1928	2*r replaced by r in the exponential term of the particle momentum
1929	equation.<br>
1930	Error in output of yz-slice information removed.</td> <td style="vertical-align: top;">advec_particles, header,
1931	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
1932	in case of using cloud droplets.</td> <td style="vertical-align: top;">check_parameters,
1933	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
1934	profile is calculated within<span style="font-family: monospace;">
1935	buoyancy </span>only
1936	in case of the first respective intermediate timestep. This is done in
1937	order to spare communication time and to produce identical model
1938	results with jobs which are calling<span style="font-family: monospace;"> flow_statistics </span>at
1939	different time intervals.<br> <br>
1940	Error in netcdf variable declaration for<span style="font-family: monospace;"> statistic_regions </span>/=
1941	<span style="font-style: italic;">0</span> removed.</td>
1942	<td style="vertical-align: top;">buoyancy, netcdf</td>
1943	</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
1944	topography (buildings, mountains, etc.)</span><br style="font-weight: bold;"><br>Besides
1945	the implementation of topography, this version contains several other
1946	improvements. The most important ones are listed here:<br><ul><li>The
1947	cloud droplet code has been optimized (it now runs about 100 times
1948	faster than before).</li><li>Output of time-averaged 2d/3d
1949	data (sections / volume data) is possible.</li><li>Output
1950	of 2d-section data averaged along the direction normal to this section
1951	can be done.</li><li>The user-interface has been extended
1952	in order to allow 2d-/3d-output of user-defined quantities.</li></ul>The
1953	kind of topography to be used is controlled by the new initialization
1954	parameter <span style="font-family: monospace;">topography</span>.
1955	Allowed values are <span style="font-style: italic;">'flat'</span>,
1956	<span style="font-style: italic;">'single_building'</span>,
1957	and <span style="font-style: italic;">'read_from_file'</span>.
1958	The user can define his own special topography setting within the new
1959	user-interface routine <span style="font-family: monospace;">user_init_grid</span>.
1960	For the single building case, the building (rectangular) size
1961	and position can be controlled with parameters <span style="font-family: monospace;">building_height</span>,
1962	<span style="font-family: monospace;">building_length_x</span>,
1963	<span style="font-family: monospace;">building_length_y</span>,
1964	<span style="font-family: monospace;">building_wall_left</span>,
1965	and <span style="font-family: monospace;">building_wall_south</span>.<br>
1966	<br>
1967	The topography code is already optimized (vectorized) for use on the
1968	NEC-SX6.<br><br>Output of time-averaged 2d-/3d-data can be
1969	enabled by appending the string <span style="font-style: italic;">'_av'</span>
1970	to the respective output quantities given with the new
1971	runtime-parameter <span style="font-family: monospace;">data_output</span>
1972	(see further below for the (name)changes in the parameters for data
1973	output). Example: if a time-average of the vertical cross-section of
1974	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>.
1975	In case of NetCDF-output, the time-averaged data is output to
1976	additional files (seperate from the non-averaged output). The length of
1977	the averaging interval and the temporal distance of the single
1978	instantaneous sections (volumes) entering into this averaging is
1979	controlled by the new runtime-parameters <span style="font-family: monospace;">averaging_interval</span>and
1980	<span style="font-family: monospace;">dt_averaging_input</span>.
1981	<br><br>An average normal to the direction of a
1982	cross-section can be output by setting the respective cross section
1983	index to <span style="font-style: italic;">-1</span>
1984	(example: <span style="font-family: monospace;">section_xz</span>
1985	= <span style="font-style: italic;">-1</span>).<br><br>New
1986	user-interface routines allowing the output of user-defined quantities
1987	are <span style="font-family: monospace;">user_check_data_output</span>,
1988	<span style="font-family: monospace;">user_define_netcdf_grid</span>,
1989	<span style="font-family: monospace;">user_data_output_2d</span>,
1990	<span style="font-family: monospace;">user_data_output_3d</span>,
1991	and <span style="font-family: monospace;">user_3d_data_averaging</span>.
1992	These quantities can be calculated using the new <span style="font-family: monospace;">CASE</span>-Entry <span style="font-style: italic;">'after integration'</span>
1993	in the user-interface routine <span style="font-family: monospace;">user_actions</span>.<br><br>Optimization
1994	of the cloud droplet code is mainly done by re-sorting all particles
1995	after every timestep in a way that now all particles which belong to
1996	the same grid-box (k,j,i) are stored consecutively (wthout any strides)
1997	in memory.<br> <br>
1998	Code adaptation for the IBM at the department of atmospheric sciences,
1999	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
2000	of particle tails now requires setting of the new package-parameter <span style="font-family: monospace;">use_particle_tails</span>.
2001	The new parameter skip_particles_for_tail allows only every <span style="font-family: monospace;">skip_particle_for_tail</span>'th
2002	parameter having a tail.</li><li>Initialization-parameter <span style="font-family: monospace;">e_min</span> can be
2003	used to set a lower limit for the subgrid-scale TKE (i.e. to guarantee
2004	a lower limit for the flow's Reynolds-number).</li><li>A
2005	conservation of the volume flow (through the complete xz- and
2006	yz-sections  of the total domain) can be enforced by the new
2007	initialization-parameter <span style="font-family: monospace;">conserve_volume_flow</span>.</li><li>Data
2008	output can be skipped for a given time interval from simulation start
2009	(t=0) using new runtime-parameters <span style="font-family: monospace;">skip_time_dopr</span>,
2010	<span style="font-family: monospace;">skip_time_dosp</span>,
2011	<span style="font-family: monospace;">skip_time_do2d_xy</span>,
2012	<span style="font-family: monospace;">skip_time_do2d_xz</span>,
2013	<span style="font-family: monospace;">skip_time_do2d_yz</span>,
2014	and <span style="font-family: monospace;">skip_time_do3d</span>.<br>
2015	</li><li>By default, NetCDF output is now using 64-bit
2016	offset format
2017	(large file support) on most machines. The user can switch to the
2018	32-bit offset format with the new runtime-parameter <span style="font-family: monospace;">netcdf_64bit</span>.
2019	Units 111:113  and 116 are opened for NetCDF output of
2020	time-averaged 2d-3d data.<br> </li> <li>Data
2021	logging routines are added (see file data_log.f90), which can be used
2022	for debugging purposes. Output is done on unit 20 (local file
2023	name/directory name DATA_LOG).</li> <li>New routine <span style="font-family: monospace;">exchange_horiz_2d_int</span>
2024	for  ghostpoint exchange of 2d-integer arrays. Routine <span style="font-family: monospace;">exchange_horiz_2d</span>
2025	is extended for non-cyclic boundary conditions in the non-parallel case.</li>
2026	<li>Two different methods for calculating the mixing length and
2027	the dissipation can be used in the 1d-model. These are steered by the
2028	new initializing-parameters <span style="font-family: monospace;">dissipation_1d</span>
2029	and <span style="font-family: monospace;">mixing_length_1d</span>.<br>
2030	</li>
2031	</ul></td><td style="vertical-align: top;">advec_particles,
2032	advec_s_pw,
2033	advec_s_up, advec_u_pw, advec_u_up, advec_v_pw, advec_v_up, advec_w_pw,
2034	advec_w_up, boundary_conds, buoyancy, check_open, check_parameters,
2035	close_file, coriolis, diffusion_e, diffusion_s, diffusion_u,
2036	diffusion_v, diffusion_w, diffusivities, disturb_field,
2037	disturb_heatflux, exchange_horiz_2d, exchange_horiz, flow_statistics,
2038	header, init_1d_model, init_3d_model, init_grid, init_particles,
2039	init_pegrid, modules, netcdf, package_parin, parin, poisfft,
2040	prandtl_fluxes, pres, production_e, prognostic_equations,
2041	read_3d_binary, read_var_list, run_control, time_integration,
2042	user_interface, write_3d_binary, write_var_list<br> <br> <span style="font-weight: bold;">new:</span><br>
2043	average_3d_data, data_log, sum_up_3d_data<br> <br> <span style="font-weight: bold;">renamed:<br> </span>plot_dvrp
2044	-> data_output_dvrp<br>
2045	plot_spectra -> data_output_spectra<br>
2046	plot_ts -> data_output_tseries<br>
2047	plot_1d -> data_output_profiles<br> <span style="font-weight: bold;"></span>plot_2d ->
2048	data_output_2d<br>
2049	plot_3d -> data_output_3d<br>
2050	</td></tr><tr><td style="vertical-align: top;"> </td><td> </td><td> </td><td style="vertical-align: top;">C</td><td>In
2051	parallel mode, all PEs are opening the same copy of the
2052	NAMELIST-parameter file <span style="font-family: monospace;">PARIN</span>,
2053	i.e. from now on, the file attribute "<span style="font-family: monospace;">npe</span>" must be
2054	removed from the corresponding file connection statements in the <span style="font-weight: bold;">mrun</span> configuration
2055	file (.mrun.config).<br><br>A
2056	large number of parameter names and local filenames have been changed
2057	(see list below). Most of them are parameters concerning data
2058	output (do). The former denotations "plot" and "pl" have been changed
2059	to "data_output" and "do", respectively. In addition to these changes,
2060	the names of many internal PALM parameters and variables have also
2061	changed.<br><br>Restart runs now require setting of the
2062	initialization-parameter <span style="font-family: monospace;">initializing_actions</span>
2063	= <span style="font-style: italic;">'read_restart_data'</span>.<br>
2064	<br>
2065	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>,
2066	etc., which are controlling the position of the particle source and the
2067	number of particles within this source, are now 1d-arrays. This allows
2068	to define different particle sources for different particle groups.<br>
2069	<br>
2070	The number of particle groups has to be set by the user (no automatic
2071	calculation from the value of parameter <span style="font-family: monospace;">density_ratio</span>
2072	any more)<span style="font-style: italic;"></span>.
2073	Variable <span style="font-family: monospace;">idum</span>
2074	in type <span style="font-family: monospace;">particle_type</span>
2075	has been renamed <span style="font-family: monospace;">tail_id</span>.<br><br>Output
2076	for units 15 and 17 flushed in <span style="font-family: monospace;">init_1d_model</span>.<br><br>List
2077	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>
2078	</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
2079	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>
2080	</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>
2081	</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>
2082	</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>
2083	</td></tr><tr><td>dt_plts</td><td>dt_dots</td><td></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>
2084	</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>
2085	</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>
2086	</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>
2087	</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>
2088	</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>
2089	</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>
2090	</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>
2091	</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>
2092	</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>
2093	</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
2094	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>
2095	</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>
2096	</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>
2097	</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>
2098	</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>
2099	</td></tr><tr><td>pl_spectra</td><td>data_output_sp</td><td></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>
2100	</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>
2101	</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>
2102	</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>
2103	</td></tr></tbody></table></td><td style="vertical-align: top;">advec_particles,
2104	advec_s_bc, check_parameters, check_open, close_file,
2105	data_output_dvrp,  data_output_profiles, data_output_tseries,
2106	data_output_2d, data_output_3d, flow_statistics, header, init_1d_model,
2107	init_3d_model, init_dvrp, init_particles, init_pegrid, init_slope,
2108	modules, netcdf, package_parin, palm, parin, print_1d, read_var_list,
2109	run_control, time_integration, timestep, write_compressed,
2110	write_var_list<br>
2111	</td></tr><tr><td> </td><td> </td><td> </td><td style="vertical-align: top;">E</td><td>Error in
2112	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
2113	boundary has been fixed.<br> <br>
2114	Error removed getting the variable ids for <span style="font-family: monospace;">_ext</span> for
2115	profiles and time series.<br><br>NetCDF calls in <span style="font-family: monospace;">data_output_tseries</span>
2116	only if NetCDF output is switched on.<br><br>Output of the
2117	initial geostrophic wind profile corrected.<br><br>Maximum
2118	possibel timestep for Runge-Kutta-schemes reduced, error concerning
2119	initialization of  <span style="font-family: monospace;">l_black</span>
2120	removed (both in <span style="font-family: monospace;">init_1d_model</span>).<br>
2121	</td><td style="vertical-align: top;">advec_particles,
2122	data_output_tseries, header, init_particles, init_1d_model, netcdf<br>
2123	</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
2124	the cache-optimized PALM code.<br><br>OpenMP
2125	directives have been added where necessary. Still further tuning will
2126	be necessary to get optimum performance. Other parts of the code than
2127	the cache-optimized code still need to be (OpenMP-) parallelized. <br><br>So
2128	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>
2129	and <span style="font-family: monospace;">-O</span>,
2130	i.e. when the Option <span style="font-family: monospace;">-O</span>
2131	is given, the <span style="font-family: monospace;">-T</span>
2132	argument is interpreted as the number of threads to be used. When <span style="font-family: monospace;">-O</span> is given,
2133	the number of MPI tasks per node is automatically set to <span style="font-style: italic;">1</span>.<br><br>Beside
2134	the additional compiler directives, the main code change required by
2135	the OpenMP parallelization is that global sums are now calculated by
2136	first calculating local sums on each thread. As the next step, local
2137	sums are calculated from these thread sums for each MPI task before the
2138	global sum is computed via MPI_ALLREDUCE.  For storing the
2139	thread
2140	sums, arrays sums_l and sums_l_l now have three dimensions where the
2141	number of elements of the third dimension is equal to the number of
2142	OpenMP threads.</td><td align="left" valign="top">buoyancy,
2143	cpu_statistics, diffusivities, flow_statistics, header, init_pegrid,
2144	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
2145	correction for Piacsek & Williams advection scheme: keep u and
2146	v
2147	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>
2148	nzb_s_inner(j,i) replaced by nzb in determination of z_i.<br><br>Errors
2149	removed in the computation of the diabatic mixing length (<span style="font-family: monospace;">init_1d_model.f90</span>).<br><br>Error
2150	removed in extend mode when checking whether the selected cross
2151	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,
2152	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
2153	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,
2154	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-
2155	and 3d-datasets now contain the exact coordinates of the variables
2156	along x and y with respect to the positions where they are defined on
2157	the staggered grid.<br><br>NetCDF datasets of cross
2158	sections (e.g. <span style="font-family: monospace;">DATA_2D_XY_NETCDF</span>)
2159	are only opened if the respective cross sections are really requested
2160	by the settings of parameter <span style="font-family: monospace;">data_output</span>.</td><td align="left" valign="top">check_parameters,
2161	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>
2162	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
2163	scale velocities can (optionally) be included for calculating the
2164	particle advection, using the method of Weil et al. (2004, JAS, 61,
2165	2877-2887). This method is switched on by the new particle package
2166	parameter <span style="font-family: monospace;">use_sgs_for_particles</span>.
2167	This also forces the Euler/upstream method to be used for time
2168	advancement of the TKE (see new parameter <span style="font-family: monospace;">use_upstream_for_tke</span>).
2169	The minimum timestep during the sub-timesteps is controlled by
2170	parameter <span style="font-family: monospace;">dt_min_part</span>.
2171	The data type <span style="font-family: monospace;">particle_type</span>
2172	has additional new attributes <span style="font-family: monospace;">e_m</span>,
2173	<span style="font-family: monospace;">dt_sum</span>,
2174	and <span style="font-family: monospace;">speed_x/y/z_sgs</span>.<br><br>Other
2175	new particle features: output of particle quantities as timeseries in
2176	NetCDF format (on local file <span style="font-family: monospace;">DATA_1D_PTS_NETCDF</span>).
2177	The output time interval is controlled by parameter <span style="font-family: monospace;">dt_dopts</span>.
2178	Particle advection can be switched off after some time using parameter <span style="font-family: monospace;">end_time_prel</span>.
2179	More than one particle per point can be started with parameter <span style="font-family: monospace;">particles_per_point</span>.<br><br>Additional
2180	parameter in function <span style="font-family: monospace;">random_gauss</span>
2181	which limits the range of the created random numbers to five times the
2182	standard deviation (=1). Seeds <span style="font-family: monospace;">iran</span>
2183	and <span style="font-family: monospace;">iran_part</span>
2184	are stored for restart runs.</td><td align="left" valign="top">advec_particles,
2185	check_open, check_parameters, close_file, diffusion_e,
2186	disturb_heatflux, header, init_3d_model, init_particles, modules,
2187	netcdf, package_parin, parin, prognostic_equations, random_gauss,
2188	read_3d_binary, read_var_list, time_integration, write_3d_binary,
2189	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
2190	after call of subroutine <span style="font-family: monospace;">init_3d_model</span>.
2191	Generation of <span style="font-family: monospace;">run_description_header</span>
2192	is moved from routines <span style="font-family: monospace;">palm</span>
2193	and <span style="font-family: monospace;">header</span>
2194	to <span style="font-family: monospace;">check_parameters</span>.
2195	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,
2196	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
2197	do2d_unit and do3d_unit now defined as 2d-arrays. Before, in some
2198	cases, the units of variables in the 2d- and 3d-NetCDF-files have been
2199	wrong.<br><br>In routine <span style="font-family: monospace;">poisfft</span> default
2200	setting of the thread number tn in case of not using OpenMP.<br><br>Error
2201	removed in the non-parallel part of routine <span style="font-family: monospace;">flow_statistics</span>
2202	(number of arguments of array <span style="font-family: monospace;">sums_l</span>).<br><br>Error
2203	removed which appeared if the user had decreased the value of <span style="font-family: monospace;">dt_dopr</span> within
2204	a job chain and if simulataneous time averaging of profiles was
2205	switched on.</td><td align="left" valign="top">check_parameters,
2206	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
2207	particle group, seperate output of timeseries for each of the groups.<br><br>New
2208	initial parameter <span style="font-family: monospace;">dz_max</span>,
2209	which limits the vertical gridspacing in case of a vertically stretched
2210	grid.</td><td style="vertical-align: top;">data_output_ptseries,
2211	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
2212	for the last Runge-Kutta-substep. <br><span style="font-weight: bold;">Attention:</span> <br>
2213	The content of the testresult-file (run control output) has changed
2214	due to this modification.<br><br>Output of xz and yz cross
2215	sections now up to gridpoint nzt+1.<br><br>Default settings
2216	of particle start positions changed.</td><td style="vertical-align: top;">check_open, close_file,
2217	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
2218	arrays (t.._m) needed for the Runge-Kutta schemes.<br><br>Bugfix
2219	in index array initialization for line- or point-like topography
2220	structures.<br><br>Bugfix: yv coordinates are now used for
2221	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
2222	is the last revision before switching to the subversion revison control
2223	system!<br><br>Informative output to the job protocoll in
2224	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
2225	are now read from local file <span style="font-family: monospace;">ENVPAR</span>
2226	instead of getting them by a system call.<br><br>For
2227	interpolation in <span style="font-family: monospace;">advec_particles</span>,
2228	allways level k is used.</td><td style="vertical-align: top;">advec_particles,
2229	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>:
2230	new particles are released only if <span style="font-family: monospace;">end_time_prel</span>
2231	> <span style="font-family: monospace;">simulated_time</span>, transfer
2232	of particles when x < -0.5*dx (0.0 before), etc., index i,j used
2233	instead of cartesian (x,y) coordinate to check for transfer because
2234	this failed under very rare conditions, calculation of number of
2235	particles with same radius as the current particle (cloud droplet code).<br><br>Allocation
2236	of <span style="font-family: monospace;">tail_mask</span>
2237	and <span style="font-family: monospace;">new_tail_id</span>
2238	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
2239	the top with new inipar parameters <span style="font-family: monospace;">top_heatflux</span>
2240	and <span style="font-family: monospace;">use_top_fluxes</span>.
2241	New 2d-arrays <span style="font-family: monospace;">qswst</span>,
2242	<span style="font-family: monospace;">qswst_m</span>,
2243	<span style="font-family: monospace;">tswst</span>
2244	and <span style="font-family: monospace;">tswst_m</span>
2245	are used to store this flux. Use of fluxes are controlled with new
2246	index variable <span style="font-family: monospace;">nzt_diff</span>.
2247	A Neumann boundary condition for temperature can be applied under these
2248	conditions.<br><br>Additionally, a Dirichlet condition for
2249	temperature can be used at the top.<br><br><span style="font-weight: bold;">Attention:</span> <br>
2250	The content of the testresult-file (run control output) has changed
2251	due to this modification.</td><td style="vertical-align: top;">check_parameters,
2252	diffusion_s, flow_statistics, header, init_grid, init_3d_model,
2253	modules, parin, production_e, prognostic_equations, read_var_list,
2254	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
2255	scalars are now solved up to gridpoint nzt (formerly nzt-1).
2256	Boundary conditions for scalars at top adjusted respectively (now
2257	applied only at nzt+1).<br><br>The
2258	default top boundary condition for temperature has been renamed to <span style="font-style: italic;">'initial_gradient'</span>.<br><br>Calls
2259	of dvrp_output_local,
2260	which were commented out for a long time, are now activated for all
2261	streams.</td><td style="vertical-align: top;">advec_s_pw,
2262	boundary_conds, calc_precipitation, check_parameters, diffusion_e,
2263	diffusion_s, impact_of_latent_heat, init_dvrp, init_pt_anomaly,
2264	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
2265	pointer any more.<br><br>Bugfix in init_particles:
2266	MPI_REAL
2267	argument in MPI_ALLREDUCE
2268	replaced by<br>MPI_INTEGER
2269	(caused error on NEC only).<br><br>Bugfix:  ddzw now
2270	dimensioned 1:nzt"+1".</td><td style="vertical-align: top;">diffusion_e, diffusion_s,
2271	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
2272	inipar-parameter <span style="font-family: Courier New,Courier,monospace;">pt_reference</span>. If given, this value is used as the
2273	reference that is used in the buoyancy terms (otherwise, the instantaneous
2274	horizontally averaged temperature is used).<br><br>New d3par-parameter <span style="font-family: Courier New,Courier,monospace;">netcdf_64bit_3d</span>
2275	to switch on and especially to switch off 64bit offset for 3D
2276	files only (because still some pd-software is unable to handle 64bit
2277	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,
2278	average_3d_data, buoyancy, calc_precipitation, check_open,
2279	check_parameters, data_output_2d, diffusion_e, diffusion_u,
2280	diffusion_v, diffusion_w, diffusivities, header, impact_of_latent_heat,
2281	init_particles, init_3d_model, modules, netcdf, parin, production_e,
2282	read_var_list, read_3d_binary, sum_up_3d_data, user_interface,
2283	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
2284	non-cyclic boundary conditions of this revision still contain some bugs
2285	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
2286	FFT-method for solving the Poisson-equation is now working with Neumann
2287	boundary conditions both at the bottom and the top. This requires
2288	adjustments of the tridiagonal coefficients and subtracting the
2289	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>
2290	are regarded for volume flow control in case they have been set zero
2291	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,
2292	advec_u_up, advec_v_pw, advec_v_up, asselin_filter, boundary_conds, check_parameters,
2293	coriolis, data_output_dvrp, data_output_ptseries, data_output_ts,
2294	data_output_2d, data_output_3d, diffusion_u, diffusion_v,
2295	disturb_field, exchange_horiz, exchange_horiz_2d, flow_statistics, header, init_grid,
2296	init_particles, init_pegrid, init_rankine, init_pt_anomaly,
2297	init_1d_model, init_3d_model, modules, palm, package_parin, parin,
2298	poisfft, poismg, prandtl_fluxes, pres, production_e,
2299	prognostic_equations, read_var_list, read_3d_binary, sor,
2300	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,
2301	library paths, etc.) as well as the host identifier (local_host) are
2302	now specified in the configuration file. This generally allows to install
2303	PALM on any kind of Linux-, IBM-AIX-, or NEC-SX-system by adding
2304	appropriate
2305	settings to the configuration file. A description is added to chapter
2306	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,
2307	check_open, cpu_log, cpu_statistics, data_output_dvrp, flow_statistics,
2308	header, init_dvrp, init_particles, init_1d_model, init_dvrp,
2309	init_pegrid, local_getenv, local_system, local_tremain,
2310	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>
2311	replaced by multiplication of the inverse. For performance
2312	optimisation, this is done in the loop calculating the divergence
2313	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
2314	density is calculated from the equation of state for seawater after
2315	each timestep, using the algorithm proposed by Jackett et al. (2006, J.
2316	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>".
2317	Saturation at k=nzb is assumed for the atmosphere coupled to ocean.
2318	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>
2319	</td><td style="vertical-align: top;">boundary_conds,
2320	check_open, check_parameters, diffusion_u, diffusion_v,
2321	flow_statistics, header, init_pegrid, init_rankine, init_3d_model,
2322	local_stop, modules, palm, parin, prandtl_fluxes, pres,
2323	prognostic_equations, read_var_list, read_3d_binary, swap_timelevel,
2324	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>),
2325	it is called after the first substep instead of the last. In that case,
2326	random perturbations are also added to the velocity field after the
2327	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>,
2328	respectively. The radiation boundary condition is used for every
2329	Runge-Kutta substep. Velocity phase speeds for the radiation boundary
2330	conditions are calculated for the first Runge-Kutta substep only and
2331	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>
2332	are defined for this purpose. Several index errors are removed from the
2333	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,
2334	advec_u_up, advec_v_pw, advec_v_up, boundary_conds, buoyancy,
2335	check_parameters, coriolis, diffusion_u, diffusion_v, header,
2336	init_pegrid, init_3d_model, modules, poismg, production_e,
2337	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
2338	be used to prescribe a plant canopy type. The default case is a
2339	homogeneous plant canopy. Heterogeneous distributions of the leaf area
2340	density and the canopy drag coefficient can be defined in the new
2341	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,
2342	check_parameters, data_output_dvrp, header, init_3d_model, init_grid,
2343	init_particles, init_pegrid, modules, package_parin,
2344	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>.
2345	This update serves two purposes: - it avoids errors in calculations
2346	with humidity/scalar/salinity and prescribed non-zero wall heatflux, -
2347	it prepares PALM for a possible assignment of wall fluxes of
2348	humidity/scalar/salinity in a future releases.</td><td style="vertical-align: top;">buoyancy,
2349	check_open, data_output_dvrp, diffusion_s, diffusivities,
2350	flow_statistics, header, init_3d_model, init_dvrp, init_grid, modules,
2351	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,
2352	check_parameters, combine_plot_fields, diffusion_s, diffusivities,
2353	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
2354	turbulence recycling method of Kataoka and Mizuno (2002) has been
2355	implemented. A precursor run must be used to initialize the main run
2356	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>).
2357	The precursor run may have a smaller domain than the main run, which
2358	helps to spare CPU time. New parameters for steering the recycling
2359	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
2360	new feature related with the recycling method is that within a job
2361	chain, the number of processors or the virtual processor grid is now
2362	allowed to change. Such a change modifies the domain decomposition
2363	and requires that the PEs within a restart job have to know from which
2364	file(s) they have to read their restart data (up to now there has been
2365	a one to one relation between the restart files and the PEs, i.e.
2366	processor 4 only reads data from file "_0004"). Informations about the
2367	subdomain index limits of all restart files are now written by PE0 (to
2368	file "_0000"). Also, all variables containing global values which do
2369	not depend on the subdomain are written to file "_0000" only. In a
2370	restart run, this file is opened by all PEs to read these global values
2371	and the informations about the subdomain index limits. Depending on
2372	these index limit information it is decided which restart file(s)
2373	has/have to be opened in order to read the complete data necessary for
2374	the current subdomain.<br><br>The plant canopy model has been extended
2375	to the prognostic equation for the potential temperature
2376	and passive scalar, as proposed by Watanabe (2004) and Shaw and
2377	Schumann (1992).<br><br>Particle advection adjusted for ocean runs.<br><br>Grid
2378	coarsening (multigrid method) is limited to subdomains (i.e. no
2379	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,
2380	header, init_3d_model, init_particles, init_pegrid, modules, netcdf, parin, particle_boundary_conds, plant_canopy_model,
2381
2382	prognostic_equations, read_3d_binary, read_var_list, time_integration,
2383	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
2384	of the integrated version of the profile function for momentum for
2385	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
2386	lateral edges of the plant canopy introduced. Before, smaller values of
2387	the leaf area density than those applied in the prognostic equation for
2388	the vertical velocity were used in the prognostic equations for u and v
2389	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>
2390	removed. This was used, since on IBM machines the process rank could be
2391	changed when the final communicator was defined, in order to save the
2392	preliminary processor-id for opening the binary output file for
2393	restarts (unit 14), because otherwise a mismatch occured when reading
2394	this file in a restart job. This mechanism is not needed any more since
2395	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>
2396	as an automatic array instead of providing the memory by a dummy
2397	argument. This spares one copy loop per transposition. Order of indices
2398	in the 3D loops in some of the transpose routines have been rearranged
2399	for better cache utilization. Both have been suggested by Roland
2400	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,
2401	advec_u_ups, advec_v_ups, advec_w_ups, calc_spectra, check_open,
2402	check_parameters, cpu_statistics, data_output_profiles,
2403	data_output_spectra, flow_statistics, header, init_1d_model,
2404	init_3d_model, modules, netcdf, palm, parin, poisfft, production_e,
2405	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:
2406	modification of the calculation of the vertical turbulent momentum
2407	fluxes u'w' and v'w'; the first usws that is computed corresponds to
2408	-u'w'/u* and not as priorily assumed to (-u'w')**0.5, the first vsws
2409	that is computed corresponds to -v'w'/u* and not as priorily assumed to
2410	(-v'w')**0.5. Therefore, the intermediate result for usws has to be
2411	multiplied by -u* instead by itself in order to get u'w'. Accordingly,
2412	the intermediate result for vsws has to be multiplied by -u* instead by
2413	itself in order to get v'w'. As u* is calculated for the position of a
2414	scalar an additional interpolation of u* to the position of u and v,
2415	respectively, is necessary. As u* is not determined for the ghost
2416	points on each PE, an additional exchange of information from
2417	neighbouring PEs is necessary. Tests showed that this
2418	decreases u* by some 10% and increases TKE and momentum fluxes by some
2419	10% because friction was underestimated and momentum fluxes were
2420	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;">
2421	The content of the testresult-file (run control output) has changed
2422	due to the above bugfix.</span><br><br>Bugfix:
2423	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:
2424	Construction of vertical profiles when 10 gradients have been specified
2425	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:
2426	Lengths of those characters that are needed for the output of the
2427	characteristic levels of potential temperature, the geostrophic wind,
2428	scalar concentration, humidity and leaf area density to the header file
2429	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>
2430	was written on the binary file, which caused that NetCDF files newly
2431	created by restart files (no append of existing files!) contained
2432	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,
2433	check_parameters, cpu_statistics, diffusion_s, flow_statistics,
2434	init_3d_model, init_dvrp, local_stop, plant_canopy_model, poismg,
2435	prandtl_fluxes, pres, read_3d_binary, user_interface, wall_fluxes,
2436	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
2437	release contains further additions, changes, and bugfixes for the
2438	SGI-ICE system, as well as important changes like the splitting of the
2439	user-interface into single files, a complete revision of the
2440	pre-compiling mechanism allowing to use different make-depositories
2441	simultaneously, and a revision of the reading-mechanism from restart
2442	files, which has no more restrictions in case that the previous and
2443	current run have different domain/subdomain sizes. A new handling of
2444	all kind of output messages is introduced with this release and will be
2445	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,
2446	check_parameters, data_output_dvrp, init_dvrp, init_pegrid, local_stop,
2447	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>
2448	changed to INTEGER(8) in order to avoid "out of range" problems, which
2449	result in measured negative time intervals. (cpu_log, local_tremain,
2450	local_tremain_ini)<br><br>Reading mechanism from restart files
2451	completely revised. The subdomain/total domain size is now allowed to
2452	vary arbitrarily between the current and previous run. (read_var_list,
2453	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>).
2454	One depository per block (given in the config-file) is created. Always
2455	all files from the source directory are copied to the respective
2456	depository. No additional file checks are done any more (mrun version
2457	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,
2458	check_parameters, cpu_log, init_grid, local_stop, local_tremain,
2459	local_tremain_ini, modules, netcdf, read_3d_binary, read_var_list,
2460	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,
2461	user_3d_data_averaging, user_actions, user_advec_particles,
2462	user_check_data_output, user_check_data_output_pr, user_data_output_2d,
2463	user_data_output_3d, user_data_output_dvrp, user_define_netcdf_grid,
2464	user_dvrp_coltab, user_header, user_init_3d_model, user_init,
2465	user_init_grid, user_init_particles, user_init_plant_canopy,
2466	user_last_actions, user_parin, user_parin, user_particle_attributes,
2467	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
2468	removed: as the thermal stratification is not taken into account for
2469	the evaluation of the wall fluxes at vertical walls, the eddy viscosity
2470	<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,
2471	calc_spectra, check_for_restart, cpu_statistics, data_output_2d,
2472	header, inflow_turbulence, init_cloud_physics, production_e,
2473	read_3d_binary, timestep<br><br>combine_plot_fields</td></tr>
2474	</tbody>
2475	</table> <b><blink>Attention:</blink></b>
2476	If<tt> make </tt>is not used
2477	for
2478	compiling,
2479	<b>all routines</b> have to be re-compiled after every
2480	change
2481	to <b>modules.f90!</b>
2482	<br>
2483	<br>
2484	<h2><a name="Kapitel2.0"></a>2.0  How
2485	to change the model source
2486	code</h2>
2487	Änderungen, Erweiterungen oder Fehlerkorrekturen am Modellcode
2488	(gemeint
2489	sind alle Modellteile, die nicht zur benutzereigenen Software
2490	gehören)
2491	erfordern vom jeweiligen Benutzer Gruppenzugehörigkeit zur
2492	Gruppe
2493	<tt>"palm"</tt>.
2494	Zu dieser Gruppe gehören alle Benutzer, die aktiv an der
2495	Modellentwicklung
2496	mitwirken (im weiteren "Modellarbeitsgruppe" genannt).
2497	<p>Die einzelnen Quelltextdateien des Modells werden mit RCS
2498	(Revision
2499	Control System) verwaltet. Grundlegende Kenntnisse über dieses
2500	System
2501	werden im weiteren vorausgesetzt.
2502	</p><p>Änderungen am Modellcode erfordern die
2503	Durchführung
2504	bestimmter
2505	Aktionen in einer festgelegten Reihenfolge, die nun beschrieben werden
2506	sollen.
2507	</p><ol> <li>Konzeptplanung.</li> <li>Diskussion
2508	der geplanten Änderungen in der
2509	Modellarbeitsgruppe.</li> <li>Auschecken der
2510	benötigten Quelltextdateien,
2511	Durchführung der
2512	Änderungen und Test des Modells. Die Modul-Datei <tt>modules.f90</tt>
2513	sollte nur dann ausgecheckt werden, wenn dort aufgeführte
2514	Variablen
2515	verändert werden. Neu geschaffene Variablen sollten
2516	während
2517	der
2518	Testphase in ein ebenfalls temporär neu zu schaffendes Modul
2519	geschrieben
2520	werden, das von den jeweiligen Programmteilen benutzt werden muss
2521	(Einfügen
2522	entsprechender USE-Anweisungen). Die in den einzelnen Dateien
2523	durchgeführten
2524	Arbeiten müssen in den Kopfzeilen (unter "Aktuelle
2525	Aenderungen")
2526	der
2527	Dateien vermerkt werden. Dies tut man am besten noch <b>bevor</b>
2528	man
2529	die
2530	eigentlichen Änderungen durchführt (sonst droht das
2531	Vergessen...).</li> <li>Zum Abschluß der Tests
2532	sollte mit dem Modell eine
2533	Kontrollrechnung
2534	durchgeführt und die Ergebnisse mit denen des sogenannten
2535	Standardlaufes
2536	verglichen werden. Diese Rechnung ist mit der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">Konfigurationsdatei</a>
2537	und der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">Parameterdatei</a>
2538	durchzuführen, die auch zum Testen der Modellinstallation
2539	verwendet
2540	werden (s. <a href="Anwendung/Kapitel_5.0.html">Kapitel
2541	5.0</a> der
2542	Anwenderdokumentation).
2543	Die Ergebnisdatei mit dem lokalen Namen <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM-1/Dokumentationen/Anwendung/Kapitel_3.4.html#RUN_CONTROL">RUN_CONTROL</a>
2544	ist dann mit der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">Beispiel-Ergebnisdatei</a>
2545	zu vergleichen (Hinweis: Kopien der Konfigurationsdatei, Parameterdatei
2546	und Beispiel-Ergebnisdatei erhält man durch anklicken der
2547	entsprechenden
2548	Links mit der linken Maustaste bei gleichzeitig gedrückter
2549	<SHIFT>-Taste).
2550	Werden Abweichungen zwischen den beiden Ergebnisdateien festgestellt,
2551	so
2552	ist unbedingt eine Diskussion in der Modellarbeitsgruppe notwendig.</li>
2553	<li>Nach Durchführung der Tests müssen bei
2554	Bedarf die
2555	vorläufig
2556	im temporären Modul eingetragenen Variablen in die
2557	eigentlichen
2558	Module
2559	des Modells übertragen werden. Dazu ist die Modul-Datei <tt>modules.f90</tt>
2560	auszuchecken. Nach Eintrag der Variablen sollte das Modell noch einmal
2561	testweise übersetzt werden, um Sytaxfehler
2562	auszuschließen
2563	(evtl.
2564	auch noch einmal einen Probelauf starten). Die Verwendung des
2565	temporären
2566	Moduls ist aus allen entsprechenden Programmteilen zu entfernen.</li>
2567	<li>Vergabe einer neuen Versionsnummer (Variable <tt>version</tt>
2568	im
2569	Modul <tt>steuer</tt>),
2570	Bsp.: 2.3c. Kleinere Änderungen werden durch
2571	angehängten
2572	kleinen
2573	Buchstaben kenntlich gemacht, größere
2574	Änderungen durch
2575	die Zahl hinter dem Punkt. Eine Inkrementierung der Zahl vor dem Punkt
2576	geschieht nur bei ganz grundsätzlichen Revisionen des Modells,
2577	die
2578	weite Teile des Modellcodes betreffen.</li> <li>Nun
2579	können die ausgecheckten Dateien wieder eingecheckt
2580	werden.
2581	Vor
2582	dem Einchecken sind in den Dateien die Vermerke unter "Aktuelle
2583	Aenderungen"
2584	zu entfernen und beim check-in - Kommando als Log-Text anzugeben. Sie
2585	erscheinen
2586	dann in der jeweiligen Datei unter "Fruehere Aenderungen" zusammen mit
2587	der vom RCS-System vergebenen Versionsnummer (dafür sorgt die
2588	$Log:
2589	... $ - Zeile, die in jeder Quelltextdatei steht).</li> <li>Eine
2590	Zusammenfassung der durchgeführten Arbeiten ist im <a href="#Kapitel1.0">Kapitel
2591	1.0</a> einzutragen.</li> <li>Die
2592	Modellarbeitsgruppe ist über den Abschluß der
2593	durchgeführten
2594	Arbeiten zu informieren.</li>
2595	</ol><h2>
2596	<a name="Kapitel3.0"></a>3.0  Description
2597	of selected parts of the
2598	model source code</h2>
2599	<b>This chapter is still under construction (Feb. 04).</b>
2600	<p>Dieser Abschnitt verweist auf vorhandene Beschreibungen der
2601	genauen
2602	Funktionsweise einzelner, spezieller Modellteile. Dazu gehört
2603	z.B.
2604	die Beschreibung bestimmter numerischer Verfahren (auch ihr
2605	theoretischer
2606	Hintergrund), die Erklärung besonderer Prinzipien bei der
2607	Parallelisierung
2608	oder Erläuterungen zur Vorgehensweise bei der Lösung
2609	bestimmter
2610	Aufgaben (z.B. der Berechnung horizontal gemittelter
2611	Größen).
2612	<br>Die Beschreibungen liegen in jeweils getrennten Dokumenten,
2613	in der
2614	Regel als TeX- und/oder Postscript-Datei vor und sind über die
2615	folgenden
2616	Links zugänglich.
2617	<br>
2618	</p><ul> <li> <a name="UPS"></a>upstream-spline
2619	advection scheme ( <a href="Upstream_Spline/ups.ps">.ps</a>
2620	)</li> <li> <a name="Cloud_physics"></a>cloud
2621	physics module ( <a href="Cloud_physics/wolken.pdf">.pdf</a>
2622	)</li> <li> <a name="Bitkompression"></a>Datenkompression
2623	mit dem Verfahren
2624	der <a href="Bitkompression/kompression.html">Bitverschiebung</a></li>
2625	<li> <a name="Runge-kutta"></a>Runge-Kutta
2626	time integration scheme ( <a href="numerik.heiko/zeitschrittverfahren.pdf">.pdf</a>
2627	)</li>
2628	</ul><br>
2629
2630	<br>
2631	<br>
2632	<br>
2633	<br>
2634	<br>
2635	<br>
2636	<br>
2637	</body></html>

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