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[5]	1	<!DOCTYPE html PUBLIC "-//w3c//dtd html 4.0 transitional//en">
	2	<html><head>
[77]	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>
[62]	4	<body><font size="+4">PALM
[5]	5	</font>a
	6	<b>pa</b>rallelized
	7	<b>L</b>ES <b>m</b>odel
[62]	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
[197]	14	model version:</b></td> <td><span style="font-weight: bold;">3.5</span></td> </tr>
[62]	15	<tr nosave=""> <td nosave=""><b>Last
	16	change of this document</b>: </td> <td nosave=""><b>$Id: technical_documentation.html 198 2008-09-17 08:55:28Z raasch $</b></td> </tr>
	17	</tbody>
	18	</table><hr width="100%">
[5]	19	<p><font size="+2">Table of contents</font>
[62]	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
[5]	27	of
	28	the model source code <br>
	29	</p>
[62]	30	</ul><b>Please note: Parts of this document are still in
	31	German. We
[5]	32	apologize
	33	for any inconvenience.</b>
[62]	34	<br>
	35	<h2><a name="Kapitel1.0"></a>1.0
	36	History of changes</h2>
[5]	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.
[62]	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
[5]	54	(initializing_actions, end_time,
	55	fcl_factor, use_prior_plot1d_parameters), zusätzliche
	56	Überprüfung
[62]	57	von Parametern auf Zulässigkeit (prandtl_layer, psolver, nx,
	58	ny,
[5]	59	nz,
[62]	60	fcl_factor), Höhe der Schnittebenen der Horizontalschnitte
	61	wird
[5]	62	auf
[62]	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
[5]	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
[62]	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,
[5]	79	init_pegrid,
	80	local_getenv, local_system, local_tremain, local_tremain_ini, poisfft</td>
[62]	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
[5]	84	Vorgehensweise von
[62]	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
[5]	89	ausserhalb der k-Schleife,
[62]	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
[5]	94	(Piascek-Williams)
[62]	95	bei k=1. Terme werden nun überall gleich berechnet. Evtl.
	96	leichte
[5]	97	Erhöhung der Varianzen in Oberflächennähe.</td>
[62]	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
[5]	102	noch bei
[62]	103	k=1. Unrealistische sekundäre Maxima in den Km-Profilen
	104	oberhalb
[5]	105	der
[62]	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
[5]	112	simulierter
[62]	113	Zeit bei Fortsetzungsläufen korrigiert.  <p>Berechnung
	114	von cross_uxmin(1) und cross_uxmax(1) aus den
[5]	115	Werten von
[62]	116	ug und vg entfernt. Lieferte falsche Wertebereiche für Plots
	117	von
[5]	118	Vertikalprofilen,
	119	wenn im ersten Koordinatenkreuz nicht die Windgeschwindigkeiten
	120	gezeichnet
[62]	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
[5]	125	der Initialparameter
	126	rif_max und rif_min einstellbar (Werte waren bisher fest auf -2.0, +1.0
[62]	127	eingestellt).</td> <td>check_parameters, header,
	128	init_1d_model, modules, parin,
[5]	129	prandtl_fluxes,
[62]	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 =
[5]	133	"<i>set_constant_profiles</i>"
[62]	134	und "<i>set_1d-model_profiles</i>" korrigiert.  <p>2D-Plotausgabe
	135	von u* und theta* korrigiert. Hier wurden
[5]	136	bisher falsche
[62]	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
[5]	143	Datei RUN_CONTROL
[62]	144	um einige Kommastellen erweitert.  <p>Lieferung von
	145	ausführlicheren Informationen bei
[5]	146	Programmabbruch
[62]	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
[5]	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
[62]	156	des Schwerkraftvektors. Dadurch erhält auch die u-Komponente
	157	der
[5]	158	Windgeschwindigkeit
[62]	159	einen Anteil der Auftriebskraft.  <p>Diese
	160	Implementierung ist noch nicht abgeschlossen. Die
[5]	161	Simulation von
	162	Kaltluftabflüssen erfordert bisher noch Eingriffe "von Hand".</p>
[62]	163	</td> <td>buoyancy, check_parameters, header, leap_frog,
	164	modules,
[5]	165	parin, prandtl_fluxes,
[62]	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
[5]	169	I/O auf
[62]	170	T3E-Rechnern.  <p>Ermittelung wahrer I/O-Zeiten
	171	für binäre
[5]	172	Ein-/Ausgabe auf
[62]	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
[5]	180	zwingend den
	181	Einsatz der MPI-Version mpt.1.2.0.1. In dieser neuen Version tritt auch
[62]	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
[5]	188	von Impuls
[62]	189	und skalaren Größen (neue UP's, s. rechts).
	190	Berechnung von
[5]	191	Variablen
[62]	192	für spezielle Advektionsverfahren in eigenständiges
	193	UP
[5]	194	ausgelagert
[62]	195	(<tt>init_advec</tt> + eigenes Modul <tt>advection</tt>).
	196	Reines
[5]	197	Euler-/Upstream-Verfahren
[62]	198	kann gerechnet werden.  <p>Schnelle binäre I/O
	199	(s. 15/12/98) wieder abgeschaltet, da
[5]	200	Dateien
[62]	201	nicht wieder einlesbar sind. Druckstörung (p) wird zu Beginn
	202	auf 0
[5]	203	gesetzt, damit sie keine Tendenzen im ersten Zeitschritt hervorruft.</p>
[62]	204	</td> <td>advec_s_bc, check_open, check_parameters,
	205	flow_statistics,
[5]	206	header,
	207	init_3d_model, init_grid, leap_frog, modules, parin, plot_2d, plot_ts,
[62]	208	read_var_list, timestep, write_3d_binary, write_var_list  <p><b>Neu:</b>
	209	<br>
[5]	210	advec_s_ups, advec_u_ups, advec_v_ups, advec_w_ups, init_advec,
	211	long_filter,
[62]	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
[5]	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>
[62]	224	<td>check_parameters, diffusion_e, diffusion_pt, diffusivities,
[5]	225	header,
	226	init_advec, long_filter, modules, production_e, spline_x, spline_y,
[62]	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
[5]	231	TKE,
	232	Korrektur der Dichteberechnung (war falsch bei Galilei-Transformation)</td>
[62]	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
[5]	239	des
	240	Upstream-Verfahrens
[62]	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,
[5]	246	modules,
[62]	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.
[5]	252	Beim
	253	binären Einlesen dürfen Records nicht mit dem Trick "<tt>READ
[62]	254	(..) idum</tt>" überlesen werden. Zeitmessungen auf T3E
	255	erfolgen
[5]	256	jetzt
[62]	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
[5]	263	Wahl der
	264	numerischen Begrenzer für das Upstream - Spline - Verfahren.</td>
[62]	265	<td>check_parameters, header, init_3d_model, leap_frog, modules,
[5]	266	parin,
[62]	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
[5]	274	möglich.
	275	Ausgabe erfolgt im dvr-Format. Bisher noch nicht nutzbar, da noch
	276	Einstellmöglichkeiten
[62]	277	für die Partikelquelle(n) fehlen. <b>Wichtig:</b>
	278	Die Benutzung
[5]	279	der
	280	vtk-Software erfordert die zusätzliche mrun-Option <tt>-g</tt>.
	281	Das
[62]	282	Hauptprogramm <tt>parles</tt> wird in diesem Fall zum
	283	Unterprogramm
[5]	284	und
[62]	285	von einem c++-Programm aus aufgerufen.</td> <td>header,
	286	init_3d_model, init_pegrid, leap_frog, modules,
[5]	287	parin, parles,
[62]	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
[5]	294	umgestellt.
[62]	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
[5]	300	t3eh
	301	möglich. Ausgabe erfolgt im dvr-Format. Bisher noch nicht
	302	allgemein
	303	nutzbar, da noch diverse manuelle Eingriffe nötig sind.</td>
[62]	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
[5]	311	zwar nicht
[62]	312	nur bei  <tt>k = nzb, nzt+1</tt> sondern auch
	313	bei  <tt>k =
[5]	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
[62]	319	den Drucklöser modifiziert. Soweit bis jetzt abzusehen, hat
	320	diese
	321	Änderung nur minimale Auswirkungen auf den Prognoseverlauf.
	322	Evtl.
[5]	323	gibt es stärkere Auswirkungen bei exzessivem Auftreten von
	324	Schwerewellen
	325	am oberen Rand (die dort aber eigentlich sowieso nicht
	326	hingehören).  <br>
[62]	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
[5]	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>
[62]	337	<p>3D-Feldvariablen (u, v, w, pt, e, km, kh) sowie einige
[5]	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
[62]	345	die jeweilige Neuzuordnung der Targets entfällt das
	346	Umspeichern
[5]	347	der
[62]	348	Zeitebenen komplett (Zeitersparung: ca. 5% der
	349	Gesamtrechenzeit).  <br>
[5]	350	Die Umordnung der Zeitebenen wurde ins neue UP <tt>swap_timelevel</tt>
[62]	351	ausgelagert.  <br> <b>Wichtig:</b> Die
	352	Übersetzungszeiten haben durch die
[5]	353	Einführung
	354	der Pointer t.w. sehr deutlich zugenommen (<tt>leap_frog</tt>
	355	benötigt
[62]	356	jetzt z.B. ca. 60 Sekunden). Außerdem benötigt der
	357	Compiler
[5]	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,
[62]	361	t3ej2) bzw. 45 (t3eb) und 96 (vpp) haben.  <br> <b>Achtung:</b>
	362	bislang wurde diese Änderung nur für
[5]	363	das
[62]	364	reine Leapfrog-Verfahren getestet!  </p> <p>Neue
	365	Laderoption "<tt>-D preset=nan</tt>" empfohlen (s.
[5]	366	Beispiel-Konfigurationsdatei).
[62]	367	Ebenso empfehlenswert für Debug-Läufe: Compileroption
	368	"<tt>-ei</tt>".
[5]	369	Diese bewirkt einen Programmabbruch, falls mit nicht initialisierten
	370	Variablen
	371	gearbeitet wird (ist aber zeitaufwendig in der Ausführung!).</p>
[62]	372	</td> <td>boundary_conds, check_parameters, header,
	373	init_3d_model,
[5]	374	leap_frog,
[62]	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
[5]	380	aufgerufen. Dies
	381	geschah bisher fälschlicherweise erst danach, sodass der
	382	Zeitfilter
[62]	383	asymmetrisch arbeitete.  <br> <b>Achtung:</b>
	384	diese Änderung hat Auswirkungen auf den
[5]	385	Prognoseverlauf.
	386	Die Testergebnis-Datei wurde entsprechend geändert.</td>
[62]	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>
[5]	390	Der Asselin-Filter im 1D-Modell wird nun auch vor der Umordnung der
[62]	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 -
[5]	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
[62]	402	Impulsflüsse.  </p> <p>Bei der
	403	Berechnung der Diffusion der Temperatur werden die
[5]	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
[62]	411	Anwachsen der Grenzschicht mit der Zeit.  </p> <p><b>Achtung:</b>
	412	diese Änderungen haben Auswirkungen auf
[5]	413	den Prognoseverlauf.
[62]	414	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
	415	<td nosave="" valign="top">init_1d_model,
	416	asselin_filter,
[5]	417	diffusion_u, diffusion_v,  <br>
[62]	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
[5]	425	Änderungen
	426	in zahlreichen Programmteilen notwendig (Beschreibung <a href="#Cloud_physics">siehe
	427	unten</a> ). Im einzelnen wurden folgende Unprogramme
[62]	428	geändert:  <br> <b>modules</b>:
	429	<br>1) Bereitstellung neuer 3D-, 2D- und 1D-Felder für
	430	die Prognose
[5]	431	des Gesamtwassergehaltes  <br>
	432	2) "cloud_parameters" als neues Modul mit wolkenphysikalischen
[62]	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,
[5]	437	write_3d_binary: </b>In/Output
	438	der neuen Initialisierungsparamter und Felder für
[62]	439	Fortsetzungsläufe </font> <br> <font color="#000000"><b>check_parameters:</b>
	440	Initialisierung
[5]	441	des
[62]	442	Feuchteprofils und Ausgabe von neuen Vertikalprofilen: </font>
	443	<br> <font color="#ff0000">vpt</font><font color="#000000">: virtuelle
[5]	444	poteniellen
[62]	445	Temperatur,</font> <br> <font color="#ff0000">lpt</font><font color="#000000">:
[5]	446	potentielle
[62]	447	Flüssigwassertemperatur,</font> <br> <font color="#ff0000">q</font><font color="#000000">:
	448	Gesamtwassergehalt,</font> <br> <font color="#ff0000">qv</font><font color="#000000">:
[5]	449	spezifische
[62]	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">:
[5]	452	Auftriebsfluss (subskalig, aufgelöst, gesamt),</font> <br>
[62]	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
[5]	460	Wolkenphysik
	461	eingefügt, außerdem Formatnummern erweitert um Platz
	462	für
[62]	463	weitere Ausgaben zu schaffen  <br> <b>leap_frog:</b>
	464	<br>
[5]	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>
[62]	469	3) veraenderter Aufruf von diffusivities  <br> <b><tt>b</tt>oundary_conds,
	470	asselin_filter, swap_timelevel,
[5]	471	flow_statistics: </b>Anpassung
[62]	472	an Feuchtebehandlung  <br> <b>plot2d, plot3d</b>:
	473	Ausgabemöglichkeiten von q und ql <br> <b>buoyancy</b>:
	474	Anpassung des Autriebstermes an
[5]	475	Feuchtebehandlung
	476	durch neue Übergabeparameter: Temperatur + Nummer des
	477	entsprechenden
[62]	478	mittleren Temperaturprofils  <br> <b>diffusion_e</b>:
	479	Anpassung der Mischungswegberechnung an
[5]	480	Feuchtebehandlung
[62]	481	durch Variation der Übergabeparameter  <br> <b>production_e</b>:
	482	TKE-Produktion durch Auftriebskräfte an
[5]	483	Feuchtebehandlung
[62]	484	angepasst  <br> <b>diffusivities</b>:
	485	siehe diffusion_e  <br> <b>prandtl-fluxes</b>:
	486	Prandtl-Schicht fuer den
[5]	487	Gesamtwassergehalt
[62]	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
[5]	494	Gleichungen
[62]	495	aus leap_frog, zusätzliche porgnostische Gleichung
	496	für den
	497	Gesamtwassergehalt  <br> <b>diffusion_s</b>:
	498	Berechnung der Diffusion skalarer
[5]	499	Größen
	500	(Temperatur und Gesamtwassergehalt), ersetzt diffusion_pt  <br>
[62]	501	<b>calc_liquid_water_content</b>: Berechnung des
	502	Flüssigwassergehalts  <br> <b>calc_radiation</b>:
	503	Parametrisierung langwelliger
[5]	504	Strahlungsprozesse
	505	über des Schema der effektiven Emissivität  <br>
[62]	506	<b>calc_precipitation</b>:Parametrisierung von
[5]	507	Niederschlagsprozessen
[62]	508	mit Hilfe eines vereinfachten Kesslerschemas  <br> <b>impact_of_latent_heat</b>:
	509	Berücksichtigung der durch
[5]	510	Niederschlagsprozesse
	511	zurückbleibenden latenten Waerme innerhalb eines
[62]	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
[5]	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
[62]	555	deshalb nach Abschluss eines kompletten Modelllaufs erfolgen.
	556	</p> <p><b>Achtung:</b> diese
	557	Änderungen haben Auswirkungen auf
[5]	558	den Prognoseverlauf.
[62]	559	Die Testergebnis-Datei wurde entsprechend geändert.</p> </td>
	560	<td nosave="" valign="top">modules, parin,
	561	read_var_list,
[5]	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,
[62]	567	write_3d_binary  <p><b>Neu:</b> <br>
[5]	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>
[62]	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
[5]	573	noch kleine
[62]	574	Änderungen an den Unterprogrammen diffusion_e, production_e
	575	und
[5]	576	diffusivities
	577	vorgenommen. In allen genannten  <br>
	578	Unterprogrammen wurde bisher ein strengeres Kriterium zur Bestimmung
[62]	579	der Schichtungsverhältnisse verwendet. Ein Modellvergleich
	580	zeigte
[5]	581	jedoch, dass dadurch die Diffusion im Bereich der Inversion zu gross
[62]	582	wird.  <p>Eine weitere Ergänzung betrifft die
[5]	583	Advektionsverfahren:  <br>
[62]	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
[5]	588	den Prognoseverlauf.
[62]	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
[5]	595	dvrp-Software.
	596	Grafik-Ausgaben im dvr-Format sind mittlerweile begrenzt nutzbar
	597	(Isooberflächen
[62]	598	sind darstellbar, siehe neue Laufparameter  <tt>dt_dvrp,
	599	threshold</tt>),
[5]	600	es wird aber in der Anwendung in naher Zukunft noch diverse
	601	Änderungen
	602	geben. Partikelausgabe vorerst nicht mehr möglich (Verlagerung
[62]	603	schon).</td> <td>header, init_particles, init_3d_model,
	604	leap_frog, modules,
[5]	605	parin, parles,
[62]	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
[5]	614	sehr
	615	viele SENDRECV-Aufrufe eingespart.  <br>
[62]	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
[5]	623	Änderungen
	624	am Header-Format wurde Testergebnis-Datei geändert.</td>
[62]	625	<td>advec_s_bc, check_open, header, init_pegrid, modules, parin,
[5]	626	read_var_list,
[62]	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
[5]	631	Vorgabe
	632	eines stabil geschichteten Temperaturprofils mit konstantem Gradienten.
	633	Hinzuschalten von Feuchte funktioniert für Hangrechnungen noch
[62]	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
[5]	640	gesetzt.
	641	Ein Nichtsetzen der Randbedingungen führte zu Fehlern bei der
	642	Ausgabe
[62]	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
[5]	647	von <tt>prognostic_equation</tt>
[62]	648	aufgerufen werden und an die Pointer-Variablen übergeben
	649	werden,
[5]	650	sind
	651	jetzt explizite Interfaces vereinbart (neues Modul <tt>pointer_interfaces</tt>).
	652	Auch im Vereinbarungsteil der entsprechenden Unterprogramme sind diese
[62]	653	Übergabeparameter jetzt aus Konsistenzgründen (und
	654	weil es
[5]	655	sonst
	656	Laufzeitfehler gibt) als Pointer-Variablen deklariert. Mit dieser
	657	Änderung
[62]	658	ist der große Speicher- und CPU-Zeit-Bedarf beim
	659	Übersetzen
	660	von prognostic_equations wieder auf ein erträgliches
	661	Maß
[5]	662	reduziert.  <br>
	663	Im Rahmen dieser Änderungen wurde auch an diffusion_e ein
	664	Hilfsfeld
	665	weniger übergeben.  <br>
[62]	666	Aus nicht vollständig gekärten Gründen haben
	667	sich die
	668	Zahlen in der Testergebnis-Datei minimal geändert (und zwar
	669	die
[5]	670	Spalte
	671	mit der Gesamtdivergenz nach Aufruf des Drucklösers).</td>
[62]	672	<td>advec_s_bc, buoyancy, diffusion_e, diffusion_s, diffusion_u,
[5]	673	diffusion_v,
	674	diffusion_w, disturb_field, modules, production_e, prognostic_equations</td>
[62]	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
[5]	678	Flüssigwassergehalt
[62]	679	werden gesetzt. Dies wäre bereits nach Einführung der
	680	Pointer
[5]	681	zwingend notwendig gewesen. Rechnungen mit vorgegebener
	682	Oberflächentemperatur
[62]	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
[5]	687	k=nzb und
	688	k=nzt+1 berechnet, um die Randwerte auch für Ausgabezwecke
[62]	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,
[5]	693	die zwar
[62]	694	zum Modell gehören, standardmäßig aber
	695	nicht mit
[5]	696	übersetzt
	697	werden, um so unter anderem Kompilationszeit einzusparen. Siehe neues
	698	Kapitel
[62]	699	3.7 in der Modelldokumentation.  <p>Einsatz der
	700	dvrp-Software wurde vollständig
[5]	701	überarbeitet.
	702	Sie ist nun als Software-Paket optional im Modell einsetzbar. Siehe
	703	überarbeitetes
[62]	704	Kapitel 4.5.6 in der Modelldokumentation.  </p> <p>Die
	705	Prognose der Partikelverlagerung ist ebenfalls in ein
[5]	706	optionales
[62]	707	Software-Paket ausgelagert.</p> </td> <td>advec_particles,
	708	header, init_3d_model, init_dvrp,
[5]	709	init_particles,
	710	init_pegrid, modules, parin, parles, plot_dvrp, prognostic_equations,
	711	read_var_list,
[62]	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
[5]	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>
[62]	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.
[5]	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>
[62]	728	<td>advec_particles, check_cpu_time, check_open, cpu_auswertung,
[5]	729	init_1d_model,
	730	init_3d_model, init_particles, modules.f90, parin, parles, plot_2d,
[62]	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,
[5]	743	package_parin,
[62]	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>
[5]	749	wurde deshalb von <tt>calc_spectra.f90</tt> nach <tt>modules.f90</tt>
	750	geschoben
[62]	751	(neuer Initialisierungsparameter <tt>fft_method</tt>).
	752	<br>Flüsse können jetzt bei k=1
	753	unabhängig von der
[5]	754	Verwendung
	755	einer Prandtl-Schicht vorgegeben werden (neuer
[62]	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>
[5]	761	Modell kann auf DEC-Workstations eingesetzt werden (-D <tt>dec</tt>).
[62]	762	<br>Zusätzliche Zeitmessungen mit dvrp-Software.
	763	Schreiben von
[5]	764	Partikel-Informationen
	765	ist optional (neuer Parameter <tt>write_particle_informations</tt>).</td>
[62]	766	<td>advec_particles, calc_spectra, check_parameters,
[5]	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
[62]	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>
[5]	776	fehlte in disturb_field.  <br>
	777	Wertebereich von theta* in Prandtl-Fluxes eingeschränkt, weil
[62]	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
[5]	782	Feuchte),
	783	dazu neuer Initialisierungsparameter <tt>passive_scalar</tt>.
[62]	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,
[5]	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,
[62]	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.
[5]	797	Version vom
	798	25/01/01 brach deswegen bei Fortsetzungsläufen ab.  <br>
[62]	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.
[5]	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
[62]	811	von <tt>pres, advec_s_bc, poisfft, production_e, sor </tt>sowie
	812	den
[5]	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
[62]	817	(bisher geschah dies erst nach Aufruf des Drucklösers), haben
	818	sich
[5]	819	die Zahlen in der Testergebnis-Datei geändert. Die mittleren
	820	Profile
[62]	821	sind aber unbeeinflusst.  <p>Eine weitere kleinere
	822	Änderung der Testergebnis-Daten
[5]	823	wird dadurch
	824	verursacht, dass jetzt der Parameter <tt>adjust_mixing_length</tt>
	825	defaultmäßig <tt>.FALSE.</tt>
[62]	826	ist und der Mischungsweg grundsätzlich zusätzlich
	827	auf  <tt>0.7
[5]	828	* zu</tt>   begrenzt wird. Falls <tt>adjust_mixing_length=T</tt>,
[62]	829	wird jetzt der Mischungsweg in <tt>diffusivities</tt>
	830	analog zu <tt>diffusion_e</tt>
[5]	831	an allen Gitterpunkten modifiziert. <b>Achtung: </b>Diese
	832	Änderungen
[62]	833	können bei anderen Simulationen t.w. erhebliche Auswirkungen
	834	auf
[5]	835	die
[62]	836	oberflächennahen Ergebnisse haben.  </p> <p><b>Kleinere
	837	Änderungen:</b> In <tt>init_cloud_physics</tt>
[5]	838	wird
[62]	839	der Wert der Variablen <tt>surface_pressure</tt> in hPa
	840	belassen
[5]	841	(bisher
	842	Umwandlung in Pa).  <br>
	843	Die Namelist-Namen der Software-Pakete sind  t.w.
	844	geändert.  <br>
[62]	845	Unit 14 (binäre Ausgabe für
	846	Fortsetzungsläufe) wird
[5]	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
[62]	855	Galilei-Transformation.  </p> <p>Restliche
	856	deutsche Variablen-, Unterprogramm- und Modulnamen
[5]	857	wurden
	858	ins Englische übersetzt. Davon sind fast alle Programmteile
	859	betroffen
[62]	860	(nicht in rechter Spalte aufgeführt).</p> </td> <td>advec_particles,
	861	advec_s_bc, advec_s_ups, advec_u_ups,
[5]	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,
[62]	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
[5]	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,
[62]	886	damit die durch sie vereinbarten Variablen während der
	887	Rechnung in
	888	keinem Fall undefiniert werden können (diese Gefahr besteht
	889	z.B.
[5]	890	auf
[62]	891	SGI-Origin-Maschinen).</td> <td>advec_particles, header,
	892	init_dvrp, init_particles,
[5]	893	modules.f90, package_parin,
[62]	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,
[5]	903	init_pegrid, modules,
[62]	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
[5]	909	Schwänzen
	910	versehen werden. Die Ausgabe der dvrp-Plotdaten durch einen separaten
	911	PE
[62]	912	ist möglich (mrun-Option "<tt>-p dvrp_graphics+1PE</tt>").
	913	Der
[5]	914	Kommunikator <tt>MPI_COMM_WORLD</tt>
[62]	915	wurde deshalb durch  <tt>comm_palm</tt>
	916	ersetzt.  <p>Reduzierung des Mischungsweges im
	917	Wandbereich kann wahlweise
[5]	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
[62]	922	Grundstroms am unteren Rand wurde verbessert.  </p> <p>Generelle
	923	Verwendung der bodennahen vertikalen
[5]	924	Impulsflüsse in
	925	den Diffusionstermen von u und v, immer wenn diese als Randbedingung
	926	vorgegeben
[62]	927	sind (gemäß <tt>use_surface_fluxes</tt>,
	928	- bisher wurde
[5]	929	dies
	930	nur bei eingeschalteter Prandtl-Schicht gemacht). Schubspannungen
	931	können
	932	jetzt als Randbedingungen vorgegeben werden (allerdings unter
	933	zuhilfenahme
[62]	934	benutzereigener Software).  </p> <p>Zusätzliche
	935	Schnittstellen für benutzereigene
[5]	936	Software in
[62]	937	allen Tendenztermen, in <tt>flow_statistics,</tt> und
	938	für
[5]	939	Partikel-
	940	bzw. dvrp-Programmteile (Bestimmung von Partikeleigenschaften,
	941	Festlegung
[62]	942	von Farbtabellen).  </p> <p><b>Achtung: </b>Diese
	943	Änderungen können bei
[5]	944	Simulationen mit
[62]	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,
[5]	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>
[62]	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
[5]	964	Energieproduktionsterme möglich.
[62]	965	Stördruck wird bei der FFT-Methode nicht mehr durch
	966	Aufsummieren
[5]	967	der
[62]	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
[5]	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
[62]	978	an den seitlichen Rändern der Teilgebiete).  <p><b>Achtung:</b>
	979	Der Inhalt der Testergebnis-Datei ändert
[5]	980	sich durch
[62]	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
[5]	985	ändern. Einschalten
	986	der Partikeladvektion bei Fortsetzungsläufen möglich.</td>
[62]	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
[5]	992	möglich.
[62]	993	Partikeldaten können für spätere Analysen
	994	auf Datei
[5]	995	geschrieben
[62]	996	werden (Unit 85). <tt>PARTICLE</tt>-Datentyp
	997	enthält
[5]	998	Informationen
[62]	999	über Partikelgeschwindigkeitskomponenten und
	1000	Startposition.  <p>Skalartransport sowie entsprechende
	1001	Datenausgaben können
[5]	1002	durch
	1003	eigene Parameter gesteuert werden (nicht mehr über die
[62]	1004	Feuchteparameter).  </p> <p>Im Fall von
	1005	pdims(1)=1 (eindimensionales virtuelles
[5]	1006	Prozessornetz in
	1007	y-Richtung) werden die zyklischen Randbedingungen in x-Richtung durch
	1008	direktes
[62]	1009	Umspeichern anstatt durch  <tt>sendrecv </tt>realisiert.
	1010	Ebenso
[5]	1011	werden
[62]	1012	die Transponierungen xz, yz, zx  und zy eingespart (es wird
	1013	aber
[5]	1014	weiter
[62]	1015	umsortiert).  </p> <p>Im Fall von
	1016	3D-Plotausgaben Aufruf von ftpcopy-Script durch
[5]	1017	batch_scp-Script
	1018	ersetzt (dient der Ermittelung von Dateizyklusnummern als Information
	1019	für
[62]	1020	die AVS-fld-Datei).  </p> <p>Bei fehlerhafter
	1021	Eröffnung einer CPU_MEASURES-Datei
[5]	1022	werden erneute
[62]	1023	Eröffnungsversuche durchgeführt.</p> </td>
	1024	<td>advec_particles, check_open, check_parameters,
[5]	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,
[62]	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
[5]	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
[62]	1038	fälschlicherweise die Zeitebene t+dt verwendet. Asselin-Filter
	1039	ist
[5]	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
[62]	1044	Optimierung.  <p>Fehler bei Berechnung von
	1045	Ausgabezeitpunkten eliminiert (trat
[5]	1046	auf, wenn
[62]	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
[5]	1051	sich durch
[62]	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
[5]	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
[62]	1069	interpoliert.</p> </td> <td nosave="">advec_particles,
	1070	check_parameters, cpu_log,
[5]	1071	global_min_max,
[62]	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
[5]	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
[62]	1083	als Argumente übergeben. Die Tendenzunterprogramme sind als
	1084	Module
	1085	geschrieben, die mittels Technik der überladenen Funktionen
	1086	auch
[5]	1087	ohne
[62]	1088	diese Indices i und j aufgerufen werden können, und dann wie
	1089	in
[5]	1090	früheren
[62]	1091	Versionen funktionieren (d.h. in ihnen laufen die Schleifen
	1092	über
[5]	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
[62]	1100	Gleichungen in einer einzigen (i,j)-Schleife gerechnet. </p> <p><b>Kommunikationsoptimierung:</b>
	1101	Zusätzliche
[5]	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>
[62]	1112	<p><b>Kleinere Anpassungen:</b> String-Vergleiche
	1113	erfordern beim
[5]	1114	IBM-Compiler
[62]	1115	in der Regel den Einsatz der TRIM-Funktion, um
	1116	überschüssige
[5]	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
[62]	1121	(günstiger, um Gefahr von eventuellen Speicherlecks zu
	1122	vermeiden).
[5]	1123	Einige Feldoperationen wurden wegen schlechter Performance auf der IBM
[62]	1124	entfernt (s. pres). </p> <p><b>Achtung: </b>Die
	1125	Übersetzung des Modells erfordert
[5]	1126	aufgrund
	1127	der Vielzahl nunmehr eingesetzter Module die Verwendung des
	1128	make-Mechanismus,
[62]	1129	um die korrekte Reihenfolge bei der Übersetzung der
	1130	Programmteile
	1131	zu gewährleisten. Die Beschreibung dieser
	1132	Abhängigkeiten
[5]	1133	erfolgt
[62]	1134	in der Datei<tt> Makefile</tt>, die zusammen mit den
	1135	Programmdateien
[5]	1136	abgelegt
[62]	1137	ist und ebenfalls unter RCS-Verwaltung steht. </p> <p>Im
	1138	User-Interface ist das Unterprogramm<tt> user_actions </tt>nun
[5]	1139	ebenfalls
[62]	1140	als Modul geschrieben und bedient sich der Methode der
	1141	überladenen
[5]	1142	Funktionen. Existierende benutzereigene Software muss entsprechend
	1143	angepasst
[62]	1144	werden.</p> </td> <td>advec_s_pw, advec_s_up,
	1145	advec_u_pw, advec_u_up, advec_v_pw,
[5]	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,
[62]	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
[5]	1165	werden und
	1166	einen Dichteunterschied zum umgebenden Fluid haben. Zur Steuerung dient
	1167	der neue Paketparameter <tt>density_ratio</tt>.</td>
[62]	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
[5]	1173	und q entfernt
	1174	(obere Feldgrenze von 10 konnte in <tt>pt_vertical_gradient_level_ind</tt>
[62]	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
[5]	1181	entfernt, die
[62]	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
[5]	1190	runtime (d3par)
[62]	1191	parameters <tt>restart_time</tt> and <tt>dt_restart</tt>.
	1192	Run
[5]	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.
[62]	1200	Remaining cpu-time is also evaluated on IBM-Regatta.</td> <td valign="top">cpu_log, cpu_statistics,
[5]	1201	check_parameters,header, leap_frog,
[62]	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
[5]	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.
[62]	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>
[5]	1218	Additional optimization of the hybrid-solver for multinode usage
	1219	(overlapping
[62]	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
[5]	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
[62]	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
[5]	1237	sendrecv
[62]	1238	in case of a 1d-decomposition along <tt>x</tt>. SENDRECV
	1239	replaced by
[5]	1240	nonblocking
	1241	routines ISEND and IRECV in <tt>exchange_horiz.f90</tt>. </p>
[62]	1242	<p>Speed optimization by removing MINVAL/MAXVAL calls and by
[5]	1243	handling <br>
	1244	the "abs" case in a different way than the min/max cases (routine <tt>global_min_max</tt>).</p>
[62]	1245	</td> <td valign="top">asselin_filter, check_open,
	1246	exchange_horiz,
[5]	1247	global_min_max,
	1248	init_3d_model, init_pegrid, parin, poisfft_hybrid, read_var_list,
	1249	timestep,
[62]	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)).
[5]	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>,
[62]	1257	which is set to 1.8 in <tt>modules.f90</tt>. The factor
	1258	0.7 was the
[5]	1259	possible
[62]	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
[5]	1264	MPI_FINALIZE is called before STOP in case of a parallel environment. </p>
[62]	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,
[5]	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,
[62]	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
[5]	1281	particles in
	1282	case of zero density ratio. Steering of variables by dvrp browser
[62]	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
[5]	1287	(needed
	1288	on linux machines <br>
	1289	due to the little/big endian problem). Updates for new version of dvrp
[62]	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
[5]	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
[62]	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>
[5]	1307	is added, where cache optimizations are undone. The tendency
	1308	subroutines
[62]	1309	called by <tt>prognostic_equations_vec</tt> contain the
	1310	full 3d-loops
[5]	1311	(compared
	1312	with the cache-optimized versions where only loops over k are carried
	1313	out).
[62]	1314	Additionally, a new pressure solver <tt>poisfft_hybrid_vec</tt>
	1315	is
[5]	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>.
[62]	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>
[5]	1325	which
	1326	caused run time errors on IBM and NEC due to compiler problems. </p>
[62]	1327	<p>Reading of environment variable <tt>tasks_per_node</tt>
	1328	moved
[5]	1329	from routine <tt>poisfft_hybrid</tt>
[62]	1330	to routine <tt>parin</tt>. </p> <p><b>Changes
	1331	in makefile:</b> modules and user_interface now
[5]	1332	depend on
	1333	the f90 files, dependency of singleton added, LDFLAGS moved to the end
[62]	1334	of PROG rule, temperton_fft added.</p> </td> <td valign="top">advec_s_pw, advec_s_up, advec_u_pw, advec_u_up,
[5]	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,
[62]	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
[5]	1349	calling sor
[62]	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
[5]	1355	(for equal
[62]	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
[5]	1362	the right
[62]	1363	column!</p> </td> <td valign="top">asselin_filter,
	1364	check_parameters, diffusion_e,
[5]	1365	diffusivities,
	1366	disturb_field, global_min_max, header, local_tremain, modules, parin,
	1367	poisfft_hybrid,
[62]	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
[5]	1371	(velocity must
[62]	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
[5]	1378	decomposition.
	1379	Abort in case of Temperton fft, if number of gridpoints along x and/or
[62]	1380	y contain illegal factors.  </p> <p>Index values
	1381	for the extrema found in global_min_max are
[5]	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>
[62]	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,
[5]	1388	global_min_max, init_pegrid,
[62]	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>
[5]	1392	and <tt>host</tt>
[62]	1393	(<tt>hybrid_solver</tt> must not be used for a
	1394	2d-domain-decomposition, <tt>host</tt>
[5]	1395	should be set by setting environment variable <tt>localhost</tt>).
[62]	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
[5]	1402	and Intel
[62]	1403	FORTRAN compiler (ifc)</b> <p>So far, only absolutely
	1404	neccessary changes have been done
[5]	1405	(possible
[62]	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
[5]	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
[62]	1414	module (named <tt>mpi</tt>).  I did not find out
	1415	how character
[5]	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
[62]	1421	PE. </p> <p>On the MUK-cluster, only PE0 is able to read
	1422	the values of
[5]	1423	environment
	1424	variables. Therefore, these values are communicated via broadcast to
	1425	the
[62]	1426	other PEs. </p> <p>1d-decomposition is set as the default
	1427	on Linux Clusters.
[5]	1428	Character
[62]	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,
[5]	1433	init_pegrid, local_getenv,
[62]	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>,
[5]	1437	which allows correct measurements for jobs running over the 24:00
[62]	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
[5]	1443	integral divisor
[62]	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
[5]	1448	removed. It
	1449	was caused by the Linux changes of version 2.7 and led to program abort
[62]	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
[5]	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>
[62]	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,
[5]	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>.
[62]	1471	<p>Particle groups implemented. New data type<tt>
[5]	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>
[62]	1476	diameter</tt>. Parameter name<tt> uniform_psize</tt>
	1477	changed to<tt>
[5]	1478	dvrp_psize</tt>.
	1479	Parameters<tt> density_ratio </tt>is now an array.</p>
[62]	1480	</td> <td valign="top">advec_particles, check_open,
	1481	exchange_horiz,
[5]	1482	header, init_particles,
[62]	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
[5]	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
[62]	1490	numbers. New binary version 2.2. <p>Buffer is flushed for file
	1491	RUN_CONTROL immediately after every
[5]	1492	output
[62]	1493	on IBM and Linux cluster.</p> </td> <td valign="top">advec_particles,
	1494	disturb_field, init_3d_model,
[5]	1495	init_particles,
[62]	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
[5]	1500	is now
	1501	taken from array hom instead of array sums (otherwise inconsistence in
[62]	1502	case of using more than one statistical region). <p>Information
	1503	about the time of the last timestep change added
[5]	1504	to the
[62]	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
[5]	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
[62]	1514	former default leapfrog scheme.  The intermediate steps, which
	1515	are
[5]	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;">
[62]	1518	leap_frog</span>, but this routine will be renamed soon).
	1519	Steering
[5]	1520	variables<span style="font-family: monospace;">
[62]	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>.
[5]	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;">
[62]	1528	timestep_scheme_steering</span>. <p>When using Runge-Kutta
	1529	schemes,  the timestep increment
[5]	1530	is freely
	1531	allowed to adjust after each timestep (the older schemes are using some
[62]	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
[5]	1536	not automatically called in case of timestep changes, when Runge-Kutta
[62]	1537	schemes are switched on. </p> <p>The old leapfrog scheme
	1538	is still implemented and should
[5]	1539	produce the
[62]	1540	same results as in the previous version(s)! </p> <p>Depending
	1541	on the user experience, further adjustments to the
[5]	1542	Runge-Kutta
	1543	schemes may be necessary within the next minor versions.  </p>
[62]	1544	<p><span style="font-weight: bold;">Attention:</span>
	1545	<br>
[5]	1546	The content of the testresult-file (run control output) has
	1547	significantly
[62]	1548	changed due to the new default timestep scheme!</p> </td> <td style="vertical-align: top;">check_parameters, header,
[5]	1549	init_3d_model,
	1550	init_rankine, leap_frog, modules, prognostic_equations, read_var_list,
[62]	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
[5]	1554	subroutine<span style="font-family: monospace;">
[62]	1555	allocate_prt_memory </span>on demand only. <p>Type<span style="font-family: monospace;"> log </span>(used
[5]	1556	for
	1557	cpu time measurements) changed to<span style="font-family: monospace;">
[62]	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
[5]	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;">
[62]	1565	init_particles</span>), in order to avoid the possibility of
	1566	hanging
[5]	1567	jobs,
	1568	which may occur if unit 80 is opened within routine<span style="font-family: monospace;">
[62]	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
[5]	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;">
[62]	1578	nzb_2d </span>in many of the three-dimensional loops. So
	1579	far, all
[5]	1580	elements of this array are set to<span style="font-family: monospace;">
[62]	1581	nzb</span>. <p>This change should not effect simulation
	1582	results and cpu time
[5]	1583	in any
[62]	1584	way.</p> </td> <td style="vertical-align: top;">advec_s_pw,
	1585	advec_s_up,
[5]	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,
[62]	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
[5]	1595	removed in
	1596	the run control output in case of Runge-Kutta schemes. Also, the
	1597	timestep
[62]	1598	increment limitation is removed for the Runge-Kutta schemes. <p><span style="font-weight: bold;">Attention:</span> <br>
[5]	1599	The content of the testresult-file (run control output) has changed
[62]	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
[5]	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>)
[62]	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
[5]	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.
[62]	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
[5]	1625	all processors. This new feature is switched on by setting the
[62]	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
[5]	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
[62]	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
[5]	1641	faster when running PALM on more than one node of the IBM-Regatta,
[62]	1642	although the difference is not very big. The <span style="font-family: monospace;">poisfft</span>-code
	1643	for a
[5]	1644	decomposition along y has still a poor performance and needs further
[62]	1645	optimization.<br> <br>
[5]	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
[62]	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
[5]	1654	quantity arrays are allocated for previous timelevels only in case of
[62]	1655	leapfrog scheme.<br> <br>
[5]	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
[62]	1660	internal compiler errors).<br> </td> <td style="vertical-align: top;">advec_s_ups, advec_u_ups,
[5]	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,
[62]	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>
[5]	1670	For all transpositions, MPI_ALLTOALL is used instead of MPI_ALLTOALLV.
[62]	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,
[5]	1680	flow_statistics, header, init_1d_model, init_3d_model, init_advec,
	1681	init_pegrid, palm, parin, poisfft, poisfft_hybrid, production_e,
[62]	1682	prognostic_equations, read_var_list, sline_x, spline_y, write_var_list<span style="font-weight: bold;"><br> <br>
[5]	1683	new:</span><br>
[62]	1684	fft_xy, read_3d_binary, time_integration, transpose<br> <br>
	1685	<span style="font-weight: bold;">deleted:</span><br>
[5]	1686	fft_for_1d_decomp, leap_frog, transpose_xy, transpose_xz, transpose_yx,
[62]	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
[5]	1690	particle-package removed, which sometimes caused aborts of restart runs
[62]	1691	on IBM.<br> <br>
[5]	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>
[62]	1694	<br>
[5]	1695	Function fft (singleton method) replaced by subroutine fftn due to
[62]	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
[5]	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
[62]	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
[5]	1710	additional arguments. Boundary conditions are set with new
[62]	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>).
[5]	1718	Non-cyclic conditions require the use of the multigrid-method for
[62]	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>
[5]	1723	Minor changes:<br>
[62]	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,
[5]	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>
[62]	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
[5]	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;">
[62]	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>
[5]	1744	The content of the testresult-file (run control output) has changed
[62]	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,
[5]	1752	diffusivities, modules, poismg, pres, time_integration,
[62]	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>
[5]	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
[62]	1759	faster).<br> <br>
[5]	1760	Two errors concerning switch to PE0 (multigrid method) removed from<span style="font-family: monospace;"> init_pegrid</span>.<br>
[62]	1761	<br>
	1762	Two errors in<span style="font-family: monospace;">
	1763	plot_2d </span>removed:
[5]	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
[62]	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>
[5]	1773	Wrong re-definition of dx2 and dy2 in<span style="font-family: monospace;"> sor </span>removed.<br>
[62]	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
[5]	1781	incompatibilities between non-cyclic lateral boundary conditions and
[62]	1782	other schemes.<br> <br>
	1783	fcl_factor renamed cfl_factor.<br> <br>
[5]	1784	New local array sums_ll declared in flow_statistics instead of
[62]	1785	temporarily using sums_l.<br> <br>
[5]	1786	crmax (maximum number of crosses allowed in a plot of vertical
[62]	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
[5]	1792	time counters regarding a possible decrease of the output time interval
[62]	1793	in case of restart runs.<br> <br>
[5]	1794	Error removed in Dirichlet bottom boundary conditions for pt and q in
[62]	1795	case of Runge-Kutta schemes.<br> <br> <span style="font-weight: bold;">batch_scp</span> calls
	1796	(needed
[5]	1797	for determining correct filenames for AVS-fld-files) is given the
[62]	1798	remote username as an additional argument.<br> <br>
	1799	Default setting of outflow_damping_width corrected.<br> <br>
[5]	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
[62]	1802	resulting too small timesteps.<br> <br>
[5]	1803	Implicit counters i renamed i9 in modules due to declaration conflicts
[62]	1804	with i in other subroutines (reported by Portland compiler).<br> </td>
	1805	<td style="vertical-align: top;">advec_particles,
	1806	boundary_conds,
[5]	1807	check_open, check_parameters, init_1d_model, modules, time_integration<br>
[62]	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>
[5]	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
[62]	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>
[5]	1818	Output of cross sections for qv, vpt and lwp (liquid water path).<br>
[62]	1819	</td> <td style="vertical-align: top;">advec_particles,
	1820	check_open,
[5]	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>
[62]	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
[5]	1826	number of spectra (formerly, the number of spectra was given by n-1)<br>
[62]	1827	<br>
[5]	1828	Abort if <span style="font-family: monospace;">poisfft_hybrid</span>
[62]	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
[5]	1844	implemented, which explicitly simulates single cloud droplets,
	1845	including droplet growth by condensation and collision. Using this code
[62]	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
[5]	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,
[62]	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>
[5]	1887	No opening of units 101 - 108 in case of missing NetCDF support.</td>
[62]	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
[5]	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
[62]	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,
[5]	1905	check_parameters, coriolis, header, init_1d_model, modules, parin,
	1906	prognostic_equations, read_var_list, spline_z, write_var_list<br>
[62]	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
[5]	1908	and
[62]	1909	v_0 in production_e.f90 removed.<br> <br> <span style="font-weight: bold;">Attention:</span> <br>
[5]	1910	The content of the testresult-file (run control output) has changed
[62]	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
[5]	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
[62]	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
[5]	1936	in case of the first respective intermediate timestep. This is done in
	1937	order to spare communication time and to produce identical model
[62]	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
[5]	1945	the implementation of topography, this version contains several other
[62]	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>
[5]	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
[62]	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
[5]	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)
[62]	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
[5]	2005	conservation of the volume flow (through the complete xz- and
	2006	yz-sections  of the total domain) can be enforced by the new
[62]	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
[5]	2017	(large file support) on most machines. The user can switch to the
[62]	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
[5]	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
[62]	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
[5]	2027	the dissipation can be used in the 1d-model. These are steered by the
[62]	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,
[5]	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,
[62]	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>
[5]	2045	plot_spectra -> data_output_spectra<br>
	2046	plot_ts -> data_output_tseries<br>
[62]	2047	plot_1d -> data_output_profiles<br> <span style="font-weight: bold;"></span>plot_2d ->
	2048	data_output_2d<br>
[5]	2049	plot_3d -> data_output_3d<br>
[62]	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
[5]	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
[62]	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>
[5]	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>
[62]	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>
[5]	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>
[62]	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>
[5]	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>
[62]	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
[5]	2125	directives have been added where necessary. Still further tuning will
	2126	be necessary to get optimum performance. Other parts of the code than
[62]	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
[5]	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
[62]	2138	global sum is computed via MPI_ALLREDUCE.  For storing the
	2139	thread
[5]	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
[62]	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-
[5]	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
[62]	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
[5]	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
[62]	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,
[5]	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,
[62]	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
[5]	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
[62]	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>
[5]	2213	The content of the testresult-file (run control output) has changed
[62]	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
[5]	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
[62]	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>
[45]	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,
[40]	2252	diffusion_s, flow_statistics, header, init_grid, init_3d_model,
	2253	modules, parin, production_e, prognostic_equations, read_var_list,
[62]	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
[77]	2255	scalars are now solved up to gridpoint nzt (formerly nzt-1).
[62]	2256	Boundary conditions for scalars at top adjusted respectively (now
[77]	2257	applied only at nzt+1).<br><br>The
[62]	2258	default top boundary condition for temperature has been renamed to <span style="font-style: italic;">'initial_gradient'</span>.<br><br>Calls
[77]	2259	of dvrp_output_local,
[62]	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,
[40]	2262	boundary_conds, calc_precipitation, check_parameters, diffusion_e,
	2263	diffusion_s, impact_of_latent_heat, init_dvrp, init_pt_anomaly,
[77]	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,
[83]	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,
[90]	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
[98]	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
[97]	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.
[110]	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.
[111]	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,
[110]	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,
[139]	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,
[198]	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>
[62]	2437	</tbody>
	2438	</table> <b><blink>Attention:</blink></b>
	2439	If<tt> make </tt>is not used
[5]	2440	for
	2441	compiling,
[62]	2442	<b>all routines</b> have to be re-compiled after every
	2443	change
[5]	2444	to <b>modules.f90!</b>
[62]	2445	<br>
	2446	<br>
	2447	<h2><a name="Kapitel2.0"></a>2.0  How
	2448	to change the model source
[5]	2449	code</h2>
	2450	Änderungen, Erweiterungen oder Fehlerkorrekturen am Modellcode
	2451	(gemeint
	2452	sind alle Modellteile, die nicht zur benutzereigenen Software
	2453	gehören)
[62]	2454	erfordern vom jeweiligen Benutzer Gruppenzugehörigkeit zur
	2455	Gruppe
[5]	2456	<tt>"palm"</tt>.
	2457	Zu dieser Gruppe gehören alle Benutzer, die aktiv an der
	2458	Modellentwicklung
	2459	mitwirken (im weiteren "Modellarbeitsgruppe" genannt).
[62]	2460	<p>Die einzelnen Quelltextdateien des Modells werden mit RCS
	2461	(Revision
[5]	2462	Control System) verwaltet. Grundlegende Kenntnisse über dieses
	2463	System
	2464	werden im weiteren vorausgesetzt.
[62]	2465	</p><p>Änderungen am Modellcode erfordern die
	2466	Durchführung
[5]	2467	bestimmter
	2468	Aktionen in einer festgelegten Reihenfolge, die nun beschrieben werden
	2469	sollen.
[62]	2470	</p><ol> <li>Konzeptplanung.</li> <li>Diskussion
	2471	der geplanten Änderungen in der
	2472	Modellarbeitsgruppe.</li> <li>Auschecken der
	2473	benötigten Quelltextdateien,
[5]	2474	Durchführung der
	2475	Änderungen und Test des Modells. Die Modul-Datei <tt>modules.f90</tt>
	2476	sollte nur dann ausgecheckt werden, wenn dort aufgeführte
	2477	Variablen
[62]	2478	verändert werden. Neu geschaffene Variablen sollten
	2479	während
[5]	2480	der
	2481	Testphase in ein ebenfalls temporär neu zu schaffendes Modul
	2482	geschrieben
	2483	werden, das von den jeweiligen Programmteilen benutzt werden muss
	2484	(Einfügen
	2485	entsprechender USE-Anweisungen). Die in den einzelnen Dateien
	2486	durchgeführten
[62]	2487	Arbeiten müssen in den Kopfzeilen (unter "Aktuelle
	2488	Aenderungen")
[5]	2489	der
[62]	2490	Dateien vermerkt werden. Dies tut man am besten noch <b>bevor</b>
	2491	man
[5]	2492	die
	2493	eigentlichen Änderungen durchführt (sonst droht das
[62]	2494	Vergessen...).</li> <li>Zum Abschluß der Tests
	2495	sollte mit dem Modell eine
[5]	2496	Kontrollrechnung
	2497	durchgeführt und die Ergebnisse mit denen des sogenannten
	2498	Standardlaufes
	2499	verglichen werden. Diese Rechnung ist mit der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/.mrun.config">Konfigurationsdatei</a>
	2500	und der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_p3d">Parameterdatei</a>
	2501	durchzuführen, die auch zum Testen der Modellinstallation
	2502	verwendet
[62]	2503	werden (s. <a href="Anwendung/Kapitel_5.0.html">Kapitel
	2504	5.0</a> der
[5]	2505	Anwenderdokumentation).
	2506	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>
	2507	ist dann mit der <a href="http://www.muk.uni-hannover.de/%7Eraasch/PALM_group/INSTALL/example_rc">Beispiel-Ergebnisdatei</a>
	2508	zu vergleichen (Hinweis: Kopien der Konfigurationsdatei, Parameterdatei
	2509	und Beispiel-Ergebnisdatei erhält man durch anklicken der
	2510	entsprechenden
	2511	Links mit der linken Maustaste bei gleichzeitig gedrückter
	2512	<SHIFT>-Taste).
	2513	Werden Abweichungen zwischen den beiden Ergebnisdateien festgestellt,
	2514	so
	2515	ist unbedingt eine Diskussion in der Modellarbeitsgruppe notwendig.</li>
[62]	2516	<li>Nach Durchführung der Tests müssen bei
	2517	Bedarf die
[5]	2518	vorläufig
[62]	2519	im temporären Modul eingetragenen Variablen in die
	2520	eigentlichen
[5]	2521	Module
	2522	des Modells übertragen werden. Dazu ist die Modul-Datei <tt>modules.f90</tt>
	2523	auszuchecken. Nach Eintrag der Variablen sollte das Modell noch einmal
[62]	2524	testweise übersetzt werden, um Sytaxfehler
	2525	auszuschließen
[5]	2526	(evtl.
	2527	auch noch einmal einen Probelauf starten). Die Verwendung des
	2528	temporären
	2529	Moduls ist aus allen entsprechenden Programmteilen zu entfernen.</li>
[62]	2530	<li>Vergabe einer neuen Versionsnummer (Variable <tt>version</tt>
	2531	im
[5]	2532	Modul <tt>steuer</tt>),
[62]	2533	Bsp.: 2.3c. Kleinere Änderungen werden durch
	2534	angehängten
[5]	2535	kleinen
[62]	2536	Buchstaben kenntlich gemacht, größere
	2537	Änderungen durch
[5]	2538	die Zahl hinter dem Punkt. Eine Inkrementierung der Zahl vor dem Punkt
[62]	2539	geschieht nur bei ganz grundsätzlichen Revisionen des Modells,
	2540	die
	2541	weite Teile des Modellcodes betreffen.</li> <li>Nun
	2542	können die ausgecheckten Dateien wieder eingecheckt
[5]	2543	werden.
	2544	Vor
	2545	dem Einchecken sind in den Dateien die Vermerke unter "Aktuelle
	2546	Aenderungen"
	2547	zu entfernen und beim check-in - Kommando als Log-Text anzugeben. Sie
	2548	erscheinen
	2549	dann in der jeweiligen Datei unter "Fruehere Aenderungen" zusammen mit
	2550	der vom RCS-System vergebenen Versionsnummer (dafür sorgt die
	2551	$Log:
[62]	2552	... $ - Zeile, die in jeder Quelltextdatei steht).</li> <li>Eine
	2553	Zusammenfassung der durchgeführten Arbeiten ist im <a href="#Kapitel1.0">Kapitel
	2554	1.0</a> einzutragen.</li> <li>Die
	2555	Modellarbeitsgruppe ist über den Abschluß der
[5]	2556	durchgeführten
	2557	Arbeiten zu informieren.</li>
[62]	2558	</ol><h2>
	2559	<a name="Kapitel3.0"></a>3.0  Description
	2560	of selected parts of the
[5]	2561	model source code</h2>
	2562	<b>This chapter is still under construction (Feb. 04).</b>
[62]	2563	<p>Dieser Abschnitt verweist auf vorhandene Beschreibungen der
	2564	genauen
	2565	Funktionsweise einzelner, spezieller Modellteile. Dazu gehört
	2566	z.B.
[5]	2567	die Beschreibung bestimmter numerischer Verfahren (auch ihr
	2568	theoretischer
	2569	Hintergrund), die Erklärung besonderer Prinzipien bei der
	2570	Parallelisierung
	2571	oder Erläuterungen zur Vorgehensweise bei der Lösung
	2572	bestimmter
	2573	Aufgaben (z.B. der Berechnung horizontal gemittelter
	2574	Größen).
[62]	2575	<br>Die Beschreibungen liegen in jeweils getrennten Dokumenten,
	2576	in der
[5]	2577	Regel als TeX- und/oder Postscript-Datei vor und sind über die
	2578	folgenden
	2579	Links zugänglich.
[62]	2580	<br>
	2581	</p><ul> <li> <a name="UPS"></a>upstream-spline
	2582	advection scheme ( <a href="Upstream_Spline/ups.ps">.ps</a>
	2583	)</li> <li> <a name="Cloud_physics"></a>cloud
	2584	physics module ( <a href="Cloud_physics/wolken.pdf">.pdf</a>
	2585	)</li> <li> <a name="Bitkompression"></a>Datenkompression
	2586	mit dem Verfahren
[5]	2587	der <a href="Bitkompression/kompression.html">Bitverschiebung</a></li>
[62]	2588	<li> <a name="Runge-kutta"></a>Runge-Kutta
	2589	time integration scheme ( <a href="numerik.heiko/zeitschrittverfahren.pdf">.pdf</a>
[5]	2590	)</li>
[62]	2591	</ul><br>
[5]	2592
[62]	2593	<br>
	2594	<br>
	2595	<br>
	2596	<br>
	2597	<br>
	2598	<br>
	2599	<br>
[139]	2600	</body></html>

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