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Last change on this file since 4330 was 4329, checked in by motisi, 5 years ago

Renamed wall_flags_0 to wall_flags_static_0

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/palm/branches/chemistry/SOURCE/init_3d_model.f90	2047-3190,3218-3297
/palm/branches/forwind/SOURCE/init_3d_model.f90	1564-1913
/palm/branches/mosaik_M2/init_3d_model.f90	2360-3471
/palm/branches/palm4u/SOURCE/init_3d_model.f90	2540-2692
/palm/branches/rans/SOURCE/init_3d_model.f90	2078-3128
/palm/branches/resler/SOURCE/init_3d_model.f90	2023-4285
/palm/branches/salsa/SOURCE/init_3d_model.f90	2503-3581

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1	!> @file init_3d_model.f90
2	!------------------------------------------------------------------------------!
3	! This file is part of the PALM model system.
4	!
5	! PALM is free software: you can redistribute it and/or modify it under the
6	! terms of the GNU General Public License as published by the Free Software
7	! Foundation, either version 3 of the License, or (at your option) any later
8	! version.
9	!
10	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
11	! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
12	! A PARTICULAR PURPOSE. See the GNU General Public License for more details.
13	!
14	! You should have received a copy of the GNU General Public License along with
15	! PALM. If not, see <http://www.gnu.org/licenses/>.
16	!
17	! Copyright 1997-2019 Leibniz Universitaet Hannover
18	!------------------------------------------------------------------------------!
19	!
20	! Current revisions:
21	! ------------------
22	!
23	!
24	! Former revisions:
25	! -----------------
26	! $Id: init_3d_model.f90 4329 2019-12-10 15:46:36Z knoop $
27	! Renamed wall_flags_0 to wall_flags_static_0
28	!
29	! 4286 2019-10-30 16:01:14Z resler
30	! implement new palm_date_time_mod
31	!
32	! 4223 2019-09-10 09:20:47Z gronemeier
33	! Deallocate temporary string array since it may be re-used to read different
34	! input data in other modules
35	!
36	! 4186 2019-08-23 16:06:14Z suehring
37	! Design change, use variables defined in netcdf_data_input_mod to read netcd
38	! variables rather than define local ones.
39	!
40	! 4185 2019-08-23 13:49:38Z oliver.maas
41	! For initializing_actions = ' cyclic_fill':
42	! Overwrite u_init, v_init, pt_init, q_init and s_init with the
43	! (temporally) and horizontally averaged vertical profiles from the end
44	! of the prerun, because these profiles shall be used as the basic state
45	! for the rayleigh damping and the pt_damping.
46	!
47	! 4182 2019-08-22 15:20:23Z scharf
48	! Corrected "Former revisions" section
49	!
50	! 4168 2019-08-16 13:50:17Z suehring
51	! Replace function get_topography_top_index by topo_top_ind
52	!
53	! 4151 2019-08-09 08:24:30Z suehring
54	! Add netcdf directive around input calls (fix for last commit)
55	!
56	! 4150 2019-08-08 20:00:47Z suehring
57	! Input of additional surface variables independent on land- or urban-surface
58	! model
59	!
60	! 4131 2019-08-02 11:06:18Z monakurppa
61	! Allocate sums and sums_l to allow profile output for salsa variables.
62	!
63	! 4130 2019-08-01 13:04:13Z suehring
64	! Effectively reduce 3D initialization to 1D initial profiles. This is because
65	! 3D initialization produces structures in the w-component that are correlated
66	! with the processor grid for some unknown reason
67	!
68	! 4090 2019-07-11 15:06:47Z Giersch
69	! Unused variables removed
70	!
71	! 4088 2019-07-11 13:57:56Z Giersch
72	! Pressure and density profile calculations revised using basic functions
73	!
74	! 4048 2019-06-21 21:00:21Z knoop
75	! Further modularization of particle code components
76	!
77	! 4017 2019-06-06 12:16:46Z schwenkel
78	! Convert most location messages to debug messages to reduce output in
79	! job logfile to a minimum
80	!
81	!
82	! unused variable removed
83	!
84	! 3937 2019-04-29 15:09:07Z suehring
85	! Move initialization of synthetic turbulence generator behind initialization
86	! of offline nesting. Remove call for stg_adjust, as this is now already done
87	! in stg_init.
88	!
89	! 3900 2019-04-16 15:17:43Z suehring
90	! Fix problem with LOD = 2 initialization
91	!
92	! 3885 2019-04-11 11:29:34Z kanani
93	! Changes related to global restructuring of location messages and introduction
94	! of additional debug messages
95	!
96	! 3849 2019-04-01 16:35:16Z knoop
97	! Move initialization of rmask before initializing user_init_arrays
98	!
99	! 3711 2019-01-31 13:44:26Z knoop
100	! Introduced module_interface_init_checks for post-init checks in modules
101	!
102	! 3700 2019-01-26 17:03:42Z knoop
103	! Some interface calls moved to module_interface + cleanup
104	!
105	! 3648 2019-01-02 16:35:46Z suehring
106	! Rename subroutines for surface-data output
107	!
108	! Revision 1.1 1998/03/09 16:22:22 raasch
109	! Initial revision
110	!
111	!
112	! Description:
113	! ------------
114	!> Allocation of arrays and initialization of the 3D model via
115	!> a) pre-run the 1D model
116	!> or
117	!> b) pre-set constant linear profiles
118	!> or
119	!> c) read values of a previous run
120	!------------------------------------------------------------------------------!
121	SUBROUTINE init_3d_model
122
123
124	USE advec_ws
125
126	USE arrays_3d
127
128	USE basic_constants_and_equations_mod, &
129	ONLY: c_p, g, l_v, pi, exner_function, exner_function_invers, &
130	ideal_gas_law_rho, ideal_gas_law_rho_pt, barometric_formula
131
132	USE bulk_cloud_model_mod, &
133	ONLY: bulk_cloud_model
134
135	USE chem_modules, &
136	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
137
138	USE control_parameters
139
140	USE grid_variables, &
141	ONLY: dx, dy, ddx2_mg, ddy2_mg
142
143	USE indices
144
145	USE kinds
146
147	USE lsf_nudging_mod, &
148	ONLY: ls_forcing_surf
149
150	USE model_1d_mod, &
151	ONLY: init_1d_model, l1d, u1d, v1d
152
153	USE module_interface, &
154	ONLY: module_interface_init_arrays, &
155	module_interface_init, &
156	module_interface_init_checks
157
158	USE multi_agent_system_mod, &
159	ONLY: agents_active, mas_init
160
161	USE netcdf_interface, &
162	ONLY: dots_max
163
164	USE netcdf_data_input_mod, &
165	ONLY: char_fill, &
166	check_existence, &
167	close_input_file, &
168	get_attribute, &
169	get_variable, &
170	init_3d, &
171	input_pids_static, &
172	inquire_num_variables, &
173	inquire_variable_names, &
174	input_file_static, &
175	netcdf_data_input_init_3d, &
176	num_var_pids, &
177	open_read_file, &
178	pids_id, &
179	real_2d, &
180	vars_pids
181
182	USE nesting_offl_mod, &
183	ONLY: nesting_offl_init
184
185	USE palm_date_time_mod, &
186	ONLY: set_reference_date_time
187
188	USE pegrid
189
190	#if defined( __parallel )
191	USE pmc_interface, &
192	ONLY: nested_run
193	#endif
194
195	USE random_function_mod
196
197	USE random_generator_parallel, &
198	ONLY: init_parallel_random_generator
199
200	USE read_restart_data_mod, &
201	ONLY: rrd_read_parts_of_global, rrd_local
202
203	USE statistics, &
204	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, &
205	statistic_regions, sums, sums_divnew_l, sums_divold_l, sums_l, &
206	sums_l_l, sums_wsts_bc_l, ts_value, &
207	weight_pres, weight_substep
208
209	USE synthetic_turbulence_generator_mod, &
210	ONLY: stg_init, use_syn_turb_gen
211
212	USE surface_layer_fluxes_mod, &
213	ONLY: init_surface_layer_fluxes
214
215	USE surface_mod, &
216	ONLY : init_single_surface_properties, &
217	init_surface_arrays, &
218	init_surfaces, &
219	surf_def_h, &
220	surf_def_v, &
221	surf_lsm_h, &
222	surf_usm_h
223
224	#if defined( _OPENACC )
225	USE surface_mod, &
226	ONLY : bc_h
227	#endif
228
229	USE surface_data_output_mod, &
230	ONLY: surface_data_output_init
231
232	USE transpose_indices
233
234	IMPLICIT NONE
235
236	INTEGER(iwp) :: i !< grid index in x direction
237	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
238	INTEGER(iwp) :: j !< grid index in y direction
239	INTEGER(iwp) :: k !< grid index in z direction
240	INTEGER(iwp) :: k_surf !< surface level index
241	INTEGER(iwp) :: l !< running index over surface orientation
242	INTEGER(iwp) :: m !< index of surface element in surface data type
243	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
244	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
245	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
246	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
247	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
248	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
249	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
250	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
251	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
252	INTEGER(iwp) :: sr !< index of statistic region
253
254	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on subdomain
255
256	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on subdomain
257	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on subdomain
258
259
260
261	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain inital profiles
262	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
263
264	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
265	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
266
267	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
268	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
269
270	REAL(wp), DIMENSION(:), ALLOCATABLE :: mean_surface_level_height_l !< mean surface level height on subdomain
271	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_l !< total number of non-topography grid points on subdomain
272	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_tmp !< total number of non-topography grid points
273
274	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
275
276	CALL location_message( 'model initialization', 'start' )
277	!
278	!-- Set reference date-time
279	CALL set_reference_date_time( date_time_str=origin_date_time )
280
281	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
282	!
283	!-- Allocate arrays
284	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
285	mean_surface_level_height_l(0:statistic_regions), &
286	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
287	ngp_3d(0:statistic_regions), &
288	ngp_3d_inner(0:statistic_regions), &
289	ngp_3d_inner_l(0:statistic_regions), &
290	ngp_3d_inner_tmp(0:statistic_regions), &
291	sums_divnew_l(0:statistic_regions), &
292	sums_divold_l(0:statistic_regions) )
293	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
294	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
295	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
296	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
297	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
298	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
299	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
300	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
301	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
302	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
303	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
304	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
305
306	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
307	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
308	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
309
310	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
311	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
312	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
313	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
314	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
315	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
316	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
317	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
318	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
319	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
320	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
321	IF ( .NOT. neutral ) THEN
322	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
323	ENDIF
324	!
325	!-- Pre-set masks for regional statistics. Default is the total model domain.
326	!-- Ghost points are excluded because counting values at the ghost boundaries
327	!-- would bias the statistics
328	rmask = 1.0_wp
329	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
330	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
331	!
332	!-- Following array is required for perturbation pressure within the iterative
333	!-- pressure solvers. For the multistep schemes (Runge-Kutta), array p holds
334	!-- the weighted average of the substeps and cannot be used in the Poisson
335	!-- solver.
336	IF ( psolver == 'sor' ) THEN
337	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
338	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
339	!
340	!-- For performance reasons, multigrid is using one ghost layer only
341	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
342	ENDIF
343
344	!
345	!-- Array for storing constant coeffficients of the tridiagonal solver
346	IF ( psolver == 'poisfft' ) THEN
347	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
348	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
349	ENDIF
350
351	IF ( humidity ) THEN
352	!
353	!-- 3D-humidity
354	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
355	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
356	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
357	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
358	ENDIF
359
360	IF ( passive_scalar ) THEN
361
362	!
363	!-- 3D scalar arrays
364	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
365	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
366	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
367
368	ENDIF
369
370	!
371	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to
372	!-- non-zero values later in ocean_init
373	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
374	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
375	u_stokes_zu(:) = 0.0_wp
376	u_stokes_zw(:) = 0.0_wp
377	v_stokes_zu(:) = 0.0_wp
378	v_stokes_zw(:) = 0.0_wp
379
380	!
381	!-- Allocation of anelastic and Boussinesq approximation specific arrays
382	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
383	ALLOCATE( rho_air(nzb:nzt+1) )
384	ALLOCATE( rho_air_zw(nzb:nzt+1) )
385	ALLOCATE( drho_air(nzb:nzt+1) )
386	ALLOCATE( drho_air_zw(nzb:nzt+1) )
387	!
388	!-- Density profile calculation for anelastic and Boussinesq approximation
389	!-- In case of a Boussinesq approximation, a constant density is calculated
390	!-- mainly for output purposes. This density do not need to be considered
391	!-- in the model's system of equations.
392	IF ( TRIM( approximation ) == 'anelastic' ) THEN
393	DO k = nzb, nzt+1
394	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
395	exner_function(surface_pressure * 100.0_wp), &
396	surface_pressure * 100.0_wp)
397
398	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
399	ENDDO
400
401	DO k = nzb, nzt
402	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
403	ENDDO
404
405	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
406	+ 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
407
408	ELSE
409	DO k = nzb, nzt+1
410	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
411	exner_function(surface_pressure * 100.0_wp), &
412	surface_pressure * 100.0_wp)
413
414	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
415	ENDDO
416
417	DO k = nzb, nzt
418	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
419	ENDDO
420
421	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
422	+ 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
423
424	ENDIF
425	!
426	!-- compute the inverse density array in order to avoid expencive divisions
427	drho_air = 1.0_wp / rho_air
428	drho_air_zw = 1.0_wp / rho_air_zw
429
430	!
431	!-- Allocation of flux conversion arrays
432	ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
433	ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
434	ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
435	ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
436	ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
437	ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )
438
439	!
440	!-- calculate flux conversion factors according to approximation and in-/output mode
441	DO k = nzb, nzt+1
442
443	IF ( TRIM( flux_input_mode ) == 'kinematic' ) THEN
444	heatflux_input_conversion(k) = rho_air_zw(k)
445	waterflux_input_conversion(k) = rho_air_zw(k)
446	momentumflux_input_conversion(k) = rho_air_zw(k)
447	ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
448	heatflux_input_conversion(k) = 1.0_wp / c_p
449	waterflux_input_conversion(k) = 1.0_wp / l_v
450	momentumflux_input_conversion(k) = 1.0_wp
451	ENDIF
452
453	IF ( TRIM( flux_output_mode ) == 'kinematic' ) THEN
454	heatflux_output_conversion(k) = drho_air_zw(k)
455	waterflux_output_conversion(k) = drho_air_zw(k)
456	momentumflux_output_conversion(k) = drho_air_zw(k)
457	ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
458	heatflux_output_conversion(k) = c_p
459	waterflux_output_conversion(k) = l_v
460	momentumflux_output_conversion(k) = 1.0_wp
461	ENDIF
462
463	IF ( .NOT. humidity ) THEN
464	waterflux_input_conversion(k) = 1.0_wp
465	waterflux_output_conversion(k) = 1.0_wp
466	ENDIF
467
468	ENDDO
469
470	!
471	!-- In case of multigrid method, compute grid lengths and grid factors for the
472	!-- grid levels with respective density on each grid
473	IF ( psolver(1:9) == 'multigrid' ) THEN
474
475	ALLOCATE( ddx2_mg(maximum_grid_level) )
476	ALLOCATE( ddy2_mg(maximum_grid_level) )
477	ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
478	ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
479	ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
480	ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
481	ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
482	ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
483	ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )
484
485	dzu_mg(:,maximum_grid_level) = dzu
486	rho_air_mg(:,maximum_grid_level) = rho_air
487	!
488	!-- Next line to ensure an equally spaced grid.
489	dzu_mg(1,maximum_grid_level) = dzu(2)
490	rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) + &
491	(rho_air(nzb) - rho_air(nzb+1))
492
493	dzw_mg(:,maximum_grid_level) = dzw
494	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
495	nzt_l = nzt
496	DO l = maximum_grid_level-1, 1, -1
497	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
498	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
499	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + (rho_air_mg(nzb,l+1) - rho_air_mg(nzb+1,l+1))
500	rho_air_zw_mg(nzb,l) = rho_air_zw_mg(nzb,l+1) + (rho_air_zw_mg(nzb,l+1) - rho_air_zw_mg(nzb+1,l+1))
501	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
502	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
503	nzt_l = nzt_l / 2
504	DO k = 2, nzt_l+1
505	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
506	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
507	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
508	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
509	ENDDO
510	ENDDO
511
512	nzt_l = nzt
513	dx_l = dx
514	dy_l = dy
515	DO l = maximum_grid_level, 1, -1
516	ddx2_mg(l) = 1.0_wp / dx_l**2
517	ddy2_mg(l) = 1.0_wp / dy_l**2
518	DO k = nzb+1, nzt_l
519	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
520	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
521	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
522	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
523	ENDDO
524	nzt_l = nzt_l / 2
525	dx_l = dx_l * 2.0_wp
526	dy_l = dy_l * 2.0_wp
527	ENDDO
528
529	ENDIF
530
531	!
532	!-- 1D-array for large scale subsidence velocity
533	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
534	ALLOCATE ( w_subs(nzb:nzt+1) )
535	w_subs = 0.0_wp
536	ENDIF
537
538	!
539	!-- Arrays to store velocity data from t-dt and the phase speeds which
540	!-- are needed for radiation boundary conditions
541	IF ( bc_radiation_l ) THEN
542	ALLOCATE( u_m_l(nzb:nzt+1,nysg:nyng,1:2), &
543	v_m_l(nzb:nzt+1,nysg:nyng,0:1), &
544	w_m_l(nzb:nzt+1,nysg:nyng,0:1) )
545	ENDIF
546	IF ( bc_radiation_r ) THEN
547	ALLOCATE( u_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
548	v_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
549	w_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx) )
550	ENDIF
551	IF ( bc_radiation_l .OR. bc_radiation_r ) THEN
552	ALLOCATE( c_u(nzb:nzt+1,nysg:nyng), c_v(nzb:nzt+1,nysg:nyng), &
553	c_w(nzb:nzt+1,nysg:nyng) )
554	ENDIF
555	IF ( bc_radiation_s ) THEN
556	ALLOCATE( u_m_s(nzb:nzt+1,0:1,nxlg:nxrg), &
557	v_m_s(nzb:nzt+1,1:2,nxlg:nxrg), &
558	w_m_s(nzb:nzt+1,0:1,nxlg:nxrg) )
559	ENDIF
560	IF ( bc_radiation_n ) THEN
561	ALLOCATE( u_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
562	v_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
563	w_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg) )
564	ENDIF
565	IF ( bc_radiation_s .OR. bc_radiation_n ) THEN
566	ALLOCATE( c_u(nzb:nzt+1,nxlg:nxrg), c_v(nzb:nzt+1,nxlg:nxrg), &
567	c_w(nzb:nzt+1,nxlg:nxrg) )
568	ENDIF
569	IF ( bc_radiation_l .OR. bc_radiation_r .OR. bc_radiation_s .OR. &
570	bc_radiation_n ) THEN
571	ALLOCATE( c_u_m_l(nzb:nzt+1), c_v_m_l(nzb:nzt+1), c_w_m_l(nzb:nzt+1) )
572	ALLOCATE( c_u_m(nzb:nzt+1), c_v_m(nzb:nzt+1), c_w_m(nzb:nzt+1) )
573	ENDIF
574
575	!
576	!-- Initial assignment of the pointers
577	IF ( .NOT. neutral ) THEN
578	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
579	ELSE
580	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
581	ENDIF
582	u => u_1; u_p => u_2; tu_m => u_3
583	v => v_1; v_p => v_2; tv_m => v_3
584	w => w_1; w_p => w_2; tw_m => w_3
585
586	IF ( humidity ) THEN
587	q => q_1; q_p => q_2; tq_m => q_3
588	vpt => vpt_1
589	ENDIF
590
591	IF ( passive_scalar ) THEN
592	s => s_1; s_p => s_2; ts_m => s_3
593	ENDIF
594
595	!
596	!-- Initialize surface arrays
597	CALL init_surface_arrays
598	!
599	!-- Allocate arrays for other modules
600	CALL module_interface_init_arrays
601
602
603	!
604	!-- Allocate arrays containing the RK coefficient for calculation of
605	!-- perturbation pressure and turbulent fluxes. At this point values are
606	!-- set for pressure calculation during initialization (where no timestep
607	!-- is done). Further below the values needed within the timestep scheme
608	!-- will be set.
609	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
610	weight_pres(1:intermediate_timestep_count_max) )
611	weight_substep = 1.0_wp
612	weight_pres = 1.0_wp
613	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
614
615	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
616
617	!
618	!-- Initialize time series
619	ts_value = 0.0_wp
620
621	!
622	!-- Initialize local summation arrays for routine flow_statistics.
623	!-- This is necessary because they may not yet have been initialized when they
624	!-- are called from flow_statistics (or - depending on the chosen model run -
625	!-- are never initialized)
626	sums_divnew_l = 0.0_wp
627	sums_divold_l = 0.0_wp
628	sums_l_l = 0.0_wp
629	sums_wsts_bc_l = 0.0_wp
630
631	!
632	!-- Initialize model variables
633	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
634	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
635	!
636	!-- Initialization with provided input data derived from larger-scale model
637	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
638	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
639	!
640	!-- Read initial 1D profiles or 3D data from NetCDF file, depending
641	!-- on the provided level-of-detail.
642	!-- At the moment, only u, v, w, pt and q are provided.
643	CALL netcdf_data_input_init_3d
644	!
645	!-- Please note, Inifor provides data from nzb+1 to nzt.
646	!-- Bottom and top boundary conditions for Inifor profiles are already
647	!-- set (just after reading), so that this is not necessary here.
648	!-- Depending on the provided level-of-detail, initial Inifor data is
649	!-- either stored on data type (lod=1), or directly on 3D arrays (lod=2).
650	!-- In order to obtain also initial profiles in case of lod=2 (which
651	!-- is required for e.g. damping), average over 3D data.
652	IF( init_3d%lod_u == 1 ) THEN
653	u_init = init_3d%u_init
654	ELSEIF( init_3d%lod_u == 2 ) THEN
655	ALLOCATE( init_l(nzb:nzt+1) )
656	DO k = nzb, nzt+1
657	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
658	ENDDO
659	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
660
661	#if defined( __parallel )
662	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, &
663	MPI_REAL, MPI_SUM, comm2d, ierr )
664	#else
665	u_init = init_l
666	#endif
667	DEALLOCATE( init_l )
668
669	ENDIF
670
671	IF( init_3d%lod_v == 1 ) THEN
672	v_init = init_3d%v_init
673	ELSEIF( init_3d%lod_v == 2 ) THEN
674	ALLOCATE( init_l(nzb:nzt+1) )
675	DO k = nzb, nzt+1
676	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
677	ENDDO
678	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
679
680	#if defined( __parallel )
681	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, &
682	MPI_REAL, MPI_SUM, comm2d, ierr )
683	#else
684	v_init = init_l
685	#endif
686	DEALLOCATE( init_l )
687	ENDIF
688	IF( .NOT. neutral ) THEN
689	IF( init_3d%lod_pt == 1 ) THEN
690	pt_init = init_3d%pt_init
691	ELSEIF( init_3d%lod_pt == 2 ) THEN
692	ALLOCATE( init_l(nzb:nzt+1) )
693	DO k = nzb, nzt+1
694	init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
695	ENDDO
696	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
697
698	#if defined( __parallel )
699	CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1, &
700	MPI_REAL, MPI_SUM, comm2d, ierr )
701	#else
702	pt_init = init_l
703	#endif
704	DEALLOCATE( init_l )
705	ENDIF
706	ENDIF
707
708
709	IF( humidity ) THEN
710	IF( init_3d%lod_q == 1 ) THEN
711	q_init = init_3d%q_init
712	ELSEIF( init_3d%lod_q == 2 ) THEN
713	ALLOCATE( init_l(nzb:nzt+1) )
714	DO k = nzb, nzt+1
715	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
716	ENDDO
717	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
718
719	#if defined( __parallel )
720	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, &
721	MPI_REAL, MPI_SUM, comm2d, ierr )
722	#else
723	q_init = init_l
724	#endif
725	DEALLOCATE( init_l )
726	ENDIF
727	ENDIF
728
729	!
730	!-- Write initial profiles onto 3D arrays.
731	!-- Work-around, 3D initialization of u,v,w creates artificial
732	!-- structures wich correlate with the processor grid. The reason
733	!-- for this is still unknown. To work-around this, 3D initialization
734	!-- will be effectively reduce to a 1D initialization where no such
735	!-- artificial structures appear.
736	DO i = nxlg, nxrg
737	DO j = nysg, nyng
738	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) &
739	u(:,j,i) = u_init(:)
740	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) &
741	v(:,j,i) = v_init(:)
742	IF( .NOT. neutral .AND. &
743	( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
744	pt(:,j,i) = pt_init(:)
745	IF( humidity .AND. &
746	( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
747	q(:,j,i) = q_init(:)
748	ENDDO
749	ENDDO
750	!
751	!-- Set geostrophic wind components.
752	IF ( init_3d%from_file_ug ) THEN
753	ug(:) = init_3d%ug_init(:)
754	ENDIF
755	IF ( init_3d%from_file_vg ) THEN
756	vg(:) = init_3d%vg_init(:)
757	ENDIF
758	!
759	!-- Set bottom and top boundary condition for geostrophic wind
760	ug(nzt+1) = ug(nzt)
761	vg(nzt+1) = vg(nzt)
762	ug(nzb) = ug(nzb+1)
763	vg(nzb) = vg(nzb+1)
764	!
765	!-- Set inital w to 0
766	w = 0.0_wp
767
768	IF ( passive_scalar ) THEN
769	DO i = nxlg, nxrg
770	DO j = nysg, nyng
771	s(:,j,i) = s_init
772	ENDDO
773	ENDDO
774	ENDIF
775
776	!
777	!-- Set velocity components at non-atmospheric / oceanic grid points to
778	!-- zero.
779	u = MERGE( u, 0.0_wp, BTEST( wall_flags_static_0, 1 ) )
780	v = MERGE( v, 0.0_wp, BTEST( wall_flags_static_0, 2 ) )
781	w = MERGE( w, 0.0_wp, BTEST( wall_flags_static_0, 3 ) )
782	!
783	!-- Initialize surface variables, e.g. friction velocity, momentum
784	!-- fluxes, etc.
785	CALL init_surfaces
786
787	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
788	!
789	!-- Initialization via computed 1D-model profiles
790	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
791
792	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
793	!
794	!-- Use solutions of the 1D model as initial profiles,
795	!-- start 1D model
796	CALL init_1d_model
797	!
798	!-- Transfer initial profiles to the arrays of the 3D model
799	DO i = nxlg, nxrg
800	DO j = nysg, nyng
801	pt(:,j,i) = pt_init
802	u(:,j,i) = u1d
803	v(:,j,i) = v1d
804	ENDDO
805	ENDDO
806
807	IF ( humidity ) THEN
808	DO i = nxlg, nxrg
809	DO j = nysg, nyng
810	q(:,j,i) = q_init
811	ENDDO
812	ENDDO
813	ENDIF
814
815	IF ( passive_scalar ) THEN
816	DO i = nxlg, nxrg
817	DO j = nysg, nyng
818	s(:,j,i) = s_init
819	ENDDO
820	ENDDO
821	ENDIF
822	!
823	!-- Store initial profiles for output purposes etc.
824	IF ( .NOT. constant_diffusion ) THEN
825	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
826	ENDIF
827	!
828	!-- Set velocities back to zero
829	u = MERGE( u, 0.0_wp, BTEST( wall_flags_static_0, 1 ) )
830	v = MERGE( v, 0.0_wp, BTEST( wall_flags_static_0, 2 ) )
831	!
832	!-- WARNING: The extra boundary conditions set after running the
833	!-- ------- 1D model impose an error on the divergence one layer
834	!-- below the topography; need to correct later
835	!-- ATTENTION: Provisional correction for Piacsek & Williams
836	!-- --------- advection scheme: keep u and v zero one layer below
837	!-- the topography.
838	IF ( ibc_uv_b == 1 ) THEN
839	!
840	!-- Neumann condition
841	DO i = nxl-1, nxr+1
842	DO j = nys-1, nyn+1
843	u(nzb,j,i) = u(nzb+1,j,i)
844	v(nzb,j,i) = v(nzb+1,j,i)
845	ENDDO
846	ENDDO
847
848	ENDIF
849	!
850	!-- Initialize surface variables, e.g. friction velocity, momentum
851	!-- fluxes, etc.
852	CALL init_surfaces
853
854	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
855
856	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
857	THEN
858
859	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
860
861	!
862	!-- Use constructed initial profiles (velocity constant with height,
863	!-- temperature profile with constant gradient)
864	DO i = nxlg, nxrg
865	DO j = nysg, nyng
866	pt(:,j,i) = pt_init
867	u(:,j,i) = u_init
868	v(:,j,i) = v_init
869	ENDDO
870	ENDDO
871	!
872	!-- Mask topography
873	u = MERGE( u, 0.0_wp, BTEST( wall_flags_static_0, 1 ) )
874	v = MERGE( v, 0.0_wp, BTEST( wall_flags_static_0, 2 ) )
875	!
876	!-- Set initial horizontal velocities at the lowest computational grid
877	!-- levels to zero in order to avoid too small time steps caused by the
878	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
879	!-- in the limiting formula!).
880	!-- Please note, in case land- or urban-surface model is used and a
881	!-- spinup is applied, masking the lowest computational level is not
882	!-- possible as MOST as well as energy-balance parametrizations will not
883	!-- work with zero wind velocity.
884	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
885	DO i = nxlg, nxrg
886	DO j = nysg, nyng
887	DO k = nzb, nzt
888	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
889	BTEST( wall_flags_static_0(k,j,i), 20 ) )
890	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
891	BTEST( wall_flags_static_0(k,j,i), 21 ) )
892	ENDDO
893	ENDDO
894	ENDDO
895	ENDIF
896
897	IF ( humidity ) THEN
898	DO i = nxlg, nxrg
899	DO j = nysg, nyng
900	q(:,j,i) = q_init
901	ENDDO
902	ENDDO
903	ENDIF
904
905	IF ( passive_scalar ) THEN
906	DO i = nxlg, nxrg
907	DO j = nysg, nyng
908	s(:,j,i) = s_init
909	ENDDO
910	ENDDO
911	ENDIF
912
913	!
914	!-- Compute initial temperature field and other constants used in case
915	!-- of a sloping surface
916	IF ( sloping_surface ) CALL init_slope
917	!
918	!-- Initialize surface variables, e.g. friction velocity, momentum
919	!-- fluxes, etc.
920	CALL init_surfaces
921
922	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
923
924	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
925	THEN
926
927	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
928	!
929	!-- Pre-initialize surface variables, i.e. setting start- and end-indices
930	!-- at each (j,i)-location. Please note, this does not supersede
931	!-- user-defined initialization of surface quantities.
932	CALL init_surfaces
933	!
934	!-- Initialization will completely be done by the user
935	CALL user_init_3d_model
936
937	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
938
939	ENDIF
940
941	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
942
943	!
944	!-- Bottom boundary
945	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
946	u(nzb,:,:) = 0.0_wp
947	v(nzb,:,:) = 0.0_wp
948	ENDIF
949
950	!
951	!-- Apply channel flow boundary condition
952	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
953	u(nzt+1,:,:) = 0.0_wp
954	v(nzt+1,:,:) = 0.0_wp
955	ENDIF
956
957	!
958	!-- Calculate virtual potential temperature
959	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
960
961	!
962	!-- Store initial profiles for output purposes etc.. Please note, in case of
963	!-- initialization of u, v, w, pt, and q via output data derived from larger
964	!-- scale models, data will not be horizontally homogeneous. Actually, a mean
965	!-- profile should be calculated before.
966	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
967	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
968	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
969	hom(nzb,1,5,:) = 0.0_wp
970	hom(nzb,1,6,:) = 0.0_wp
971	ENDIF
972	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
973
974	IF ( humidity ) THEN
975	!
976	!-- Store initial profile of total water content, virtual potential
977	!-- temperature
978	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
979	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
980	!
981	!-- Store initial profile of mixing ratio and potential
982	!-- temperature
983	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
984	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
985	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
986	ENDIF
987	ENDIF
988
989	!
990	!-- Store initial scalar profile
991	IF ( passive_scalar ) THEN
992	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
993	ENDIF
994
995	!
996	!-- Initialize the random number generators (from numerical recipes)
997	CALL random_function_ini
998
999	IF ( random_generator == 'random-parallel' ) THEN
1000	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
1001	ENDIF
1002	!
1003	!-- Set the reference state to be used in the buoyancy terms (for ocean runs
1004	!-- the reference state will be set (overwritten) in init_ocean)
1005	IF ( use_single_reference_value ) THEN
1006	IF ( .NOT. humidity ) THEN
1007	ref_state(:) = pt_reference
1008	ELSE
1009	ref_state(:) = vpt_reference
1010	ENDIF
1011	ELSE
1012	IF ( .NOT. humidity ) THEN
1013	ref_state(:) = pt_init(:)
1014	ELSE
1015	ref_state(:) = vpt(:,nys,nxl)
1016	ENDIF
1017	ENDIF
1018
1019	!
1020	!-- For the moment, vertical velocity is zero
1021	w = 0.0_wp
1022
1023	!
1024	!-- Initialize array sums (must be defined in first call of pres)
1025	sums = 0.0_wp
1026
1027	!
1028	!-- In case of iterative solvers, p must get an initial value
1029	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
1030	!
1031	!-- Impose vortex with vertical axis on the initial velocity profile
1032	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
1033	CALL init_rankine
1034	ENDIF
1035
1036	!
1037	!-- Impose temperature anomaly (advection test only) or warm air bubble
1038	!-- close to surface
1039	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1040	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1041	CALL init_pt_anomaly
1042	ENDIF
1043
1044	!
1045	!-- If required, change the surface temperature at the start of the 3D run
1046	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1047	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1048	ENDIF
1049
1050	!
1051	!-- If required, change the surface humidity/scalar at the start of the 3D
1052	!-- run
1053	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1054	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1055
1056	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1057	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1058
1059
1060	!
1061	!-- Initialize old and new time levels.
1062	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1063	pt_p = pt; u_p = u; v_p = v; w_p = w
1064
1065	IF ( humidity ) THEN
1066	tq_m = 0.0_wp
1067	q_p = q
1068	ENDIF
1069
1070	IF ( passive_scalar ) THEN
1071	ts_m = 0.0_wp
1072	s_p = s
1073	ENDIF
1074
1075	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1076
1077	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1078	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1079	THEN
1080
1081	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1082	!
1083	!-- Initialize surface elements and its attributes, e.g. heat- and
1084	!-- momentumfluxes, roughness, scaling parameters. As number of surface
1085	!-- elements might be different between runs, e.g. in case of cyclic fill,
1086	!-- and not all surface elements are read, surface elements need to be
1087	!-- initialized before.
1088	!-- Please note, in case of cyclic fill, surfaces should be initialized
1089	!-- after restart data is read, else, individual settings of surface
1090	!-- parameters will be overwritten from data of precursor run, hence,
1091	!-- init_surfaces is called a second time after reading the restart data.
1092	CALL init_surfaces
1093	!
1094	!-- When reading data for cyclic fill of 3D prerun data files, read
1095	!-- some of the global variables from the restart file which are required
1096	!-- for initializing the inflow
1097	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1098
1099	DO i = 0, io_blocks-1
1100	IF ( i == io_group ) THEN
1101	CALL rrd_read_parts_of_global
1102	ENDIF
1103	#if defined( __parallel )
1104	CALL MPI_BARRIER( comm2d, ierr )
1105	#endif
1106	ENDDO
1107
1108	ENDIF
1109
1110	!
1111	!-- Read processor specific binary data from restart file
1112	DO i = 0, io_blocks-1
1113	IF ( i == io_group ) THEN
1114	CALL rrd_local
1115	ENDIF
1116	#if defined( __parallel )
1117	CALL MPI_BARRIER( comm2d, ierr )
1118	#endif
1119	ENDDO
1120	!
1121	!-- In case of cyclic fill, call init_surfaces a second time, so that
1122	!-- surface properties such as heat fluxes are initialized as prescribed.
1123	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) &
1124	CALL init_surfaces
1125
1126	!
1127	!-- In case of complex terrain and cyclic fill method as initialization,
1128	!-- shift initial data in the vertical direction for each point in the
1129	!-- x-y-plane depending on local surface height
1130	IF ( complex_terrain .AND. &
1131	TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1132	DO i = nxlg, nxrg
1133	DO j = nysg, nyng
1134	nz_u_shift = topo_top_ind(j,i,1)
1135	nz_v_shift = topo_top_ind(j,i,2)
1136	nz_w_shift = topo_top_ind(j,i,3)
1137	nz_s_shift = topo_top_ind(j,i,0)
1138
1139	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1140
1141	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1142
1143	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1144
1145	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1146	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1147	ENDDO
1148	ENDDO
1149	ENDIF
1150	!
1151	!-- Initialization of the turbulence recycling method
1152	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1153	turbulent_inflow ) THEN
1154	!
1155	!-- First store the profiles to be used at the inflow.
1156	!-- These profiles are the (temporally) and horizontally averaged vertical
1157	!-- profiles from the prerun. Alternatively, prescribed profiles
1158	!-- for u,v-components can be used.
1159	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the
1160	!-- (temporally) and horizontally averaged vertical profiles from the end
1161	!-- of the prerun, because these profiles shall be used as the basic state
1162	!-- for the rayleigh damping and the pt_damping.
1163	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1164
1165	IF ( use_prescribed_profile_data ) THEN
1166	mean_inflow_profiles(:,1) = u_init ! u
1167	mean_inflow_profiles(:,2) = v_init ! v
1168	ELSE
1169	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1170	u_init(:) = hom_sum(:,1,0)
1171	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1172	v_init(:) = hom_sum(:,2,0)
1173	ENDIF
1174	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1175	pt_init(:) = hom_sum(:,4,0)
1176	IF ( humidity ) &
1177	mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1178	q_init(:) = hom_sum(:,41,0)
1179	IF ( passive_scalar ) &
1180	mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1181	s_init(:) = hom_sum(:,115,0)
1182	!
1183	!-- In case of complex terrain, determine vertical displacement at inflow
1184	!-- boundary and adjust mean inflow profiles
1185	IF ( complex_terrain ) THEN
1186	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1187	nz_u_shift_l = topo_top_ind(j,i,1)
1188	nz_v_shift_l = topo_top_ind(j,i,2)
1189	nz_w_shift_l = topo_top_ind(j,i,3)
1190	nz_s_shift_l = topo_top_ind(j,i,0)
1191	ELSE
1192	nz_u_shift_l = 0
1193	nz_v_shift_l = 0
1194	nz_w_shift_l = 0
1195	nz_s_shift_l = 0
1196	ENDIF
1197
1198	#if defined( __parallel )
1199	CALL MPI_ALLREDUCE(nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, &
1200	MPI_MAX, comm2d, ierr)
1201	CALL MPI_ALLREDUCE(nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, &
1202	MPI_MAX, comm2d, ierr)
1203	CALL MPI_ALLREDUCE(nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, &
1204	MPI_MAX, comm2d, ierr)
1205	CALL MPI_ALLREDUCE(nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, &
1206	MPI_MAX, comm2d, ierr)
1207	#else
1208	nz_u_shift = nz_u_shift_l
1209	nz_v_shift = nz_v_shift_l
1210	nz_w_shift = nz_w_shift_l
1211	nz_s_shift = nz_s_shift_l
1212	#endif
1213
1214	mean_inflow_profiles(:,1) = 0.0_wp
1215	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1216
1217	mean_inflow_profiles(:,2) = 0.0_wp
1218	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1219
1220	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1221
1222	ENDIF
1223
1224	!
1225	!-- If necessary, adjust the horizontal flow field to the prescribed
1226	!-- profiles
1227	IF ( use_prescribed_profile_data ) THEN
1228	DO i = nxlg, nxrg
1229	DO j = nysg, nyng
1230	DO k = nzb, nzt+1
1231	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1232	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1233	ENDDO
1234	ENDDO
1235	ENDDO
1236	ENDIF
1237
1238	!
1239	!-- Use these mean profiles at the inflow (provided that Dirichlet
1240	!-- conditions are used)
1241	IF ( bc_dirichlet_l ) THEN
1242	DO j = nysg, nyng
1243	DO k = nzb, nzt+1
1244	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1245	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1246	w(k,j,nxlg:-1) = 0.0_wp
1247	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1248	IF ( humidity ) &
1249	q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1250	IF ( passive_scalar ) &
1251	s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1252	ENDDO
1253	ENDDO
1254	ENDIF
1255
1256	!
1257	!-- Calculate the damping factors to be used at the inflow. For a
1258	!-- turbulent inflow the turbulent fluctuations have to be limited
1259	!-- vertically because otherwise the turbulent inflow layer will grow
1260	!-- in time.
1261	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1262	!
1263	!-- Default: use the inversion height calculated by the prerun; if
1264	!-- this is zero, inflow_damping_height must be explicitly
1265	!-- specified.
1266	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1267	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1268	ELSE
1269	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1270	'explicitly specified because&the inversion height ', &
1271	'calculated by the prerun is zero.'
1272	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1273	ENDIF
1274
1275	ENDIF
1276
1277	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1278	!
1279	!-- Default for the transition range: one tenth of the undamped
1280	!-- layer
1281	inflow_damping_width = 0.1_wp * inflow_damping_height
1282
1283	ENDIF
1284
1285	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1286
1287	DO k = nzb, nzt+1
1288
1289	IF ( zu(k) <= inflow_damping_height ) THEN
1290	inflow_damping_factor(k) = 1.0_wp
1291	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1292	inflow_damping_factor(k) = 1.0_wp - &
1293	( zu(k) - inflow_damping_height ) / &
1294	inflow_damping_width
1295	ELSE
1296	inflow_damping_factor(k) = 0.0_wp
1297	ENDIF
1298
1299	ENDDO
1300
1301	ENDIF
1302
1303	!
1304	!-- Inside buildings set velocities back to zero
1305	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1306	topography /= 'flat' ) THEN
1307	!
1308	!-- Inside buildings set velocities back to zero.
1309	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1310	!-- maybe revise later.
1311	DO i = nxlg, nxrg
1312	DO j = nysg, nyng
1313	DO k = nzb, nzt
1314	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
1315	BTEST( wall_flags_static_0(k,j,i), 1 ) )
1316	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
1317	BTEST( wall_flags_static_0(k,j,i), 2 ) )
1318	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, &
1319	BTEST( wall_flags_static_0(k,j,i), 3 ) )
1320	ENDDO
1321	ENDDO
1322	ENDDO
1323
1324	ENDIF
1325
1326	!
1327	!-- Calculate initial temperature field and other constants used in case
1328	!-- of a sloping surface
1329	IF ( sloping_surface ) CALL init_slope
1330
1331	!
1332	!-- Initialize new time levels (only done in order to set boundary values
1333	!-- including ghost points)
1334	pt_p = pt; u_p = u; v_p = v; w_p = w
1335	IF ( humidity ) THEN
1336	q_p = q
1337	ENDIF
1338	IF ( passive_scalar ) s_p = s
1339	!
1340	!-- Allthough tendency arrays are set in prognostic_equations, they have
1341	!-- have to be predefined here because they are used (but multiplied with 0)
1342	!-- there before they are set.
1343	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1344	IF ( humidity ) THEN
1345	tq_m = 0.0_wp
1346	ENDIF
1347	IF ( passive_scalar ) ts_m = 0.0_wp
1348
1349	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1350
1351	ELSE
1352	!
1353	!-- Actually this part of the programm should not be reached
1354	message_string = 'unknown initializing problem'
1355	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1356	ENDIF
1357
1358
1359	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1360	!
1361	!-- Initialize old timelevels needed for radiation boundary conditions
1362	IF ( bc_radiation_l ) THEN
1363	u_m_l(:,:,:) = u(:,:,1:2)
1364	v_m_l(:,:,:) = v(:,:,0:1)
1365	w_m_l(:,:,:) = w(:,:,0:1)
1366	ENDIF
1367	IF ( bc_radiation_r ) THEN
1368	u_m_r(:,:,:) = u(:,:,nx-1:nx)
1369	v_m_r(:,:,:) = v(:,:,nx-1:nx)
1370	w_m_r(:,:,:) = w(:,:,nx-1:nx)
1371	ENDIF
1372	IF ( bc_radiation_s ) THEN
1373	u_m_s(:,:,:) = u(:,0:1,:)
1374	v_m_s(:,:,:) = v(:,1:2,:)
1375	w_m_s(:,:,:) = w(:,0:1,:)
1376	ENDIF
1377	IF ( bc_radiation_n ) THEN
1378	u_m_n(:,:,:) = u(:,ny-1:ny,:)
1379	v_m_n(:,:,:) = v(:,ny-1:ny,:)
1380	w_m_n(:,:,:) = w(:,ny-1:ny,:)
1381	ENDIF
1382
1383	ENDIF
1384
1385	!
1386	!-- Calculate the initial volume flow at the right and north boundary
1387	IF ( conserve_volume_flow ) THEN
1388
1389	IF ( use_prescribed_profile_data ) THEN
1390
1391	volume_flow_initial_l = 0.0_wp
1392	volume_flow_area_l = 0.0_wp
1393
1394	IF ( nxr == nx ) THEN
1395	DO j = nys, nyn
1396	DO k = nzb+1, nzt
1397	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1398	u_init(k) * dzw(k) &
1399	* MERGE( 1.0_wp, 0.0_wp, &
1400	BTEST( wall_flags_static_0(k,j,nxr), 1 )&
1401	)
1402
1403	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1404	* MERGE( 1.0_wp, 0.0_wp, &
1405	BTEST( wall_flags_static_0(k,j,nxr), 1 )&
1406	)
1407	ENDDO
1408	ENDDO
1409	ENDIF
1410
1411	IF ( nyn == ny ) THEN
1412	DO i = nxl, nxr
1413	DO k = nzb+1, nzt
1414	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1415	v_init(k) * dzw(k) &
1416	* MERGE( 1.0_wp, 0.0_wp, &
1417	BTEST( wall_flags_static_0(k,nyn,i), 2 )&
1418	)
1419	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1420	* MERGE( 1.0_wp, 0.0_wp, &
1421	BTEST( wall_flags_static_0(k,nyn,i), 2 )&
1422	)
1423	ENDDO
1424	ENDDO
1425	ENDIF
1426
1427	#if defined( __parallel )
1428	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1429	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1430	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1431	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1432
1433	#else
1434	volume_flow_initial = volume_flow_initial_l
1435	volume_flow_area = volume_flow_area_l
1436	#endif
1437
1438	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1439
1440	volume_flow_initial_l = 0.0_wp
1441	volume_flow_area_l = 0.0_wp
1442
1443	IF ( nxr == nx ) THEN
1444	DO j = nys, nyn
1445	DO k = nzb+1, nzt
1446	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1447	hom_sum(k,1,0) * dzw(k) &
1448	* MERGE( 1.0_wp, 0.0_wp, &
1449	BTEST( wall_flags_static_0(k,j,nx), 1 ) &
1450	)
1451	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1452	* MERGE( 1.0_wp, 0.0_wp, &
1453	BTEST( wall_flags_static_0(k,j,nx), 1 ) &
1454	)
1455	ENDDO
1456	ENDDO
1457	ENDIF
1458
1459	IF ( nyn == ny ) THEN
1460	DO i = nxl, nxr
1461	DO k = nzb+1, nzt
1462	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1463	hom_sum(k,2,0) * dzw(k) &
1464	* MERGE( 1.0_wp, 0.0_wp, &
1465	BTEST( wall_flags_static_0(k,ny,i), 2 ) &
1466	)
1467	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1468	* MERGE( 1.0_wp, 0.0_wp, &
1469	BTEST( wall_flags_static_0(k,ny,i), 2 ) &
1470	)
1471	ENDDO
1472	ENDDO
1473	ENDIF
1474
1475	#if defined( __parallel )
1476	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1477	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1478	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1479	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1480
1481	#else
1482	volume_flow_initial = volume_flow_initial_l
1483	volume_flow_area = volume_flow_area_l
1484	#endif
1485
1486	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1487
1488	volume_flow_initial_l = 0.0_wp
1489	volume_flow_area_l = 0.0_wp
1490
1491	IF ( nxr == nx ) THEN
1492	DO j = nys, nyn
1493	DO k = nzb+1, nzt
1494	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1495	u(k,j,nx) * dzw(k) &
1496	* MERGE( 1.0_wp, 0.0_wp, &
1497	BTEST( wall_flags_static_0(k,j,nx), 1 ) &
1498	)
1499	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1500	* MERGE( 1.0_wp, 0.0_wp, &
1501	BTEST( wall_flags_static_0(k,j,nx), 1 ) &
1502	)
1503	ENDDO
1504	ENDDO
1505	ENDIF
1506
1507	IF ( nyn == ny ) THEN
1508	DO i = nxl, nxr
1509	DO k = nzb+1, nzt
1510	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1511	v(k,ny,i) * dzw(k) &
1512	* MERGE( 1.0_wp, 0.0_wp, &
1513	BTEST( wall_flags_static_0(k,ny,i), 2 ) &
1514	)
1515	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1516	* MERGE( 1.0_wp, 0.0_wp, &
1517	BTEST( wall_flags_static_0(k,ny,i), 2 ) &
1518	)
1519	ENDDO
1520	ENDDO
1521	ENDIF
1522
1523	#if defined( __parallel )
1524	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1525	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1526	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1527	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1528
1529	#else
1530	volume_flow_initial = volume_flow_initial_l
1531	volume_flow_area = volume_flow_area_l
1532	#endif
1533
1534	ENDIF
1535
1536	!
1537	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated
1538	!-- from u\|v_bulk instead
1539	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1540	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1541	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1542	ENDIF
1543
1544	ENDIF
1545	!
1546	!-- In the following, surface properties can be further initialized with
1547	!-- input from static driver file.
1548	!-- At the moment this affects only default surfaces. For example,
1549	!-- roughness length or sensible / latent heat fluxes can be initialized
1550	!-- heterogeneously for default surfaces. Therefore, a generic routine
1551	!-- from netcdf_data_input_mod is called to read a 2D array.
1552	IF ( input_pids_static ) THEN
1553	!
1554	!-- Allocate memory for possible static input
1555	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1556	tmp_2d%var = 0.0_wp
1557	!
1558	!-- Open the static input file
1559	#if defined( __netcdf )
1560	CALL open_read_file( TRIM( input_file_static ) // &
1561	TRIM( coupling_char ), &
1562	pids_id )
1563
1564	CALL inquire_num_variables( pids_id, num_var_pids )
1565	!
1566	!-- Allocate memory to store variable names and read them
1567	ALLOCATE( vars_pids(1:num_var_pids) )
1568	CALL inquire_variable_names( pids_id, vars_pids )
1569	!
1570	!-- Input roughness length.
1571	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1572	!
1573	!-- Read _FillValue attribute
1574	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, &
1575	.FALSE., 'z0' )
1576	!
1577	!-- Read variable
1578	CALL get_variable( pids_id, 'z0', tmp_2d%var, &
1579	nxl, nxr, nys, nyn )
1580	!
1581	!-- Initialize roughness length. Note, z0 will be only initialized at
1582	!-- default-type surfaces. At natural or urban z0 is implicitly
1583	!-- initialized bythe respective parameter lists.
1584	!-- Initialize horizontal surface elements.
1585	CALL init_single_surface_properties( surf_def_h(0)%z0, &
1586	tmp_2d%var, &
1587	surf_def_h(0)%ns, &
1588	tmp_2d%fill, &
1589	surf_def_h(0)%i, &
1590	surf_def_h(0)%j )
1591	!
1592	!-- Initialize roughness also at vertical surface elements.
1593	!-- Note, the actual 2D input arrays are only defined on the
1594	!-- subdomain. Therefore, pass the index arrays with their respective
1595	!-- offset values.
1596	DO l = 0, 3
1597	CALL init_single_surface_properties( &
1598	surf_def_v(l)%z0, &
1599	tmp_2d%var, &
1600	surf_def_v(l)%ns, &
1601	tmp_2d%fill, &
1602	surf_def_v(l)%i + surf_def_v(l)%ioff, &
1603	surf_def_v(l)%j + surf_def_v(l)%joff )
1604	ENDDO
1605
1606	ENDIF
1607	!
1608	!-- Additional variables, e.g. shf, qsws, etc, can be initialized the
1609	!-- same way.
1610
1611	!
1612	!-- Finally, close the input file and deallocate temporary arrays
1613	DEALLOCATE( vars_pids )
1614
1615	CALL close_input_file( pids_id )
1616	#endif
1617	DEALLOCATE( tmp_2d%var )
1618	ENDIF
1619	!
1620	!-- Finally, if random_heatflux is set, disturb shf at horizontal
1621	!-- surfaces. Actually, this should be done in surface_mod, where all other
1622	!-- initializations of surface quantities are done. However, this
1623	!-- would create a ring dependency, hence, it is done here. Maybe delete
1624	!-- disturb_heatflux and tranfer the respective code directly into the
1625	!-- initialization in surface_mod.
1626	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1627	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1628
1629	IF ( use_surface_fluxes .AND. constant_heatflux .AND. &
1630	random_heatflux ) THEN
1631	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1632	IF ( surf_lsm_h%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h )
1633	IF ( surf_usm_h%ns >= 1 ) CALL disturb_heatflux( surf_usm_h )
1634	ENDIF
1635	ENDIF
1636
1637	!
1638	!-- Compute total sum of grid points and the mean surface level height for each
1639	!-- statistic region. These are mainly used for horizontal averaging of
1640	!-- turbulence statistics.
1641	!-- ngp_2dh: number of grid points of a horizontal cross section through the
1642	!-- respective statistic region
1643	!-- ngp_3d: number of grid points of the respective statistic region
1644	ngp_2dh_outer_l = 0
1645	ngp_2dh_outer = 0
1646	ngp_2dh_s_inner_l = 0
1647	ngp_2dh_s_inner = 0
1648	ngp_2dh_l = 0
1649	ngp_2dh = 0
1650	ngp_3d_inner_l = 0.0_wp
1651	ngp_3d_inner = 0
1652	ngp_3d = 0
1653	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1654
1655	mean_surface_level_height = 0.0_wp
1656	mean_surface_level_height_l = 0.0_wp
1657	!
1658	!-- To do: New concept for these non-topography grid points!
1659	DO sr = 0, statistic_regions
1660	DO i = nxl, nxr
1661	DO j = nys, nyn
1662	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1663	!
1664	!-- All xy-grid points
1665	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1666	!
1667	!-- Determine mean surface-level height. In case of downward-
1668	!-- facing walls are present, more than one surface level exist.
1669	!-- In this case, use the lowest surface-level height.
1670	IF ( surf_def_h(0)%start_index(j,i) <= &
1671	surf_def_h(0)%end_index(j,i) ) THEN
1672	m = surf_def_h(0)%start_index(j,i)
1673	k = surf_def_h(0)%k(m)
1674	mean_surface_level_height_l(sr) = &
1675	mean_surface_level_height_l(sr) + zw(k-1)
1676	ENDIF
1677	IF ( surf_lsm_h%start_index(j,i) <= &
1678	surf_lsm_h%end_index(j,i) ) THEN
1679	m = surf_lsm_h%start_index(j,i)
1680	k = surf_lsm_h%k(m)
1681	mean_surface_level_height_l(sr) = &
1682	mean_surface_level_height_l(sr) + zw(k-1)
1683	ENDIF
1684	IF ( surf_usm_h%start_index(j,i) <= &
1685	surf_usm_h%end_index(j,i) ) THEN
1686	m = surf_usm_h%start_index(j,i)
1687	k = surf_usm_h%k(m)
1688	mean_surface_level_height_l(sr) = &
1689	mean_surface_level_height_l(sr) + zw(k-1)
1690	ENDIF
1691
1692	k_surf = k - 1
1693
1694	DO k = nzb, nzt+1
1695	!
1696	!-- xy-grid points above topography
1697	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1698	MERGE( 1, 0, BTEST( wall_flags_static_0(k,j,i), 24 ) )
1699
1700	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1701	MERGE( 1, 0, BTEST( wall_flags_static_0(k,j,i), 22 ) )
1702
1703	ENDDO
1704	!
1705	!-- All grid points of the total domain above topography
1706	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1707
1708
1709
1710	ENDIF
1711	ENDDO
1712	ENDDO
1713	ENDDO
1714
1715	sr = statistic_regions + 1
1716	#if defined( __parallel )
1717	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1718	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, &
1719	comm2d, ierr )
1720	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1721	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, &
1722	MPI_INTEGER, MPI_SUM, comm2d, ierr )
1723	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1724	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), &
1725	(nz+2)*sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1726	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1727	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, &
1728	MPI_SUM, comm2d, ierr )
1729	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1730	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1731	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), &
1732	mean_surface_level_height(0), sr, MPI_REAL, &
1733	MPI_SUM, comm2d, ierr )
1734	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1735	#else
1736	ngp_2dh = ngp_2dh_l
1737	ngp_2dh_outer = ngp_2dh_outer_l
1738	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1739	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1740	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1741	#endif
1742
1743	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1744	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1745
1746	!
1747	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics,
1748	!-- buoyancy, etc. A zero value will occur for cases where all grid points of
1749	!-- the respective subdomain lie below the surface topography
1750	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1751	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), &
1752	ngp_3d_inner(:) )
1753	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1754
1755	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, &
1756	ngp_3d_inner_l, ngp_3d_inner_tmp )
1757	!
1758	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1759	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1760	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1761	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1762	CALL ls_forcing_surf ( simulated_time )
1763	ENDIF
1764	ENDIF
1765	!
1766	!-- Initializae 3D offline nesting in COSMO model and read data from
1767	!-- external NetCDF file.
1768	IF ( nesting_offline ) CALL nesting_offl_init
1769	!
1770	!-- Initialize quantities for special advections schemes
1771	CALL init_advec
1772
1773	!
1774	!-- Impose random perturbation on the horizontal velocity field and then
1775	!-- remove the divergences from the velocity field at the initial stage
1776	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1777	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1778	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1779
1780	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1781	!
1782	!-- Needed for both disturb_field and pres
1783	!$ACC DATA &
1784	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1785	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1786	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1787
1788	CALL disturb_field( 'u', tend, u )
1789	CALL disturb_field( 'v', tend, v )
1790
1791	!$ACC DATA &
1792	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1793	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1794	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1795	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1796	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1797	!$ACC COPYIN(wall_flags_static_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1798	!$ACC COPYIN(bc_h(0:1)) &
1799	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1800	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1801	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1802	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1803	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1804	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1805
1806	n_sor = nsor_ini
1807	CALL pres
1808	n_sor = nsor
1809
1810	!$ACC END DATA
1811	!$ACC END DATA
1812
1813	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1814
1815	ENDIF
1816
1817	IF ( .NOT. ocean_mode ) THEN
1818
1819	ALLOCATE( hyp(nzb:nzt+1) )
1820	ALLOCATE( d_exner(nzb:nzt+1) )
1821	ALLOCATE( exner(nzb:nzt+1) )
1822	ALLOCATE( hyrho(nzb:nzt+1) )
1823	!
1824	!-- Check temperature in case of too large domain height
1825	DO k = nzb, nzt+1
1826	IF ( ( pt_surface * exner_function(surface_pressure * 100.0_wp) - g/c_p * zu(k) ) < 0.0_wp ) THEN
1827	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, &
1828	') = ', zu(k)
1829	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1830	ENDIF
1831	ENDDO
1832
1833	!
1834	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1835	hyp = barometric_formula(zu, pt_surface * exner_function(surface_pressure * 100.0_wp), surface_pressure * 100.0_wp)
1836	d_exner = exner_function_invers(hyp)
1837	exner = 1.0_wp / exner_function_invers(hyp)
1838	hyrho = ideal_gas_law_rho_pt(hyp, pt_init)
1839	!
1840	!-- Compute reference density
1841	rho_surface = ideal_gas_law_rho(surface_pressure * 100.0_wp, pt_surface * exner_function(surface_pressure * 100.0_wp))
1842
1843	ENDIF
1844
1845	!
1846	!-- If required, initialize particles
1847	IF ( agents_active ) CALL mas_init
1848	!
1849	!-- Initialization of synthetic turbulence generator
1850	IF ( use_syn_turb_gen ) CALL stg_init
1851	!
1852	!-- Initializing actions for all other modules
1853	CALL module_interface_init
1854	!
1855	!-- Initialize surface layer (done after LSM as roughness length are required
1856	!-- for initialization
1857	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1858	!
1859	!-- Initialize surface data output
1860	IF ( surface_output ) CALL surface_data_output_init
1861	!
1862	!-- Initialize the ws-scheme.
1863	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1864	!
1865	!-- Perform post-initializing checks for all other modules
1866	CALL module_interface_init_checks
1867
1868	!
1869	!-- Setting weighting factors for calculation of perturbation pressure
1870	!-- and turbulent quantities from the RK substeps
1871	IF ( TRIM(timestep_scheme) == 'runge-kutta-3' ) THEN ! for RK3-method
1872
1873	weight_substep(1) = 1._wp/6._wp
1874	weight_substep(2) = 3._wp/10._wp
1875	weight_substep(3) = 8._wp/15._wp
1876
1877	weight_pres(1) = 1._wp/3._wp
1878	weight_pres(2) = 5._wp/12._wp
1879	weight_pres(3) = 1._wp/4._wp
1880
1881	ELSEIF ( TRIM(timestep_scheme) == 'runge-kutta-2' ) THEN ! for RK2-method
1882
1883	weight_substep(1) = 1._wp/2._wp
1884	weight_substep(2) = 1._wp/2._wp
1885
1886	weight_pres(1) = 1._wp/2._wp
1887	weight_pres(2) = 1._wp/2._wp
1888
1889	ELSE ! for Euler-method
1890
1891	weight_substep(1) = 1.0_wp
1892	weight_pres(1) = 1.0_wp
1893
1894	ENDIF
1895
1896	!
1897	!-- Initialize Rayleigh damping factors
1898	rdf = 0.0_wp
1899	rdf_sc = 0.0_wp
1900	IF ( rayleigh_damping_factor /= 0.0_wp ) THEN
1901
1902	IF ( .NOT. ocean_mode ) THEN
1903	DO k = nzb+1, nzt
1904	IF ( zu(k) >= rayleigh_damping_height ) THEN
1905	rdf(k) = rayleigh_damping_factor * &
1906	( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
1907	/ ( zu(nzt) - rayleigh_damping_height ) ) &
1908	)**2
1909	ENDIF
1910	ENDDO
1911	ELSE
1912	!
1913	!-- In ocean mode, rayleigh damping is applied in the lower part of the
1914	!-- model domain
1915	DO k = nzt, nzb+1, -1
1916	IF ( zu(k) <= rayleigh_damping_height ) THEN
1917	rdf(k) = rayleigh_damping_factor * &
1918	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1919	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1920	)**2
1921	ENDIF
1922	ENDDO
1923	ENDIF
1924
1925	ENDIF
1926	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1927
1928	!
1929	!-- Initialize the starting level and the vertical smoothing factor used for
1930	!-- the external pressure gradient
1931	dp_smooth_factor = 1.0_wp
1932	IF ( dp_external ) THEN
1933	!
1934	!-- Set the starting level dp_level_ind_b only if it has not been set before
1935	!-- (e.g. in init_grid).
1936	IF ( dp_level_ind_b == 0 ) THEN
1937	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1938	dp_level_ind_b = ind_array(1) - 1 + nzb
1939	! MINLOC uses lower array bound 1
1940	ENDIF
1941	IF ( dp_smooth ) THEN
1942	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1943	DO k = dp_level_ind_b+1, nzt
1944	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1945	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1946	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1947	ENDDO
1948	ENDIF
1949	ENDIF
1950
1951	!
1952	!-- Initialize damping zone for the potential temperature in case of
1953	!-- non-cyclic lateral boundaries. The damping zone has the maximum value
1954	!-- at the inflow boundary and decreases to zero at pt_damping_width.
1955	ptdf_x = 0.0_wp
1956	ptdf_y = 0.0_wp
1957	IF ( bc_lr_dirrad ) THEN
1958	DO i = nxl, nxr
1959	IF ( ( i * dx ) < pt_damping_width ) THEN
1960	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1961	REAL( pt_damping_width - i * dx, KIND=wp ) / ( &
1962	REAL( pt_damping_width, KIND=wp ) ) ) )**2
1963	ENDIF
1964	ENDDO
1965	ELSEIF ( bc_lr_raddir ) THEN
1966	DO i = nxl, nxr
1967	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1968	ptdf_x(i) = pt_damping_factor * &
1969	SIN( pi * 0.5_wp * &
1970	( ( i - nx ) * dx + pt_damping_width ) / &
1971	REAL( pt_damping_width, KIND=wp ) )**2
1972	ENDIF
1973	ENDDO
1974	ELSEIF ( bc_ns_dirrad ) THEN
1975	DO j = nys, nyn
1976	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1977	ptdf_y(j) = pt_damping_factor * &
1978	SIN( pi * 0.5_wp * &
1979	( ( j - ny ) * dy + pt_damping_width ) / &
1980	REAL( pt_damping_width, KIND=wp ) )**2
1981	ENDIF
1982	ENDDO
1983	ELSEIF ( bc_ns_raddir ) THEN
1984	DO j = nys, nyn
1985	IF ( ( j * dy ) < pt_damping_width ) THEN
1986	ptdf_y(j) = pt_damping_factor * &
1987	SIN( pi * 0.5_wp * &
1988	( pt_damping_width - j * dy ) / &
1989	REAL( pt_damping_width, KIND=wp ) )**2
1990	ENDIF
1991	ENDDO
1992	ENDIF
1993
1994	!
1995	!-- Input binary data file is not needed anymore. This line must be placed
1996	!-- after call of user_init!
1997	CALL close_file( 13 )
1998	!
1999	!-- In case of nesting, put an barrier to assure that all parent and child
2000	!-- domains finished initialization.
2001	#if defined( __parallel )
2002	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
2003	#endif
2004
2005
2006	CALL location_message( 'model initialization', 'finished' )
2007
2008	END SUBROUTINE init_3d_model

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