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init_3d_model.f90 @ 4861

Last change on this file since 4861 was 4848, checked in by gronemeier, 4 years ago

bugfix: removed syn_turb_gen from restart files, replaced use_syn_turb_gen by syn_turb_gen

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/palm/branches/chemistry/SOURCE/init_3d_model.f90	2047-3190,3218-3297
/palm/branches/rans/SOURCE/init_3d_model.f90	2078-3128
/palm/branches/resler/SOURCE/init_3d_model.f90	2023-4492
/palm/branches/salsa/SOURCE/init_3d_model.f90	2503-3581
/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

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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 terms of the GNU General
6	! Public License as published by the Free Software Foundation, either version 3 of the License, or
7	! (at your option) any later version.
8	!
9	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the
10	! implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
11	! Public License for more details.
12	!
13	! You should have received a copy of the GNU General Public License along with PALM. If not, see
14	! <http://www.gnu.org/licenses/>.
15	!
16	! Copyright 1997-2021 Leibniz Universitaet Hannover
17	!--------------------------------------------------------------------------------------------------!
18	!
19	! Current revisions:
20	! ------------------
21	!
22	!
23	! Former revisions:
24	! -----------------
25	! $Id: init_3d_model.f90 4848 2021-01-21 15:51:51Z raasch $
26	! replaced use_syn_turb_gen by syn_turb_gen
27	!
28	! 4845 2021-01-18 11:15:37Z raasch
29	! removed allocation and initialization of arrays required for radiation boundary conditions
30	!
31	! 4828 2021-01-05 11:21:41Z Giersch
32	! Add possibility to initialize surface flux of passive scalar via static driver
33	!
34	! 4783 2020-11-13 13:58:45Z raasch
35	! bugfix for reading restart data with MPI-I/O (does not work with blockwise I/O)
36	!
37	! 4680 2020-09-16 10:20:34Z gronemeier
38	! Add option to fix date or time of the simulation
39	!
40	! 4671 2020-09-09 20:27:58Z pavelkrc
41	! Implementation of downward facing USM and LSM surfaces
42	!
43	! 4648 2020-08-25 07:52:08Z raasch
44	! file re-formatted to follow the PALM coding standard
45	!
46	! 4548 2020-05-28 19:36:45Z suehring
47	! Bugfix, move call for lsf_forcing_surf after lsf_init is called
48	!
49	! 4514 2020-04-30 16:29:59Z suehring
50	! Add possibility to initialize surface sensible and latent heat fluxes via a static driver.
51	!
52	! 4493 2020-04-10 09:49:43Z pavelkrc
53	! Overwrite u_init, v_init, pt_init, q_init and s_init with hom for all cyclic_fill-cases, not only
54	! for turbulent_inflow = .TRUE.
55	!
56	! 4360 2020-01-07 11:25:50Z suehring
57	! Introduction of wall_flags_total_0, which currently sets bits based on static topography
58	! information used in wall_flags_static_0
59	!
60	! 4329 2019-12-10 15:46:36Z motisi
61	! Renamed wall_flags_0 to wall_flags_static_0
62	!
63	! 4286 2019-10-30 16:01:14Z resler
64	! implement new palm_date_time_mod
65	!
66	! 4223 2019-09-10 09:20:47Z gronemeier
67	! Deallocate temporary string array since it may be re-used to read different input data in other
68	! modules
69	!
70	! 4186 2019-08-23 16:06:14Z suehring
71	! Design change, use variables defined in netcdf_data_input_mod to read netcd variables rather than
72	! define local ones.
73	!
74	! 4185 2019-08-23 13:49:38Z oliver.maas
75	! For initializing_actions = ' cyclic_fill':
76	! Overwrite u_init, v_init, pt_init, q_init and s_init with the (temporally) and horizontally
77	! averaged vertical profiles from the end of the prerun, because these profiles shall be used as the
78	! basic state for the rayleigh damping and the pt_damping.
79	!
80	! 4182 2019-08-22 15:20:23Z scharf
81	! Corrected "Former revisions" section
82	!
83	! 4168 2019-08-16 13:50:17Z suehring
84	! Replace function get_topography_top_index by topo_top_ind
85	!
86	! 4151 2019-08-09 08:24:30Z suehring
87	! Add netcdf directive around input calls (fix for last commit)
88	!
89	! 4150 2019-08-08 20:00:47Z suehring
90	! Input of additional surface variables independent on land- or urban-surface model
91	!
92	! 4131 2019-08-02 11:06:18Z monakurppa
93	! Allocate sums and sums_l to allow profile output for salsa variables.
94	!
95	! 4130 2019-08-01 13:04:13Z suehring
96	! Effectively reduce 3D initialization to 1D initial profiles. This is because 3D initialization
97	! produces structures in the w-component that are correlated with the processor grid for some
98	! unknown reason
99	!
100	! 4090 2019-07-11 15:06:47Z Giersch
101	! Unused variables removed
102	!
103	! 4088 2019-07-11 13:57:56Z Giersch
104	! Pressure and density profile calculations revised using basic functions
105	!
106	! 4048 2019-06-21 21:00:21Z knoop
107	! Further modularization of particle code components
108	!
109	! 4017 2019-06-06 12:16:46Z schwenkel
110	! Convert most location messages to debug messages to reduce output in job logfile to a minimum
111	!
112	! unused variable removed
113	!
114	! 3937 2019-04-29 15:09:07Z suehring
115	! Move initialization of synthetic turbulence generator behind initialization of offline nesting.
116	! Remove call for stg_adjust, as this is now already done in stg_init.
117	!
118	! 3900 2019-04-16 15:17:43Z suehring
119	! Fix problem with LOD = 2 initialization
120	!
121	! 3885 2019-04-11 11:29:34Z kanani
122	! Changes related to global restructuring of location messages and introduction of additional debug
123	! messages
124	!
125	! 3849 2019-04-01 16:35:16Z knoop
126	! Move initialization of rmask before initializing user_init_arrays
127	!
128	! 3711 2019-01-31 13:44:26Z knoop
129	! Introduced module_interface_init_checks for post-init checks in modules
130	!
131	! 3700 2019-01-26 17:03:42Z knoop
132	! Some interface calls moved to module_interface + cleanup
133	!
134	! 3648 2019-01-02 16:35:46Z suehring
135	! Rename subroutines for surface-data output
136	!
137	! Revision 1.1 1998/03/09 16:22:22 raasch
138	! Initial revision
139	!
140	!
141	! Description:
142	! ------------
143	!> Allocation of arrays and initialization of the 3D model via
144	!> a) pre-run the 1D model
145	!> or
146	!> b) pre-set constant linear profiles
147	!> or
148	!> c) read values of a previous run
149	!--------------------------------------------------------------------------------------------------!
150	SUBROUTINE init_3d_model
151
152
153	USE advec_ws
154
155	USE arrays_3d
156
157	USE basic_constants_and_equations_mod, &
158	ONLY: barometric_formula, c_p, exner_function, exner_function_invers, g, &
159	ideal_gas_law_rho, ideal_gas_law_rho_pt, l_v, pi
160
161	USE bulk_cloud_model_mod, &
162	ONLY: bulk_cloud_model
163
164	USE chem_modules, &
165	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
166
167	USE control_parameters
168
169	USE grid_variables, &
170	ONLY: dx, dy, ddx2_mg, ddy2_mg
171
172	USE indices
173
174	USE kinds
175
176	USE lsf_nudging_mod, &
177	ONLY: ls_forcing_surf
178
179	USE model_1d_mod, &
180	ONLY: init_1d_model, l1d, u1d, v1d
181
182	USE module_interface, &
183	ONLY: module_interface_init_arrays, &
184	module_interface_init, &
185	module_interface_init_checks
186
187	USE multi_agent_system_mod, &
188	ONLY: agents_active, mas_init
189
190	USE netcdf_interface, &
191	ONLY: dots_max
192
193	USE netcdf_data_input_mod, &
194	ONLY: char_fill, &
195	check_existence, &
196	close_input_file, &
197	get_attribute, &
198	get_variable, &
199	init_3d, &
200	input_pids_static, &
201	inquire_num_variables, &
202	inquire_variable_names, &
203	input_file_static, &
204	netcdf_data_input_init_3d, &
205	num_var_pids, &
206	open_read_file, &
207	pids_id, &
208	real_2d, &
209	vars_pids
210
211	USE nesting_offl_mod, &
212	ONLY: nesting_offl_init
213
214	USE palm_date_time_mod, &
215	ONLY: init_date_time
216
217	USE pegrid
218
219	#if defined( __parallel )
220	USE pmc_interface, &
221	ONLY: nested_run
222	#endif
223
224	USE random_function_mod
225
226	USE random_generator_parallel, &
227	ONLY: init_parallel_random_generator
228
229	USE read_restart_data_mod, &
230	ONLY: rrd_local, rrd_read_parts_of_global
231
232	USE statistics, &
233	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, statistic_regions, sums, &
234	sums_divnew_l, sums_divold_l, sums_l, sums_l_l, sums_wsts_bc_l, ts_value, &
235	weight_pres, weight_substep
236
237	USE synthetic_turbulence_generator_mod, &
238	ONLY: stg_init
239
240	USE surface_layer_fluxes_mod, &
241	ONLY: init_surface_layer_fluxes
242
243	USE surface_mod, &
244	ONLY : init_single_surface_properties, &
245	init_surface_arrays, &
246	init_surfaces, &
247	surf_def_h, &
248	surf_def_v, &
249	surf_lsm_h, &
250	surf_usm_h
251
252	#if defined( _OPENACC )
253	USE surface_mod, &
254	ONLY : bc_h
255	#endif
256
257	USE surface_data_output_mod, &
258	ONLY: surface_data_output_init
259
260	USE transpose_indices
261
262
263	IMPLICIT NONE
264
265	INTEGER(iwp) :: i !< grid index in x direction
266	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
267	INTEGER(iwp) :: j !< grid index in y direction
268	INTEGER(iwp) :: k !< grid index in z direction
269	INTEGER(iwp) :: k_surf !< surface level index
270	INTEGER(iwp) :: l !< running index over surface orientation
271	INTEGER(iwp) :: m !< index of surface element in surface data type
272	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
273	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
274	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
275	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
276	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
277	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
278	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
279	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
280	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
281	INTEGER(iwp) :: sr !< index of statistic region
282
283	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on
284	!< subdomain
285
286	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on
287	!< subdomain
288	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on
289	!< subdomain
290
291	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
292	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
293
294	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain
295	!< inital profiles
296	REAL(wp), DIMENSION(:), ALLOCATABLE :: mean_surface_level_height_l !< mean surface level height on subdomain
297	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_l !< total number of non-topography grid points on subdomain
298	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_tmp !< total number of non-topography grid points
299	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
300
301	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
302	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
303
304	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
305
306	CALL location_message( 'model initialization', 'start' )
307	!
308	!-- Set reference date-time
309	CALL init_date_time( date_time_str=origin_date_time, &
310	use_fixed_date=use_fixed_date, &
311	use_fixed_time=use_fixed_time )
312
313	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
314	!
315	!-- Allocate arrays
316	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
317	mean_surface_level_height_l(0:statistic_regions), &
318	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
319	ngp_3d(0:statistic_regions), &
320	ngp_3d_inner(0:statistic_regions), &
321	ngp_3d_inner_l(0:statistic_regions), &
322	ngp_3d_inner_tmp(0:statistic_regions), &
323	sums_divnew_l(0:statistic_regions), &
324	sums_divold_l(0:statistic_regions) )
325	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
326	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
327	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
328	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
329	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
330	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
331	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
332	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
333	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
334	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
335	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
336	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
337
338	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
339	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
340	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
341
342	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
343	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
344	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
345	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
346	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
347	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
348	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
349	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
350	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
351	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
352	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
353	IF ( .NOT. neutral ) THEN
354	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
355	ENDIF
356	!
357	!-- Pre-set masks for regional statistics. Default is the total model domain.
358	!-- Ghost points are excluded because counting values at the ghost boundaries would bias the
359	!-- statistics.
360	rmask = 1.0_wp
361	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
362	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
363	!
364	!-- Following array is required for perturbation pressure within the iterative pressure solvers. For
365	!-- the multistep schemes (Runge-Kutta), array p holds the weighted average of the substeps and
366	!-- cannot be used in the Poisson solver.
367	IF ( psolver == 'sor' ) THEN
368	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
369	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
370	!
371	!-- For performance reasons, multigrid is using one ghost layer only
372	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
373	ENDIF
374
375	!
376	!-- Array for storing constant coeffficients of the tridiagonal solver
377	IF ( psolver == 'poisfft' ) THEN
378	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
379	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
380	ENDIF
381
382	IF ( humidity ) THEN
383	!
384	!-- 3D-humidity
385	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
386	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
387	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
388	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
389	ENDIF
390
391	IF ( passive_scalar ) THEN
392
393	!
394	!-- 3D scalar arrays
395	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
396	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
397	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
398
399	ENDIF
400
401	!
402	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to non-zero values later
403	!-- in ocean_init.
404	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
405	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
406	u_stokes_zu(:) = 0.0_wp
407	u_stokes_zw(:) = 0.0_wp
408	v_stokes_zu(:) = 0.0_wp
409	v_stokes_zw(:) = 0.0_wp
410
411	!
412	!-- Allocation of anelastic and Boussinesq approximation specific arrays
413	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
414	ALLOCATE( rho_air(nzb:nzt+1) )
415	ALLOCATE( rho_air_zw(nzb:nzt+1) )
416	ALLOCATE( drho_air(nzb:nzt+1) )
417	ALLOCATE( drho_air_zw(nzb:nzt+1) )
418	!
419	!-- Density profile calculation for anelastic and Boussinesq approximation.
420	!-- In case of a Boussinesq approximation, a constant density is calculated mainly for output
421	!-- purposes. This density does not need to be considered in the model's system of equations.
422	IF ( TRIM( approximation ) == 'anelastic' ) THEN
423	DO k = nzb, nzt+1
424	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
425	exner_function(surface_pressure * 100.0_wp), &
426	surface_pressure * 100.0_wp)
427
428	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
429	ENDDO
430
431	DO k = nzb, nzt
432	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
433	ENDDO
434
435	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
436
437	ELSE
438	DO k = nzb, nzt+1
439	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
440	exner_function(surface_pressure * 100.0_wp), &
441	surface_pressure * 100.0_wp)
442
443	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
444	ENDDO
445
446	DO k = nzb, nzt
447	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
448	ENDDO
449
450	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
451
452	ENDIF
453	!
454	!-- Compute the inverse density array in order to avoid expencive divisions
455	drho_air = 1.0_wp / rho_air
456	drho_air_zw = 1.0_wp / rho_air_zw
457
458	!
459	!-- Allocation of flux conversion arrays
460	ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
461	ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
462	ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
463	ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
464	ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
465	ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )
466
467	!
468	!-- Calculate flux conversion factors according to approximation and in-/output mode
469	DO k = nzb, nzt+1
470
471	IF ( TRIM( flux_input_mode ) == 'kinematic' ) THEN
472	heatflux_input_conversion(k) = rho_air_zw(k)
473	waterflux_input_conversion(k) = rho_air_zw(k)
474	momentumflux_input_conversion(k) = rho_air_zw(k)
475	ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
476	heatflux_input_conversion(k) = 1.0_wp / c_p
477	waterflux_input_conversion(k) = 1.0_wp / l_v
478	momentumflux_input_conversion(k) = 1.0_wp
479	ENDIF
480
481	IF ( TRIM( flux_output_mode ) == 'kinematic' ) THEN
482	heatflux_output_conversion(k) = drho_air_zw(k)
483	waterflux_output_conversion(k) = drho_air_zw(k)
484	momentumflux_output_conversion(k) = drho_air_zw(k)
485	ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
486	heatflux_output_conversion(k) = c_p
487	waterflux_output_conversion(k) = l_v
488	momentumflux_output_conversion(k) = 1.0_wp
489	ENDIF
490
491	IF ( .NOT. humidity ) THEN
492	waterflux_input_conversion(k) = 1.0_wp
493	waterflux_output_conversion(k) = 1.0_wp
494	ENDIF
495
496	ENDDO
497
498	!
499	!-- In case of multigrid method, compute grid lengths and grid factors for the grid levels with
500	!-- respective density on each grid.
501	IF ( psolver(1:9) == 'multigrid' ) THEN
502
503	ALLOCATE( ddx2_mg(maximum_grid_level) )
504	ALLOCATE( ddy2_mg(maximum_grid_level) )
505	ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
506	ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
507	ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
508	ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
509	ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
510	ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
511	ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )
512
513	dzu_mg(:,maximum_grid_level) = dzu
514	rho_air_mg(:,maximum_grid_level) = rho_air
515	!
516	!-- Next line to ensure an equally spaced grid.
517	dzu_mg(1,maximum_grid_level) = dzu(2)
518	rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) + (rho_air(nzb) - rho_air(nzb+1))
519
520	dzw_mg(:,maximum_grid_level) = dzw
521	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
522	nzt_l = nzt
523	DO l = maximum_grid_level-1, 1, -1
524	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
525	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
526	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + ( rho_air_mg(nzb,l+1) - &
527	rho_air_mg(nzb+1,l+1) )
528	rho_air_zw_mg(nzb,l) = rho_air_zw_mg(nzb,l+1) + ( rho_air_zw_mg(nzb,l+1) - &
529	rho_air_zw_mg(nzb+1,l+1) )
530	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
531	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
532	nzt_l = nzt_l / 2
533	DO k = 2, nzt_l+1
534	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
535	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
536	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
537	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
538	ENDDO
539	ENDDO
540
541	nzt_l = nzt
542	dx_l = dx
543	dy_l = dy
544	DO l = maximum_grid_level, 1, -1
545	ddx2_mg(l) = 1.0_wp / dx_l**2
546	ddy2_mg(l) = 1.0_wp / dy_l**2
547	DO k = nzb+1, nzt_l
548	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
549	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
550	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
551	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
552	ENDDO
553	nzt_l = nzt_l / 2
554	dx_l = dx_l * 2.0_wp
555	dy_l = dy_l * 2.0_wp
556	ENDDO
557
558	ENDIF
559
560	!
561	!-- 1D-array for large scale subsidence velocity
562	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
563	ALLOCATE ( w_subs(nzb:nzt+1) )
564	w_subs = 0.0_wp
565	ENDIF
566
567	!
568	!-- Initial assignment of the pointers
569	IF ( .NOT. neutral ) THEN
570	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
571	ELSE
572	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
573	ENDIF
574	u => u_1; u_p => u_2; tu_m => u_3
575	v => v_1; v_p => v_2; tv_m => v_3
576	w => w_1; w_p => w_2; tw_m => w_3
577
578	IF ( humidity ) THEN
579	q => q_1; q_p => q_2; tq_m => q_3
580	vpt => vpt_1
581	ENDIF
582
583	IF ( passive_scalar ) THEN
584	s => s_1; s_p => s_2; ts_m => s_3
585	ENDIF
586
587	!
588	!-- Initialize surface arrays
589	CALL init_surface_arrays
590	!
591	!-- Allocate arrays for other modules
592	CALL module_interface_init_arrays
593
594
595	!
596	!-- Allocate arrays containing the RK coefficient for calculation of perturbation pressure and
597	!-- turbulent fluxes. At this point values are set for pressure calculation during initialization
598	!-- (where no timestep is done). Further below the values needed within the timestep scheme will be
599	!-- set.
600	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
601	weight_pres(1:intermediate_timestep_count_max) )
602	weight_substep = 1.0_wp
603	weight_pres = 1.0_wp
604	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
605
606	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
607
608	!
609	!-- Initialize time series
610	ts_value = 0.0_wp
611
612	!
613	!-- Initialize local summation arrays for routine flow_statistics.
614	!-- This is necessary because they may not yet have been initialized when they are called from
615	!-- flow_statistics (or - depending on the chosen model run - are never initialized)
616	sums_divnew_l = 0.0_wp
617	sums_divold_l = 0.0_wp
618	sums_l_l = 0.0_wp
619	sums_wsts_bc_l = 0.0_wp
620
621	!
622	!-- Initialize model variables
623	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
624	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
625	!
626	!-- Initialization with provided input data derived from larger-scale model
627	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
628	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
629	!
630	!-- Read initial 1D profiles or 3D data from NetCDF file, depending on the provided
631	!-- level-of-detail.
632	!-- At the moment, only u, v, w, pt and q are provided.
633	CALL netcdf_data_input_init_3d
634	!
635	!-- Please note, Inifor provides data from nzb+1 to nzt.
636	!-- Bottom and top boundary conditions for Inifor profiles are already set (just after
637	!-- reading), so that this is not necessary here.
638	!-- Depending on the provided level-of-detail, initial Inifor data is either stored on data
639	!-- type (lod=1), or directly on 3D arrays (lod=2).
640	!-- In order to obtain also initial profiles in case of lod=2 (which is required for e.g.
641	!-- damping), average over 3D data.
642	IF( init_3d%lod_u == 1 ) THEN
643	u_init = init_3d%u_init
644	ELSEIF( init_3d%lod_u == 2 ) THEN
645	ALLOCATE( init_l(nzb:nzt+1) )
646	DO k = nzb, nzt+1
647	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
648	ENDDO
649	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
650
651	#if defined( __parallel )
652	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
653	#else
654	u_init = init_l
655	#endif
656	DEALLOCATE( init_l )
657
658	ENDIF
659
660	IF( init_3d%lod_v == 1 ) THEN
661	v_init = init_3d%v_init
662	ELSEIF( init_3d%lod_v == 2 ) THEN
663	ALLOCATE( init_l(nzb:nzt+1) )
664	DO k = nzb, nzt+1
665	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
666	ENDDO
667	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
668
669	#if defined( __parallel )
670	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
671	#else
672	v_init = init_l
673	#endif
674	DEALLOCATE( init_l )
675	ENDIF
676	IF( .NOT. neutral ) THEN
677	IF( init_3d%lod_pt == 1 ) THEN
678	pt_init = init_3d%pt_init
679	ELSEIF( init_3d%lod_pt == 2 ) THEN
680	ALLOCATE( init_l(nzb:nzt+1) )
681	DO k = nzb, nzt+1
682	init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
683	ENDDO
684	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
685
686	#if defined( __parallel )
687	CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
688	#else
689	pt_init = init_l
690	#endif
691	DEALLOCATE( init_l )
692	ENDIF
693	ENDIF
694
695
696	IF( humidity ) THEN
697	IF( init_3d%lod_q == 1 ) THEN
698	q_init = init_3d%q_init
699	ELSEIF( init_3d%lod_q == 2 ) THEN
700	ALLOCATE( init_l(nzb:nzt+1) )
701	DO k = nzb, nzt+1
702	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
703	ENDDO
704	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
705
706	#if defined( __parallel )
707	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
708	#else
709	q_init = init_l
710	#endif
711	DEALLOCATE( init_l )
712	ENDIF
713	ENDIF
714
715	!
716	!-- Write initial profiles onto 3D arrays.
717	!-- Work-around, 3D initialization of u,v,w creates artificial structures which correlate with
718	!-- the processor grid. The reason for this is still unknown. To work-around this, 3D
719	!-- initialization will be effectively reduce to a 1D initialization where no such artificial
720	!-- structures appear.
721	DO i = nxlg, nxrg
722	DO j = nysg, nyng
723	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) u(:,j,i) = u_init(:)
724	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) v(:,j,i) = v_init(:)
725	IF( .NOT. neutral .AND. ( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
726	pt(:,j,i) = pt_init(:)
727	IF( humidity .AND. ( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
728	q(:,j,i) = q_init(:)
729	ENDDO
730	ENDDO
731	!
732	!-- Set geostrophic wind components.
733	IF ( init_3d%from_file_ug ) THEN
734	ug(:) = init_3d%ug_init(:)
735	ENDIF
736	IF ( init_3d%from_file_vg ) THEN
737	vg(:) = init_3d%vg_init(:)
738	ENDIF
739	!
740	!-- Set bottom and top boundary condition for geostrophic wind
741	ug(nzt+1) = ug(nzt)
742	vg(nzt+1) = vg(nzt)
743	ug(nzb) = ug(nzb+1)
744	vg(nzb) = vg(nzb+1)
745	!
746	!-- Set inital w to 0
747	w = 0.0_wp
748
749	IF ( passive_scalar ) THEN
750	DO i = nxlg, nxrg
751	DO j = nysg, nyng
752	s(:,j,i) = s_init
753	ENDDO
754	ENDDO
755	ENDIF
756
757	!
758	!-- Set velocity components at non-atmospheric / oceanic grid points to zero.
759	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
760	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
761	w = MERGE( w, 0.0_wp, BTEST( wall_flags_total_0, 3 ) )
762	!
763	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
764	CALL init_surfaces
765
766	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
767	!
768	!-- Initialization via computed 1D-model profiles
769	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
770
771	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
772	!
773	!-- Use solutions of the 1D model as initial profiles,
774	!-- start 1D model
775	CALL init_1d_model
776	!
777	!-- Transfer initial profiles to the arrays of the 3D model
778	DO i = nxlg, nxrg
779	DO j = nysg, nyng
780	pt(:,j,i) = pt_init
781	u(:,j,i) = u1d
782	v(:,j,i) = v1d
783	ENDDO
784	ENDDO
785
786	IF ( humidity ) THEN
787	DO i = nxlg, nxrg
788	DO j = nysg, nyng
789	q(:,j,i) = q_init
790	ENDDO
791	ENDDO
792	ENDIF
793
794	IF ( passive_scalar ) THEN
795	DO i = nxlg, nxrg
796	DO j = nysg, nyng
797	s(:,j,i) = s_init
798	ENDDO
799	ENDDO
800	ENDIF
801	!
802	!-- Store initial profiles for output purposes etc.
803	IF ( .NOT. constant_diffusion ) THEN
804	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
805	ENDIF
806	!
807	!-- Set velocities back to zero
808	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
809	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
810	!
811	!-- WARNING: The extra boundary conditions set after running the 1D model impose an error on
812	!-- -------- the divergence one layer below the topography; need to correct later
813	!-- ATTENTION: Provisional correction for Piacsek & Williams advection scheme: keep u and v
814	!-- ---------- zero one layer below the topography.
815	IF ( ibc_uv_b == 1 ) THEN
816	!
817	!-- Neumann condition
818	DO i = nxl-1, nxr+1
819	DO j = nys-1, nyn+1
820	u(nzb,j,i) = u(nzb+1,j,i)
821	v(nzb,j,i) = v(nzb+1,j,i)
822	ENDDO
823	ENDDO
824
825	ENDIF
826	!
827	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
828	CALL init_surfaces
829
830	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
831
832	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) THEN
833
834	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
835
836	!
837	!-- Use constructed initial profiles (velocity constant with height, temperature profile with
838	!-- constant gradient)
839	DO i = nxlg, nxrg
840	DO j = nysg, nyng
841	pt(:,j,i) = pt_init
842	u(:,j,i) = u_init
843	v(:,j,i) = v_init
844	ENDDO
845	ENDDO
846	!
847	!-- Mask topography
848	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
849	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
850	!
851	!-- Set initial horizontal velocities at the lowest computational grid levels to zero in order
852	!-- to avoid too small time steps caused by the diffusion limit in the initial phase of a run
853	!-- (at k=1, dz/2 occurs in the limiting formula!).
854	!-- Please note, in case land- or urban-surface model is used and a spinup is applied, masking
855	!-- the lowest computational level is not possible as MOST as well as energy-balance
856	!-- parametrizations will not work with zero wind velocity.
857	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
858	DO i = nxlg, nxrg
859	DO j = nysg, nyng
860	DO k = nzb, nzt
861	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 20 ) )
862	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 21 ) )
863	ENDDO
864	ENDDO
865	ENDDO
866	ENDIF
867
868	IF ( humidity ) THEN
869	DO i = nxlg, nxrg
870	DO j = nysg, nyng
871	q(:,j,i) = q_init
872	ENDDO
873	ENDDO
874	ENDIF
875
876	IF ( passive_scalar ) THEN
877	DO i = nxlg, nxrg
878	DO j = nysg, nyng
879	s(:,j,i) = s_init
880	ENDDO
881	ENDDO
882	ENDIF
883
884	!
885	!-- Compute initial temperature field and other constants used in case of a sloping surface.
886	IF ( sloping_surface ) CALL init_slope
887	!
888	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
889	CALL init_surfaces
890
891	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
892
893	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) THEN
894
895	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
896	!
897	!-- Pre-initialize surface variables, i.e. setting start- and end-indices at each
898	!-- (j,i)-location. Please note, this does not supersede user-defined initialization of
899	!-- surface quantities.
900	CALL init_surfaces
901	!
902	!-- Initialization will completely be done by the user
903	CALL user_init_3d_model
904
905	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
906
907	ENDIF
908
909	IF ( debug_output ) THEN
910	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
911	ENDIF
912
913	!
914	!-- Bottom boundary
915	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
916	u(nzb,:,:) = 0.0_wp
917	v(nzb,:,:) = 0.0_wp
918	ENDIF
919
920	!
921	!-- Apply channel flow boundary condition
922	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
923	u(nzt+1,:,:) = 0.0_wp
924	v(nzt+1,:,:) = 0.0_wp
925	ENDIF
926
927	!
928	!-- Calculate virtual potential temperature
929	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
930
931	!
932	!-- Store initial profiles for output purposes etc.. Please note, in case of initialization of u,
933	!-- v, w, pt, and q via output data derived from larger scale models, data will not be
934	!-- horizontally homogeneous. Actually, a mean profile should be calculated before.
935	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
936	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
937	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
938	hom(nzb,1,5,:) = 0.0_wp
939	hom(nzb,1,6,:) = 0.0_wp
940	ENDIF
941	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
942
943	IF ( humidity ) THEN
944	!
945	!-- Store initial profile of total water content, virtual potential temperature
946	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
947	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
948	!
949	!-- Store initial profile of mixing ratio and potential temperature
950	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
951	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
952	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
953	ENDIF
954	ENDIF
955
956	!
957	!-- Store initial scalar profile
958	IF ( passive_scalar ) THEN
959	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
960	ENDIF
961
962	!
963	!-- Initialize the random number generators (from numerical recipes)
964	CALL random_function_ini
965
966	IF ( random_generator == 'random-parallel' ) THEN
967	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
968	ENDIF
969	!
970	!-- Set the reference state to be used in the buoyancy terms (for ocean runs the reference state
971	!-- will be set (overwritten) in init_ocean).
972	IF ( use_single_reference_value ) THEN
973	IF ( .NOT. humidity ) THEN
974	ref_state(:) = pt_reference
975	ELSE
976	ref_state(:) = vpt_reference
977	ENDIF
978	ELSE
979	IF ( .NOT. humidity ) THEN
980	ref_state(:) = pt_init(:)
981	ELSE
982	ref_state(:) = vpt(:,nys,nxl)
983	ENDIF
984	ENDIF
985
986	!
987	!-- For the moment, vertical velocity is zero
988	w = 0.0_wp
989
990	!
991	!-- Initialize array sums (must be defined in first call of pres)
992	sums = 0.0_wp
993
994	!
995	!-- In case of iterative solvers, p must get an initial value
996	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
997	!
998	!-- Impose vortex with vertical axis on the initial velocity profile
999	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
1000	CALL init_rankine
1001	ENDIF
1002
1003	!
1004	!-- Impose temperature anomaly (advection test only) or warm air bubble close to surface.
1005	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1006	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1007	CALL init_pt_anomaly
1008	ENDIF
1009
1010	!
1011	!-- If required, change the surface temperature at the start of the 3D run
1012	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1013	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1014	ENDIF
1015
1016	!
1017	!-- If required, change the surface humidity/scalar at the start of the 3D
1018	!-- run
1019	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1020	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1021
1022	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1023	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1024
1025
1026	!
1027	!-- Initialize old and new time levels.
1028	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1029	pt_p = pt; u_p = u; v_p = v; w_p = w
1030
1031	IF ( humidity ) THEN
1032	tq_m = 0.0_wp
1033	q_p = q
1034	ENDIF
1035
1036	IF ( passive_scalar ) THEN
1037	ts_m = 0.0_wp
1038	s_p = s
1039	ENDIF
1040
1041	IF ( debug_output ) THEN
1042	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1043	ENDIF
1044
1045	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1046	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1047	THEN
1048
1049	IF ( debug_output ) THEN
1050	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1051	ENDIF
1052	!
1053	!-- Initialize surface elements and its attributes, e.g. heat- and momentumfluxes, roughness,
1054	!-- scaling parameters. As number of surface elements might be different between runs, e.g. in
1055	!-- case of cyclic fill, and not all surface elements are read, surface elements need to be
1056	!-- initialized before.
1057	!-- Please note, in case of cyclic fill, surfaces should be initialized after restart data is
1058	!-- read, else, individual settings of surface parameters will be overwritten from data of
1059	!-- precursor run, hence, init_surfaces is called a second time after reading the restart data.
1060	CALL init_surfaces
1061	!
1062	!-- When reading data for cyclic fill of 3D prerun data files, read some of the global variables
1063	!-- from the restart file which are required for initializing the inflow
1064	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1065
1066	!
1067	!-- Blockwise I/O does not work together with MPI-I/O
1068	IF ( restart_data_format_input(1:3) == 'mpi' ) THEN
1069	CALL rrd_read_parts_of_global
1070	ELSE
1071	DO i = 0, io_blocks-1
1072	IF ( i == io_group ) THEN
1073	CALL rrd_read_parts_of_global
1074	ENDIF
1075	#if defined( __parallel )
1076	CALL MPI_BARRIER( comm2d, ierr )
1077	#endif
1078	ENDDO
1079	ENDIF
1080
1081	ENDIF
1082
1083	!
1084	!-- Read processor specific binary data from restart file.
1085	!-- Blockwise I/O does not work together with MPI-I/O
1086	IF ( restart_data_format_input(1:3) == 'mpi' ) THEN
1087	CALL rrd_local
1088	ELSE
1089	DO i = 0, io_blocks-1
1090	IF ( i == io_group ) THEN
1091	CALL rrd_local
1092	ENDIF
1093	#if defined( __parallel )
1094	CALL MPI_BARRIER( comm2d, ierr )
1095	#endif
1096	ENDDO
1097	ENDIF
1098
1099
1100	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1101
1102	!
1103	!-- In case of cyclic fill, call init_surfaces a second time, so that surface properties such
1104	!-- as heat fluxes are initialized as prescribed.
1105	CALL init_surfaces
1106
1107	!
1108	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the horizontally mean (hom)
1109	!-- vertical profiles from the end of the prerun, because these profiles shall be used as the
1110	!-- reference state for the rayleigh damping and the pt_damping. This is especially important
1111	!-- for the use of large_scale_subsidence, because the reference temperature in the free
1112	!-- atmosphere changes in time.
1113	u_init(:) = hom_sum(:,1,0)
1114	v_init(:) = hom_sum(:,2,0)
1115	pt_init(:) = hom_sum(:,4,0)
1116	IF ( humidity ) q_init(:) = hom_sum(:,41,0)
1117	IF ( passive_scalar ) s_init(:) = hom_sum(:,115,0)
1118	ENDIF
1119	!
1120	!-- In case of complex terrain and cyclic fill method as initialization, shift initial data in
1121	!-- the vertical direction for each point in the x-y-plane depending on local surface height.
1122	IF ( complex_terrain .AND. TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1123	DO i = nxlg, nxrg
1124	DO j = nysg, nyng
1125	nz_u_shift = topo_top_ind(j,i,1)
1126	nz_v_shift = topo_top_ind(j,i,2)
1127	nz_w_shift = topo_top_ind(j,i,3)
1128	nz_s_shift = topo_top_ind(j,i,0)
1129
1130	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1131
1132	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1133
1134	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1135
1136	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1137	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1138	ENDDO
1139	ENDDO
1140	ENDIF
1141	!
1142	!-- Initialization of the turbulence recycling method
1143	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. turbulent_inflow ) THEN
1144	!
1145	!-- First store the profiles to be used at the inflow.
1146	!-- These profiles are the (temporally) and horizontally averaged vertical profiles from the
1147	!-- prerun. Alternatively, prescribed profiles for u,v-components can be used.
1148	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1149
1150	IF ( use_prescribed_profile_data ) THEN
1151	mean_inflow_profiles(:,1) = u_init ! u
1152	mean_inflow_profiles(:,2) = v_init ! v
1153	ELSE
1154	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1155	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1156	ENDIF
1157	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1158	IF ( humidity ) mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1159	IF ( passive_scalar ) mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1160
1161	!
1162	!-- In case of complex terrain, determine vertical displacement at inflow boundary and adjust
1163	!-- mean inflow profiles
1164	IF ( complex_terrain ) THEN
1165	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1166	nz_u_shift_l = topo_top_ind(j,i,1)
1167	nz_v_shift_l = topo_top_ind(j,i,2)
1168	nz_w_shift_l = topo_top_ind(j,i,3)
1169	nz_s_shift_l = topo_top_ind(j,i,0)
1170	ELSE
1171	nz_u_shift_l = 0
1172	nz_v_shift_l = 0
1173	nz_w_shift_l = 0
1174	nz_s_shift_l = 0
1175	ENDIF
1176
1177	#if defined( __parallel )
1178	CALL MPI_ALLREDUCE( nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1179	CALL MPI_ALLREDUCE( nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1180	CALL MPI_ALLREDUCE( nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1181	CALL MPI_ALLREDUCE( nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1182	#else
1183	nz_u_shift = nz_u_shift_l
1184	nz_v_shift = nz_v_shift_l
1185	nz_w_shift = nz_w_shift_l
1186	nz_s_shift = nz_s_shift_l
1187	#endif
1188
1189	mean_inflow_profiles(:,1) = 0.0_wp
1190	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1191
1192	mean_inflow_profiles(:,2) = 0.0_wp
1193	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1194
1195	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1196
1197	ENDIF
1198
1199	!
1200	!-- If necessary, adjust the horizontal flow field to the prescribed profiles
1201	IF ( use_prescribed_profile_data ) THEN
1202	DO i = nxlg, nxrg
1203	DO j = nysg, nyng
1204	DO k = nzb, nzt+1
1205	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1206	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1207	ENDDO
1208	ENDDO
1209	ENDDO
1210	ENDIF
1211
1212	!
1213	!-- Use these mean profiles at the inflow (provided that Dirichlet conditions are used)
1214	IF ( bc_dirichlet_l ) THEN
1215	DO j = nysg, nyng
1216	DO k = nzb, nzt+1
1217	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1218	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1219	w(k,j,nxlg:-1) = 0.0_wp
1220	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1221	IF ( humidity ) q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1222	IF ( passive_scalar ) s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1223	ENDDO
1224	ENDDO
1225	ENDIF
1226
1227	!
1228	!-- Calculate the damping factors to be used at the inflow. For a turbulent inflow the
1229	!-- turbulent fluctuations have to be limited vertically because otherwise the turbulent
1230	!-- inflow layer will grow in time.
1231	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1232	!
1233	!-- Default: use the inversion height calculated by the prerun; if this is zero,
1234	!-- inflow_damping_height must be explicitly specified.
1235	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1236	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1237	ELSE
1238	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1239	'explicitly specified because&the inversion height ', &
1240	'calculated by the prerun is zero.'
1241	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1242	ENDIF
1243
1244	ENDIF
1245
1246	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1247	!
1248	!-- Default for the transition range: one tenth of the undamped layer
1249	inflow_damping_width = 0.1_wp * inflow_damping_height
1250
1251	ENDIF
1252
1253	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1254
1255	DO k = nzb, nzt+1
1256
1257	IF ( zu(k) <= inflow_damping_height ) THEN
1258	inflow_damping_factor(k) = 1.0_wp
1259	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1260	inflow_damping_factor(k) = 1.0_wp - &
1261	( zu(k) - inflow_damping_height ) / inflow_damping_width
1262	ELSE
1263	inflow_damping_factor(k) = 0.0_wp
1264	ENDIF
1265
1266	ENDDO
1267
1268	ENDIF
1269
1270	!
1271	!-- Inside buildings set velocities back to zero
1272	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. topography /= 'flat' ) THEN
1273	!
1274	!-- Inside buildings set velocities back to zero.
1275	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1276	!-- maybe revise later.
1277	DO i = nxlg, nxrg
1278	DO j = nysg, nyng
1279	DO k = nzb, nzt
1280	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 1 ) )
1281	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 2 ) )
1282	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 3 ) )
1283	ENDDO
1284	ENDDO
1285	ENDDO
1286
1287	ENDIF
1288
1289	!
1290	!-- Calculate initial temperature field and other constants used in case of a sloping surface
1291	IF ( sloping_surface ) CALL init_slope
1292
1293	!
1294	!-- Initialize new time levels (only done in order to set boundary values including ghost points)
1295	pt_p = pt; u_p = u; v_p = v; w_p = w
1296	IF ( humidity ) THEN
1297	q_p = q
1298	ENDIF
1299	IF ( passive_scalar ) s_p = s
1300	!
1301	!-- Allthough tendency arrays are set in prognostic_equations, they have have to be predefined
1302	!-- here because they are used (but multiplied with 0) there before they are set.
1303	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1304	IF ( humidity ) THEN
1305	tq_m = 0.0_wp
1306	ENDIF
1307	IF ( passive_scalar ) ts_m = 0.0_wp
1308
1309	IF ( debug_output ) THEN
1310	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1311	ENDIF
1312
1313	ELSE
1314	!
1315	!-- Actually this part of the programm should not be reached
1316	message_string = 'unknown initializing problem'
1317	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1318	ENDIF
1319
1320	!
1321	!-- Calculate the initial volume flow at the right and north boundary
1322	IF ( conserve_volume_flow ) THEN
1323
1324	IF ( use_prescribed_profile_data ) THEN
1325
1326	volume_flow_initial_l = 0.0_wp
1327	volume_flow_area_l = 0.0_wp
1328
1329	IF ( nxr == nx ) THEN
1330	DO j = nys, nyn
1331	DO k = nzb+1, nzt
1332	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1333	u_init(k) * dzw(k) &
1334	* MERGE( 1.0_wp, 0.0_wp, &
1335	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1336	)
1337
1338	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1339	* MERGE( 1.0_wp, 0.0_wp, &
1340	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1341	)
1342	ENDDO
1343	ENDDO
1344	ENDIF
1345
1346	IF ( nyn == ny ) THEN
1347	DO i = nxl, nxr
1348	DO k = nzb+1, nzt
1349	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1350	v_init(k) * dzw(k) &
1351	* MERGE( 1.0_wp, 0.0_wp, &
1352	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1353	)
1354	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1355	* MERGE( 1.0_wp, 0.0_wp, &
1356	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1357	)
1358	ENDDO
1359	ENDDO
1360	ENDIF
1361
1362	#if defined( __parallel )
1363	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1364	MPI_SUM, comm2d, ierr )
1365	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1366	comm2d, ierr )
1367
1368	#else
1369	volume_flow_initial = volume_flow_initial_l
1370	volume_flow_area = volume_flow_area_l
1371	#endif
1372
1373	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1374
1375	volume_flow_initial_l = 0.0_wp
1376	volume_flow_area_l = 0.0_wp
1377
1378	IF ( nxr == nx ) THEN
1379	DO j = nys, nyn
1380	DO k = nzb+1, nzt
1381	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1382	hom_sum(k,1,0) * dzw(k) &
1383	* MERGE( 1.0_wp, 0.0_wp, &
1384	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1385	)
1386	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1387	* MERGE( 1.0_wp, 0.0_wp, &
1388	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1389	)
1390	ENDDO
1391	ENDDO
1392	ENDIF
1393
1394	IF ( nyn == ny ) THEN
1395	DO i = nxl, nxr
1396	DO k = nzb+1, nzt
1397	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1398	hom_sum(k,2,0) * dzw(k) &
1399	* MERGE( 1.0_wp, 0.0_wp, &
1400	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1401	)
1402	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1403	* MERGE( 1.0_wp, 0.0_wp, &
1404	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1405	)
1406	ENDDO
1407	ENDDO
1408	ENDIF
1409
1410	#if defined( __parallel )
1411	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1412	MPI_SUM, comm2d, ierr )
1413	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1414	comm2d, ierr )
1415
1416	#else
1417	volume_flow_initial = volume_flow_initial_l
1418	volume_flow_area = volume_flow_area_l
1419	#endif
1420
1421	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1422
1423	volume_flow_initial_l = 0.0_wp
1424	volume_flow_area_l = 0.0_wp
1425
1426	IF ( nxr == nx ) THEN
1427	DO j = nys, nyn
1428	DO k = nzb+1, nzt
1429	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1430	u(k,j,nx) * dzw(k) &
1431	* MERGE( 1.0_wp, 0.0_wp, &
1432	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1433	)
1434	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1435	* MERGE( 1.0_wp, 0.0_wp, &
1436	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1437	)
1438	ENDDO
1439	ENDDO
1440	ENDIF
1441
1442	IF ( nyn == ny ) THEN
1443	DO i = nxl, nxr
1444	DO k = nzb+1, nzt
1445	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1446	v(k,ny,i) * dzw(k) &
1447	* MERGE( 1.0_wp, 0.0_wp, &
1448	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1449	)
1450	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1451	* MERGE( 1.0_wp, 0.0_wp, &
1452	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1453	)
1454	ENDDO
1455	ENDDO
1456	ENDIF
1457
1458	#if defined( __parallel )
1459	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1460	MPI_SUM, comm2d, ierr )
1461	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1462	comm2d, ierr )
1463
1464	#else
1465	volume_flow_initial = volume_flow_initial_l
1466	volume_flow_area = volume_flow_area_l
1467	#endif
1468
1469	ENDIF
1470
1471	!
1472	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated from u\|v_bulk instead
1473	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1474	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1475	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1476	ENDIF
1477
1478	ENDIF
1479	!
1480	!-- In the following, surface properties can be further initialized with input from static driver
1481	!-- file.
1482	!-- At the moment this affects only default surfaces. For example, roughness length or sensible /
1483	!-- latent heat fluxes can be initialized heterogeneously for default surfaces. Therefore, a generic
1484	!-- routine from netcdf_data_input_mod is called to read a 2D array.
1485	IF ( input_pids_static ) THEN
1486	!
1487	!-- Allocate memory for possible static input
1488	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1489	tmp_2d%var = 0.0_wp
1490	!
1491	!-- Open the static input file
1492	#if defined( __netcdf )
1493	CALL open_read_file( TRIM( input_file_static ) // &
1494	TRIM( coupling_char ), pids_id )
1495
1496	CALL inquire_num_variables( pids_id, num_var_pids )
1497	!
1498	!-- Allocate memory to store variable names and read them
1499	ALLOCATE( vars_pids(1:num_var_pids) )
1500	CALL inquire_variable_names( pids_id, vars_pids )
1501	!
1502	!-- Input roughness length.
1503	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1504	!
1505	!-- Read _FillValue attribute
1506	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'z0' )
1507	!
1508	!-- Read variable
1509	CALL get_variable( pids_id, 'z0', tmp_2d%var, nxl, nxr, nys, nyn )
1510	!
1511	!-- Initialize roughness length. Note, z0 will be only initialized at default-type surfaces.
1512	!-- At natural or urban z0 is implicitly initialized by the respective parameter lists.
1513	!-- Initialize horizontal surface elements.
1514	CALL init_single_surface_properties( surf_def_h(0)%z0, tmp_2d%var, surf_def_h(0)%ns, &
1515	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1516	!
1517	!-- Initialize roughness also at vertical surface elements.
1518	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1519	!-- index arrays with their respective offset values.
1520	DO l = 0, 3
1521	CALL init_single_surface_properties( surf_def_v(l)%z0, tmp_2d%var, surf_def_v(l)%ns, &
1522	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1523	surf_def_v(l)%j+surf_def_v(l)%joff )
1524	ENDDO
1525
1526	ENDIF
1527	!
1528	!-- Input surface sensible heat flux.
1529	IF ( check_existence( vars_pids, 'shf' ) ) THEN
1530	!
1531	!-- Read _FillValue attribute
1532	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'shf' )
1533	!
1534	!-- Read variable
1535	CALL get_variable( pids_id, 'shf', tmp_2d%var, nxl, nxr, nys, nyn )
1536	!
1537	!-- Initialize heat flux. Note, shf will be only initialized at default-type surfaces. At
1538	!-- natural or urban shf is implicitly initialized by the respective parameter lists.
1539	!-- Initialize horizontal surface elements.
1540	CALL init_single_surface_properties( surf_def_h(0)%shf, tmp_2d%var, surf_def_h(0)%ns, &
1541	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1542	!
1543	!-- Initialize heat flux also at vertical surface elements.
1544	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1545	!-- index arrays with their respective offset values.
1546	DO l = 0, 3
1547	CALL init_single_surface_properties( surf_def_v(l)%shf, tmp_2d%var, surf_def_v(l)%ns, &
1548	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1549	surf_def_v(l)%j+surf_def_v(l)%joff )
1550	ENDDO
1551
1552	ENDIF
1553	!
1554	!-- Input surface latent heat flux.
1555	IF ( humidity ) THEN
1556	IF ( check_existence( vars_pids, 'qsws' ) ) THEN
1557	!
1558	!-- Read _FillValue attribute
1559	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'qsws' )
1560	!
1561	!-- Read variable
1562	CALL get_variable( pids_id, 'qsws', tmp_2d%var, nxl, nxr, nys, nyn )
1563	!
1564	!-- Initialize latent heat flux. Note, qsws will be only initialized at default-type surfaces.
1565	!-- At natural or urban qsws is implicitly initialized by the respective parameter lists.
1566	!-- Initialize horizontal surface elements.
1567	CALL init_single_surface_properties( surf_def_h(0)%qsws, tmp_2d%var, surf_def_h(0)%ns,&
1568	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1569	!
1570	!-- Initialize latent heat flux also at vertical surface elements.
1571	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1572	!-- index arrays with their respective offset values.
1573	DO l = 0, 3
1574	CALL init_single_surface_properties( surf_def_v(l)%qsws, tmp_2d%var, &
1575	surf_def_v(l)%ns, tmp_2d%fill, &
1576	surf_def_v(l)%i+surf_def_v(l)%ioff, &
1577	surf_def_v(l)%j+surf_def_v(l)%joff )
1578	ENDDO
1579
1580	ENDIF
1581	ENDIF
1582	!
1583	!-- Input passive scalar flux.
1584	IF ( passive_scalar ) THEN
1585	IF ( check_existence( vars_pids, 'ssws' ) ) THEN
1586	!
1587	!-- Read _FillValue attribute
1588	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'ssws' )
1589	!
1590	!-- Read variable
1591	CALL get_variable( pids_id, 'ssws', tmp_2d%var, nxl, nxr, nys, nyn )
1592	!
1593	!-- Initialize passive scalar flux. Initialize horizontal surface elements.
1594	CALL init_single_surface_properties( surf_def_h(0)%ssws, tmp_2d%var, surf_def_h(0)%ns,&
1595	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1596
1597	DO l = 0, 3
1598	CALL init_single_surface_properties( surf_def_v(l)%ssws, tmp_2d%var, &
1599	surf_def_v(l)%ns, tmp_2d%fill, &
1600	surf_def_v(l)%i+surf_def_v(l)%ioff, &
1601	surf_def_v(l)%j+surf_def_v(l)%joff )
1602	ENDDO
1603
1604	ENDIF
1605	ENDIF
1606	!
1607	!-- Additional variables, can be initialized the
1608	!-- same way.
1609
1610	!
1611	!-- Finally, close the input file and deallocate temporary arrays
1612	DEALLOCATE( vars_pids )
1613
1614	CALL close_input_file( pids_id )
1615	#endif
1616	DEALLOCATE( tmp_2d%var )
1617	ENDIF
1618	!
1619	!-- Finally, if random_heatflux is set, disturb shf at horizontal surfaces. Actually, this should be
1620	!-- done in surface_mod, where all other initializations of surface quantities are done. However,
1621	!-- this would create a ring dependency, hence, it is done here. Maybe delete disturb_heatflux and
1622	!-- tranfer the respective code directly into the 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. random_heatflux ) THEN
1627	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1628	IF ( surf_lsm_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h(0) )
1629	IF ( surf_usm_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_usm_h(0) )
1630	ENDIF
1631	ENDIF
1632
1633	!
1634	!-- Compute total sum of grid points and the mean surface level height for each statistic region.
1635	!-- These are mainly used for horizontal averaging of turbulence statistics.
1636	!-- ngp_2dh: number of grid points of a horizontal cross section through the respective statistic
1637	!-- region
1638	!-- ngp_3d: number of grid points of the respective statistic region
1639	ngp_2dh_outer_l = 0
1640	ngp_2dh_outer = 0
1641	ngp_2dh_s_inner_l = 0
1642	ngp_2dh_s_inner = 0
1643	ngp_2dh_l = 0
1644	ngp_2dh = 0
1645	ngp_3d_inner_l = 0.0_wp
1646	ngp_3d_inner = 0
1647	ngp_3d = 0
1648	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1649
1650	mean_surface_level_height = 0.0_wp
1651	mean_surface_level_height_l = 0.0_wp
1652	!
1653	!-- To do: New concept for these non-topography grid points!
1654	DO sr = 0, statistic_regions
1655	DO i = nxl, nxr
1656	DO j = nys, nyn
1657	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1658	!
1659	!-- All xy-grid points
1660	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1661	!
1662	!-- Determine mean surface-level height. In case of downward-facing walls are present,
1663	!-- more than one surface level exist.
1664	!-- In this case, use the lowest surface-level height.
1665	IF ( surf_def_h(0)%start_index(j,i) <= surf_def_h(0)%end_index(j,i) ) THEN
1666	m = surf_def_h(0)%start_index(j,i)
1667	k = surf_def_h(0)%k(m)
1668	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1669	ENDIF
1670	IF ( surf_lsm_h(0)%start_index(j,i) <= surf_lsm_h(0)%end_index(j,i) ) THEN
1671	m = surf_lsm_h(0)%start_index(j,i)
1672	k = surf_lsm_h(0)%k(m)
1673	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1674	ENDIF
1675	IF ( surf_usm_h(0)%start_index(j,i) <= surf_usm_h(0)%end_index(j,i) ) THEN
1676	m = surf_usm_h(0)%start_index(j,i)
1677	k = surf_usm_h(0)%k(m)
1678	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1679	ENDIF
1680
1681	k_surf = k - 1
1682
1683	DO k = nzb, nzt+1
1684	!
1685	!-- xy-grid points above topography
1686	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1687	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 24 ) )
1688
1689	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1690	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 22 ) )
1691
1692	ENDDO
1693	!
1694	!-- All grid points of the total domain above topography
1695	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1696
1697
1698
1699	ENDIF
1700	ENDDO
1701	ENDDO
1702	ENDDO
1703
1704	sr = statistic_regions + 1
1705	#if defined( __parallel )
1706	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1707	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1708	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1709	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, MPI_INTEGER, MPI_SUM, &
1710	comm2d, ierr )
1711	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1712	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), (nz+2)*sr, MPI_INTEGER, &
1713	MPI_SUM, comm2d, ierr )
1714	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1715	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, MPI_SUM, comm2d, &
1716	ierr )
1717	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1718	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1719	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), mean_surface_level_height(0), sr, MPI_REAL,&
1720	MPI_SUM, comm2d, ierr )
1721	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1722	#else
1723	ngp_2dh = ngp_2dh_l
1724	ngp_2dh_outer = ngp_2dh_outer_l
1725	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1726	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1727	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1728	#endif
1729
1730	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1731	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1732
1733	!
1734	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics, buoyancy, etc. A
1735	!-- zero value will occur for cases where all grid points of the respective subdomain lie below the
1736	!-- surface topography
1737	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1738	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), ngp_3d_inner(:) )
1739	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1740
1741	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, ngp_3d_inner_l, &
1742	ngp_3d_inner_tmp )
1743
1744	!
1745	!-- Initializae 3D offline nesting in COSMO model and read data from
1746	!-- external NetCDF file.
1747	IF ( nesting_offline ) CALL nesting_offl_init
1748	!
1749	!-- Initialize quantities for special advections schemes
1750	CALL init_advec
1751
1752	!
1753	!-- Impose random perturbation on the horizontal velocity field and then
1754	!-- remove the divergences from the velocity field at the initial stage
1755	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1756	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1757	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1758
1759	IF ( debug_output ) THEN
1760	CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1761	ENDIF
1762	!
1763	!-- Needed for both disturb_field and pres
1764	!$ACC DATA &
1765	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1766	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1767	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1768
1769	CALL disturb_field( 'u', tend, u )
1770	CALL disturb_field( 'v', tend, v )
1771
1772	!$ACC DATA &
1773	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1774	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1775	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1776	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1777	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1778	!$ACC COPYIN(wall_flags_total_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1779	!$ACC COPYIN(bc_h(0:1)) &
1780	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1781	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1782	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1783	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1784	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1785	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1786
1787	n_sor = nsor_ini
1788	CALL pres
1789	n_sor = nsor
1790
1791	!$ACC END DATA
1792	!$ACC END DATA
1793
1794	IF ( debug_output ) THEN
1795	CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1796	ENDIF
1797
1798	ENDIF
1799
1800	IF ( .NOT. ocean_mode ) THEN
1801
1802	ALLOCATE( hyp(nzb:nzt+1) )
1803	ALLOCATE( d_exner(nzb:nzt+1) )
1804	ALLOCATE( exner(nzb:nzt+1) )
1805	ALLOCATE( hyrho(nzb:nzt+1) )
1806	!
1807	!-- Check temperature in case of too large domain height
1808	DO k = nzb, nzt+1
1809	IF ( ( pt_surface * exner_function( surface_pressure * 100.0_wp ) - g/c_p * zu(k) ) &
1810	< 0.0_wp ) THEN
1811	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, ') = ', zu(k)
1812	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1813	ENDIF
1814	ENDDO
1815
1816	!
1817	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1818	hyp = barometric_formula( zu, pt_surface * exner_function( surface_pressure * 100.0_wp ),&
1819	surface_pressure * 100.0_wp )
1820	d_exner = exner_function_invers( hyp )
1821	exner = 1.0_wp / exner_function_invers( hyp )
1822	hyrho = ideal_gas_law_rho_pt( hyp, pt_init )
1823	!
1824	!-- Compute reference density
1825	rho_surface = ideal_gas_law_rho( surface_pressure * 100.0_wp, &
1826	pt_surface * exner_function( surface_pressure * 100.0_wp ) )
1827
1828	ENDIF
1829
1830	!
1831	!-- If required, initialize particles
1832	IF ( agents_active ) CALL mas_init
1833	!
1834	!-- Initialization of synthetic turbulence generator
1835	IF ( syn_turb_gen ) CALL stg_init
1836	!
1837	!-- Initializing actions for all other modules
1838	CALL module_interface_init
1839	!
1840	!-- Initialize surface layer (done after LSM as roughness length are required for initialization
1841	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1842	!
1843	!-- Initialize surface data output
1844	IF ( surface_output ) CALL surface_data_output_init
1845	!
1846	!-- Initialize the ws-scheme.
1847	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1848	!
1849	!-- Perform post-initializing checks for all other modules
1850	CALL module_interface_init_checks
1851
1852	!
1853	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1854	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1855	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1856	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1857	CALL ls_forcing_surf( simulated_time )
1858	ENDIF
1859	ENDIF
1860	!
1861	!-- Setting weighting factors for calculation of perturbation pressure and turbulent quantities from
1862	!-- the RK substeps.
1863	IF ( TRIM( timestep_scheme ) == 'runge-kutta-3' ) THEN ! for RK3-method
1864
1865	weight_substep(1) = 1._wp/6._wp
1866	weight_substep(2) = 3._wp/10._wp
1867	weight_substep(3) = 8._wp/15._wp
1868
1869	weight_pres(1) = 1._wp/3._wp
1870	weight_pres(2) = 5._wp/12._wp
1871	weight_pres(3) = 1._wp/4._wp
1872
1873	ELSEIF ( TRIM( timestep_scheme ) == 'runge-kutta-2' ) THEN ! for RK2-method
1874
1875	weight_substep(1) = 1._wp/2._wp
1876	weight_substep(2) = 1._wp/2._wp
1877
1878	weight_pres(1) = 1._wp/2._wp
1879	weight_pres(2) = 1._wp/2._wp
1880
1881	ELSE ! for Euler-method
1882
1883	weight_substep(1) = 1.0_wp
1884	weight_pres(1) = 1.0_wp
1885
1886	ENDIF
1887
1888	!
1889	!-- Initialize Rayleigh damping factors
1890	rdf = 0.0_wp
1891	rdf_sc = 0.0_wp
1892	IF ( rayleigh_damping_factor /= 0.0_wp ) THEN
1893
1894	IF ( .NOT. ocean_mode ) THEN
1895	DO k = nzb+1, nzt
1896	IF ( zu(k) >= rayleigh_damping_height ) THEN
1897	rdf(k) = rayleigh_damping_factor * &
1898	( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
1899	/ ( zu(nzt) - rayleigh_damping_height ) ) &
1900	)**2
1901	ENDIF
1902	ENDDO
1903	ELSE
1904	!
1905	!-- In ocean mode, rayleigh damping is applied in the lower part of the model domain
1906	DO k = nzt, nzb+1, -1
1907	IF ( zu(k) <= rayleigh_damping_height ) THEN
1908	rdf(k) = rayleigh_damping_factor * &
1909	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1910	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1911	)**2
1912	ENDIF
1913	ENDDO
1914	ENDIF
1915
1916	ENDIF
1917	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1918
1919	!
1920	!-- Initialize the starting level and the vertical smoothing factor used for the external pressure
1921	!-- gradient
1922	dp_smooth_factor = 1.0_wp
1923	IF ( dp_external ) THEN
1924	!
1925	!-- Set the starting level dp_level_ind_b only if it has not been set before (e.g. in init_grid).
1926	IF ( dp_level_ind_b == 0 ) THEN
1927	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1928	dp_level_ind_b = ind_array(1) - 1 + nzb
1929	! MINLOC uses lower array bound 1
1930	ENDIF
1931	IF ( dp_smooth ) THEN
1932	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1933	DO k = dp_level_ind_b+1, nzt
1934	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1935	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1936	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1937	ENDDO
1938	ENDIF
1939	ENDIF
1940
1941	!
1942	!-- Initialize damping zone for the potential temperature in case of non-cyclic lateral boundaries.
1943	!-- The damping zone has the maximum value at the inflow boundary and decreases to zero at
1944	!-- pt_damping_width.
1945	ptdf_x = 0.0_wp
1946	ptdf_y = 0.0_wp
1947	IF ( bc_lr_dirrad ) THEN
1948	DO i = nxl, nxr
1949	IF ( ( i * dx ) < pt_damping_width ) THEN
1950	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1951	REAL( pt_damping_width - i * dx, KIND=wp ) / &
1952	REAL( pt_damping_width, KIND=wp ) ) )**2
1953	ENDIF
1954	ENDDO
1955	ELSEIF ( bc_lr_raddir ) THEN
1956	DO i = nxl, nxr
1957	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1958	ptdf_x(i) = pt_damping_factor * SIN( pi * 0.5_wp * &
1959	( ( i - nx ) * dx + pt_damping_width ) / &
1960	REAL( pt_damping_width, KIND=wp ) )**2
1961	ENDIF
1962	ENDDO
1963	ELSEIF ( bc_ns_dirrad ) THEN
1964	DO j = nys, nyn
1965	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1966	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1967	( ( j - ny ) * dy + pt_damping_width ) / &
1968	REAL( pt_damping_width, KIND=wp ) )**2
1969	ENDIF
1970	ENDDO
1971	ELSEIF ( bc_ns_raddir ) THEN
1972	DO j = nys, nyn
1973	IF ( ( j * dy ) < pt_damping_width ) THEN
1974	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1975	( pt_damping_width - j * dy ) / &
1976	REAL( pt_damping_width, KIND=wp ) )**2
1977	ENDIF
1978	ENDDO
1979	ENDIF
1980
1981	!
1982	!-- Input binary data file is not needed anymore. This line must be placed after call of user_init!
1983	CALL close_file( 13 )
1984	!
1985	!-- In case of nesting, put an barrier to assure that all parent and child domains finished
1986	!-- initialization.
1987	#if defined( __parallel )
1988	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
1989	#endif
1990
1991
1992	CALL location_message( 'model initialization', 'finished' )
1993
1994	END SUBROUTINE init_3d_model

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