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source: palm/trunk/SOURCE/init_3d_model.f90 @ 364

Last change on this file since 364 was 359, checked in by letzel, 15 years ago
Bugfix for extended NetCDF files: In order to avoid 'data mode' errors if updated attributes are larger than their original size, NF90_PUT_ATT is called in 'define mode' enclosed by NF90_REDEF and NF90_ENDDEF calls. This implies a possible performance loss; an alternative strategy would be to ensure equal attribute size in a job chain. (netcdf) Changed: For extended NetCDF files, the updated title attribute includes an update of time_average_text where appropriate. (netcdf) Bugfix: correction of initial volume flow for non-flat topography (init_3d_model) Bugfix: zero initialization of arrays within buildings for 'cyclic_fill' (init_3d_model) New: MPI debug option (mrun) Documentation updates: topography file format (chapter 3.5.4) NC identifier range expanded to 444 (appendix_a)
Property svn:keywords set to `Id`
File size: 54.9 KB

Line
1	#if defined( __ibmy_special )
2	@PROCESS NOOPTimize
3	#endif
4	SUBROUTINE init_3d_model
5
6	!------------------------------------------------------------------------------!
7	! Current revisions:
8	! -----------------
9	! bugfix: correction of initial volume flow for non-flat topography
10	! bugfix: zero initialization of arrays within buildings for 'cyclic_fill'
11	! bugfix: avoid that ngp_2dh_s_inner becomes zero
12	! initializing_actions='read_data_for_recycling' renamed to 'cyclic_fill', now
13	! independent of turbulent_inflow
14	! Output of messages replaced by message handling routine.
15	! Set the starting level and the vertical smoothing factor used for
16	! the external pressure gradient
17	! +conserve_volume_flow_mode: 'default', 'initial_profiles', 'inflow_profile'
18	! and 'bulk_velocity'
19	! If the inversion height calculated by the prerun is zero,
20	! inflow_damping_height must be explicitly specified.
21	!
22	! Former revisions:
23	! -----------------
24	! $Id: init_3d_model.f90 359 2009-08-19 16:56:44Z letzel $
25	!
26	! 181 2008-07-30 07:07:47Z raasch
27	! bugfix: zero assignments to tendency arrays in case of restarts,
28	! further extensions and modifications in the initialisation of the plant
29	! canopy model,
30	! allocation of hom_sum moved to parin, initialization of spectrum_x\|y directly
31	! after allocating theses arrays,
32	! read data for recycling added as new initialization option,
33	! dummy allocation for diss
34	!
35	! 138 2007-11-28 10:03:58Z letzel
36	! New counter ngp_2dh_s_inner.
37	! Allow new case bc_uv_t = 'dirichlet_0' for channel flow.
38	! Corrected calculation of initial volume flow for 'set_1d-model_profiles' and
39	! 'set_constant_profiles' in case of buildings in the reference cross-sections.
40	!
41	! 108 2007-08-24 15:10:38Z letzel
42	! Flux initialization in case of coupled runs, +momentum fluxes at top boundary,
43	! +arrays for phase speed c_u, c_v, c_w, indices for u\|v\|w_m_l\|r changed
44	! +qswst_remote in case of atmosphere model with humidity coupled to ocean
45	! Rayleigh damping for ocean, optionally calculate km and kh from initial
46	! TKE e_init
47	!
48	! 97 2007-06-21 08:23:15Z raasch
49	! Initialization of salinity, call of init_ocean
50	!
51	! 87 2007-05-22 15:46:47Z raasch
52	! var_hom and var_sum renamed pr_palm
53	!
54	! 75 2007-03-22 09:54:05Z raasch
55	! Arrays for radiation boundary conditions are allocated (u_m_l, u_m_r, etc.),
56	! bugfix for cases with the outflow damping layer extending over more than one
57	! subdomain, moisture renamed humidity,
58	! new initializing action "by_user" calls user_init_3d_model,
59	! precipitation_amount/rate, ts_value are allocated, +module netcdf_control,
60	! initial velocities at nzb+1 are regarded for volume
61	! flow control in case they have been set zero before (to avoid small timesteps)
62	! -uvmean_outflow, uxrp, vynp eliminated
63	!
64	! 19 2007-02-23 04:53:48Z raasch
65	! +handling of top fluxes
66	!
67	! RCS Log replace by Id keyword, revision history cleaned up
68	!
69	! Revision 1.49 2006/08/22 15:59:07 raasch
70	! No optimization of this file on the ibmy (Yonsei Univ.)
71	!
72	! Revision 1.1 1998/03/09 16:22:22 raasch
73	! Initial revision
74	!
75	!
76	! Description:
77	! ------------
78	! Allocation of arrays and initialization of the 3D model via
79	! a) pre-run the 1D model
80	! or
81	! b) pre-set constant linear profiles
82	! or
83	! c) read values of a previous run
84	!------------------------------------------------------------------------------!
85
86	USE arrays_3d
87	USE averaging
88	USE cloud_parameters
89	USE constants
90	USE control_parameters
91	USE cpulog
92	USE indices
93	USE interfaces
94	USE model_1d
95	USE netcdf_control
96	USE particle_attributes
97	USE pegrid
98	USE profil_parameter
99	USE random_function_mod
100	USE statistics
101
102	IMPLICIT NONE
103
104	INTEGER :: i, ind_array(1), j, k, sr
105
106	INTEGER, DIMENSION(:), ALLOCATABLE :: ngp_2dh_l, ngp_3d_inner_l
107
108	INTEGER, DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l, &
109	ngp_2dh_s_inner_l
110
111	REAL :: a, b
112
113	REAL, DIMENSION(1:2) :: volume_flow_area_l, volume_flow_initial_l
114
115
116	!
117	!-- Allocate arrays
118	ALLOCATE( ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
119	ngp_3d(0:statistic_regions), &
120	ngp_3d_inner(0:statistic_regions), &
121	ngp_3d_inner_l(0:statistic_regions), &
122	sums_divnew_l(0:statistic_regions), &
123	sums_divold_l(0:statistic_regions) )
124	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt) )
125	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
126	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
127	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
128	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
129	rmask(nys-1:nyn+1,nxl-1:nxr+1,0:statistic_regions), &
130	sums(nzb:nzt+1,pr_palm+max_pr_user), &
131	sums_l(nzb:nzt+1,pr_palm+max_pr_user,0:threads_per_task-1), &
132	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
133	sums_up_fraction_l(10,3,0:statistic_regions), &
134	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions), &
135	ts_value(var_ts,0:statistic_regions) )
136	ALLOCATE( km_damp_x(nxl-1:nxr+1), km_damp_y(nys-1:nyn+1) )
137
138	ALLOCATE( rif_1(nys-1:nyn+1,nxl-1:nxr+1), shf_1(nys-1:nyn+1,nxl-1:nxr+1), &
139	ts(nys-1:nyn+1,nxl-1:nxr+1), tswst_1(nys-1:nyn+1,nxl-1:nxr+1), &
140	us(nys-1:nyn+1,nxl-1:nxr+1), usws_1(nys-1:nyn+1,nxl-1:nxr+1), &
141	uswst_1(nys-1:nyn+1,nxl-1:nxr+1), &
142	vsws_1(nys-1:nyn+1,nxl-1:nxr+1), &
143	vswst_1(nys-1:nyn+1,nxl-1:nxr+1), z0(nys-1:nyn+1,nxl-1:nxr+1) )
144
145	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
146	!
147	!-- Leapfrog scheme needs two timelevels of diffusion quantities
148	ALLOCATE( rif_2(nys-1:nyn+1,nxl-1:nxr+1), &
149	shf_2(nys-1:nyn+1,nxl-1:nxr+1), &
150	tswst_2(nys-1:nyn+1,nxl-1:nxr+1), &
151	usws_2(nys-1:nyn+1,nxl-1:nxr+1), &
152	uswst_2(nys-1:nyn+1,nxl-1:nxr+1), &
153	vswst_2(nys-1:nyn+1,nxl-1:nxr+1), &
154	vsws_2(nys-1:nyn+1,nxl-1:nxr+1) )
155	ENDIF
156
157	ALLOCATE( d(nzb+1:nzta,nys:nyna,nxl:nxra), &
158	e_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
159	e_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
160	e_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
161	kh_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
162	km_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
163	p(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
164	pt_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
165	pt_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
166	pt_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
167	tend(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
168	u_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
169	u_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
170	u_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
171	v_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
172	v_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
173	v_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
174	w_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
175	w_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
176	w_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
177
178	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
179	ALLOCATE( kh_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
180	km_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
181	ENDIF
182
183	IF ( humidity .OR. passive_scalar ) THEN
184	!
185	!-- 2D-humidity/scalar arrays
186	ALLOCATE ( qs(nys-1:nyn+1,nxl-1:nxr+1), &
187	qsws_1(nys-1:nyn+1,nxl-1:nxr+1), &
188	qswst_1(nys-1:nyn+1,nxl-1:nxr+1) )
189
190	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
191	ALLOCATE( qsws_2(nys-1:nyn+1,nxl-1:nxr+1), &
192	qswst_2(nys-1:nyn+1,nxl-1:nxr+1) )
193	ENDIF
194	!
195	!-- 3D-humidity/scalar arrays
196	ALLOCATE( q_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
197	q_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
198	q_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
199
200	!
201	!-- 3D-arrays needed for humidity only
202	IF ( humidity ) THEN
203	ALLOCATE( vpt_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
204
205	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
206	ALLOCATE( vpt_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
207	ENDIF
208
209	IF ( cloud_physics ) THEN
210	!
211	!-- Liquid water content
212	ALLOCATE ( ql_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
213	!
214	!-- Precipitation amount and rate (only needed if output is switched)
215	ALLOCATE( precipitation_amount(nys-1:nyn+1,nxl-1:nxr+1), &
216	precipitation_rate(nys-1:nyn+1,nxl-1:nxr+1) )
217	ENDIF
218
219	IF ( cloud_droplets ) THEN
220	!
221	!-- Liquid water content, change in liquid water content,
222	!-- real volume of particles (with weighting), volume of particles
223	ALLOCATE ( ql_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
224	ql_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
225	ql_v(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
226	ql_vp(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
227	ENDIF
228
229	ENDIF
230
231	ENDIF
232
233	IF ( ocean ) THEN
234	ALLOCATE( saswsb_1(nys-1:nyn+1,nxl-1:nxr+1), &
235	saswst_1(nys-1:nyn+1,nxl-1:nxr+1) )
236	ALLOCATE( rho_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
237	sa_1(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
238	sa_2(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
239	sa_3(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
240	rho => rho_1 ! routine calc_mean_profile requires density to be a
241	! pointer
242	IF ( humidity_remote ) THEN
243	ALLOCATE( qswst_remote(nys-1:nyn+1,nxl-1:nxr+1) )
244	qswst_remote = 0.0
245	ENDIF
246	ENDIF
247
248	!
249	!-- 3D-array for storing the dissipation, needed for calculating the sgs
250	!-- particle velocities
251	IF ( use_sgs_for_particles ) THEN
252	ALLOCATE ( diss(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
253	ELSE
254	ALLOCATE ( diss(2,2,2) ) ! required because diss is used as a
255	! formal parameter
256	ENDIF
257
258	IF ( dt_dosp /= 9999999.9 ) THEN
259	ALLOCATE( spectrum_x( 1:nx/2, 1:10, 1:10 ), &
260	spectrum_y( 1:ny/2, 1:10, 1:10 ) )
261	spectrum_x = 0.0
262	spectrum_y = 0.0
263	ENDIF
264
265	!
266	!-- 3D-arrays for the leaf area density and the canopy drag coefficient
267	IF ( plant_canopy ) THEN
268	ALLOCATE ( lad_s(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
269	lad_u(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
270	lad_v(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
271	lad_w(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
272	cdc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
273
274	IF ( passive_scalar ) THEN
275	ALLOCATE ( sls(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
276	sec(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
277	ENDIF
278
279	IF ( cthf /= 0.0 ) THEN
280	ALLOCATE ( lai(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1), &
281	canopy_heat_flux(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
282	ENDIF
283
284	ENDIF
285
286	!
287	!-- 4D-array for storing the Rif-values at vertical walls
288	IF ( topography /= 'flat' ) THEN
289	ALLOCATE( rif_wall(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1,1:4) )
290	rif_wall = 0.0
291	ENDIF
292
293	!
294	!-- Velocities at nzb+1 needed for volume flow control
295	IF ( conserve_volume_flow ) THEN
296	ALLOCATE( u_nzb_p1_for_vfc(nys:nyn), v_nzb_p1_for_vfc(nxl:nxr) )
297	u_nzb_p1_for_vfc = 0.0
298	v_nzb_p1_for_vfc = 0.0
299	ENDIF
300
301	!
302	!-- Arrays to store velocity data from t-dt and the phase speeds which
303	!-- are needed for radiation boundary conditions
304	IF ( outflow_l ) THEN
305	ALLOCATE( u_m_l(nzb:nzt+1,nys-1:nyn+1,1:2), &
306	v_m_l(nzb:nzt+1,nys-1:nyn+1,0:1), &
307	w_m_l(nzb:nzt+1,nys-1:nyn+1,0:1) )
308	ENDIF
309	IF ( outflow_r ) THEN
310	ALLOCATE( u_m_r(nzb:nzt+1,nys-1:nyn+1,nx-1:nx), &
311	v_m_r(nzb:nzt+1,nys-1:nyn+1,nx-1:nx), &
312	w_m_r(nzb:nzt+1,nys-1:nyn+1,nx-1:nx) )
313	ENDIF
314	IF ( outflow_l .OR. outflow_r ) THEN
315	ALLOCATE( c_u(nzb:nzt+1,nys-1:nyn+1), c_v(nzb:nzt+1,nys-1:nyn+1), &
316	c_w(nzb:nzt+1,nys-1:nyn+1) )
317	ENDIF
318	IF ( outflow_s ) THEN
319	ALLOCATE( u_m_s(nzb:nzt+1,0:1,nxl-1:nxr+1), &
320	v_m_s(nzb:nzt+1,1:2,nxl-1:nxr+1), &
321	w_m_s(nzb:nzt+1,0:1,nxl-1:nxr+1) )
322	ENDIF
323	IF ( outflow_n ) THEN
324	ALLOCATE( u_m_n(nzb:nzt+1,ny-1:ny,nxl-1:nxr+1), &
325	v_m_n(nzb:nzt+1,ny-1:ny,nxl-1:nxr+1), &
326	w_m_n(nzb:nzt+1,ny-1:ny,nxl-1:nxr+1) )
327	ENDIF
328	IF ( outflow_s .OR. outflow_n ) THEN
329	ALLOCATE( c_u(nzb:nzt+1,nxl-1:nxr+1), c_v(nzb:nzt+1,nxl-1:nxr+1), &
330	c_w(nzb:nzt+1,nxl-1:nxr+1) )
331	ENDIF
332
333	!
334	!-- Initial assignment of the pointers
335	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
336
337	rif_m => rif_1; rif => rif_2
338	shf_m => shf_1; shf => shf_2
339	tswst_m => tswst_1; tswst => tswst_2
340	usws_m => usws_1; usws => usws_2
341	uswst_m => uswst_1; uswst => uswst_2
342	vsws_m => vsws_1; vsws => vsws_2
343	vswst_m => vswst_1; vswst => vswst_2
344	e_m => e_1; e => e_2; e_p => e_3; te_m => e_3
345	kh_m => kh_1; kh => kh_2
346	km_m => km_1; km => km_2
347	pt_m => pt_1; pt => pt_2; pt_p => pt_3; tpt_m => pt_3
348	u_m => u_1; u => u_2; u_p => u_3; tu_m => u_3
349	v_m => v_1; v => v_2; v_p => v_3; tv_m => v_3
350	w_m => w_1; w => w_2; w_p => w_3; tw_m => w_3
351
352	IF ( humidity .OR. passive_scalar ) THEN
353	qsws_m => qsws_1; qsws => qsws_2
354	qswst_m => qswst_1; qswst => qswst_2
355	q_m => q_1; q => q_2; q_p => q_3; tq_m => q_3
356	IF ( humidity ) vpt_m => vpt_1; vpt => vpt_2
357	IF ( cloud_physics ) ql => ql_1
358	IF ( cloud_droplets ) THEN
359	ql => ql_1
360	ql_c => ql_2
361	ENDIF
362	ENDIF
363
364	ELSE
365
366	rif => rif_1
367	shf => shf_1
368	tswst => tswst_1
369	usws => usws_1
370	uswst => uswst_1
371	vsws => vsws_1
372	vswst => vswst_1
373	e => e_1; e_p => e_2; te_m => e_3; e_m => e_3
374	kh => kh_1
375	km => km_1
376	pt => pt_1; pt_p => pt_2; tpt_m => pt_3; pt_m => pt_3
377	u => u_1; u_p => u_2; tu_m => u_3; u_m => u_3
378	v => v_1; v_p => v_2; tv_m => v_3; v_m => v_3
379	w => w_1; w_p => w_2; tw_m => w_3; w_m => w_3
380
381	IF ( humidity .OR. passive_scalar ) THEN
382	qsws => qsws_1
383	qswst => qswst_1
384	q => q_1; q_p => q_2; tq_m => q_3; q_m => q_3
385	IF ( humidity ) vpt => vpt_1
386	IF ( cloud_physics ) ql => ql_1
387	IF ( cloud_droplets ) THEN
388	ql => ql_1
389	ql_c => ql_2
390	ENDIF
391	ENDIF
392
393	IF ( ocean ) THEN
394	saswsb => saswsb_1
395	saswst => saswst_1
396	sa => sa_1; sa_p => sa_2; tsa_m => sa_3
397	ENDIF
398
399	ENDIF
400
401	!
402	!-- Initialize model variables
403	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
404	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
405	!
406	!-- First model run of a possible job queue.
407	!-- Initial profiles of the variables must be computes.
408	IF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
409	!
410	!-- Use solutions of the 1D model as initial profiles,
411	!-- start 1D model
412	CALL init_1d_model
413	!
414	!-- Transfer initial profiles to the arrays of the 3D model
415	DO i = nxl-1, nxr+1
416	DO j = nys-1, nyn+1
417	e(:,j,i) = e1d
418	kh(:,j,i) = kh1d
419	km(:,j,i) = km1d
420	pt(:,j,i) = pt_init
421	u(:,j,i) = u1d
422	v(:,j,i) = v1d
423	ENDDO
424	ENDDO
425
426	IF ( humidity .OR. passive_scalar ) THEN
427	DO i = nxl-1, nxr+1
428	DO j = nys-1, nyn+1
429	q(:,j,i) = q_init
430	ENDDO
431	ENDDO
432	ENDIF
433
434	IF ( .NOT. constant_diffusion ) THEN
435	DO i = nxl-1, nxr+1
436	DO j = nys-1, nyn+1
437	e(:,j,i) = e1d
438	ENDDO
439	ENDDO
440	!
441	!-- Store initial profiles for output purposes etc.
442	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
443
444	IF ( prandtl_layer ) THEN
445	rif = rif1d(nzb+1)
446	ts = 0.0 ! could actually be computed more accurately in the
447	! 1D model. Update when opportunity arises.
448	us = us1d
449	usws = usws1d
450	vsws = vsws1d
451	ELSE
452	ts = 0.0 ! must be set, because used in
453	rif = 0.0 ! flowste
454	us = 0.0
455	usws = 0.0
456	vsws = 0.0
457	ENDIF
458
459	ELSE
460	e = 0.0 ! must be set, because used in
461	rif = 0.0 ! flowste
462	ts = 0.0
463	us = 0.0
464	usws = 0.0
465	vsws = 0.0
466	ENDIF
467	uswst = top_momentumflux_u
468	vswst = top_momentumflux_v
469
470	!
471	!-- In every case qs = 0.0 (see also pt)
472	!-- This could actually be computed more accurately in the 1D model.
473	!-- Update when opportunity arises!
474	IF ( humidity .OR. passive_scalar ) qs = 0.0
475
476	!
477	!-- inside buildings set velocities back to zero
478	IF ( topography /= 'flat' ) THEN
479	DO i = nxl-1, nxr+1
480	DO j = nys-1, nyn+1
481	u(nzb:nzb_u_inner(j,i),j,i) = 0.0
482	v(nzb:nzb_v_inner(j,i),j,i) = 0.0
483	ENDDO
484	ENDDO
485	IF ( conserve_volume_flow ) THEN
486	IF ( nxr == nx ) THEN
487	DO j = nys, nyn
488	DO k = nzb + 1, nzb_u_inner(j,nx)
489	u_nzb_p1_for_vfc(j) = u_nzb_p1_for_vfc(j) + &
490	u1d(k) * dzu(k)
491	ENDDO
492	ENDDO
493	ENDIF
494	IF ( nyn == ny ) THEN
495	DO i = nxl, nxr
496	DO k = nzb + 1, nzb_v_inner(ny,i)
497	v_nzb_p1_for_vfc(i) = v_nzb_p1_for_vfc(i) + &
498	v1d(k) * dzu(k)
499	ENDDO
500	ENDDO
501	ENDIF
502	ENDIF
503	!
504	!-- WARNING: The extra boundary conditions set after running the
505	!-- ------- 1D model impose an error on the divergence one layer
506	!-- below the topography; need to correct later
507	!-- ATTENTION: Provisional correction for Piacsek & Williams
508	!-- --------- advection scheme: keep u and v zero one layer below
509	!-- the topography.
510	IF ( ibc_uv_b == 0 ) THEN
511	!
512	!-- Satisfying the Dirichlet condition with an extra layer below
513	!-- the surface where the u and v component change their sign.
514	DO i = nxl-1, nxr+1
515	DO j = nys-1, nyn+1
516	IF ( nzb_u_inner(j,i) == 0 ) u(0,j,i) = -u(1,j,i)
517	IF ( nzb_v_inner(j,i) == 0 ) v(0,j,i) = -v(1,j,i)
518	ENDDO
519	ENDDO
520
521	ELSE
522	!
523	!-- Neumann condition
524	DO i = nxl-1, nxr+1
525	DO j = nys-1, nyn+1
526	IF ( nzb_u_inner(j,i) == 0 ) u(0,j,i) = u(1,j,i)
527	IF ( nzb_v_inner(j,i) == 0 ) v(0,j,i) = v(1,j,i)
528	ENDDO
529	ENDDO
530
531	ENDIF
532
533	ENDIF
534
535	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
536	THEN
537	!
538	!-- Use constructed initial profiles (velocity constant with height,
539	!-- temperature profile with constant gradient)
540	DO i = nxl-1, nxr+1
541	DO j = nys-1, nyn+1
542	pt(:,j,i) = pt_init
543	u(:,j,i) = u_init
544	v(:,j,i) = v_init
545	ENDDO
546	ENDDO
547
548	!
549	!-- Set initial horizontal velocities at the lowest computational grid
550	!-- levels to zero in order to avoid too small time steps caused by the
551	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
552	!-- in the limiting formula!). The original values are stored to be later
553	!-- used for volume flow control.
554	DO i = nxl-1, nxr+1
555	DO j = nys-1, nyn+1
556	u(nzb:nzb_u_inner(j,i)+1,j,i) = 0.0
557	v(nzb:nzb_v_inner(j,i)+1,j,i) = 0.0
558	ENDDO
559	ENDDO
560	IF ( conserve_volume_flow ) THEN
561	IF ( nxr == nx ) THEN
562	DO j = nys, nyn
563	DO k = nzb + 1, nzb_u_inner(j,nx) + 1
564	u_nzb_p1_for_vfc(j) = u_nzb_p1_for_vfc(j) + &
565	u_init(k) * dzu(k)
566	ENDDO
567	ENDDO
568	ENDIF
569	IF ( nyn == ny ) THEN
570	DO i = nxl, nxr
571	DO k = nzb + 1, nzb_v_inner(ny,i) + 1
572	v_nzb_p1_for_vfc(i) = v_nzb_p1_for_vfc(i) + &
573	v_init(k) * dzu(k)
574	ENDDO
575	ENDDO
576	ENDIF
577	ENDIF
578
579	IF ( humidity .OR. passive_scalar ) THEN
580	DO i = nxl-1, nxr+1
581	DO j = nys-1, nyn+1
582	q(:,j,i) = q_init
583	ENDDO
584	ENDDO
585	ENDIF
586
587	IF ( ocean ) THEN
588	DO i = nxl-1, nxr+1
589	DO j = nys-1, nyn+1
590	sa(:,j,i) = sa_init
591	ENDDO
592	ENDDO
593	ENDIF
594
595	IF ( constant_diffusion ) THEN
596	km = km_constant
597	kh = km / prandtl_number
598	e = 0.0
599	ELSEIF ( e_init > 0.0 ) THEN
600	DO k = nzb+1, nzt
601	km(k,:,:) = 0.1 * l_grid(k) * SQRT( e_init )
602	ENDDO
603	km(nzb,:,:) = km(nzb+1,:,:)
604	km(nzt+1,:,:) = km(nzt,:,:)
605	kh = km / prandtl_number
606	e = e_init
607	ELSE
608	IF ( .NOT. ocean ) THEN
609	kh = 0.01 ! there must exist an initial diffusion, because
610	km = 0.01 ! otherwise no TKE would be produced by the
611	! production terms, as long as not yet
612	! e = (u/cm)*2 at k=nzb+1
613	ELSE
614	kh = 0.00001
615	km = 0.00001
616	ENDIF
617	e = 0.0
618	ENDIF
619	rif = 0.0
620	ts = 0.0
621	us = 0.0
622	usws = 0.0
623	uswst = top_momentumflux_u
624	vsws = 0.0
625	vswst = top_momentumflux_v
626	IF ( humidity .OR. passive_scalar ) qs = 0.0
627
628	!
629	!-- Compute initial temperature field and other constants used in case
630	!-- of a sloping surface
631	IF ( sloping_surface ) CALL init_slope
632
633	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
634	THEN
635	!
636	!-- Initialization will completely be done by the user
637	CALL user_init_3d_model
638
639	ENDIF
640
641	!
642	!-- Apply channel flow boundary condition
643	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
644
645	u(nzt+1,:,:) = 0.0
646	v(nzt+1,:,:) = 0.0
647
648	!-- For the Dirichlet condition to be correctly applied at the top, set
649	!-- ug and vg to zero there
650	ug(nzt+1) = 0.0
651	vg(nzt+1) = 0.0
652
653	ENDIF
654
655	!
656	!-- Calculate virtual potential temperature
657	IF ( humidity ) vpt = pt * ( 1.0 + 0.61 * q )
658
659	!
660	!-- Store initial profiles for output purposes etc.
661	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
662	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
663	IF ( ibc_uv_b == 0 ) THEN
664	hom(nzb,1,5,:) = -hom(nzb+1,1,5,:) ! due to satisfying the Dirichlet
665	hom(nzb,1,6,:) = -hom(nzb+1,1,6,:) ! condition with an extra layer
666	! below the surface where the u and v component change their sign
667	ENDIF
668	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
669	hom(:,1,23,:) = SPREAD( km(:,nys,nxl), 2, statistic_regions+1 )
670	hom(:,1,24,:) = SPREAD( kh(:,nys,nxl), 2, statistic_regions+1 )
671
672	IF ( ocean ) THEN
673	!
674	!-- Store initial salinity profile
675	hom(:,1,26,:) = SPREAD( sa(:,nys,nxl), 2, statistic_regions+1 )
676	ENDIF
677
678	IF ( humidity ) THEN
679	!
680	!-- Store initial profile of total water content, virtual potential
681	!-- temperature
682	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
683	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
684	IF ( cloud_physics .OR. cloud_droplets ) THEN
685	!
686	!-- Store initial profile of specific humidity and potential
687	!-- temperature
688	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
689	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
690	ENDIF
691	ENDIF
692
693	IF ( passive_scalar ) THEN
694	!
695	!-- Store initial scalar profile
696	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
697	ENDIF
698
699	!
700	!-- Initialize fluxes at bottom surface
701	IF ( use_surface_fluxes ) THEN
702
703	IF ( constant_heatflux ) THEN
704	!
705	!-- Heat flux is prescribed
706	IF ( random_heatflux ) THEN
707	CALL disturb_heatflux
708	ELSE
709	shf = surface_heatflux
710	!
711	!-- Over topography surface_heatflux is replaced by wall_heatflux(0)
712	IF ( TRIM( topography ) /= 'flat' ) THEN
713	DO i = nxl-1, nxr+1
714	DO j = nys-1, nyn+1
715	IF ( nzb_s_inner(j,i) /= 0 ) THEN
716	shf(j,i) = wall_heatflux(0)
717	ENDIF
718	ENDDO
719	ENDDO
720	ENDIF
721	ENDIF
722	IF ( ASSOCIATED( shf_m ) ) shf_m = shf
723	ENDIF
724
725	!
726	!-- Determine the near-surface water flux
727	IF ( humidity .OR. passive_scalar ) THEN
728	IF ( constant_waterflux ) THEN
729	qsws = surface_waterflux
730	IF ( ASSOCIATED( qsws_m ) ) qsws_m = qsws
731	ENDIF
732	ENDIF
733
734	ENDIF
735
736	!
737	!-- Initialize fluxes at top surface
738	!-- Currently, only the heatflux and salinity flux can be prescribed.
739	!-- The latent flux is zero in this case!
740	IF ( use_top_fluxes ) THEN
741
742	IF ( constant_top_heatflux ) THEN
743	!
744	!-- Heat flux is prescribed
745	tswst = top_heatflux
746	IF ( ASSOCIATED( tswst_m ) ) tswst_m = tswst
747
748	IF ( humidity .OR. passive_scalar ) THEN
749	qswst = 0.0
750	IF ( ASSOCIATED( qswst_m ) ) qswst_m = qswst
751	ENDIF
752
753	IF ( ocean ) THEN
754	saswsb = bottom_salinityflux
755	saswst = top_salinityflux
756	ENDIF
757	ENDIF
758
759	!
760	!-- Initialization in case of a coupled model run
761	IF ( coupling_mode == 'ocean_to_atmosphere' ) THEN
762	tswst = 0.0
763	IF ( ASSOCIATED( tswst_m ) ) tswst_m = tswst
764	ENDIF
765
766	ENDIF
767
768	!
769	!-- Initialize Prandtl layer quantities
770	IF ( prandtl_layer ) THEN
771
772	z0 = roughness_length
773
774	IF ( .NOT. constant_heatflux ) THEN
775	!
776	!-- Surface temperature is prescribed. Here the heat flux cannot be
777	!-- simply estimated, because therefore rif, u* and theta* would have
778	!-- to be computed by iteration. This is why the heat flux is assumed
779	!-- to be zero before the first time step. It approaches its correct
780	!-- value in the course of the first few time steps.
781	shf = 0.0
782	IF ( ASSOCIATED( shf_m ) ) shf_m = 0.0
783	ENDIF
784
785	IF ( humidity .OR. passive_scalar ) THEN
786	IF ( .NOT. constant_waterflux ) THEN
787	qsws = 0.0
788	IF ( ASSOCIATED( qsws_m ) ) qsws_m = 0.0
789	ENDIF
790	ENDIF
791
792	ENDIF
793
794	!
795	!-- Calculate the initial volume flow at the right and north boundary
796	IF ( conserve_volume_flow ) THEN
797
798	volume_flow_initial_l = 0.0
799	volume_flow_area_l = 0.0
800
801	IF ( nxr == nx ) THEN
802	DO j = nys, nyn
803	DO k = nzb_2d(j,nx) + 1, nzt
804	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
805	u(k,j,nx) * dzu(k)
806	volume_flow_area_l(1) = volume_flow_area_l(1) + dzu(k)
807	ENDDO
808	!
809	!-- Correction if velocity at nzb+1 has been set zero further above
810	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
811	u_nzb_p1_for_vfc(j)
812	ENDDO
813	ENDIF
814
815	IF ( nyn == ny ) THEN
816	DO i = nxl, nxr
817	DO k = nzb_2d(ny,i) + 1, nzt
818	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
819	v(k,ny,i) * dzu(k)
820	volume_flow_area_l(2) = volume_flow_area_l(2) + dzu(k)
821	ENDDO
822	!
823	!-- Correction if velocity at nzb+1 has been set zero further above
824	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
825	v_nzb_p1_for_vfc(i)
826	ENDDO
827	ENDIF
828
829	#if defined( __parallel )
830	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
831	2, MPI_REAL, MPI_SUM, comm2d, ierr )
832	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
833	2, MPI_REAL, MPI_SUM, comm2d, ierr )
834	#else
835	volume_flow_initial = volume_flow_initial_l
836	volume_flow_area = volume_flow_area_l
837	#endif
838	!
839	!-- In case of 'bulk_velocity' mode, volume_flow_initial is overridden
840	!-- and calculated from u\|v_bulk instead.
841	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
842	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
843	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
844	ENDIF
845
846	ENDIF
847
848	!
849	!-- For the moment, perturbation pressure and vertical velocity are zero
850	p = 0.0; w = 0.0
851
852	!
853	!-- Initialize array sums (must be defined in first call of pres)
854	sums = 0.0
855
856	!
857	!-- Treating cloud physics, liquid water content and precipitation amount
858	!-- are zero at beginning of the simulation
859	IF ( cloud_physics ) THEN
860	ql = 0.0
861	IF ( precipitation ) precipitation_amount = 0.0
862	ENDIF
863
864	!
865	!-- Impose vortex with vertical axis on the initial velocity profile
866	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
867	CALL init_rankine
868	ENDIF
869
870	!
871	!-- Impose temperature anomaly (advection test only)
872	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 ) THEN
873	CALL init_pt_anomaly
874	ENDIF
875
876	!
877	!-- If required, change the surface temperature at the start of the 3D run
878	IF ( pt_surface_initial_change /= 0.0 ) THEN
879	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
880	ENDIF
881
882	!
883	!-- If required, change the surface humidity/scalar at the start of the 3D
884	!-- run
885	IF ( ( humidity .OR. passive_scalar ) .AND. &
886	q_surface_initial_change /= 0.0 ) THEN
887	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
888	ENDIF
889
890	!
891	!-- Initialize the random number generator (from numerical recipes)
892	CALL random_function_ini
893
894	!
895	!-- Impose random perturbation on the horizontal velocity field and then
896	!-- remove the divergences from the velocity field
897	IF ( create_disturbances ) THEN
898	CALL disturb_field( nzb_u_inner, tend, u )
899	CALL disturb_field( nzb_v_inner, tend, v )
900	n_sor = nsor_ini
901	CALL pres
902	n_sor = nsor
903	ENDIF
904
905	!
906	!-- Once again set the perturbation pressure explicitly to zero in order to
907	!-- assure that it does not generate any divergences in the first time step.
908	!-- At t=0 the velocity field is free of divergence (as constructed above).
909	!-- Divergences being created during a time step are not yet known and thus
910	!-- cannot be corrected during the time step yet.
911	p = 0.0
912
913	!
914	!-- Initialize old and new time levels.
915	IF ( timestep_scheme(1:5) /= 'runge' ) THEN
916	e_m = e; pt_m = pt; u_m = u; v_m = v; w_m = w; kh_m = kh; km_m = km
917	ELSE
918	te_m = 0.0; tpt_m = 0.0; tu_m = 0.0; tv_m = 0.0; tw_m = 0.0
919	ENDIF
920	e_p = e; pt_p = pt; u_p = u; v_p = v; w_p = w
921
922	IF ( humidity .OR. passive_scalar ) THEN
923	IF ( ASSOCIATED( q_m ) ) q_m = q
924	IF ( timestep_scheme(1:5) == 'runge' ) tq_m = 0.0
925	q_p = q
926	IF ( humidity .AND. ASSOCIATED( vpt_m ) ) vpt_m = vpt
927	ENDIF
928
929	IF ( ocean ) THEN
930	tsa_m = 0.0
931	sa_p = sa
932	ENDIF
933
934
935	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
936	TRIM( initializing_actions ) == 'cyclic_fill' ) &
937	THEN
938	!
939	!-- When reading data for cyclic fill of 3D prerun data, first read
940	!-- some of the global variables from restart file
941	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
942
943	WRITE (9,*) 'before read_parts_of_var_list'
944	CALL local_flush( 9 )
945	CALL read_parts_of_var_list
946	WRITE (9,*) 'after read_parts_of_var_list'
947	CALL local_flush( 9 )
948	CALL close_file( 13 )
949
950	!
951	!-- Initialization of the turbulence recycling method
952	IF ( turbulent_inflow ) THEN
953	!
954	!-- Store temporally and horizontally averaged vertical profiles to be
955	!-- used as mean inflow profiles
956	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,5) )
957
958	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
959	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
960	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
961	mean_inflow_profiles(:,5) = hom_sum(:,8,0) ! e
962
963	!
964	!-- Use these mean profiles for the inflow (provided that Dirichlet
965	!-- conditions are used)
966	IF ( inflow_l ) THEN
967	DO j = nys-1, nyn+1
968	DO k = nzb, nzt+1
969	u(k,j,-1) = mean_inflow_profiles(k,1)
970	v(k,j,-1) = mean_inflow_profiles(k,2)
971	w(k,j,-1) = 0.0
972	pt(k,j,-1) = mean_inflow_profiles(k,4)
973	e(k,j,-1) = mean_inflow_profiles(k,5)
974	ENDDO
975	ENDDO
976	ENDIF
977
978	!
979	!-- Calculate the damping factors to be used at the inflow. For a
980	!-- turbulent inflow the turbulent fluctuations have to be limited
981	!-- vertically because otherwise the turbulent inflow layer will grow
982	!-- in time.
983	IF ( inflow_damping_height == 9999999.9 ) THEN
984	!
985	!-- Default: use the inversion height calculated by the prerun; if
986	!-- this is zero, inflow_damping_height must be explicitly
987	!-- specified.
988	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0 ) THEN
989	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
990	ELSE
991	WRITE( message_string, * ) 'inflow_damping_height must be ',&
992	'explicitly specified because&the inversion height ', &
993	'calculated by the prerun is zero.'
994	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
995	ENDIF
996
997	ENDIF
998
999	IF ( inflow_damping_width == 9999999.9 ) THEN
1000	!
1001	!-- Default for the transition range: one tenth of the undamped
1002	!-- layer
1003	inflow_damping_width = 0.1 * inflow_damping_height
1004
1005	ENDIF
1006
1007	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1008
1009	DO k = nzb, nzt+1
1010
1011	IF ( zu(k) <= inflow_damping_height ) THEN
1012	inflow_damping_factor(k) = 1.0
1013	ELSEIF ( zu(k) <= inflow_damping_height + &
1014	inflow_damping_width ) THEN
1015	inflow_damping_factor(k) = 1.0 - &
1016	( zu(k) - inflow_damping_height ) / &
1017	inflow_damping_width
1018	ELSE
1019	inflow_damping_factor(k) = 0.0
1020	ENDIF
1021
1022	ENDDO
1023	ENDIF
1024
1025	ENDIF
1026
1027	!
1028	!-- Read binary data from restart file
1029	WRITE (9,*) 'before read_3d_binary'
1030	CALL local_flush( 9 )
1031	CALL read_3d_binary
1032	WRITE (9,*) 'after read_3d_binary'
1033	CALL local_flush( 9 )
1034
1035	!
1036	!-- Inside buildings set velocities and TKE back to zero
1037	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1038	topography /= 'flat' ) THEN
1039	!
1040	!-- Correction of initial volume flow
1041	IF ( conserve_volume_flow ) THEN
1042	IF ( nxr == nx ) THEN
1043	DO j = nys, nyn
1044	DO k = nzb + 1, nzb_u_inner(j,nx)
1045	u_nzb_p1_for_vfc(j) = u_nzb_p1_for_vfc(j) + &
1046	u(k,j,nx) * dzu(k)
1047	ENDDO
1048	ENDDO
1049	ENDIF
1050	IF ( nyn == ny ) THEN
1051	DO i = nxl, nxr
1052	DO k = nzb + 1, nzb_v_inner(ny,i)
1053	v_nzb_p1_for_vfc(i) = v_nzb_p1_for_vfc(i) + &
1054	v(k,ny,i) * dzu(k)
1055	ENDDO
1056	ENDDO
1057	ENDIF
1058	ENDIF
1059
1060	!
1061	!-- Inside buildings set velocities and TKE back to zero.
1062	!-- Other scalars (pt, q, s, km, kh, p, sa, ...) are ignored at present,
1063	!-- maybe revise later.
1064	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1065	DO i = nxl-1, nxr+1
1066	DO j = nys-1, nyn+1
1067	u (nzb:nzb_u_inner(j,i),j,i) = 0.0
1068	v (nzb:nzb_v_inner(j,i),j,i) = 0.0
1069	w (nzb:nzb_w_inner(j,i),j,i) = 0.0
1070	e (nzb:nzb_w_inner(j,i),j,i) = 0.0
1071	u_m(nzb:nzb_u_inner(j,i),j,i) = 0.0
1072	v_m(nzb:nzb_v_inner(j,i),j,i) = 0.0
1073	w_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1074	e_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1075	tu_m(nzb:nzb_u_inner(j,i),j,i) = 0.0
1076	tv_m(nzb:nzb_v_inner(j,i),j,i) = 0.0
1077	tw_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1078	te_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1079	tpt_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1080	ENDDO
1081	ENDDO
1082	ELSE
1083	DO i = nxl-1, nxr+1
1084	DO j = nys-1, nyn+1
1085	u (nzb:nzb_u_inner(j,i),j,i) = 0.0
1086	v (nzb:nzb_v_inner(j,i),j,i) = 0.0
1087	w (nzb:nzb_w_inner(j,i),j,i) = 0.0
1088	e (nzb:nzb_w_inner(j,i),j,i) = 0.0
1089	u_m(nzb:nzb_u_inner(j,i),j,i) = 0.0
1090	v_m(nzb:nzb_v_inner(j,i),j,i) = 0.0
1091	w_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1092	e_m(nzb:nzb_w_inner(j,i),j,i) = 0.0
1093	u_p(nzb:nzb_u_inner(j,i),j,i) = 0.0
1094	v_p(nzb:nzb_v_inner(j,i),j,i) = 0.0
1095	w_p(nzb:nzb_w_inner(j,i),j,i) = 0.0
1096	e_p(nzb:nzb_w_inner(j,i),j,i) = 0.0
1097	ENDDO
1098	ENDDO
1099	ENDIF
1100
1101	ENDIF
1102
1103	!
1104	!-- Calculate the initial volume flow at the right and north boundary
1105	IF ( conserve_volume_flow .AND. &
1106	TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1107
1108	volume_flow_initial_l = 0.0
1109	volume_flow_area_l = 0.0
1110
1111	IF ( nxr == nx ) THEN
1112	DO j = nys, nyn
1113	DO k = nzb_2d(j,nx) + 1, nzt
1114	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1115	u(k,j,nx) * dzu(k)
1116	volume_flow_area_l(1) = volume_flow_area_l(1) + dzu(k)
1117	ENDDO
1118	!
1119	!-- Correction if velocity inside buildings has been set to zero
1120	!-- further above
1121	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1122	u_nzb_p1_for_vfc(j)
1123	ENDDO
1124	ENDIF
1125
1126	IF ( nyn == ny ) THEN
1127	DO i = nxl, nxr
1128	DO k = nzb_2d(ny,i) + 1, nzt
1129	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1130	v(k,ny,i) * dzu(k)
1131	volume_flow_area_l(2) = volume_flow_area_l(2) + dzu(k)
1132	ENDDO
1133	!
1134	!-- Correction if velocity inside buildings has been set to zero
1135	!-- further above
1136	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1137	v_nzb_p1_for_vfc(i)
1138	ENDDO
1139	ENDIF
1140
1141	#if defined( __parallel )
1142	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1143	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1144	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1145	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1146	#else
1147	volume_flow_initial = volume_flow_initial_l
1148	volume_flow_area = volume_flow_area_l
1149	#endif
1150	ENDIF
1151
1152
1153	!
1154	!-- Calculate initial temperature field and other constants used in case
1155	!-- of a sloping surface
1156	IF ( sloping_surface ) CALL init_slope
1157
1158	!
1159	!-- Initialize new time levels (only done in order to set boundary values
1160	!-- including ghost points)
1161	e_p = e; pt_p = pt; u_p = u; v_p = v; w_p = w
1162	IF ( humidity .OR. passive_scalar ) q_p = q
1163	IF ( ocean ) sa_p = sa
1164
1165	!
1166	!-- Allthough tendency arrays are set in prognostic_equations, they have
1167	!-- have to be predefined here because they are used (but multiplied with 0)
1168	!-- there before they are set.
1169	IF ( timestep_scheme(1:5) == 'runge' ) THEN
1170	te_m = 0.0; tpt_m = 0.0; tu_m = 0.0; tv_m = 0.0; tw_m = 0.0
1171	IF ( humidity .OR. passive_scalar ) tq_m = 0.0
1172	IF ( ocean ) tsa_m = 0.0
1173	ENDIF
1174
1175	ELSE
1176	!
1177	!-- Actually this part of the programm should not be reached
1178	message_string = 'unknown initializing problem'
1179	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1180	ENDIF
1181
1182
1183	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1184	!
1185	!-- Initialize old timelevels needed for radiation boundary conditions
1186	IF ( outflow_l ) THEN
1187	u_m_l(:,:,:) = u(:,:,1:2)
1188	v_m_l(:,:,:) = v(:,:,0:1)
1189	w_m_l(:,:,:) = w(:,:,0:1)
1190	ENDIF
1191	IF ( outflow_r ) THEN
1192	u_m_r(:,:,:) = u(:,:,nx-1:nx)
1193	v_m_r(:,:,:) = v(:,:,nx-1:nx)
1194	w_m_r(:,:,:) = w(:,:,nx-1:nx)
1195	ENDIF
1196	IF ( outflow_s ) THEN
1197	u_m_s(:,:,:) = u(:,0:1,:)
1198	v_m_s(:,:,:) = v(:,1:2,:)
1199	w_m_s(:,:,:) = w(:,0:1,:)
1200	ENDIF
1201	IF ( outflow_n ) THEN
1202	u_m_n(:,:,:) = u(:,ny-1:ny,:)
1203	v_m_n(:,:,:) = v(:,ny-1:ny,:)
1204	w_m_n(:,:,:) = w(:,ny-1:ny,:)
1205	ENDIF
1206
1207	ENDIF
1208
1209	!
1210	!-- Initialization of the leaf area density
1211	IF ( plant_canopy ) THEN
1212
1213	SELECT CASE ( TRIM( canopy_mode ) )
1214
1215	CASE( 'block' )
1216
1217	DO i = nxl-1, nxr+1
1218	DO j = nys-1, nyn+1
1219	lad_s(:,j,i) = lad(:)
1220	cdc(:,j,i) = drag_coefficient
1221	IF ( passive_scalar ) THEN
1222	sls(:,j,i) = leaf_surface_concentration
1223	sec(:,j,i) = scalar_exchange_coefficient
1224	ENDIF
1225	ENDDO
1226	ENDDO
1227
1228	CASE DEFAULT
1229
1230	!
1231	!-- The DEFAULT case is reached either if the parameter
1232	!-- canopy mode contains a wrong character string or if the
1233	!-- user has coded a special case in the user interface.
1234	!-- There, the subroutine user_init_plant_canopy checks
1235	!-- which of these two conditions applies.
1236	CALL user_init_plant_canopy
1237
1238	END SELECT
1239
1240	CALL exchange_horiz( lad_s )
1241	CALL exchange_horiz( cdc )
1242
1243	IF ( passive_scalar ) THEN
1244	CALL exchange_horiz( sls )
1245	CALL exchange_horiz( sec )
1246	ENDIF
1247
1248	!
1249	!-- Sharp boundaries of the plant canopy in horizontal directions
1250	!-- In vertical direction the interpolation is retained, as the leaf
1251	!-- area density is initialised by prescribing a vertical profile
1252	!-- consisting of piecewise linear segments. The upper boundary
1253	!-- of the plant canopy is now defined by lad_w(pch_index,:,:) = 0.0.
1254
1255	DO i = nxl, nxr
1256	DO j = nys, nyn
1257	DO k = nzb, nzt+1
1258	IF ( lad_s(k,j,i) > 0.0 ) THEN
1259	lad_u(k,j,i) = lad_s(k,j,i)
1260	lad_u(k,j,i+1) = lad_s(k,j,i)
1261	lad_v(k,j,i) = lad_s(k,j,i)
1262	lad_v(k,j+1,i) = lad_s(k,j,i)
1263	ENDIF
1264	ENDDO
1265	DO k = nzb, nzt
1266	lad_w(k,j,i) = 0.5 * ( lad_s(k+1,j,i) + lad_s(k,j,i) )
1267	ENDDO
1268	ENDDO
1269	ENDDO
1270
1271	lad_w(pch_index,:,:) = 0.0
1272	lad_w(nzt+1,:,:) = lad_w(nzt,:,:)
1273
1274	CALL exchange_horiz( lad_u )
1275	CALL exchange_horiz( lad_v )
1276	CALL exchange_horiz( lad_w )
1277
1278	!
1279	!-- Initialisation of the canopy heat source distribution
1280	IF ( cthf /= 0.0 ) THEN
1281	!
1282	!-- Piecewise evaluation of the leaf area index by
1283	!-- integration of the leaf area density
1284	lai(:,:,:) = 0.0
1285	DO i = nxl-1, nxr+1
1286	DO j = nys-1, nyn+1
1287	DO k = pch_index-1, 0, -1
1288	lai(k,j,i) = lai(k+1,j,i) + &
1289	( 0.5 * ( lad_w(k+1,j,i) + &
1290	lad_s(k+1,j,i) ) * &
1291	( zw(k+1) - zu(k+1) ) ) + &
1292	( 0.5 * ( lad_w(k,j,i) + &
1293	lad_s(k+1,j,i) ) * &
1294	( zu(k+1) - zw(k) ) )
1295	ENDDO
1296	ENDDO
1297	ENDDO
1298
1299	!
1300	!-- Evaluation of the upward kinematic vertical heat flux within the
1301	!-- canopy
1302	DO i = nxl-1, nxr+1
1303	DO j = nys-1, nyn+1
1304	DO k = 0, pch_index
1305	canopy_heat_flux(k,j,i) = cthf * &
1306	exp( -0.6 * lai(k,j,i) )
1307	ENDDO
1308	ENDDO
1309	ENDDO
1310
1311	!
1312	!-- The near surface heat flux is derived from the heat flux
1313	!-- distribution within the canopy
1314	shf(:,:) = canopy_heat_flux(0,:,:)
1315
1316	IF ( ASSOCIATED( shf_m ) ) shf_m = shf
1317
1318	ENDIF
1319
1320	ENDIF
1321
1322	!
1323	!-- If required, initialize dvrp-software
1324	IF ( dt_dvrp /= 9999999.9 ) CALL init_dvrp
1325
1326	IF ( ocean ) THEN
1327	!
1328	!-- Initialize quantities needed for the ocean model
1329	CALL init_ocean
1330	ELSE
1331	!
1332	!-- Initialize quantities for handling cloud physics
1333	!-- This routine must be called before init_particles, because
1334	!-- otherwise, array pt_d_t, needed in data_output_dvrp (called by
1335	!-- init_particles) is not defined.
1336	CALL init_cloud_physics
1337	ENDIF
1338
1339	!
1340	!-- If required, initialize particles
1341	IF ( particle_advection ) CALL init_particles
1342
1343	!
1344	!-- Initialize quantities for special advections schemes
1345	CALL init_advec
1346
1347	!
1348	!-- Initialize Rayleigh damping factors
1349	rdf = 0.0
1350	IF ( rayleigh_damping_factor /= 0.0 ) THEN
1351	IF ( .NOT. ocean ) THEN
1352	DO k = nzb+1, nzt
1353	IF ( zu(k) >= rayleigh_damping_height ) THEN
1354	rdf(k) = rayleigh_damping_factor * &
1355	( SIN( pi * 0.5 * ( zu(k) - rayleigh_damping_height ) &
1356	/ ( zu(nzt) - rayleigh_damping_height ) )&
1357	)**2
1358	ENDIF
1359	ENDDO
1360	ELSE
1361	DO k = nzt, nzb+1, -1
1362	IF ( zu(k) <= rayleigh_damping_height ) THEN
1363	rdf(k) = rayleigh_damping_factor * &
1364	( SIN( pi * 0.5 * ( rayleigh_damping_height - zu(k) ) &
1365	/ ( rayleigh_damping_height - zu(nzb+1)))&
1366	)**2
1367	ENDIF
1368	ENDDO
1369	ENDIF
1370	ENDIF
1371
1372	!
1373	!-- Initialize the starting level and the vertical smoothing factor used for
1374	!-- the external pressure gradient
1375	dp_smooth_factor = 1.0
1376	IF ( dp_external ) THEN
1377	!
1378	!-- Set the starting level dp_level_ind_b only if it has not been set before
1379	!-- (e.g. in init_grid).
1380	IF ( dp_level_ind_b == 0 ) THEN
1381	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1382	dp_level_ind_b = ind_array(1) - 1 + nzb
1383	! MINLOC uses lower array bound 1
1384	ENDIF
1385	IF ( dp_smooth ) THEN
1386	dp_smooth_factor(:dp_level_ind_b) = 0.0
1387	DO k = dp_level_ind_b+1, nzt
1388	dp_smooth_factor(k) = 0.5 * ( 1.0 + SIN( pi * &
1389	( REAL( k - dp_level_ind_b ) / &
1390	REAL( nzt - dp_level_ind_b ) - 0.5 ) ) )
1391	ENDDO
1392	ENDIF
1393	ENDIF
1394
1395	!
1396	!-- Initialize diffusivities used within the outflow damping layer in case of
1397	!-- non-cyclic lateral boundaries. A linear increase is assumed over the first
1398	!-- half of the width of the damping layer
1399	IF ( bc_lr == 'dirichlet/radiation' ) THEN
1400
1401	DO i = nxl-1, nxr+1
1402	IF ( i >= nx - outflow_damping_width ) THEN
1403	km_damp_x(i) = km_damp_max * MIN( 1.0, &
1404	( i - ( nx - outflow_damping_width ) ) / &
1405	REAL( outflow_damping_width/2 ) &
1406	)
1407	ELSE
1408	km_damp_x(i) = 0.0
1409	ENDIF
1410	ENDDO
1411
1412	ELSEIF ( bc_lr == 'radiation/dirichlet' ) THEN
1413
1414	DO i = nxl-1, nxr+1
1415	IF ( i <= outflow_damping_width ) THEN
1416	km_damp_x(i) = km_damp_max * MIN( 1.0, &
1417	( outflow_damping_width - i ) / &
1418	REAL( outflow_damping_width/2 ) &
1419	)
1420	ELSE
1421	km_damp_x(i) = 0.0
1422	ENDIF
1423	ENDDO
1424
1425	ENDIF
1426
1427	IF ( bc_ns == 'dirichlet/radiation' ) THEN
1428
1429	DO j = nys-1, nyn+1
1430	IF ( j >= ny - outflow_damping_width ) THEN
1431	km_damp_y(j) = km_damp_max * MIN( 1.0, &
1432	( j - ( ny - outflow_damping_width ) ) / &
1433	REAL( outflow_damping_width/2 ) &
1434	)
1435	ELSE
1436	km_damp_y(j) = 0.0
1437	ENDIF
1438	ENDDO
1439
1440	ELSEIF ( bc_ns == 'radiation/dirichlet' ) THEN
1441
1442	DO j = nys-1, nyn+1
1443	IF ( j <= outflow_damping_width ) THEN
1444	km_damp_y(j) = km_damp_max * MIN( 1.0, &
1445	( outflow_damping_width - j ) / &
1446	REAL( outflow_damping_width/2 ) &
1447	)
1448	ELSE
1449	km_damp_y(j) = 0.0
1450	ENDIF
1451	ENDDO
1452
1453	ENDIF
1454
1455	!
1456	!-- Initialize local summation arrays for UP flow_statistics. This is necessary
1457	!-- because they may not yet have been initialized when they are called from
1458	!-- flow_statistics (or - depending on the chosen model run - are never
1459	!-- initialized)
1460	sums_divnew_l = 0.0
1461	sums_divold_l = 0.0
1462	sums_l_l = 0.0
1463	sums_up_fraction_l = 0.0
1464	sums_wsts_bc_l = 0.0
1465
1466	!
1467	!-- Pre-set masks for regional statistics. Default is the total model domain.
1468	rmask = 1.0
1469
1470	!
1471	!-- User-defined initializing actions. Check afterwards, if maximum number
1472	!-- of allowed timeseries is not exceeded
1473	CALL user_init
1474
1475	IF ( dots_num > dots_max ) THEN
1476	WRITE( message_string, * ) 'number of time series quantities exceeds', &
1477	' its maximum of dots_max = ', dots_max, &
1478	' &Please increase dots_max in modules.f90.'
1479	CALL message( 'init_3d_model', 'PA0194', 1, 2, 0, 6, 0 )
1480	ENDIF
1481
1482	!
1483	!-- Input binary data file is not needed anymore. This line must be placed
1484	!-- after call of user_init!
1485	CALL close_file( 13 )
1486
1487	!
1488	!-- Compute total sum of active mask grid points
1489	!-- ngp_2dh: number of grid points of a horizontal cross section through the
1490	!-- total domain
1491	!-- ngp_3d: number of grid points of the total domain
1492	ngp_2dh_outer_l = 0
1493	ngp_2dh_outer = 0
1494	ngp_2dh_s_inner_l = 0
1495	ngp_2dh_s_inner = 0
1496	ngp_2dh_l = 0
1497	ngp_2dh = 0
1498	ngp_3d_inner_l = 0
1499	ngp_3d_inner = 0
1500	ngp_3d = 0
1501	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1502
1503	DO sr = 0, statistic_regions
1504	DO i = nxl, nxr
1505	DO j = nys, nyn
1506	IF ( rmask(j,i,sr) == 1.0 ) THEN
1507	!
1508	!-- All xy-grid points
1509	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1510	!
1511	!-- xy-grid points above topography
1512	DO k = nzb_s_outer(j,i), nz + 1
1513	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + 1
1514	ENDDO
1515	DO k = nzb_s_inner(j,i), nz + 1
1516	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + 1
1517	ENDDO
1518	!
1519	!-- All grid points of the total domain above topography
1520	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + &
1521	( nz - nzb_s_inner(j,i) + 2 )
1522	ENDIF
1523	ENDDO
1524	ENDDO
1525	ENDDO
1526
1527	sr = statistic_regions + 1
1528	#if defined( __parallel )
1529	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, &
1530	comm2d, ierr )
1531	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, &
1532	MPI_INTEGER, MPI_SUM, comm2d, ierr )
1533	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), &
1534	(nz+2)*sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1535	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner(0), sr, MPI_INTEGER, &
1536	MPI_SUM, comm2d, ierr )
1537	#else
1538	ngp_2dh = ngp_2dh_l
1539	ngp_2dh_outer = ngp_2dh_outer_l
1540	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1541	ngp_3d_inner = ngp_3d_inner_l
1542	#endif
1543
1544	ngp_3d = ngp_2dh * ( nz + 2 )
1545
1546	!
1547	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics,
1548	!-- buoyancy, etc. A zero value will occur for cases where all grid points of
1549	!-- the respective subdomain lie below the surface topography
1550	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1551	ngp_3d_inner = MAX( 1, ngp_3d_inner(:) )
1552	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1553
1554	DEALLOCATE( ngp_2dh_l, ngp_2dh_outer_l, ngp_3d_inner_l )
1555
1556
1557	END SUBROUTINE init_3d_model

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