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Last change on this file since 4660 was 4648, checked in by raasch, 4 years ago

files re-formatted to follow the PALM coding standard

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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
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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 1997-2020 Leibniz Universitaet Hannover
17	!--------------------------------------------------------------------------------------------------!
18	!
19	! Current revisions:
20	! ------------------
21	!
22	!
23	! Former revisions:
24	! -----------------
25	! $Id: init_3d_model.f90 4648 2020-08-25 07:52:08Z pavelkrc $
26	! file re-formatted to follow the PALM coding standard
27	!
28	! 4548 2020-05-28 19:36:45Z suehring
29	! Bugfix, move call for lsf_forcing_surf after lsf_init is called
30	!
31	! 4514 2020-04-30 16:29:59Z suehring
32	! Add possibility to initialize surface sensible and latent heat fluxes via a static driver.
33	!
34	! 4493 2020-04-10 09:49:43Z pavelkrc
35	! Overwrite u_init, v_init, pt_init, q_init and s_init with hom for all cyclic_fill-cases, not only
36	! for turbulent_inflow = .TRUE.
37	!
38	! 4360 2020-01-07 11:25:50Z suehring
39	! Introduction of wall_flags_total_0, which currently sets bits based on static topography
40	! information used in wall_flags_static_0
41	!
42	! 4329 2019-12-10 15:46:36Z motisi
43	! Renamed wall_flags_0 to wall_flags_static_0
44	!
45	! 4286 2019-10-30 16:01:14Z resler
46	! implement new palm_date_time_mod
47	!
48	! 4223 2019-09-10 09:20:47Z gronemeier
49	! Deallocate temporary string array since it may be re-used to read different input data in other
50	! modules
51	!
52	! 4186 2019-08-23 16:06:14Z suehring
53	! Design change, use variables defined in netcdf_data_input_mod to read netcd variables rather than
54	! define local ones.
55	!
56	! 4185 2019-08-23 13:49:38Z oliver.maas
57	! For initializing_actions = ' cyclic_fill':
58	! Overwrite u_init, v_init, pt_init, q_init and s_init with the (temporally) and horizontally
59	! averaged vertical profiles from the end of the prerun, because these profiles shall be used as the
60	! basic state for the rayleigh damping and the pt_damping.
61	!
62	! 4182 2019-08-22 15:20:23Z scharf
63	! Corrected "Former revisions" section
64	!
65	! 4168 2019-08-16 13:50:17Z suehring
66	! Replace function get_topography_top_index by topo_top_ind
67	!
68	! 4151 2019-08-09 08:24:30Z suehring
69	! Add netcdf directive around input calls (fix for last commit)
70	!
71	! 4150 2019-08-08 20:00:47Z suehring
72	! Input of additional surface variables independent on land- or urban-surface model
73	!
74	! 4131 2019-08-02 11:06:18Z monakurppa
75	! Allocate sums and sums_l to allow profile output for salsa variables.
76	!
77	! 4130 2019-08-01 13:04:13Z suehring
78	! Effectively reduce 3D initialization to 1D initial profiles. This is because 3D initialization
79	! produces structures in the w-component that are correlated with the processor grid for some
80	! unknown reason
81	!
82	! 4090 2019-07-11 15:06:47Z Giersch
83	! Unused variables removed
84	!
85	! 4088 2019-07-11 13:57:56Z Giersch
86	! Pressure and density profile calculations revised using basic functions
87	!
88	! 4048 2019-06-21 21:00:21Z knoop
89	! Further modularization of particle code components
90	!
91	! 4017 2019-06-06 12:16:46Z schwenkel
92	! Convert most location messages to debug messages to reduce output in job logfile to a minimum
93	!
94	! unused variable removed
95	!
96	! 3937 2019-04-29 15:09:07Z suehring
97	! Move initialization of synthetic turbulence generator behind initialization of offline nesting.
98	! Remove call for stg_adjust, as this is now already done in stg_init.
99	!
100	! 3900 2019-04-16 15:17:43Z suehring
101	! Fix problem with LOD = 2 initialization
102	!
103	! 3885 2019-04-11 11:29:34Z kanani
104	! Changes related to global restructuring of location messages and introduction of additional debug
105	! messages
106	!
107	! 3849 2019-04-01 16:35:16Z knoop
108	! Move initialization of rmask before initializing user_init_arrays
109	!
110	! 3711 2019-01-31 13:44:26Z knoop
111	! Introduced module_interface_init_checks for post-init checks in modules
112	!
113	! 3700 2019-01-26 17:03:42Z knoop
114	! Some interface calls moved to module_interface + cleanup
115	!
116	! 3648 2019-01-02 16:35:46Z suehring
117	! Rename subroutines for surface-data output
118	!
119	! Revision 1.1 1998/03/09 16:22:22 raasch
120	! Initial revision
121	!
122	!
123	! Description:
124	! ------------
125	!> Allocation of arrays and initialization of the 3D model via
126	!> a) pre-run the 1D model
127	!> or
128	!> b) pre-set constant linear profiles
129	!> or
130	!> c) read values of a previous run
131	!--------------------------------------------------------------------------------------------------!
132	SUBROUTINE init_3d_model
133
134
135	USE advec_ws
136
137	USE arrays_3d
138
139	USE basic_constants_and_equations_mod, &
140	ONLY: barometric_formula, c_p, exner_function, exner_function_invers, g, &
141	ideal_gas_law_rho, ideal_gas_law_rho_pt, l_v, pi
142
143	USE bulk_cloud_model_mod, &
144	ONLY: bulk_cloud_model
145
146	USE chem_modules, &
147	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
148
149	USE control_parameters
150
151	USE grid_variables, &
152	ONLY: dx, dy, ddx2_mg, ddy2_mg
153
154	USE indices
155
156	USE kinds
157
158	USE lsf_nudging_mod, &
159	ONLY: ls_forcing_surf
160
161	USE model_1d_mod, &
162	ONLY: init_1d_model, l1d, u1d, v1d
163
164	USE module_interface, &
165	ONLY: module_interface_init_arrays, &
166	module_interface_init, &
167	module_interface_init_checks
168
169	USE multi_agent_system_mod, &
170	ONLY: agents_active, mas_init
171
172	USE netcdf_interface, &
173	ONLY: dots_max
174
175	USE netcdf_data_input_mod, &
176	ONLY: char_fill, &
177	check_existence, &
178	close_input_file, &
179	get_attribute, &
180	get_variable, &
181	init_3d, &
182	input_pids_static, &
183	inquire_num_variables, &
184	inquire_variable_names, &
185	input_file_static, &
186	netcdf_data_input_init_3d, &
187	num_var_pids, &
188	open_read_file, &
189	pids_id, &
190	real_2d, &
191	vars_pids
192
193	USE nesting_offl_mod, &
194	ONLY: nesting_offl_init
195
196	USE palm_date_time_mod, &
197	ONLY: set_reference_date_time
198
199	USE pegrid
200
201	#if defined( __parallel )
202	USE pmc_interface, &
203	ONLY: nested_run
204	#endif
205
206	USE random_function_mod
207
208	USE random_generator_parallel, &
209	ONLY: init_parallel_random_generator
210
211	USE read_restart_data_mod, &
212	ONLY: rrd_local, rrd_read_parts_of_global
213
214	USE statistics, &
215	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, statistic_regions, sums, &
216	sums_divnew_l, sums_divold_l, sums_l, sums_l_l, sums_wsts_bc_l, ts_value, &
217	weight_pres, weight_substep
218
219	USE synthetic_turbulence_generator_mod, &
220	ONLY: stg_init, use_syn_turb_gen
221
222	USE surface_layer_fluxes_mod, &
223	ONLY: init_surface_layer_fluxes
224
225	USE surface_mod, &
226	ONLY : init_single_surface_properties, &
227	init_surface_arrays, &
228	init_surfaces, &
229	surf_def_h, &
230	surf_def_v, &
231	surf_lsm_h, &
232	surf_usm_h
233
234	#if defined( _OPENACC )
235	USE surface_mod, &
236	ONLY : bc_h
237	#endif
238
239	USE surface_data_output_mod, &
240	ONLY: surface_data_output_init
241
242	USE transpose_indices
243
244
245	IMPLICIT NONE
246
247	INTEGER(iwp) :: i !< grid index in x direction
248	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
249	INTEGER(iwp) :: j !< grid index in y direction
250	INTEGER(iwp) :: k !< grid index in z direction
251	INTEGER(iwp) :: k_surf !< surface level index
252	INTEGER(iwp) :: l !< running index over surface orientation
253	INTEGER(iwp) :: m !< index of surface element in surface data type
254	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
255	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
256	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
257	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
258	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
259	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
260	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
261	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
262	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
263	INTEGER(iwp) :: sr !< index of statistic region
264
265	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on
266	!< subdomain
267
268	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on
269	!< subdomain
270	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on
271	!< subdomain
272
273	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
274	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
275
276	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain
277	!< inital profiles
278	REAL(wp), DIMENSION(:), ALLOCATABLE :: mean_surface_level_height_l !< mean surface level height on subdomain
279	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_l !< total number of non-topography grid points on subdomain
280	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_tmp !< total number of non-topography grid points
281	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
282
283	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
284	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
285
286	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
287
288	CALL location_message( 'model initialization', 'start' )
289	!
290	!-- Set reference date-time
291	CALL set_reference_date_time( date_time_str=origin_date_time )
292
293	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
294	!
295	!-- Allocate arrays
296	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
297	mean_surface_level_height_l(0:statistic_regions), &
298	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
299	ngp_3d(0:statistic_regions), &
300	ngp_3d_inner(0:statistic_regions), &
301	ngp_3d_inner_l(0:statistic_regions), &
302	ngp_3d_inner_tmp(0:statistic_regions), &
303	sums_divnew_l(0:statistic_regions), &
304	sums_divold_l(0:statistic_regions) )
305	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
306	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
307	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
308	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
309	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
310	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
311	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
312	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
313	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
314	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
315	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
316	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
317
318	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
319	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
320	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
321
322	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
323	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
324	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
325	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
326	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
327	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
328	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
329	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
330	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
331	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
332	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
333	IF ( .NOT. neutral ) THEN
334	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
335	ENDIF
336	!
337	!-- Pre-set masks for regional statistics. Default is the total model domain.
338	!-- Ghost points are excluded because counting values at the ghost boundaries would bias the
339	!-- statistics.
340	rmask = 1.0_wp
341	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
342	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
343	!
344	!-- Following array is required for perturbation pressure within the iterative pressure solvers. For
345	!-- the multistep schemes (Runge-Kutta), array p holds the weighted average of the substeps and
346	!-- cannot be used in the Poisson solver.
347	IF ( psolver == 'sor' ) THEN
348	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
349	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
350	!
351	!-- For performance reasons, multigrid is using one ghost layer only
352	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
353	ENDIF
354
355	!
356	!-- Array for storing constant coeffficients of the tridiagonal solver
357	IF ( psolver == 'poisfft' ) THEN
358	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
359	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
360	ENDIF
361
362	IF ( humidity ) THEN
363	!
364	!-- 3D-humidity
365	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
366	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
367	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
368	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
369	ENDIF
370
371	IF ( passive_scalar ) THEN
372
373	!
374	!-- 3D scalar arrays
375	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
376	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
377	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
378
379	ENDIF
380
381	!
382	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to non-zero values later
383	!-- in ocean_init.
384	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
385	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
386	u_stokes_zu(:) = 0.0_wp
387	u_stokes_zw(:) = 0.0_wp
388	v_stokes_zu(:) = 0.0_wp
389	v_stokes_zw(:) = 0.0_wp
390
391	!
392	!-- Allocation of anelastic and Boussinesq approximation specific arrays
393	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
394	ALLOCATE( rho_air(nzb:nzt+1) )
395	ALLOCATE( rho_air_zw(nzb:nzt+1) )
396	ALLOCATE( drho_air(nzb:nzt+1) )
397	ALLOCATE( drho_air_zw(nzb:nzt+1) )
398	!
399	!-- Density profile calculation for anelastic and Boussinesq approximation.
400	!-- In case of a Boussinesq approximation, a constant density is calculated mainly for output
401	!-- purposes. This density does not need to be considered in the model's system of equations.
402	IF ( TRIM( approximation ) == 'anelastic' ) THEN
403	DO k = nzb, nzt+1
404	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
405	exner_function(surface_pressure * 100.0_wp), &
406	surface_pressure * 100.0_wp)
407
408	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
409	ENDDO
410
411	DO k = nzb, nzt
412	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
413	ENDDO
414
415	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
416
417	ELSE
418	DO k = nzb, nzt+1
419	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
420	exner_function(surface_pressure * 100.0_wp), &
421	surface_pressure * 100.0_wp)
422
423	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
424	ENDDO
425
426	DO k = nzb, nzt
427	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
428	ENDDO
429
430	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
431
432	ENDIF
433	!
434	!-- Compute the inverse density array in order to avoid expencive divisions
435	drho_air = 1.0_wp / rho_air
436	drho_air_zw = 1.0_wp / rho_air_zw
437
438	!
439	!-- Allocation of flux conversion arrays
440	ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
441	ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
442	ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
443	ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
444	ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
445	ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )
446
447	!
448	!-- Calculate flux conversion factors according to approximation and in-/output mode
449	DO k = nzb, nzt+1
450
451	IF ( TRIM( flux_input_mode ) == 'kinematic' ) THEN
452	heatflux_input_conversion(k) = rho_air_zw(k)
453	waterflux_input_conversion(k) = rho_air_zw(k)
454	momentumflux_input_conversion(k) = rho_air_zw(k)
455	ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
456	heatflux_input_conversion(k) = 1.0_wp / c_p
457	waterflux_input_conversion(k) = 1.0_wp / l_v
458	momentumflux_input_conversion(k) = 1.0_wp
459	ENDIF
460
461	IF ( TRIM( flux_output_mode ) == 'kinematic' ) THEN
462	heatflux_output_conversion(k) = drho_air_zw(k)
463	waterflux_output_conversion(k) = drho_air_zw(k)
464	momentumflux_output_conversion(k) = drho_air_zw(k)
465	ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
466	heatflux_output_conversion(k) = c_p
467	waterflux_output_conversion(k) = l_v
468	momentumflux_output_conversion(k) = 1.0_wp
469	ENDIF
470
471	IF ( .NOT. humidity ) THEN
472	waterflux_input_conversion(k) = 1.0_wp
473	waterflux_output_conversion(k) = 1.0_wp
474	ENDIF
475
476	ENDDO
477
478	!
479	!-- In case of multigrid method, compute grid lengths and grid factors for the grid levels with
480	!-- respective density on each grid.
481	IF ( psolver(1:9) == 'multigrid' ) THEN
482
483	ALLOCATE( ddx2_mg(maximum_grid_level) )
484	ALLOCATE( ddy2_mg(maximum_grid_level) )
485	ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
486	ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
487	ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
488	ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
489	ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
490	ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
491	ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )
492
493	dzu_mg(:,maximum_grid_level) = dzu
494	rho_air_mg(:,maximum_grid_level) = rho_air
495	!
496	!-- Next line to ensure an equally spaced grid.
497	dzu_mg(1,maximum_grid_level) = dzu(2)
498	rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) + (rho_air(nzb) - rho_air(nzb+1))
499
500	dzw_mg(:,maximum_grid_level) = dzw
501	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
502	nzt_l = nzt
503	DO l = maximum_grid_level-1, 1, -1
504	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
505	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
506	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + ( rho_air_mg(nzb,l+1) - &
507	rho_air_mg(nzb+1,l+1) )
508	rho_air_zw_mg(nzb,l) = rho_air_zw_mg(nzb,l+1) + ( rho_air_zw_mg(nzb,l+1) - &
509	rho_air_zw_mg(nzb+1,l+1) )
510	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
511	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
512	nzt_l = nzt_l / 2
513	DO k = 2, nzt_l+1
514	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
515	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
516	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
517	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
518	ENDDO
519	ENDDO
520
521	nzt_l = nzt
522	dx_l = dx
523	dy_l = dy
524	DO l = maximum_grid_level, 1, -1
525	ddx2_mg(l) = 1.0_wp / dx_l**2
526	ddy2_mg(l) = 1.0_wp / dy_l**2
527	DO k = nzb+1, nzt_l
528	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
529	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
530	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
531	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
532	ENDDO
533	nzt_l = nzt_l / 2
534	dx_l = dx_l * 2.0_wp
535	dy_l = dy_l * 2.0_wp
536	ENDDO
537
538	ENDIF
539
540	!
541	!-- 1D-array for large scale subsidence velocity
542	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
543	ALLOCATE ( w_subs(nzb:nzt+1) )
544	w_subs = 0.0_wp
545	ENDIF
546
547	!
548	!-- Arrays to store velocity data from t-dt and the phase speeds which are needed for radiation
549	!-- boundary conditions.
550	IF ( bc_radiation_l ) THEN
551	ALLOCATE( u_m_l(nzb:nzt+1,nysg:nyng,1:2), &
552	v_m_l(nzb:nzt+1,nysg:nyng,0:1), &
553	w_m_l(nzb:nzt+1,nysg:nyng,0:1) )
554	ENDIF
555	IF ( bc_radiation_r ) THEN
556	ALLOCATE( u_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
557	v_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
558	w_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx) )
559	ENDIF
560	IF ( bc_radiation_l .OR. bc_radiation_r ) THEN
561	ALLOCATE( c_u(nzb:nzt+1,nysg:nyng), c_v(nzb:nzt+1,nysg:nyng), c_w(nzb:nzt+1,nysg:nyng) )
562	ENDIF
563	IF ( bc_radiation_s ) THEN
564	ALLOCATE( u_m_s(nzb:nzt+1,0:1,nxlg:nxrg), &
565	v_m_s(nzb:nzt+1,1:2,nxlg:nxrg), &
566	w_m_s(nzb:nzt+1,0:1,nxlg:nxrg) )
567	ENDIF
568	IF ( bc_radiation_n ) THEN
569	ALLOCATE( u_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
570	v_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg), &
571	w_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg) )
572	ENDIF
573	IF ( bc_radiation_s .OR. bc_radiation_n ) THEN
574	ALLOCATE( c_u(nzb:nzt+1,nxlg:nxrg), c_v(nzb:nzt+1,nxlg:nxrg), c_w(nzb:nzt+1,nxlg:nxrg) )
575	ENDIF
576	IF ( bc_radiation_l .OR. bc_radiation_r .OR. bc_radiation_s .OR. bc_radiation_n ) THEN
577	ALLOCATE( c_u_m_l(nzb:nzt+1), c_v_m_l(nzb:nzt+1), c_w_m_l(nzb:nzt+1) )
578	ALLOCATE( c_u_m(nzb:nzt+1), c_v_m(nzb:nzt+1), c_w_m(nzb:nzt+1) )
579	ENDIF
580
581	!
582	!-- Initial assignment of the pointers
583	IF ( .NOT. neutral ) THEN
584	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
585	ELSE
586	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
587	ENDIF
588	u => u_1; u_p => u_2; tu_m => u_3
589	v => v_1; v_p => v_2; tv_m => v_3
590	w => w_1; w_p => w_2; tw_m => w_3
591
592	IF ( humidity ) THEN
593	q => q_1; q_p => q_2; tq_m => q_3
594	vpt => vpt_1
595	ENDIF
596
597	IF ( passive_scalar ) THEN
598	s => s_1; s_p => s_2; ts_m => s_3
599	ENDIF
600
601	!
602	!-- Initialize surface arrays
603	CALL init_surface_arrays
604	!
605	!-- Allocate arrays for other modules
606	CALL module_interface_init_arrays
607
608
609	!
610	!-- Allocate arrays containing the RK coefficient for calculation of perturbation pressure and
611	!-- turbulent fluxes. At this point values are set for pressure calculation during initialization
612	!-- (where no timestep is done). Further below the values needed within the timestep scheme will be
613	!-- set.
614	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
615	weight_pres(1:intermediate_timestep_count_max) )
616	weight_substep = 1.0_wp
617	weight_pres = 1.0_wp
618	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
619
620	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
621
622	!
623	!-- Initialize time series
624	ts_value = 0.0_wp
625
626	!
627	!-- Initialize local summation arrays for routine flow_statistics.
628	!-- This is necessary because they may not yet have been initialized when they are called from
629	!-- flow_statistics (or - depending on the chosen model run - are never initialized)
630	sums_divnew_l = 0.0_wp
631	sums_divold_l = 0.0_wp
632	sums_l_l = 0.0_wp
633	sums_wsts_bc_l = 0.0_wp
634
635	!
636	!-- Initialize model variables
637	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
638	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
639	!
640	!-- Initialization with provided input data derived from larger-scale model
641	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
642	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
643	!
644	!-- Read initial 1D profiles or 3D data from NetCDF file, depending on the provided
645	!-- level-of-detail.
646	!-- At the moment, only u, v, w, pt and q are provided.
647	CALL netcdf_data_input_init_3d
648	!
649	!-- Please note, Inifor provides data from nzb+1 to nzt.
650	!-- Bottom and top boundary conditions for Inifor profiles are already set (just after
651	!-- reading), so that this is not necessary here.
652	!-- Depending on the provided level-of-detail, initial Inifor data is either stored on data
653	!-- type (lod=1), or directly on 3D arrays (lod=2).
654	!-- In order to obtain also initial profiles in case of lod=2 (which is required for e.g.
655	!-- damping), average over 3D data.
656	IF( init_3d%lod_u == 1 ) THEN
657	u_init = init_3d%u_init
658	ELSEIF( init_3d%lod_u == 2 ) THEN
659	ALLOCATE( init_l(nzb:nzt+1) )
660	DO k = nzb, nzt+1
661	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
662	ENDDO
663	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
664
665	#if defined( __parallel )
666	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
667	#else
668	u_init = init_l
669	#endif
670	DEALLOCATE( init_l )
671
672	ENDIF
673
674	IF( init_3d%lod_v == 1 ) THEN
675	v_init = init_3d%v_init
676	ELSEIF( init_3d%lod_v == 2 ) THEN
677	ALLOCATE( init_l(nzb:nzt+1) )
678	DO k = nzb, nzt+1
679	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
680	ENDDO
681	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
682
683	#if defined( __parallel )
684	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
685	#else
686	v_init = init_l
687	#endif
688	DEALLOCATE( init_l )
689	ENDIF
690	IF( .NOT. neutral ) THEN
691	IF( init_3d%lod_pt == 1 ) THEN
692	pt_init = init_3d%pt_init
693	ELSEIF( init_3d%lod_pt == 2 ) THEN
694	ALLOCATE( init_l(nzb:nzt+1) )
695	DO k = nzb, nzt+1
696	init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
697	ENDDO
698	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
699
700	#if defined( __parallel )
701	CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
702	#else
703	pt_init = init_l
704	#endif
705	DEALLOCATE( init_l )
706	ENDIF
707	ENDIF
708
709
710	IF( humidity ) THEN
711	IF( init_3d%lod_q == 1 ) THEN
712	q_init = init_3d%q_init
713	ELSEIF( init_3d%lod_q == 2 ) THEN
714	ALLOCATE( init_l(nzb:nzt+1) )
715	DO k = nzb, nzt+1
716	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
717	ENDDO
718	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
719
720	#if defined( __parallel )
721	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
722	#else
723	q_init = init_l
724	#endif
725	DEALLOCATE( init_l )
726	ENDIF
727	ENDIF
728
729	!
730	!-- Write initial profiles onto 3D arrays.
731	!-- Work-around, 3D initialization of u,v,w creates artificial structures which correlate with
732	!-- the processor grid. The reason for this is still unknown. To work-around this, 3D
733	!-- initialization will be effectively reduce to a 1D initialization where no such artificial
734	!-- structures appear.
735	DO i = nxlg, nxrg
736	DO j = nysg, nyng
737	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) u(:,j,i) = u_init(:)
738	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) v(:,j,i) = v_init(:)
739	IF( .NOT. neutral .AND. ( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
740	pt(:,j,i) = pt_init(:)
741	IF( humidity .AND. ( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
742	q(:,j,i) = q_init(:)
743	ENDDO
744	ENDDO
745	!
746	!-- Set geostrophic wind components.
747	IF ( init_3d%from_file_ug ) THEN
748	ug(:) = init_3d%ug_init(:)
749	ENDIF
750	IF ( init_3d%from_file_vg ) THEN
751	vg(:) = init_3d%vg_init(:)
752	ENDIF
753	!
754	!-- Set bottom and top boundary condition for geostrophic wind
755	ug(nzt+1) = ug(nzt)
756	vg(nzt+1) = vg(nzt)
757	ug(nzb) = ug(nzb+1)
758	vg(nzb) = vg(nzb+1)
759	!
760	!-- Set inital w to 0
761	w = 0.0_wp
762
763	IF ( passive_scalar ) THEN
764	DO i = nxlg, nxrg
765	DO j = nysg, nyng
766	s(:,j,i) = s_init
767	ENDDO
768	ENDDO
769	ENDIF
770
771	!
772	!-- Set velocity components at non-atmospheric / oceanic grid points to zero.
773	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
774	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
775	w = MERGE( w, 0.0_wp, BTEST( wall_flags_total_0, 3 ) )
776	!
777	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
778	CALL init_surfaces
779
780	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
781	!
782	!-- Initialization via computed 1D-model profiles
783	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
784
785	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
786	!
787	!-- Use solutions of the 1D model as initial profiles,
788	!-- start 1D model
789	CALL init_1d_model
790	!
791	!-- Transfer initial profiles to the arrays of the 3D model
792	DO i = nxlg, nxrg
793	DO j = nysg, nyng
794	pt(:,j,i) = pt_init
795	u(:,j,i) = u1d
796	v(:,j,i) = v1d
797	ENDDO
798	ENDDO
799
800	IF ( humidity ) THEN
801	DO i = nxlg, nxrg
802	DO j = nysg, nyng
803	q(:,j,i) = q_init
804	ENDDO
805	ENDDO
806	ENDIF
807
808	IF ( passive_scalar ) THEN
809	DO i = nxlg, nxrg
810	DO j = nysg, nyng
811	s(:,j,i) = s_init
812	ENDDO
813	ENDDO
814	ENDIF
815	!
816	!-- Store initial profiles for output purposes etc.
817	IF ( .NOT. constant_diffusion ) THEN
818	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
819	ENDIF
820	!
821	!-- Set velocities back to zero
822	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
823	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
824	!
825	!-- WARNING: The extra boundary conditions set after running the 1D model impose an error on
826	!-- -------- the divergence one layer below the topography; need to correct later
827	!-- ATTENTION: Provisional correction for Piacsek & Williams advection scheme: keep u and v
828	!-- ---------- zero one layer below the topography.
829	IF ( ibc_uv_b == 1 ) THEN
830	!
831	!-- Neumann condition
832	DO i = nxl-1, nxr+1
833	DO j = nys-1, nyn+1
834	u(nzb,j,i) = u(nzb+1,j,i)
835	v(nzb,j,i) = v(nzb+1,j,i)
836	ENDDO
837	ENDDO
838
839	ENDIF
840	!
841	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
842	CALL init_surfaces
843
844	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
845
846	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) THEN
847
848	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
849
850	!
851	!-- Use constructed initial profiles (velocity constant with height, temperature profile with
852	!-- constant gradient)
853	DO i = nxlg, nxrg
854	DO j = nysg, nyng
855	pt(:,j,i) = pt_init
856	u(:,j,i) = u_init
857	v(:,j,i) = v_init
858	ENDDO
859	ENDDO
860	!
861	!-- Mask topography
862	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
863	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
864	!
865	!-- Set initial horizontal velocities at the lowest computational grid levels to zero in order
866	!-- to avoid too small time steps caused by the diffusion limit in the initial phase of a run
867	!-- (at k=1, dz/2 occurs in the limiting formula!).
868	!-- Please note, in case land- or urban-surface model is used and a spinup is applied, masking
869	!-- the lowest computational level is not possible as MOST as well as energy-balance
870	!-- parametrizations will not work with zero wind velocity.
871	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
872	DO i = nxlg, nxrg
873	DO j = nysg, nyng
874	DO k = nzb, nzt
875	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 20 ) )
876	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 21 ) )
877	ENDDO
878	ENDDO
879	ENDDO
880	ENDIF
881
882	IF ( humidity ) THEN
883	DO i = nxlg, nxrg
884	DO j = nysg, nyng
885	q(:,j,i) = q_init
886	ENDDO
887	ENDDO
888	ENDIF
889
890	IF ( passive_scalar ) THEN
891	DO i = nxlg, nxrg
892	DO j = nysg, nyng
893	s(:,j,i) = s_init
894	ENDDO
895	ENDDO
896	ENDIF
897
898	!
899	!-- Compute initial temperature field and other constants used in case of a sloping surface.
900	IF ( sloping_surface ) CALL init_slope
901	!
902	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
903	CALL init_surfaces
904
905	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
906
907	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) THEN
908
909	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
910	!
911	!-- Pre-initialize surface variables, i.e. setting start- and end-indices at each
912	!-- (j,i)-location. Please note, this does not supersede user-defined initialization of
913	!-- surface quantities.
914	CALL init_surfaces
915	!
916	!-- Initialization will completely be done by the user
917	CALL user_init_3d_model
918
919	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
920
921	ENDIF
922
923	IF ( debug_output ) THEN
924	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
925	ENDIF
926
927	!
928	!-- Bottom boundary
929	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
930	u(nzb,:,:) = 0.0_wp
931	v(nzb,:,:) = 0.0_wp
932	ENDIF
933
934	!
935	!-- Apply channel flow boundary condition
936	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
937	u(nzt+1,:,:) = 0.0_wp
938	v(nzt+1,:,:) = 0.0_wp
939	ENDIF
940
941	!
942	!-- Calculate virtual potential temperature
943	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
944
945	!
946	!-- Store initial profiles for output purposes etc.. Please note, in case of initialization of u,
947	!-- v, w, pt, and q via output data derived from larger scale models, data will not be
948	!-- horizontally homogeneous. Actually, a mean profile should be calculated before.
949	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
950	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
951	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
952	hom(nzb,1,5,:) = 0.0_wp
953	hom(nzb,1,6,:) = 0.0_wp
954	ENDIF
955	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
956
957	IF ( humidity ) THEN
958	!
959	!-- Store initial profile of total water content, virtual potential temperature
960	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
961	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
962	!
963	!-- Store initial profile of mixing ratio and potential temperature
964	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
965	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
966	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
967	ENDIF
968	ENDIF
969
970	!
971	!-- Store initial scalar profile
972	IF ( passive_scalar ) THEN
973	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
974	ENDIF
975
976	!
977	!-- Initialize the random number generators (from numerical recipes)
978	CALL random_function_ini
979
980	IF ( random_generator == 'random-parallel' ) THEN
981	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
982	ENDIF
983	!
984	!-- Set the reference state to be used in the buoyancy terms (for ocean runs the reference state
985	!-- will be set (overwritten) in init_ocean).
986	IF ( use_single_reference_value ) THEN
987	IF ( .NOT. humidity ) THEN
988	ref_state(:) = pt_reference
989	ELSE
990	ref_state(:) = vpt_reference
991	ENDIF
992	ELSE
993	IF ( .NOT. humidity ) THEN
994	ref_state(:) = pt_init(:)
995	ELSE
996	ref_state(:) = vpt(:,nys,nxl)
997	ENDIF
998	ENDIF
999
1000	!
1001	!-- For the moment, vertical velocity is zero
1002	w = 0.0_wp
1003
1004	!
1005	!-- Initialize array sums (must be defined in first call of pres)
1006	sums = 0.0_wp
1007
1008	!
1009	!-- In case of iterative solvers, p must get an initial value
1010	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
1011	!
1012	!-- Impose vortex with vertical axis on the initial velocity profile
1013	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
1014	CALL init_rankine
1015	ENDIF
1016
1017	!
1018	!-- Impose temperature anomaly (advection test only) or warm air bubble close to surface.
1019	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1020	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1021	CALL init_pt_anomaly
1022	ENDIF
1023
1024	!
1025	!-- If required, change the surface temperature at the start of the 3D run
1026	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1027	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1028	ENDIF
1029
1030	!
1031	!-- If required, change the surface humidity/scalar at the start of the 3D
1032	!-- run
1033	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1034	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1035
1036	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1037	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1038
1039
1040	!
1041	!-- Initialize old and new time levels.
1042	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1043	pt_p = pt; u_p = u; v_p = v; w_p = w
1044
1045	IF ( humidity ) THEN
1046	tq_m = 0.0_wp
1047	q_p = q
1048	ENDIF
1049
1050	IF ( passive_scalar ) THEN
1051	ts_m = 0.0_wp
1052	s_p = s
1053	ENDIF
1054
1055	IF ( debug_output ) THEN
1056	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1057	ENDIF
1058
1059	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1060	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1061	THEN
1062
1063	IF ( debug_output ) THEN
1064	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1065	ENDIF
1066	!
1067	!-- Initialize surface elements and its attributes, e.g. heat- and momentumfluxes, roughness,
1068	!-- scaling parameters. As number of surface elements might be different between runs, e.g. in
1069	!-- case of cyclic fill, and not all surface elements are read, surface elements need to be
1070	!-- initialized before.
1071	!-- Please note, in case of cyclic fill, surfaces should be initialized after restart data is
1072	!-- read, else, individual settings of surface parameters will be overwritten from data of
1073	!-- precursor run, hence, init_surfaces is called a second time after reading the restart data.
1074	CALL init_surfaces
1075	!
1076	!-- When reading data for cyclic fill of 3D prerun data files, read some of the global variables
1077	!-- from the restart file which are required for initializing the inflow
1078	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1079
1080	DO i = 0, io_blocks-1
1081	IF ( i == io_group ) THEN
1082	CALL rrd_read_parts_of_global
1083	ENDIF
1084	#if defined( __parallel )
1085	CALL MPI_BARRIER( comm2d, ierr )
1086	#endif
1087	ENDDO
1088
1089	ENDIF
1090
1091	!
1092	!-- Read processor specific binary data from restart file
1093	DO i = 0, io_blocks-1
1094	IF ( i == io_group ) THEN
1095	CALL rrd_local
1096	ENDIF
1097	#if defined( __parallel )
1098	CALL MPI_BARRIER( comm2d, ierr )
1099	#endif
1100	ENDDO
1101
1102
1103	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1104
1105	!
1106	!-- In case of cyclic fill, call init_surfaces a second time, so that surface properties such
1107	!-- as heat fluxes are initialized as prescribed.
1108	CALL init_surfaces
1109
1110	!
1111	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the horizontally mean (hom)
1112	!-- vertical profiles from the end of the prerun, because these profiles shall be used as the
1113	!-- reference state for the rayleigh damping and the pt_damping. This is especially important
1114	!-- for the use of large_scale_subsidence, because the reference temperature in the free
1115	!-- atmosphere changes in time.
1116	u_init(:) = hom_sum(:,1,0)
1117	v_init(:) = hom_sum(:,2,0)
1118	pt_init(:) = hom_sum(:,4,0)
1119	IF ( humidity ) q_init(:) = hom_sum(:,41,0)
1120	IF ( passive_scalar ) s_init(:) = hom_sum(:,115,0)
1121	ENDIF
1122	!
1123	!-- In case of complex terrain and cyclic fill method as initialization, shift initial data in
1124	!-- the vertical direction for each point in the x-y-plane depending on local surface height.
1125	IF ( complex_terrain .AND. TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1126	DO i = nxlg, nxrg
1127	DO j = nysg, nyng
1128	nz_u_shift = topo_top_ind(j,i,1)
1129	nz_v_shift = topo_top_ind(j,i,2)
1130	nz_w_shift = topo_top_ind(j,i,3)
1131	nz_s_shift = topo_top_ind(j,i,0)
1132
1133	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1134
1135	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1136
1137	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1138
1139	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1140	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1141	ENDDO
1142	ENDDO
1143	ENDIF
1144	!
1145	!-- Initialization of the turbulence recycling method
1146	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. turbulent_inflow ) THEN
1147	!
1148	!-- First store the profiles to be used at the inflow.
1149	!-- These profiles are the (temporally) and horizontally averaged vertical profiles from the
1150	!-- prerun. Alternatively, prescribed profiles for u,v-components can be used.
1151	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1152
1153	IF ( use_prescribed_profile_data ) THEN
1154	mean_inflow_profiles(:,1) = u_init ! u
1155	mean_inflow_profiles(:,2) = v_init ! v
1156	ELSE
1157	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1158	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1159	ENDIF
1160	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1161	IF ( humidity ) mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1162	IF ( passive_scalar ) mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1163
1164	!
1165	!-- In case of complex terrain, determine vertical displacement at inflow boundary and adjust
1166	!-- mean inflow profiles
1167	IF ( complex_terrain ) THEN
1168	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1169	nz_u_shift_l = topo_top_ind(j,i,1)
1170	nz_v_shift_l = topo_top_ind(j,i,2)
1171	nz_w_shift_l = topo_top_ind(j,i,3)
1172	nz_s_shift_l = topo_top_ind(j,i,0)
1173	ELSE
1174	nz_u_shift_l = 0
1175	nz_v_shift_l = 0
1176	nz_w_shift_l = 0
1177	nz_s_shift_l = 0
1178	ENDIF
1179
1180	#if defined( __parallel )
1181	CALL MPI_ALLREDUCE( nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1182	CALL MPI_ALLREDUCE( nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1183	CALL MPI_ALLREDUCE( nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1184	CALL MPI_ALLREDUCE( nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1185	#else
1186	nz_u_shift = nz_u_shift_l
1187	nz_v_shift = nz_v_shift_l
1188	nz_w_shift = nz_w_shift_l
1189	nz_s_shift = nz_s_shift_l
1190	#endif
1191
1192	mean_inflow_profiles(:,1) = 0.0_wp
1193	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1194
1195	mean_inflow_profiles(:,2) = 0.0_wp
1196	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1197
1198	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1199
1200	ENDIF
1201
1202	!
1203	!-- If necessary, adjust the horizontal flow field to the prescribed profiles
1204	IF ( use_prescribed_profile_data ) THEN
1205	DO i = nxlg, nxrg
1206	DO j = nysg, nyng
1207	DO k = nzb, nzt+1
1208	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1209	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1210	ENDDO
1211	ENDDO
1212	ENDDO
1213	ENDIF
1214
1215	!
1216	!-- Use these mean profiles at the inflow (provided that Dirichlet conditions are used)
1217	IF ( bc_dirichlet_l ) THEN
1218	DO j = nysg, nyng
1219	DO k = nzb, nzt+1
1220	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1221	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1222	w(k,j,nxlg:-1) = 0.0_wp
1223	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1224	IF ( humidity ) q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1225	IF ( passive_scalar ) s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1226	ENDDO
1227	ENDDO
1228	ENDIF
1229
1230	!
1231	!-- Calculate the damping factors to be used at the inflow. For a turbulent inflow the
1232	!-- turbulent fluctuations have to be limited vertically because otherwise the turbulent
1233	!-- inflow layer will grow in time.
1234	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1235	!
1236	!-- Default: use the inversion height calculated by the prerun; if this is zero,
1237	!-- inflow_damping_height must be explicitly specified.
1238	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1239	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1240	ELSE
1241	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1242	'explicitly specified because&the inversion height ', &
1243	'calculated by the prerun is zero.'
1244	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1245	ENDIF
1246
1247	ENDIF
1248
1249	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1250	!
1251	!-- Default for the transition range: one tenth of the undamped layer
1252	inflow_damping_width = 0.1_wp * inflow_damping_height
1253
1254	ENDIF
1255
1256	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1257
1258	DO k = nzb, nzt+1
1259
1260	IF ( zu(k) <= inflow_damping_height ) THEN
1261	inflow_damping_factor(k) = 1.0_wp
1262	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1263	inflow_damping_factor(k) = 1.0_wp - &
1264	( zu(k) - inflow_damping_height ) / inflow_damping_width
1265	ELSE
1266	inflow_damping_factor(k) = 0.0_wp
1267	ENDIF
1268
1269	ENDDO
1270
1271	ENDIF
1272
1273	!
1274	!-- Inside buildings set velocities back to zero
1275	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. topography /= 'flat' ) THEN
1276	!
1277	!-- Inside buildings set velocities back to zero.
1278	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1279	!-- maybe revise later.
1280	DO i = nxlg, nxrg
1281	DO j = nysg, nyng
1282	DO k = nzb, nzt
1283	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 1 ) )
1284	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 2 ) )
1285	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 3 ) )
1286	ENDDO
1287	ENDDO
1288	ENDDO
1289
1290	ENDIF
1291
1292	!
1293	!-- Calculate initial temperature field and other constants used in case of a sloping surface
1294	IF ( sloping_surface ) CALL init_slope
1295
1296	!
1297	!-- Initialize new time levels (only done in order to set boundary values including ghost points)
1298	pt_p = pt; u_p = u; v_p = v; w_p = w
1299	IF ( humidity ) THEN
1300	q_p = q
1301	ENDIF
1302	IF ( passive_scalar ) s_p = s
1303	!
1304	!-- Allthough tendency arrays are set in prognostic_equations, they have have to be predefined
1305	!-- here because they are used (but multiplied with 0) there before they are set.
1306	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1307	IF ( humidity ) THEN
1308	tq_m = 0.0_wp
1309	ENDIF
1310	IF ( passive_scalar ) ts_m = 0.0_wp
1311
1312	IF ( debug_output ) THEN
1313	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1314	ENDIF
1315
1316	ELSE
1317	!
1318	!-- Actually this part of the programm should not be reached
1319	message_string = 'unknown initializing problem'
1320	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1321	ENDIF
1322
1323
1324	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1325	!
1326	!-- Initialize old timelevels needed for radiation boundary conditions
1327	IF ( bc_radiation_l ) THEN
1328	u_m_l(:,:,:) = u(:,:,1:2)
1329	v_m_l(:,:,:) = v(:,:,0:1)
1330	w_m_l(:,:,:) = w(:,:,0:1)
1331	ENDIF
1332	IF ( bc_radiation_r ) THEN
1333	u_m_r(:,:,:) = u(:,:,nx-1:nx)
1334	v_m_r(:,:,:) = v(:,:,nx-1:nx)
1335	w_m_r(:,:,:) = w(:,:,nx-1:nx)
1336	ENDIF
1337	IF ( bc_radiation_s ) THEN
1338	u_m_s(:,:,:) = u(:,0:1,:)
1339	v_m_s(:,:,:) = v(:,1:2,:)
1340	w_m_s(:,:,:) = w(:,0:1,:)
1341	ENDIF
1342	IF ( bc_radiation_n ) THEN
1343	u_m_n(:,:,:) = u(:,ny-1:ny,:)
1344	v_m_n(:,:,:) = v(:,ny-1:ny,:)
1345	w_m_n(:,:,:) = w(:,ny-1:ny,:)
1346	ENDIF
1347
1348	ENDIF
1349
1350	!
1351	!-- Calculate the initial volume flow at the right and north boundary
1352	IF ( conserve_volume_flow ) THEN
1353
1354	IF ( use_prescribed_profile_data ) THEN
1355
1356	volume_flow_initial_l = 0.0_wp
1357	volume_flow_area_l = 0.0_wp
1358
1359	IF ( nxr == nx ) THEN
1360	DO j = nys, nyn
1361	DO k = nzb+1, nzt
1362	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1363	u_init(k) * dzw(k) &
1364	* MERGE( 1.0_wp, 0.0_wp, &
1365	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1366	)
1367
1368	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1369	* MERGE( 1.0_wp, 0.0_wp, &
1370	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1371	)
1372	ENDDO
1373	ENDDO
1374	ENDIF
1375
1376	IF ( nyn == ny ) THEN
1377	DO i = nxl, nxr
1378	DO k = nzb+1, nzt
1379	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1380	v_init(k) * dzw(k) &
1381	* MERGE( 1.0_wp, 0.0_wp, &
1382	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1383	)
1384	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1385	* MERGE( 1.0_wp, 0.0_wp, &
1386	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1387	)
1388	ENDDO
1389	ENDDO
1390	ENDIF
1391
1392	#if defined( __parallel )
1393	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1394	MPI_SUM, comm2d, ierr )
1395	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1396	comm2d, ierr )
1397
1398	#else
1399	volume_flow_initial = volume_flow_initial_l
1400	volume_flow_area = volume_flow_area_l
1401	#endif
1402
1403	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1404
1405	volume_flow_initial_l = 0.0_wp
1406	volume_flow_area_l = 0.0_wp
1407
1408	IF ( nxr == nx ) THEN
1409	DO j = nys, nyn
1410	DO k = nzb+1, nzt
1411	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1412	hom_sum(k,1,0) * dzw(k) &
1413	* MERGE( 1.0_wp, 0.0_wp, &
1414	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1415	)
1416	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1417	* MERGE( 1.0_wp, 0.0_wp, &
1418	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1419	)
1420	ENDDO
1421	ENDDO
1422	ENDIF
1423
1424	IF ( nyn == ny ) THEN
1425	DO i = nxl, nxr
1426	DO k = nzb+1, nzt
1427	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1428	hom_sum(k,2,0) * dzw(k) &
1429	* MERGE( 1.0_wp, 0.0_wp, &
1430	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1431	)
1432	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1433	* MERGE( 1.0_wp, 0.0_wp, &
1434	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1435	)
1436	ENDDO
1437	ENDDO
1438	ENDIF
1439
1440	#if defined( __parallel )
1441	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1442	MPI_SUM, comm2d, ierr )
1443	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1444	comm2d, ierr )
1445
1446	#else
1447	volume_flow_initial = volume_flow_initial_l
1448	volume_flow_area = volume_flow_area_l
1449	#endif
1450
1451	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1452
1453	volume_flow_initial_l = 0.0_wp
1454	volume_flow_area_l = 0.0_wp
1455
1456	IF ( nxr == nx ) THEN
1457	DO j = nys, nyn
1458	DO k = nzb+1, nzt
1459	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1460	u(k,j,nx) * dzw(k) &
1461	* MERGE( 1.0_wp, 0.0_wp, &
1462	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1463	)
1464	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1465	* MERGE( 1.0_wp, 0.0_wp, &
1466	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1467	)
1468	ENDDO
1469	ENDDO
1470	ENDIF
1471
1472	IF ( nyn == ny ) THEN
1473	DO i = nxl, nxr
1474	DO k = nzb+1, nzt
1475	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1476	v(k,ny,i) * dzw(k) &
1477	* MERGE( 1.0_wp, 0.0_wp, &
1478	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1479	)
1480	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1481	* MERGE( 1.0_wp, 0.0_wp, &
1482	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1483	)
1484	ENDDO
1485	ENDDO
1486	ENDIF
1487
1488	#if defined( __parallel )
1489	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1490	MPI_SUM, comm2d, ierr )
1491	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1492	comm2d, ierr )
1493
1494	#else
1495	volume_flow_initial = volume_flow_initial_l
1496	volume_flow_area = volume_flow_area_l
1497	#endif
1498
1499	ENDIF
1500
1501	!
1502	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated from u\|v_bulk instead
1503	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1504	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1505	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1506	ENDIF
1507
1508	ENDIF
1509	!
1510	!-- In the following, surface properties can be further initialized with input from static driver
1511	!-- file.
1512	!-- At the moment this affects only default surfaces. For example, roughness length or sensible /
1513	!-- latent heat fluxes can be initialized heterogeneously for default surfaces. Therefore, a generic
1514	!-- routine from netcdf_data_input_mod is called to read a 2D array.
1515	IF ( input_pids_static ) THEN
1516	!
1517	!-- Allocate memory for possible static input
1518	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1519	tmp_2d%var = 0.0_wp
1520	!
1521	!-- Open the static input file
1522	#if defined( __netcdf )
1523	CALL open_read_file( TRIM( input_file_static ) // &
1524	TRIM( coupling_char ), pids_id )
1525
1526	CALL inquire_num_variables( pids_id, num_var_pids )
1527	!
1528	!-- Allocate memory to store variable names and read them
1529	ALLOCATE( vars_pids(1:num_var_pids) )
1530	CALL inquire_variable_names( pids_id, vars_pids )
1531	!
1532	!-- Input roughness length.
1533	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1534	!
1535	!-- Read _FillValue attribute
1536	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'z0' )
1537	!
1538	!-- Read variable
1539	CALL get_variable( pids_id, 'z0', tmp_2d%var, nxl, nxr, nys, nyn )
1540	!
1541	!-- Initialize roughness length. Note, z0 will be only initialized at default-type surfaces.
1542	!-- At natural or urban z0 is implicitly initialized by the respective parameter lists.
1543	!-- Initialize horizontal surface elements.
1544	CALL init_single_surface_properties( surf_def_h(0)%z0, tmp_2d%var, surf_def_h(0)%ns, &
1545	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1546	!
1547	!-- Initialize roughness also at vertical surface elements.
1548	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1549	!-- index arrays with their respective offset values.
1550	DO l = 0, 3
1551	CALL init_single_surface_properties( surf_def_v(l)%z0, tmp_2d%var, surf_def_v(l)%ns, &
1552	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1553	surf_def_v(l)%j+surf_def_v(l)%joff )
1554	ENDDO
1555
1556	ENDIF
1557	!
1558	!-- Input surface sensible heat flux.
1559	IF ( check_existence( vars_pids, 'shf' ) ) THEN
1560	!
1561	!-- Read _FillValue attribute
1562	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'shf' )
1563	!
1564	!-- Read variable
1565	CALL get_variable( pids_id, 'shf', tmp_2d%var, nxl, nxr, nys, nyn )
1566	!
1567	!-- Initialize heat flux. Note, shf will be only initialized at default-type surfaces. At
1568	!-- natural or urban shf is implicitly initialized by the respective parameter lists.
1569	!-- Initialize horizontal surface elements.
1570	CALL init_single_surface_properties( surf_def_h(0)%shf, tmp_2d%var, surf_def_h(0)%ns, &
1571	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1572	!
1573	!-- Initialize heat flux also at vertical surface elements.
1574	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1575	!-- index arrays with their respective offset values.
1576	DO l = 0, 3
1577	CALL init_single_surface_properties( surf_def_v(l)%shf, tmp_2d%var, surf_def_v(l)%ns, &
1578	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1579	surf_def_v(l)%j+surf_def_v(l)%joff )
1580	ENDDO
1581
1582	ENDIF
1583	!
1584	!-- Input surface sensible heat flux.
1585	IF ( check_existence( vars_pids, 'qsws' ) ) THEN
1586	!
1587	!-- Read _FillValue attribute
1588	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, &
1589	.FALSE., 'qsws' )
1590	!
1591	!-- Read variable
1592	CALL get_variable( pids_id, 'qsws', tmp_2d%var, &
1593	nxl, nxr, nys, nyn )
1594	!
1595	!-- Initialize latent heat flux. Note, qsws will be only initialized at default-type surfaces.
1596	!-- At natural or urban qsws is implicitly initialized by the respective parameter lists.
1597	!-- Initialize horizontal surface elements.
1598	CALL init_single_surface_properties( surf_def_h(0)%qsws, tmp_2d%var, surf_def_h(0)%ns, &
1599	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1600	!
1601	!-- Initialize latent heat flux also at vertical surface elements.
1602	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1603	!-- index arrays with their respective offset values.
1604	DO l = 0, 3
1605	CALL init_single_surface_properties( surf_def_v(l)%qsws, tmp_2d%var, surf_def_v(l)%ns,&
1606	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1607	surf_def_v(l)%j+surf_def_v(l)%joff )
1608	ENDDO
1609
1610	ENDIF
1611	!
1612	!-- Additional variables, can be initialized the
1613	!-- same way.
1614
1615	!
1616	!-- Finally, close the input file and deallocate temporary arrays
1617	DEALLOCATE( vars_pids )
1618
1619	CALL close_input_file( pids_id )
1620	#endif
1621	DEALLOCATE( tmp_2d%var )
1622	ENDIF
1623	!
1624	!-- Finally, if random_heatflux is set, disturb shf at horizontal surfaces. Actually, this should be
1625	!-- done in surface_mod, where all other initializations of surface quantities are done. However,
1626	!-- this would create a ring dependency, hence, it is done here. Maybe delete disturb_heatflux and
1627	!-- tranfer the respective code directly into the initialization in surface_mod.
1628	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1629	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1630
1631	IF ( use_surface_fluxes .AND. constant_heatflux .AND. random_heatflux ) THEN
1632	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1633	IF ( surf_lsm_h%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h )
1634	IF ( surf_usm_h%ns >= 1 ) CALL disturb_heatflux( surf_usm_h )
1635	ENDIF
1636	ENDIF
1637
1638	!
1639	!-- Compute total sum of grid points and the mean surface level height for each statistic region.
1640	!-- These are mainly used for horizontal averaging of turbulence statistics.
1641	!-- ngp_2dh: number of grid points of a horizontal cross section through the respective statistic
1642	!-- region
1643	!-- ngp_3d: number of grid points of the respective statistic region
1644	ngp_2dh_outer_l = 0
1645	ngp_2dh_outer = 0
1646	ngp_2dh_s_inner_l = 0
1647	ngp_2dh_s_inner = 0
1648	ngp_2dh_l = 0
1649	ngp_2dh = 0
1650	ngp_3d_inner_l = 0.0_wp
1651	ngp_3d_inner = 0
1652	ngp_3d = 0
1653	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1654
1655	mean_surface_level_height = 0.0_wp
1656	mean_surface_level_height_l = 0.0_wp
1657	!
1658	!-- To do: New concept for these non-topography grid points!
1659	DO sr = 0, statistic_regions
1660	DO i = nxl, nxr
1661	DO j = nys, nyn
1662	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1663	!
1664	!-- All xy-grid points
1665	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1666	!
1667	!-- Determine mean surface-level height. In case of downward-facing walls are present,
1668	!-- more than one surface level exist.
1669	!-- In this case, use the lowest surface-level height.
1670	IF ( surf_def_h(0)%start_index(j,i) <= surf_def_h(0)%end_index(j,i) ) THEN
1671	m = surf_def_h(0)%start_index(j,i)
1672	k = surf_def_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_lsm_h%start_index(j,i) <= 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) = mean_surface_level_height_l(sr) + zw(k-1)
1679	ENDIF
1680	IF ( surf_usm_h%start_index(j,i) <= surf_usm_h%end_index(j,i) ) THEN
1681	m = surf_usm_h%start_index(j,i)
1682	k = surf_usm_h%k(m)
1683	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1684	ENDIF
1685
1686	k_surf = k - 1
1687
1688	DO k = nzb, nzt+1
1689	!
1690	!-- xy-grid points above topography
1691	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1692	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 24 ) )
1693
1694	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1695	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 22 ) )
1696
1697	ENDDO
1698	!
1699	!-- All grid points of the total domain above topography
1700	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1701
1702
1703
1704	ENDIF
1705	ENDDO
1706	ENDDO
1707	ENDDO
1708
1709	sr = statistic_regions + 1
1710	#if defined( __parallel )
1711	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1712	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1713	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1714	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, MPI_INTEGER, MPI_SUM, &
1715	comm2d, ierr )
1716	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1717	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), (nz+2)*sr, MPI_INTEGER, &
1718	MPI_SUM, comm2d, ierr )
1719	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1720	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, MPI_SUM, comm2d, &
1721	ierr )
1722	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1723	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1724	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), mean_surface_level_height(0), sr, MPI_REAL,&
1725	MPI_SUM, comm2d, ierr )
1726	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1727	#else
1728	ngp_2dh = ngp_2dh_l
1729	ngp_2dh_outer = ngp_2dh_outer_l
1730	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1731	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1732	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1733	#endif
1734
1735	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1736	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1737
1738	!
1739	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics, buoyancy, etc. A
1740	!-- zero value will occur for cases where all grid points of the respective subdomain lie below the
1741	!-- surface topography
1742	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1743	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), ngp_3d_inner(:) )
1744	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1745
1746	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, ngp_3d_inner_l, &
1747	ngp_3d_inner_tmp )
1748
1749	!
1750	!-- Initializae 3D offline nesting in COSMO model and read data from
1751	!-- external NetCDF file.
1752	IF ( nesting_offline ) CALL nesting_offl_init
1753	!
1754	!-- Initialize quantities for special advections schemes
1755	CALL init_advec
1756
1757	!
1758	!-- Impose random perturbation on the horizontal velocity field and then
1759	!-- remove the divergences from the velocity field at the initial stage
1760	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1761	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1762	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1763
1764	IF ( debug_output ) THEN
1765	CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1766	ENDIF
1767	!
1768	!-- Needed for both disturb_field and pres
1769	!$ACC DATA &
1770	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1771	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1772	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1773
1774	CALL disturb_field( 'u', tend, u )
1775	CALL disturb_field( 'v', tend, v )
1776
1777	!$ACC DATA &
1778	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1779	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1780	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1781	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1782	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1783	!$ACC COPYIN(wall_flags_total_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1784	!$ACC COPYIN(bc_h(0:1)) &
1785	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1786	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1787	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1788	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1789	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1790	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1791
1792	n_sor = nsor_ini
1793	CALL pres
1794	n_sor = nsor
1795
1796	!$ACC END DATA
1797	!$ACC END DATA
1798
1799	IF ( debug_output ) THEN
1800	CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1801	ENDIF
1802
1803	ENDIF
1804
1805	IF ( .NOT. ocean_mode ) THEN
1806
1807	ALLOCATE( hyp(nzb:nzt+1) )
1808	ALLOCATE( d_exner(nzb:nzt+1) )
1809	ALLOCATE( exner(nzb:nzt+1) )
1810	ALLOCATE( hyrho(nzb:nzt+1) )
1811	!
1812	!-- Check temperature in case of too large domain height
1813	DO k = nzb, nzt+1
1814	IF ( ( pt_surface * exner_function( surface_pressure * 100.0_wp ) - g/c_p * zu(k) ) &
1815	< 0.0_wp ) THEN
1816	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, ') = ', zu(k)
1817	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1818	ENDIF
1819	ENDDO
1820
1821	!
1822	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1823	hyp = barometric_formula( zu, pt_surface * exner_function( surface_pressure * 100.0_wp ),&
1824	surface_pressure * 100.0_wp )
1825	d_exner = exner_function_invers( hyp )
1826	exner = 1.0_wp / exner_function_invers( hyp )
1827	hyrho = ideal_gas_law_rho_pt( hyp, pt_init )
1828	!
1829	!-- Compute reference density
1830	rho_surface = ideal_gas_law_rho( surface_pressure * 100.0_wp, &
1831	pt_surface * exner_function( surface_pressure * 100.0_wp ) )
1832
1833	ENDIF
1834
1835	!
1836	!-- If required, initialize particles
1837	IF ( agents_active ) CALL mas_init
1838	!
1839	!-- Initialization of synthetic turbulence generator
1840	IF ( use_syn_turb_gen ) CALL stg_init
1841	!
1842	!-- Initializing actions for all other modules
1843	CALL module_interface_init
1844	!
1845	!-- Initialize surface layer (done after LSM as roughness length are required for initialization
1846	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1847	!
1848	!-- Initialize surface data output
1849	IF ( surface_output ) CALL surface_data_output_init
1850	!
1851	!-- Initialize the ws-scheme.
1852	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1853	!
1854	!-- Perform post-initializing checks for all other modules
1855	CALL module_interface_init_checks
1856
1857	!
1858	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1859	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1860	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1861	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1862	CALL ls_forcing_surf( simulated_time )
1863	ENDIF
1864	ENDIF
1865	!
1866	!-- Setting weighting factors for calculation of perturbation pressure and turbulent quantities from
1867	!-- 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 model domain
1911	DO k = nzt, nzb+1, -1
1912	IF ( zu(k) <= rayleigh_damping_height ) THEN
1913	rdf(k) = rayleigh_damping_factor * &
1914	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1915	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1916	)**2
1917	ENDIF
1918	ENDDO
1919	ENDIF
1920
1921	ENDIF
1922	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1923
1924	!
1925	!-- Initialize the starting level and the vertical smoothing factor used for the external pressure
1926	!-- gradient
1927	dp_smooth_factor = 1.0_wp
1928	IF ( dp_external ) THEN
1929	!
1930	!-- Set the starting level dp_level_ind_b only if it has not been set before (e.g. in init_grid).
1931	IF ( dp_level_ind_b == 0 ) THEN
1932	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1933	dp_level_ind_b = ind_array(1) - 1 + nzb
1934	! MINLOC uses lower array bound 1
1935	ENDIF
1936	IF ( dp_smooth ) THEN
1937	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1938	DO k = dp_level_ind_b+1, nzt
1939	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1940	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1941	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1942	ENDDO
1943	ENDIF
1944	ENDIF
1945
1946	!
1947	!-- Initialize damping zone for the potential temperature in case of non-cyclic lateral boundaries.
1948	!-- The damping zone has the maximum value at the inflow boundary and decreases to zero at
1949	!-- pt_damping_width.
1950	ptdf_x = 0.0_wp
1951	ptdf_y = 0.0_wp
1952	IF ( bc_lr_dirrad ) THEN
1953	DO i = nxl, nxr
1954	IF ( ( i * dx ) < pt_damping_width ) THEN
1955	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1956	REAL( pt_damping_width - i * dx, KIND=wp ) / &
1957	REAL( pt_damping_width, KIND=wp ) ) )**2
1958	ENDIF
1959	ENDDO
1960	ELSEIF ( bc_lr_raddir ) THEN
1961	DO i = nxl, nxr
1962	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1963	ptdf_x(i) = pt_damping_factor * SIN( pi * 0.5_wp * &
1964	( ( i - nx ) * dx + pt_damping_width ) / &
1965	REAL( pt_damping_width, KIND=wp ) )**2
1966	ENDIF
1967	ENDDO
1968	ELSEIF ( bc_ns_dirrad ) THEN
1969	DO j = nys, nyn
1970	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1971	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1972	( ( j - ny ) * dy + pt_damping_width ) / &
1973	REAL( pt_damping_width, KIND=wp ) )**2
1974	ENDIF
1975	ENDDO
1976	ELSEIF ( bc_ns_raddir ) THEN
1977	DO j = nys, nyn
1978	IF ( ( j * dy ) < pt_damping_width ) THEN
1979	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1980	( pt_damping_width - j * dy ) / &
1981	REAL( pt_damping_width, KIND=wp ) )**2
1982	ENDIF
1983	ENDDO
1984	ENDIF
1985
1986	!
1987	!-- Input binary data file is not needed anymore. This line must be placed after call of user_init!
1988	CALL close_file( 13 )
1989	!
1990	!-- In case of nesting, put an barrier to assure that all parent and child domains finished
1991	!-- initialization.
1992	#if defined( __parallel )
1993	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
1994	#endif
1995
1996
1997	CALL location_message( 'model initialization', 'finished' )
1998
1999	END SUBROUTINE init_3d_model

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