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Last change on this file since 4277 was 4245, checked in by pavelkrc, 5 years ago

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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	2023-4244
/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 4245 2019-09-30 08:40:37Z schwenkel $
27	! implement new palm_date_time_mod
28	!
29	! 4223 2019-09-10 09:20:47Z gronemeier
30	! Deallocate temporary string array since it may be re-used to read different
31	! input data in other modules
32	!
33	! 4186 2019-08-23 16:06:14Z suehring
34	! Design change, use variables defined in netcdf_data_input_mod to read netcd
35	! variables rather than define local ones.
36	!
37	! 4185 2019-08-23 13:49:38Z oliver.maas
38	! For initializing_actions = ' cyclic_fill':
39	! Overwrite u_init, v_init, pt_init, q_init and s_init with the
40	! (temporally) and horizontally averaged vertical profiles from the end
41	! of the prerun, because these profiles shall be used as the basic state
42	! for the rayleigh damping and the pt_damping.
43	!
44	! 4182 2019-08-22 15:20:23Z scharf
45	! Corrected "Former revisions" section
46	!
47	! 4168 2019-08-16 13:50:17Z suehring
48	! Replace function get_topography_top_index by topo_top_ind
49	!
50	! 4151 2019-08-09 08:24:30Z suehring
51	! Add netcdf directive around input calls (fix for last commit)
52	!
53	! 4150 2019-08-08 20:00:47Z suehring
54	! Input of additional surface variables independent on land- or urban-surface
55	! model
56	!
57	! 4131 2019-08-02 11:06:18Z monakurppa
58	! Allocate sums and sums_l to allow profile output for salsa variables.
59	!
60	! 4130 2019-08-01 13:04:13Z suehring
61	! Effectively reduce 3D initialization to 1D initial profiles. This is because
62	! 3D initialization produces structures in the w-component that are correlated
63	! with the processor grid for some unknown reason
64	!
65	! 4090 2019-07-11 15:06:47Z Giersch
66	! Unused variables removed
67	!
68	! 4088 2019-07-11 13:57:56Z Giersch
69	! Pressure and density profile calculations revised using basic functions
70	!
71	! 4048 2019-06-21 21:00:21Z knoop
72	! Further modularization of particle code components
73	!
74	! 4017 2019-06-06 12:16:46Z schwenkel
75	! Convert most location messages to debug messages to reduce output in
76	! job logfile to a minimum
77	!
78	!
79	! unused variable removed
80	!
81	! 3937 2019-04-29 15:09:07Z suehring
82	! Move initialization of synthetic turbulence generator behind initialization
83	! of offline nesting. Remove call for stg_adjust, as this is now already done
84	! in stg_init.
85	!
86	! 3900 2019-04-16 15:17:43Z suehring
87	! Fix problem with LOD = 2 initialization
88	!
89	! 3885 2019-04-11 11:29:34Z kanani
90	! Changes related to global restructuring of location messages and introduction
91	! of additional debug messages
92	!
93	! 3849 2019-04-01 16:35:16Z knoop
94	! Move initialization of rmask before initializing user_init_arrays
95	!
96	! 3711 2019-01-31 13:44:26Z knoop
97	! Introduced module_interface_init_checks for post-init checks in modules
98	!
99	! 3700 2019-01-26 17:03:42Z knoop
100	! Some interface calls moved to module_interface + cleanup
101	!
102	! 3648 2019-01-02 16:35:46Z suehring
103	! Rename subroutines for surface-data output
104	!
105	! Revision 1.1 1998/03/09 16:22:22 raasch
106	! Initial revision
107	!
108	!
109	! Description:
110	! ------------
111	!> Allocation of arrays and initialization of the 3D model via
112	!> a) pre-run the 1D model
113	!> or
114	!> b) pre-set constant linear profiles
115	!> or
116	!> c) read values of a previous run
117	!------------------------------------------------------------------------------!
118	SUBROUTINE init_3d_model
119
120
121	USE advec_ws
122
123	USE arrays_3d
124
125	USE basic_constants_and_equations_mod, &
126	ONLY: c_p, g, l_v, pi, exner_function, exner_function_invers, &
127	ideal_gas_law_rho, ideal_gas_law_rho_pt, barometric_formula
128
129	USE bulk_cloud_model_mod, &
130	ONLY: bulk_cloud_model
131
132	USE chem_modules, &
133	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
134
135	USE control_parameters
136
137	USE grid_variables, &
138	ONLY: dx, dy, ddx2_mg, ddy2_mg
139
140	USE indices
141
142	USE kinds
143
144	USE lsf_nudging_mod, &
145	ONLY: ls_forcing_surf
146
147	USE model_1d_mod, &
148	ONLY: init_1d_model, l1d, u1d, v1d
149
150	USE module_interface, &
151	ONLY: module_interface_init_arrays, &
152	module_interface_init, &
153	module_interface_init_checks
154
155	USE multi_agent_system_mod, &
156	ONLY: agents_active, mas_init
157
158	USE netcdf_interface, &
159	ONLY: dots_max
160
161	USE netcdf_data_input_mod, &
162	ONLY: char_fill, &
163	check_existence, &
164	close_input_file, &
165	get_attribute, &
166	get_variable, &
167	init_3d, &
168	input_pids_static, &
169	inquire_num_variables, &
170	inquire_variable_names, &
171	input_file_static, &
172	netcdf_data_input_init_3d, &
173	num_var_pids, &
174	open_read_file, &
175	pids_id, &
176	real_2d, &
177	vars_pids
178
179	USE nesting_offl_mod, &
180	ONLY: nesting_offl_init
181
182	USE palm_date_time_mod, &
183	ONLY: set_reference_date_time
184
185	USE pegrid
186
187	#if defined( __parallel )
188	USE pmc_interface, &
189	ONLY: nested_run
190	#endif
191
192	USE random_function_mod
193
194	USE random_generator_parallel, &
195	ONLY: init_parallel_random_generator
196
197	USE read_restart_data_mod, &
198	ONLY: rrd_read_parts_of_global, rrd_local
199
200	USE statistics, &
201	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, &
202	statistic_regions, sums, sums_divnew_l, sums_divold_l, sums_l, &
203	sums_l_l, sums_wsts_bc_l, ts_value, &
204	weight_pres, weight_substep
205
206	USE synthetic_turbulence_generator_mod, &
207	ONLY: stg_init, use_syn_turb_gen
208
209	USE surface_layer_fluxes_mod, &
210	ONLY: init_surface_layer_fluxes
211
212	USE surface_mod, &
213	ONLY : init_single_surface_properties, &
214	init_surface_arrays, &
215	init_surfaces, &
216	surf_def_h, &
217	surf_def_v, &
218	surf_lsm_h, &
219	surf_usm_h
220
221	#if defined( _OPENACC )
222	USE surface_mod, &
223	ONLY : bc_h
224	#endif
225
226	USE surface_data_output_mod, &
227	ONLY: surface_data_output_init
228
229	USE transpose_indices
230
231	IMPLICIT NONE
232
233	INTEGER(iwp) :: i !< grid index in x direction
234	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
235	INTEGER(iwp) :: j !< grid index in y direction
236	INTEGER(iwp) :: k !< grid index in z direction
237	INTEGER(iwp) :: k_surf !< surface level index
238	INTEGER(iwp) :: l !< running index over surface orientation
239	INTEGER(iwp) :: m !< index of surface element in surface data type
240	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
241	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
242	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
243	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
244	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
245	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
246	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
247	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
248	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
249	INTEGER(iwp) :: sr !< index of statistic region
250
251	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on subdomain
252
253	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on subdomain
254	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on subdomain
255
256
257
258	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain inital profiles
259	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
260
261	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
262	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
263
264	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
265	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
266
267	REAL(wp), DIMENSION(:), ALLOCATABLE :: mean_surface_level_height_l !< mean surface level height on subdomain
268	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_l !< total number of non-topography grid points on subdomain
269	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_tmp !< total number of non-topography grid points
270
271	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
272
273	CALL location_message( 'model initialization', 'start' )
274	!
275	!-- Set reference date-time
276	CALL set_reference_date_time( date_time_str=origin_date_time )
277
278	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
279	!
280	!-- Allocate arrays
281	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
282	mean_surface_level_height_l(0:statistic_regions), &
283	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
284	ngp_3d(0:statistic_regions), &
285	ngp_3d_inner(0:statistic_regions), &
286	ngp_3d_inner_l(0:statistic_regions), &
287	ngp_3d_inner_tmp(0:statistic_regions), &
288	sums_divnew_l(0:statistic_regions), &
289	sums_divold_l(0:statistic_regions) )
290	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
291	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
292	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
293	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
294	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
295	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
296	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
297	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
298	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
299	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
300	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
301	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
302
303	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
304	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
305	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
306
307	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
308	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
309	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
310	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
311	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
312	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
313	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
314	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
315	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
316	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
317	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
318	IF ( .NOT. neutral ) THEN
319	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
320	ENDIF
321	!
322	!-- Pre-set masks for regional statistics. Default is the total model domain.
323	!-- Ghost points are excluded because counting values at the ghost boundaries
324	!-- would bias the statistics
325	rmask = 1.0_wp
326	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
327	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
328	!
329	!-- Following array is required for perturbation pressure within the iterative
330	!-- pressure solvers. For the multistep schemes (Runge-Kutta), array p holds
331	!-- the weighted average of the substeps and cannot be used in the Poisson
332	!-- solver.
333	IF ( psolver == 'sor' ) THEN
334	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
335	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
336	!
337	!-- For performance reasons, multigrid is using one ghost layer only
338	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
339	ENDIF
340
341	!
342	!-- Array for storing constant coeffficients of the tridiagonal solver
343	IF ( psolver == 'poisfft' ) THEN
344	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
345	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
346	ENDIF
347
348	IF ( humidity ) THEN
349	!
350	!-- 3D-humidity
351	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
352	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
353	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
354	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
355	ENDIF
356
357	IF ( passive_scalar ) THEN
358
359	!
360	!-- 3D scalar arrays
361	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
362	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
363	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
364
365	ENDIF
366
367	!
368	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to
369	!-- non-zero values later in ocean_init
370	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
371	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
372	u_stokes_zu(:) = 0.0_wp
373	u_stokes_zw(:) = 0.0_wp
374	v_stokes_zu(:) = 0.0_wp
375	v_stokes_zw(:) = 0.0_wp
376
377	!
378	!-- Allocation of anelastic and Boussinesq approximation specific arrays
379	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
380	ALLOCATE( rho_air(nzb:nzt+1) )
381	ALLOCATE( rho_air_zw(nzb:nzt+1) )
382	ALLOCATE( drho_air(nzb:nzt+1) )
383	ALLOCATE( drho_air_zw(nzb:nzt+1) )
384	!
385	!-- Density profile calculation for anelastic and Boussinesq approximation
386	!-- In case of a Boussinesq approximation, a constant density is calculated
387	!-- mainly for output purposes. This density do not need to be considered
388	!-- in the model's system of equations.
389	IF ( TRIM( approximation ) == 'anelastic' ) THEN
390	DO k = nzb, nzt+1
391	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
392	exner_function(surface_pressure * 100.0_wp), &
393	surface_pressure * 100.0_wp)
394
395	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
396	ENDDO
397
398	DO k = nzb, nzt
399	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
400	ENDDO
401
402	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
403	+ 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
404
405	ELSE
406	DO k = nzb, nzt+1
407	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
408	exner_function(surface_pressure * 100.0_wp), &
409	surface_pressure * 100.0_wp)
410
411	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
412	ENDDO
413
414	DO k = nzb, nzt
415	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
416	ENDDO
417
418	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
419	+ 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
420
421	ENDIF
422	!
423	!-- compute the inverse density array in order to avoid expencive divisions
424	drho_air = 1.0_wp / rho_air
425	drho_air_zw = 1.0_wp / rho_air_zw
426
427	!
428	!-- Allocation of flux conversion arrays
429	ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
430	ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
431	ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
432	ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
433	ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
434	ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )
435
436	!
437	!-- calculate flux conversion factors according to approximation and in-/output mode
438	DO k = nzb, nzt+1
439
440	IF ( TRIM( flux_input_mode ) == 'kinematic' ) THEN
441	heatflux_input_conversion(k) = rho_air_zw(k)
442	waterflux_input_conversion(k) = rho_air_zw(k)
443	momentumflux_input_conversion(k) = rho_air_zw(k)
444	ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
445	heatflux_input_conversion(k) = 1.0_wp / c_p
446	waterflux_input_conversion(k) = 1.0_wp / l_v
447	momentumflux_input_conversion(k) = 1.0_wp
448	ENDIF
449
450	IF ( TRIM( flux_output_mode ) == 'kinematic' ) THEN
451	heatflux_output_conversion(k) = drho_air_zw(k)
452	waterflux_output_conversion(k) = drho_air_zw(k)
453	momentumflux_output_conversion(k) = drho_air_zw(k)
454	ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
455	heatflux_output_conversion(k) = c_p
456	waterflux_output_conversion(k) = l_v
457	momentumflux_output_conversion(k) = 1.0_wp
458	ENDIF
459
460	IF ( .NOT. humidity ) THEN
461	waterflux_input_conversion(k) = 1.0_wp
462	waterflux_output_conversion(k) = 1.0_wp
463	ENDIF
464
465	ENDDO
466
467	!
468	!-- In case of multigrid method, compute grid lengths and grid factors for the
469	!-- grid levels with respective density on each grid
470	IF ( psolver(1:9) == 'multigrid' ) THEN
471
472	ALLOCATE( ddx2_mg(maximum_grid_level) )
473	ALLOCATE( ddy2_mg(maximum_grid_level) )
474	ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
475	ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
476	ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
477	ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
478	ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
479	ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
480	ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )
481
482	dzu_mg(:,maximum_grid_level) = dzu
483	rho_air_mg(:,maximum_grid_level) = rho_air
484	!
485	!-- Next line to ensure an equally spaced grid.
486	dzu_mg(1,maximum_grid_level) = dzu(2)
487	rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) + &
488	(rho_air(nzb) - rho_air(nzb+1))
489
490	dzw_mg(:,maximum_grid_level) = dzw
491	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
492	nzt_l = nzt
493	DO l = maximum_grid_level-1, 1, -1
494	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
495	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
496	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + (rho_air_mg(nzb,l+1) - rho_air_mg(nzb+1,l+1))
497	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))
498	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
499	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
500	nzt_l = nzt_l / 2
501	DO k = 2, nzt_l+1
502	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
503	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
504	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
505	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
506	ENDDO
507	ENDDO
508
509	nzt_l = nzt
510	dx_l = dx
511	dy_l = dy
512	DO l = maximum_grid_level, 1, -1
513	ddx2_mg(l) = 1.0_wp / dx_l**2
514	ddy2_mg(l) = 1.0_wp / dy_l**2
515	DO k = nzb+1, nzt_l
516	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
517	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
518	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
519	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
520	ENDDO
521	nzt_l = nzt_l / 2
522	dx_l = dx_l * 2.0_wp
523	dy_l = dy_l * 2.0_wp
524	ENDDO
525
526	ENDIF
527
528	!
529	!-- 1D-array for large scale subsidence velocity
530	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
531	ALLOCATE ( w_subs(nzb:nzt+1) )
532	w_subs = 0.0_wp
533	ENDIF
534
535	!
536	!-- Arrays to store velocity data from t-dt and the phase speeds which
537	!-- are needed for radiation boundary conditions
538	IF ( bc_radiation_l ) THEN
539	ALLOCATE( u_m_l(nzb:nzt+1,nysg:nyng,1:2), &
540	v_m_l(nzb:nzt+1,nysg:nyng,0:1), &
541	w_m_l(nzb:nzt+1,nysg:nyng,0:1) )
542	ENDIF
543	IF ( bc_radiation_r ) THEN
544	ALLOCATE( u_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
545	v_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
546	w_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx) )
547	ENDIF
548	IF ( bc_radiation_l .OR. bc_radiation_r ) THEN
549	ALLOCATE( c_u(nzb:nzt+1,nysg:nyng), c_v(nzb:nzt+1,nysg:nyng), &
550	c_w(nzb:nzt+1,nysg:nyng) )
551	ENDIF
552	IF ( bc_radiation_s ) THEN
553	ALLOCATE( u_m_s(nzb:nzt+1,0:1,nxlg:nxrg), &
554	v_m_s(nzb:nzt+1,1:2,nxlg:nxrg), &
555	w_m_s(nzb:nzt+1,0:1,nxlg:nxrg) )
556	ENDIF
557	IF ( bc_radiation_n ) THEN
558	ALLOCATE( u_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
559	v_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
560	w_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg) )
561	ENDIF
562	IF ( bc_radiation_s .OR. bc_radiation_n ) THEN
563	ALLOCATE( c_u(nzb:nzt+1,nxlg:nxrg), c_v(nzb:nzt+1,nxlg:nxrg), &
564	c_w(nzb:nzt+1,nxlg:nxrg) )
565	ENDIF
566	IF ( bc_radiation_l .OR. bc_radiation_r .OR. bc_radiation_s .OR. &
567	bc_radiation_n ) THEN
568	ALLOCATE( c_u_m_l(nzb:nzt+1), c_v_m_l(nzb:nzt+1), c_w_m_l(nzb:nzt+1) )
569	ALLOCATE( c_u_m(nzb:nzt+1), c_v_m(nzb:nzt+1), c_w_m(nzb:nzt+1) )
570	ENDIF
571
572	!
573	!-- Initial assignment of the pointers
574	IF ( .NOT. neutral ) THEN
575	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
576	ELSE
577	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
578	ENDIF
579	u => u_1; u_p => u_2; tu_m => u_3
580	v => v_1; v_p => v_2; tv_m => v_3
581	w => w_1; w_p => w_2; tw_m => w_3
582
583	IF ( humidity ) THEN
584	q => q_1; q_p => q_2; tq_m => q_3
585	vpt => vpt_1
586	ENDIF
587
588	IF ( passive_scalar ) THEN
589	s => s_1; s_p => s_2; ts_m => s_3
590	ENDIF
591
592	!
593	!-- Initialize surface arrays
594	CALL init_surface_arrays
595	!
596	!-- Allocate arrays for other modules
597	CALL module_interface_init_arrays
598
599
600	!
601	!-- Allocate arrays containing the RK coefficient for calculation of
602	!-- perturbation pressure and turbulent fluxes. At this point values are
603	!-- set for pressure calculation during initialization (where no timestep
604	!-- is done). Further below the values needed within the timestep scheme
605	!-- will be set.
606	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
607	weight_pres(1:intermediate_timestep_count_max) )
608	weight_substep = 1.0_wp
609	weight_pres = 1.0_wp
610	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
611
612	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
613
614	!
615	!-- Initialize time series
616	ts_value = 0.0_wp
617
618	!
619	!-- Initialize local summation arrays for routine flow_statistics.
620	!-- This is necessary because they may not yet have been initialized when they
621	!-- are called from flow_statistics (or - depending on the chosen model run -
622	!-- are never initialized)
623	sums_divnew_l = 0.0_wp
624	sums_divold_l = 0.0_wp
625	sums_l_l = 0.0_wp
626	sums_wsts_bc_l = 0.0_wp
627
628	!
629	!-- Initialize model variables
630	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
631	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
632	!
633	!-- Initialization with provided input data derived from larger-scale model
634	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
635	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
636	!
637	!-- Read initial 1D profiles or 3D data from NetCDF file, depending
638	!-- on the provided level-of-detail.
639	!-- At the moment, only u, v, w, pt and q are provided.
640	CALL netcdf_data_input_init_3d
641	!
642	!-- Please note, Inifor provides data from nzb+1 to nzt.
643	!-- Bottom and top boundary conditions for Inifor profiles are already
644	!-- set (just after reading), so that this is not necessary here.
645	!-- Depending on the provided level-of-detail, initial Inifor data is
646	!-- either stored on data type (lod=1), or directly on 3D arrays (lod=2).
647	!-- In order to obtain also initial profiles in case of lod=2 (which
648	!-- is required for e.g. damping), average over 3D data.
649	IF( init_3d%lod_u == 1 ) THEN
650	u_init = init_3d%u_init
651	ELSEIF( init_3d%lod_u == 2 ) THEN
652	ALLOCATE( init_l(nzb:nzt+1) )
653	DO k = nzb, nzt+1
654	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
655	ENDDO
656	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
657
658	#if defined( __parallel )
659	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, &
660	MPI_REAL, MPI_SUM, comm2d, ierr )
661	#else
662	u_init = init_l
663	#endif
664	DEALLOCATE( init_l )
665
666	ENDIF
667
668	IF( init_3d%lod_v == 1 ) THEN
669	v_init = init_3d%v_init
670	ELSEIF( init_3d%lod_v == 2 ) THEN
671	ALLOCATE( init_l(nzb:nzt+1) )
672	DO k = nzb, nzt+1
673	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
674	ENDDO
675	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
676
677	#if defined( __parallel )
678	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, &
679	MPI_REAL, MPI_SUM, comm2d, ierr )
680	#else
681	v_init = init_l
682	#endif
683	DEALLOCATE( init_l )
684	ENDIF
685	IF( .NOT. neutral ) THEN
686	IF( init_3d%lod_pt == 1 ) THEN
687	pt_init = init_3d%pt_init
688	ELSEIF( init_3d%lod_pt == 2 ) THEN
689	ALLOCATE( init_l(nzb:nzt+1) )
690	DO k = nzb, nzt+1
691	init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
692	ENDDO
693	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
694
695	#if defined( __parallel )
696	CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1, &
697	MPI_REAL, MPI_SUM, comm2d, ierr )
698	#else
699	pt_init = init_l
700	#endif
701	DEALLOCATE( init_l )
702	ENDIF
703	ENDIF
704
705
706	IF( humidity ) THEN
707	IF( init_3d%lod_q == 1 ) THEN
708	q_init = init_3d%q_init
709	ELSEIF( init_3d%lod_q == 2 ) THEN
710	ALLOCATE( init_l(nzb:nzt+1) )
711	DO k = nzb, nzt+1
712	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
713	ENDDO
714	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
715
716	#if defined( __parallel )
717	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, &
718	MPI_REAL, MPI_SUM, comm2d, ierr )
719	#else
720	q_init = init_l
721	#endif
722	DEALLOCATE( init_l )
723	ENDIF
724	ENDIF
725
726	!
727	!-- Write initial profiles onto 3D arrays.
728	!-- Work-around, 3D initialization of u,v,w creates artificial
729	!-- structures wich correlate with the processor grid. The reason
730	!-- for this is still unknown. To work-around this, 3D initialization
731	!-- will be effectively reduce to a 1D initialization where no such
732	!-- artificial structures appear.
733	DO i = nxlg, nxrg
734	DO j = nysg, nyng
735	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) &
736	u(:,j,i) = u_init(:)
737	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) &
738	v(:,j,i) = v_init(:)
739	IF( .NOT. neutral .AND. &
740	( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
741	pt(:,j,i) = pt_init(:)
742	IF( humidity .AND. &
743	( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
744	q(:,j,i) = q_init(:)
745	ENDDO
746	ENDDO
747	!
748	!-- Set geostrophic wind components.
749	IF ( init_3d%from_file_ug ) THEN
750	ug(:) = init_3d%ug_init(:)
751	ENDIF
752	IF ( init_3d%from_file_vg ) THEN
753	vg(:) = init_3d%vg_init(:)
754	ENDIF
755	!
756	!-- Set bottom and top boundary condition for geostrophic wind
757	ug(nzt+1) = ug(nzt)
758	vg(nzt+1) = vg(nzt)
759	ug(nzb) = ug(nzb+1)
760	vg(nzb) = vg(nzb+1)
761	!
762	!-- Set inital w to 0
763	w = 0.0_wp
764
765	IF ( passive_scalar ) THEN
766	DO i = nxlg, nxrg
767	DO j = nysg, nyng
768	s(:,j,i) = s_init
769	ENDDO
770	ENDDO
771	ENDIF
772
773	!
774	!-- Set velocity components at non-atmospheric / oceanic grid points to
775	!-- zero.
776	u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
777	v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )
778	w = MERGE( w, 0.0_wp, BTEST( wall_flags_0, 3 ) )
779	!
780	!-- Initialize surface variables, e.g. friction velocity, momentum
781	!-- fluxes, etc.
782	CALL init_surfaces
783
784	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
785	!
786	!-- Initialization via computed 1D-model profiles
787	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
788
789	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
790	!
791	!-- Use solutions of the 1D model as initial profiles,
792	!-- start 1D model
793	CALL init_1d_model
794	!
795	!-- Transfer initial profiles to the arrays of the 3D model
796	DO i = nxlg, nxrg
797	DO j = nysg, nyng
798	pt(:,j,i) = pt_init
799	u(:,j,i) = u1d
800	v(:,j,i) = v1d
801	ENDDO
802	ENDDO
803
804	IF ( humidity ) THEN
805	DO i = nxlg, nxrg
806	DO j = nysg, nyng
807	q(:,j,i) = q_init
808	ENDDO
809	ENDDO
810	ENDIF
811
812	IF ( passive_scalar ) THEN
813	DO i = nxlg, nxrg
814	DO j = nysg, nyng
815	s(:,j,i) = s_init
816	ENDDO
817	ENDDO
818	ENDIF
819	!
820	!-- Store initial profiles for output purposes etc.
821	IF ( .NOT. constant_diffusion ) THEN
822	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
823	ENDIF
824	!
825	!-- Set velocities back to zero
826	u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
827	v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )
828	!
829	!-- WARNING: The extra boundary conditions set after running the
830	!-- ------- 1D model impose an error on the divergence one layer
831	!-- below the topography; need to correct later
832	!-- ATTENTION: Provisional correction for Piacsek & Williams
833	!-- --------- advection scheme: keep u and v zero one layer below
834	!-- the topography.
835	IF ( ibc_uv_b == 1 ) THEN
836	!
837	!-- Neumann condition
838	DO i = nxl-1, nxr+1
839	DO j = nys-1, nyn+1
840	u(nzb,j,i) = u(nzb+1,j,i)
841	v(nzb,j,i) = v(nzb+1,j,i)
842	ENDDO
843	ENDDO
844
845	ENDIF
846	!
847	!-- Initialize surface variables, e.g. friction velocity, momentum
848	!-- fluxes, etc.
849	CALL init_surfaces
850
851	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
852
853	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
854	THEN
855
856	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
857
858	!
859	!-- Use constructed initial profiles (velocity constant with height,
860	!-- temperature profile with constant gradient)
861	DO i = nxlg, nxrg
862	DO j = nysg, nyng
863	pt(:,j,i) = pt_init
864	u(:,j,i) = u_init
865	v(:,j,i) = v_init
866	ENDDO
867	ENDDO
868	!
869	!-- Mask topography
870	u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
871	v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )
872	!
873	!-- Set initial horizontal velocities at the lowest computational grid
874	!-- levels to zero in order to avoid too small time steps caused by the
875	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
876	!-- in the limiting formula!).
877	!-- Please note, in case land- or urban-surface model is used and a
878	!-- spinup is applied, masking the lowest computational level is not
879	!-- possible as MOST as well as energy-balance parametrizations will not
880	!-- work with zero wind velocity.
881	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
882	DO i = nxlg, nxrg
883	DO j = nysg, nyng
884	DO k = nzb, nzt
885	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
886	BTEST( wall_flags_0(k,j,i), 20 ) )
887	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
888	BTEST( wall_flags_0(k,j,i), 21 ) )
889	ENDDO
890	ENDDO
891	ENDDO
892	ENDIF
893
894	IF ( humidity ) THEN
895	DO i = nxlg, nxrg
896	DO j = nysg, nyng
897	q(:,j,i) = q_init
898	ENDDO
899	ENDDO
900	ENDIF
901
902	IF ( passive_scalar ) THEN
903	DO i = nxlg, nxrg
904	DO j = nysg, nyng
905	s(:,j,i) = s_init
906	ENDDO
907	ENDDO
908	ENDIF
909
910	!
911	!-- Compute initial temperature field and other constants used in case
912	!-- of a sloping surface
913	IF ( sloping_surface ) CALL init_slope
914	!
915	!-- Initialize surface variables, e.g. friction velocity, momentum
916	!-- fluxes, etc.
917	CALL init_surfaces
918
919	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
920
921	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
922	THEN
923
924	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
925	!
926	!-- Pre-initialize surface variables, i.e. setting start- and end-indices
927	!-- at each (j,i)-location. Please note, this does not supersede
928	!-- user-defined initialization of surface quantities.
929	CALL init_surfaces
930	!
931	!-- Initialization will completely be done by the user
932	CALL user_init_3d_model
933
934	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
935
936	ENDIF
937
938	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
939
940	!
941	!-- Bottom boundary
942	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
943	u(nzb,:,:) = 0.0_wp
944	v(nzb,:,:) = 0.0_wp
945	ENDIF
946
947	!
948	!-- Apply channel flow boundary condition
949	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
950	u(nzt+1,:,:) = 0.0_wp
951	v(nzt+1,:,:) = 0.0_wp
952	ENDIF
953
954	!
955	!-- Calculate virtual potential temperature
956	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
957
958	!
959	!-- Store initial profiles for output purposes etc.. Please note, in case of
960	!-- initialization of u, v, w, pt, and q via output data derived from larger
961	!-- scale models, data will not be horizontally homogeneous. Actually, a mean
962	!-- profile should be calculated before.
963	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
964	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
965	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
966	hom(nzb,1,5,:) = 0.0_wp
967	hom(nzb,1,6,:) = 0.0_wp
968	ENDIF
969	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
970
971	IF ( humidity ) THEN
972	!
973	!-- Store initial profile of total water content, virtual potential
974	!-- temperature
975	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
976	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
977	!
978	!-- Store initial profile of mixing ratio and potential
979	!-- temperature
980	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
981	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
982	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
983	ENDIF
984	ENDIF
985
986	!
987	!-- Store initial scalar profile
988	IF ( passive_scalar ) THEN
989	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
990	ENDIF
991
992	!
993	!-- Initialize the random number generators (from numerical recipes)
994	CALL random_function_ini
995
996	IF ( random_generator == 'random-parallel' ) THEN
997	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
998	ENDIF
999	!
1000	!-- Set the reference state to be used in the buoyancy terms (for ocean runs
1001	!-- the reference state will be set (overwritten) in init_ocean)
1002	IF ( use_single_reference_value ) THEN
1003	IF ( .NOT. humidity ) THEN
1004	ref_state(:) = pt_reference
1005	ELSE
1006	ref_state(:) = vpt_reference
1007	ENDIF
1008	ELSE
1009	IF ( .NOT. humidity ) THEN
1010	ref_state(:) = pt_init(:)
1011	ELSE
1012	ref_state(:) = vpt(:,nys,nxl)
1013	ENDIF
1014	ENDIF
1015
1016	!
1017	!-- For the moment, vertical velocity is zero
1018	w = 0.0_wp
1019
1020	!
1021	!-- Initialize array sums (must be defined in first call of pres)
1022	sums = 0.0_wp
1023
1024	!
1025	!-- In case of iterative solvers, p must get an initial value
1026	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
1027	!
1028	!-- Impose vortex with vertical axis on the initial velocity profile
1029	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
1030	CALL init_rankine
1031	ENDIF
1032
1033	!
1034	!-- Impose temperature anomaly (advection test only) or warm air bubble
1035	!-- close to surface
1036	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1037	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1038	CALL init_pt_anomaly
1039	ENDIF
1040
1041	!
1042	!-- If required, change the surface temperature at the start of the 3D run
1043	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1044	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1045	ENDIF
1046
1047	!
1048	!-- If required, change the surface humidity/scalar at the start of the 3D
1049	!-- run
1050	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1051	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1052
1053	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1054	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1055
1056
1057	!
1058	!-- Initialize old and new time levels.
1059	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1060	pt_p = pt; u_p = u; v_p = v; w_p = w
1061
1062	IF ( humidity ) THEN
1063	tq_m = 0.0_wp
1064	q_p = q
1065	ENDIF
1066
1067	IF ( passive_scalar ) THEN
1068	ts_m = 0.0_wp
1069	s_p = s
1070	ENDIF
1071
1072	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1073
1074	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1075	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1076	THEN
1077
1078	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1079	!
1080	!-- Initialize surface elements and its attributes, e.g. heat- and
1081	!-- momentumfluxes, roughness, scaling parameters. As number of surface
1082	!-- elements might be different between runs, e.g. in case of cyclic fill,
1083	!-- and not all surface elements are read, surface elements need to be
1084	!-- initialized before.
1085	!-- Please note, in case of cyclic fill, surfaces should be initialized
1086	!-- after restart data is read, else, individual settings of surface
1087	!-- parameters will be overwritten from data of precursor run, hence,
1088	!-- init_surfaces is called a second time after reading the restart data.
1089	CALL init_surfaces
1090	!
1091	!-- When reading data for cyclic fill of 3D prerun data files, read
1092	!-- some of the global variables from the restart file which are required
1093	!-- for initializing the inflow
1094	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1095
1096	DO i = 0, io_blocks-1
1097	IF ( i == io_group ) THEN
1098	CALL rrd_read_parts_of_global
1099	ENDIF
1100	#if defined( __parallel )
1101	CALL MPI_BARRIER( comm2d, ierr )
1102	#endif
1103	ENDDO
1104
1105	ENDIF
1106
1107	!
1108	!-- Read processor specific binary data from restart file
1109	DO i = 0, io_blocks-1
1110	IF ( i == io_group ) THEN
1111	CALL rrd_local
1112	ENDIF
1113	#if defined( __parallel )
1114	CALL MPI_BARRIER( comm2d, ierr )
1115	#endif
1116	ENDDO
1117	!
1118	!-- In case of cyclic fill, call init_surfaces a second time, so that
1119	!-- surface properties such as heat fluxes are initialized as prescribed.
1120	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) &
1121	CALL init_surfaces
1122
1123	!
1124	!-- In case of complex terrain and cyclic fill method as initialization,
1125	!-- shift initial data in the vertical direction for each point in the
1126	!-- x-y-plane depending on local surface height
1127	IF ( complex_terrain .AND. &
1128	TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1129	DO i = nxlg, nxrg
1130	DO j = nysg, nyng
1131	nz_u_shift = topo_top_ind(j,i,1)
1132	nz_v_shift = topo_top_ind(j,i,2)
1133	nz_w_shift = topo_top_ind(j,i,3)
1134	nz_s_shift = topo_top_ind(j,i,0)
1135
1136	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1137
1138	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1139
1140	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1141
1142	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1143	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1144	ENDDO
1145	ENDDO
1146	ENDIF
1147	!
1148	!-- Initialization of the turbulence recycling method
1149	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1150	turbulent_inflow ) THEN
1151	!
1152	!-- First store the profiles to be used at the inflow.
1153	!-- These profiles are the (temporally) and horizontally averaged vertical
1154	!-- profiles from the prerun. Alternatively, prescribed profiles
1155	!-- for u,v-components can be used.
1156	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the
1157	!-- (temporally) and horizontally averaged vertical profiles from the end
1158	!-- of the prerun, because these profiles shall be used as the basic state
1159	!-- for the rayleigh damping and the pt_damping.
1160	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1161
1162	IF ( use_prescribed_profile_data ) THEN
1163	mean_inflow_profiles(:,1) = u_init ! u
1164	mean_inflow_profiles(:,2) = v_init ! v
1165	ELSE
1166	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1167	u_init(:) = hom_sum(:,1,0)
1168	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1169	v_init(:) = hom_sum(:,2,0)
1170	ENDIF
1171	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1172	pt_init(:) = hom_sum(:,4,0)
1173	IF ( humidity ) &
1174	mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1175	q_init(:) = hom_sum(:,41,0)
1176	IF ( passive_scalar ) &
1177	mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1178	s_init(:) = hom_sum(:,115,0)
1179	!
1180	!-- In case of complex terrain, determine vertical displacement at inflow
1181	!-- boundary and adjust mean inflow profiles
1182	IF ( complex_terrain ) THEN
1183	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1184	nz_u_shift_l = topo_top_ind(j,i,1)
1185	nz_v_shift_l = topo_top_ind(j,i,2)
1186	nz_w_shift_l = topo_top_ind(j,i,3)
1187	nz_s_shift_l = topo_top_ind(j,i,0)
1188	ELSE
1189	nz_u_shift_l = 0
1190	nz_v_shift_l = 0
1191	nz_w_shift_l = 0
1192	nz_s_shift_l = 0
1193	ENDIF
1194
1195	#if defined( __parallel )
1196	CALL MPI_ALLREDUCE(nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, &
1197	MPI_MAX, comm2d, ierr)
1198	CALL MPI_ALLREDUCE(nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, &
1199	MPI_MAX, comm2d, ierr)
1200	CALL MPI_ALLREDUCE(nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, &
1201	MPI_MAX, comm2d, ierr)
1202	CALL MPI_ALLREDUCE(nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, &
1203	MPI_MAX, comm2d, ierr)
1204	#else
1205	nz_u_shift = nz_u_shift_l
1206	nz_v_shift = nz_v_shift_l
1207	nz_w_shift = nz_w_shift_l
1208	nz_s_shift = nz_s_shift_l
1209	#endif
1210
1211	mean_inflow_profiles(:,1) = 0.0_wp
1212	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1213
1214	mean_inflow_profiles(:,2) = 0.0_wp
1215	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1216
1217	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1218
1219	ENDIF
1220
1221	!
1222	!-- If necessary, adjust the horizontal flow field to the prescribed
1223	!-- profiles
1224	IF ( use_prescribed_profile_data ) THEN
1225	DO i = nxlg, nxrg
1226	DO j = nysg, nyng
1227	DO k = nzb, nzt+1
1228	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1229	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1230	ENDDO
1231	ENDDO
1232	ENDDO
1233	ENDIF
1234
1235	!
1236	!-- Use these mean profiles at the inflow (provided that Dirichlet
1237	!-- conditions are used)
1238	IF ( bc_dirichlet_l ) THEN
1239	DO j = nysg, nyng
1240	DO k = nzb, nzt+1
1241	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1242	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1243	w(k,j,nxlg:-1) = 0.0_wp
1244	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1245	IF ( humidity ) &
1246	q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1247	IF ( passive_scalar ) &
1248	s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1249	ENDDO
1250	ENDDO
1251	ENDIF
1252
1253	!
1254	!-- Calculate the damping factors to be used at the inflow. For a
1255	!-- turbulent inflow the turbulent fluctuations have to be limited
1256	!-- vertically because otherwise the turbulent inflow layer will grow
1257	!-- in time.
1258	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1259	!
1260	!-- Default: use the inversion height calculated by the prerun; if
1261	!-- this is zero, inflow_damping_height must be explicitly
1262	!-- specified.
1263	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1264	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1265	ELSE
1266	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1267	'explicitly specified because&the inversion height ', &
1268	'calculated by the prerun is zero.'
1269	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1270	ENDIF
1271
1272	ENDIF
1273
1274	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1275	!
1276	!-- Default for the transition range: one tenth of the undamped
1277	!-- layer
1278	inflow_damping_width = 0.1_wp * inflow_damping_height
1279
1280	ENDIF
1281
1282	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1283
1284	DO k = nzb, nzt+1
1285
1286	IF ( zu(k) <= inflow_damping_height ) THEN
1287	inflow_damping_factor(k) = 1.0_wp
1288	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1289	inflow_damping_factor(k) = 1.0_wp - &
1290	( zu(k) - inflow_damping_height ) / &
1291	inflow_damping_width
1292	ELSE
1293	inflow_damping_factor(k) = 0.0_wp
1294	ENDIF
1295
1296	ENDDO
1297
1298	ENDIF
1299
1300	!
1301	!-- Inside buildings set velocities back to zero
1302	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1303	topography /= 'flat' ) THEN
1304	!
1305	!-- Inside buildings set velocities back to zero.
1306	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1307	!-- maybe revise later.
1308	DO i = nxlg, nxrg
1309	DO j = nysg, nyng
1310	DO k = nzb, nzt
1311	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
1312	BTEST( wall_flags_0(k,j,i), 1 ) )
1313	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
1314	BTEST( wall_flags_0(k,j,i), 2 ) )
1315	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, &
1316	BTEST( wall_flags_0(k,j,i), 3 ) )
1317	ENDDO
1318	ENDDO
1319	ENDDO
1320
1321	ENDIF
1322
1323	!
1324	!-- Calculate initial temperature field and other constants used in case
1325	!-- of a sloping surface
1326	IF ( sloping_surface ) CALL init_slope
1327
1328	!
1329	!-- Initialize new time levels (only done in order to set boundary values
1330	!-- including ghost points)
1331	pt_p = pt; u_p = u; v_p = v; w_p = w
1332	IF ( humidity ) THEN
1333	q_p = q
1334	ENDIF
1335	IF ( passive_scalar ) s_p = s
1336	!
1337	!-- Allthough tendency arrays are set in prognostic_equations, they have
1338	!-- have to be predefined here because they are used (but multiplied with 0)
1339	!-- there before they are set.
1340	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1341	IF ( humidity ) THEN
1342	tq_m = 0.0_wp
1343	ENDIF
1344	IF ( passive_scalar ) ts_m = 0.0_wp
1345
1346	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1347
1348	ELSE
1349	!
1350	!-- Actually this part of the programm should not be reached
1351	message_string = 'unknown initializing problem'
1352	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1353	ENDIF
1354
1355
1356	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1357	!
1358	!-- Initialize old timelevels needed for radiation boundary conditions
1359	IF ( bc_radiation_l ) THEN
1360	u_m_l(:,:,:) = u(:,:,1:2)
1361	v_m_l(:,:,:) = v(:,:,0:1)
1362	w_m_l(:,:,:) = w(:,:,0:1)
1363	ENDIF
1364	IF ( bc_radiation_r ) THEN
1365	u_m_r(:,:,:) = u(:,:,nx-1:nx)
1366	v_m_r(:,:,:) = v(:,:,nx-1:nx)
1367	w_m_r(:,:,:) = w(:,:,nx-1:nx)
1368	ENDIF
1369	IF ( bc_radiation_s ) THEN
1370	u_m_s(:,:,:) = u(:,0:1,:)
1371	v_m_s(:,:,:) = v(:,1:2,:)
1372	w_m_s(:,:,:) = w(:,0:1,:)
1373	ENDIF
1374	IF ( bc_radiation_n ) THEN
1375	u_m_n(:,:,:) = u(:,ny-1:ny,:)
1376	v_m_n(:,:,:) = v(:,ny-1:ny,:)
1377	w_m_n(:,:,:) = w(:,ny-1:ny,:)
1378	ENDIF
1379
1380	ENDIF
1381
1382	!
1383	!-- Calculate the initial volume flow at the right and north boundary
1384	IF ( conserve_volume_flow ) THEN
1385
1386	IF ( use_prescribed_profile_data ) THEN
1387
1388	volume_flow_initial_l = 0.0_wp
1389	volume_flow_area_l = 0.0_wp
1390
1391	IF ( nxr == nx ) THEN
1392	DO j = nys, nyn
1393	DO k = nzb+1, nzt
1394	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1395	u_init(k) * dzw(k) &
1396	* MERGE( 1.0_wp, 0.0_wp, &
1397	BTEST( wall_flags_0(k,j,nxr), 1 )&
1398	)
1399
1400	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1401	* MERGE( 1.0_wp, 0.0_wp, &
1402	BTEST( wall_flags_0(k,j,nxr), 1 )&
1403	)
1404	ENDDO
1405	ENDDO
1406	ENDIF
1407
1408	IF ( nyn == ny ) THEN
1409	DO i = nxl, nxr
1410	DO k = nzb+1, nzt
1411	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1412	v_init(k) * dzw(k) &
1413	* MERGE( 1.0_wp, 0.0_wp, &
1414	BTEST( wall_flags_0(k,nyn,i), 2 )&
1415	)
1416	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1417	* MERGE( 1.0_wp, 0.0_wp, &
1418	BTEST( wall_flags_0(k,nyn,i), 2 )&
1419	)
1420	ENDDO
1421	ENDDO
1422	ENDIF
1423
1424	#if defined( __parallel )
1425	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1426	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1427	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1428	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1429
1430	#else
1431	volume_flow_initial = volume_flow_initial_l
1432	volume_flow_area = volume_flow_area_l
1433	#endif
1434
1435	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1436
1437	volume_flow_initial_l = 0.0_wp
1438	volume_flow_area_l = 0.0_wp
1439
1440	IF ( nxr == nx ) THEN
1441	DO j = nys, nyn
1442	DO k = nzb+1, nzt
1443	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1444	hom_sum(k,1,0) * dzw(k) &
1445	* MERGE( 1.0_wp, 0.0_wp, &
1446	BTEST( wall_flags_0(k,j,nx), 1 ) &
1447	)
1448	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1449	* MERGE( 1.0_wp, 0.0_wp, &
1450	BTEST( wall_flags_0(k,j,nx), 1 ) &
1451	)
1452	ENDDO
1453	ENDDO
1454	ENDIF
1455
1456	IF ( nyn == ny ) THEN
1457	DO i = nxl, nxr
1458	DO k = nzb+1, nzt
1459	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1460	hom_sum(k,2,0) * dzw(k) &
1461	* MERGE( 1.0_wp, 0.0_wp, &
1462	BTEST( wall_flags_0(k,ny,i), 2 ) &
1463	)
1464	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1465	* MERGE( 1.0_wp, 0.0_wp, &
1466	BTEST( wall_flags_0(k,ny,i), 2 ) &
1467	)
1468	ENDDO
1469	ENDDO
1470	ENDIF
1471
1472	#if defined( __parallel )
1473	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1474	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1475	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1476	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1477
1478	#else
1479	volume_flow_initial = volume_flow_initial_l
1480	volume_flow_area = volume_flow_area_l
1481	#endif
1482
1483	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1484
1485	volume_flow_initial_l = 0.0_wp
1486	volume_flow_area_l = 0.0_wp
1487
1488	IF ( nxr == nx ) THEN
1489	DO j = nys, nyn
1490	DO k = nzb+1, nzt
1491	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1492	u(k,j,nx) * dzw(k) &
1493	* MERGE( 1.0_wp, 0.0_wp, &
1494	BTEST( wall_flags_0(k,j,nx), 1 ) &
1495	)
1496	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1497	* MERGE( 1.0_wp, 0.0_wp, &
1498	BTEST( wall_flags_0(k,j,nx), 1 ) &
1499	)
1500	ENDDO
1501	ENDDO
1502	ENDIF
1503
1504	IF ( nyn == ny ) THEN
1505	DO i = nxl, nxr
1506	DO k = nzb+1, nzt
1507	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1508	v(k,ny,i) * dzw(k) &
1509	* MERGE( 1.0_wp, 0.0_wp, &
1510	BTEST( wall_flags_0(k,ny,i), 2 ) &
1511	)
1512	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1513	* MERGE( 1.0_wp, 0.0_wp, &
1514	BTEST( wall_flags_0(k,ny,i), 2 ) &
1515	)
1516	ENDDO
1517	ENDDO
1518	ENDIF
1519
1520	#if defined( __parallel )
1521	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1522	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1523	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1524	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1525
1526	#else
1527	volume_flow_initial = volume_flow_initial_l
1528	volume_flow_area = volume_flow_area_l
1529	#endif
1530
1531	ENDIF
1532
1533	!
1534	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated
1535	!-- from u\|v_bulk instead
1536	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1537	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1538	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1539	ENDIF
1540
1541	ENDIF
1542	!
1543	!-- In the following, surface properties can be further initialized with
1544	!-- input from static driver file.
1545	!-- At the moment this affects only default surfaces. For example,
1546	!-- roughness length or sensible / latent heat fluxes can be initialized
1547	!-- heterogeneously for default surfaces. Therefore, a generic routine
1548	!-- from netcdf_data_input_mod is called to read a 2D array.
1549	IF ( input_pids_static ) THEN
1550	!
1551	!-- Allocate memory for possible static input
1552	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1553	tmp_2d%var = 0.0_wp
1554	!
1555	!-- Open the static input file
1556	#if defined( __netcdf )
1557	CALL open_read_file( TRIM( input_file_static ) // &
1558	TRIM( coupling_char ), &
1559	pids_id )
1560
1561	CALL inquire_num_variables( pids_id, num_var_pids )
1562	!
1563	!-- Allocate memory to store variable names and read them
1564	ALLOCATE( vars_pids(1:num_var_pids) )
1565	CALL inquire_variable_names( pids_id, vars_pids )
1566	!
1567	!-- Input roughness length.
1568	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1569	!
1570	!-- Read _FillValue attribute
1571	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, &
1572	.FALSE., 'z0' )
1573	!
1574	!-- Read variable
1575	CALL get_variable( pids_id, 'z0', tmp_2d%var, &
1576	nxl, nxr, nys, nyn )
1577	!
1578	!-- Initialize roughness length. Note, z0 will be only initialized at
1579	!-- default-type surfaces. At natural or urban z0 is implicitly
1580	!-- initialized bythe respective parameter lists.
1581	!-- Initialize horizontal surface elements.
1582	CALL init_single_surface_properties( surf_def_h(0)%z0, &
1583	tmp_2d%var, &
1584	surf_def_h(0)%ns, &
1585	tmp_2d%fill, &
1586	surf_def_h(0)%i, &
1587	surf_def_h(0)%j )
1588	!
1589	!-- Initialize roughness also at vertical surface elements.
1590	!-- Note, the actual 2D input arrays are only defined on the
1591	!-- subdomain. Therefore, pass the index arrays with their respective
1592	!-- offset values.
1593	DO l = 0, 3
1594	CALL init_single_surface_properties( &
1595	surf_def_v(l)%z0, &
1596	tmp_2d%var, &
1597	surf_def_v(l)%ns, &
1598	tmp_2d%fill, &
1599	surf_def_v(l)%i + surf_def_v(l)%ioff, &
1600	surf_def_v(l)%j + surf_def_v(l)%joff )
1601	ENDDO
1602
1603	ENDIF
1604	!
1605	!-- Additional variables, e.g. shf, qsws, etc, can be initialized the
1606	!-- same way.
1607
1608	!
1609	!-- Finally, close the input file and deallocate temporary arrays
1610	DEALLOCATE( vars_pids )
1611
1612	CALL close_input_file( pids_id )
1613	#endif
1614	DEALLOCATE( tmp_2d%var )
1615	ENDIF
1616	!
1617	!-- Finally, if random_heatflux is set, disturb shf at horizontal
1618	!-- surfaces. Actually, this should be done in surface_mod, where all other
1619	!-- initializations of surface quantities are done. However, this
1620	!-- would create a ring dependency, hence, it is done here. Maybe delete
1621	!-- disturb_heatflux and tranfer the respective code directly into the
1622	!-- initialization in surface_mod.
1623	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1624	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1625
1626	IF ( use_surface_fluxes .AND. constant_heatflux .AND. &
1627	random_heatflux ) THEN
1628	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1629	IF ( surf_lsm_h%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h )
1630	IF ( surf_usm_h%ns >= 1 ) CALL disturb_heatflux( surf_usm_h )
1631	ENDIF
1632	ENDIF
1633
1634	!
1635	!-- Compute total sum of grid points and the mean surface level height for each
1636	!-- statistic region. These are mainly used for horizontal averaging of
1637	!-- turbulence statistics.
1638	!-- ngp_2dh: number of grid points of a horizontal cross section through the
1639	!-- respective statistic region
1640	!-- ngp_3d: number of grid points of the respective statistic region
1641	ngp_2dh_outer_l = 0
1642	ngp_2dh_outer = 0
1643	ngp_2dh_s_inner_l = 0
1644	ngp_2dh_s_inner = 0
1645	ngp_2dh_l = 0
1646	ngp_2dh = 0
1647	ngp_3d_inner_l = 0.0_wp
1648	ngp_3d_inner = 0
1649	ngp_3d = 0
1650	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1651
1652	mean_surface_level_height = 0.0_wp
1653	mean_surface_level_height_l = 0.0_wp
1654	!
1655	!-- To do: New concept for these non-topography grid points!
1656	DO sr = 0, statistic_regions
1657	DO i = nxl, nxr
1658	DO j = nys, nyn
1659	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1660	!
1661	!-- All xy-grid points
1662	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1663	!
1664	!-- Determine mean surface-level height. In case of downward-
1665	!-- facing walls are present, more than one surface level exist.
1666	!-- In this case, use the lowest surface-level height.
1667	IF ( surf_def_h(0)%start_index(j,i) <= &
1668	surf_def_h(0)%end_index(j,i) ) THEN
1669	m = surf_def_h(0)%start_index(j,i)
1670	k = surf_def_h(0)%k(m)
1671	mean_surface_level_height_l(sr) = &
1672	mean_surface_level_height_l(sr) + zw(k-1)
1673	ENDIF
1674	IF ( surf_lsm_h%start_index(j,i) <= &
1675	surf_lsm_h%end_index(j,i) ) THEN
1676	m = surf_lsm_h%start_index(j,i)
1677	k = surf_lsm_h%k(m)
1678	mean_surface_level_height_l(sr) = &
1679	mean_surface_level_height_l(sr) + zw(k-1)
1680	ENDIF
1681	IF ( surf_usm_h%start_index(j,i) <= &
1682	surf_usm_h%end_index(j,i) ) THEN
1683	m = surf_usm_h%start_index(j,i)
1684	k = surf_usm_h%k(m)
1685	mean_surface_level_height_l(sr) = &
1686	mean_surface_level_height_l(sr) + zw(k-1)
1687	ENDIF
1688
1689	k_surf = k - 1
1690
1691	DO k = nzb, nzt+1
1692	!
1693	!-- xy-grid points above topography
1694	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1695	MERGE( 1, 0, BTEST( wall_flags_0(k,j,i), 24 ) )
1696
1697	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1698	MERGE( 1, 0, BTEST( wall_flags_0(k,j,i), 22 ) )
1699
1700	ENDDO
1701	!
1702	!-- All grid points of the total domain above topography
1703	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1704
1705
1706
1707	ENDIF
1708	ENDDO
1709	ENDDO
1710	ENDDO
1711
1712	sr = statistic_regions + 1
1713	#if defined( __parallel )
1714	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1715	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, &
1716	comm2d, ierr )
1717	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1718	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, &
1719	MPI_INTEGER, MPI_SUM, comm2d, ierr )
1720	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1721	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), &
1722	(nz+2)*sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1723	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1724	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, &
1725	MPI_SUM, comm2d, ierr )
1726	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1727	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1728	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), &
1729	mean_surface_level_height(0), sr, MPI_REAL, &
1730	MPI_SUM, comm2d, ierr )
1731	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1732	#else
1733	ngp_2dh = ngp_2dh_l
1734	ngp_2dh_outer = ngp_2dh_outer_l
1735	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1736	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1737	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1738	#endif
1739
1740	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1741	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1742
1743	!
1744	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics,
1745	!-- buoyancy, etc. A zero value will occur for cases where all grid points of
1746	!-- the respective subdomain lie below the surface topography
1747	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1748	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), &
1749	ngp_3d_inner(:) )
1750	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1751
1752	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, &
1753	ngp_3d_inner_l, ngp_3d_inner_tmp )
1754	!
1755	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1756	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1757	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1758	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1759	CALL ls_forcing_surf ( simulated_time )
1760	ENDIF
1761	ENDIF
1762	!
1763	!-- Initializae 3D offline nesting in COSMO model and read data from
1764	!-- external NetCDF file.
1765	IF ( nesting_offline ) CALL nesting_offl_init
1766	!
1767	!-- Initialize quantities for special advections schemes
1768	CALL init_advec
1769
1770	!
1771	!-- Impose random perturbation on the horizontal velocity field and then
1772	!-- remove the divergences from the velocity field at the initial stage
1773	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1774	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1775	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1776
1777	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1778	!
1779	!-- Needed for both disturb_field and pres
1780	!$ACC DATA &
1781	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1782	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1783	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1784
1785	CALL disturb_field( 'u', tend, u )
1786	CALL disturb_field( 'v', tend, v )
1787
1788	!$ACC DATA &
1789	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1790	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1791	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1792	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1793	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1794	!$ACC COPYIN(wall_flags_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1795	!$ACC COPYIN(bc_h(0:1)) &
1796	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1797	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1798	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1799	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1800	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1801	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1802
1803	n_sor = nsor_ini
1804	CALL pres
1805	n_sor = nsor
1806
1807	!$ACC END DATA
1808	!$ACC END DATA
1809
1810	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1811
1812	ENDIF
1813
1814	IF ( .NOT. ocean_mode ) THEN
1815
1816	ALLOCATE( hyp(nzb:nzt+1) )
1817	ALLOCATE( d_exner(nzb:nzt+1) )
1818	ALLOCATE( exner(nzb:nzt+1) )
1819	ALLOCATE( hyrho(nzb:nzt+1) )
1820	!
1821	!-- Check temperature in case of too large domain height
1822	DO k = nzb, nzt+1
1823	IF ( ( pt_surface * exner_function(surface_pressure * 100.0_wp) - g/c_p * zu(k) ) < 0.0_wp ) THEN
1824	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, &
1825	') = ', zu(k)
1826	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1827	ENDIF
1828	ENDDO
1829
1830	!
1831	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1832	hyp = barometric_formula(zu, pt_surface * exner_function(surface_pressure * 100.0_wp), surface_pressure * 100.0_wp)
1833	d_exner = exner_function_invers(hyp)
1834	exner = 1.0_wp / exner_function_invers(hyp)
1835	hyrho = ideal_gas_law_rho_pt(hyp, pt_init)
1836	!
1837	!-- Compute reference density
1838	rho_surface = ideal_gas_law_rho(surface_pressure * 100.0_wp, pt_surface * exner_function(surface_pressure * 100.0_wp))
1839
1840	ENDIF
1841
1842	!
1843	!-- If required, initialize particles
1844	IF ( agents_active ) CALL mas_init
1845	!
1846	!-- Initialization of synthetic turbulence generator
1847	IF ( use_syn_turb_gen ) CALL stg_init
1848	!
1849	!-- Initializing actions for all other modules
1850	CALL module_interface_init
1851	!
1852	!-- Initialize surface layer (done after LSM as roughness length are required
1853	!-- for initialization
1854	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1855	!
1856	!-- Initialize surface data output
1857	IF ( surface_output ) CALL surface_data_output_init
1858	!
1859	!-- Initialize the ws-scheme.
1860	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1861	!
1862	!-- Perform post-initializing checks for all other modules
1863	CALL module_interface_init_checks
1864
1865	!
1866	!-- Setting weighting factors for calculation of perturbation pressure
1867	!-- and turbulent quantities from the RK substeps
1868	IF ( TRIM(timestep_scheme) == 'runge-kutta-3' ) THEN ! for RK3-method
1869
1870	weight_substep(1) = 1._wp/6._wp
1871	weight_substep(2) = 3._wp/10._wp
1872	weight_substep(3) = 8._wp/15._wp
1873
1874	weight_pres(1) = 1._wp/3._wp
1875	weight_pres(2) = 5._wp/12._wp
1876	weight_pres(3) = 1._wp/4._wp
1877
1878	ELSEIF ( TRIM(timestep_scheme) == 'runge-kutta-2' ) THEN ! for RK2-method
1879
1880	weight_substep(1) = 1._wp/2._wp
1881	weight_substep(2) = 1._wp/2._wp
1882
1883	weight_pres(1) = 1._wp/2._wp
1884	weight_pres(2) = 1._wp/2._wp
1885
1886	ELSE ! for Euler-method
1887
1888	weight_substep(1) = 1.0_wp
1889	weight_pres(1) = 1.0_wp
1890
1891	ENDIF
1892
1893	!
1894	!-- Initialize Rayleigh damping factors
1895	rdf = 0.0_wp
1896	rdf_sc = 0.0_wp
1897	IF ( rayleigh_damping_factor /= 0.0_wp ) THEN
1898
1899	IF ( .NOT. ocean_mode ) THEN
1900	DO k = nzb+1, nzt
1901	IF ( zu(k) >= rayleigh_damping_height ) THEN
1902	rdf(k) = rayleigh_damping_factor * &
1903	( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
1904	/ ( zu(nzt) - rayleigh_damping_height ) ) &
1905	)**2
1906	ENDIF
1907	ENDDO
1908	ELSE
1909	!
1910	!-- In ocean mode, rayleigh damping is applied in the lower part of the
1911	!-- model domain
1912	DO k = nzt, nzb+1, -1
1913	IF ( zu(k) <= rayleigh_damping_height ) THEN
1914	rdf(k) = rayleigh_damping_factor * &
1915	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1916	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1917	)**2
1918	ENDIF
1919	ENDDO
1920	ENDIF
1921
1922	ENDIF
1923	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1924
1925	!
1926	!-- Initialize the starting level and the vertical smoothing factor used for
1927	!-- the external pressure gradient
1928	dp_smooth_factor = 1.0_wp
1929	IF ( dp_external ) THEN
1930	!
1931	!-- Set the starting level dp_level_ind_b only if it has not been set before
1932	!-- (e.g. in init_grid).
1933	IF ( dp_level_ind_b == 0 ) THEN
1934	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1935	dp_level_ind_b = ind_array(1) - 1 + nzb
1936	! MINLOC uses lower array bound 1
1937	ENDIF
1938	IF ( dp_smooth ) THEN
1939	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1940	DO k = dp_level_ind_b+1, nzt
1941	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1942	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1943	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1944	ENDDO
1945	ENDIF
1946	ENDIF
1947
1948	!
1949	!-- Initialize damping zone for the potential temperature in case of
1950	!-- non-cyclic lateral boundaries. The damping zone has the maximum value
1951	!-- at the inflow boundary and decreases to zero at pt_damping_width.
1952	ptdf_x = 0.0_wp
1953	ptdf_y = 0.0_wp
1954	IF ( bc_lr_dirrad ) THEN
1955	DO i = nxl, nxr
1956	IF ( ( i * dx ) < pt_damping_width ) THEN
1957	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1958	REAL( pt_damping_width - i * dx, KIND=wp ) / ( &
1959	REAL( pt_damping_width, KIND=wp ) ) ) )**2
1960	ENDIF
1961	ENDDO
1962	ELSEIF ( bc_lr_raddir ) THEN
1963	DO i = nxl, nxr
1964	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1965	ptdf_x(i) = pt_damping_factor * &
1966	SIN( pi * 0.5_wp * &
1967	( ( i - nx ) * dx + pt_damping_width ) / &
1968	REAL( pt_damping_width, KIND=wp ) )**2
1969	ENDIF
1970	ENDDO
1971	ELSEIF ( bc_ns_dirrad ) THEN
1972	DO j = nys, nyn
1973	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1974	ptdf_y(j) = pt_damping_factor * &
1975	SIN( pi * 0.5_wp * &
1976	( ( j - ny ) * dy + pt_damping_width ) / &
1977	REAL( pt_damping_width, KIND=wp ) )**2
1978	ENDIF
1979	ENDDO
1980	ELSEIF ( bc_ns_raddir ) THEN
1981	DO j = nys, nyn
1982	IF ( ( j * dy ) < pt_damping_width ) THEN
1983	ptdf_y(j) = pt_damping_factor * &
1984	SIN( pi * 0.5_wp * &
1985	( pt_damping_width - j * dy ) / &
1986	REAL( pt_damping_width, KIND=wp ) )**2
1987	ENDIF
1988	ENDDO
1989	ENDIF
1990
1991	!
1992	!-- Input binary data file is not needed anymore. This line must be placed
1993	!-- after call of user_init!
1994	CALL close_file( 13 )
1995	!
1996	!-- In case of nesting, put an barrier to assure that all parent and child
1997	!-- domains finished initialization.
1998	#if defined( __parallel )
1999	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
2000	#endif
2001
2002
2003	CALL location_message( 'model initialization', 'finished' )
2004
2005	END SUBROUTINE init_3d_model

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