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init_3d_model.f90 @ 4845

Last change on this file since 4845 was 4845, checked in by raasch, 3 years ago

maximum phase velocities are alwasy used for radiation boundary conditions, parameter use_cmax removed

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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 4845 2021-01-18 11:15:37Z raasch $
26	! removed allocation and initialization of arrays required for radiation boundary conditions
27	!
28	! 4828 2021-01-05 11:21:41Z Giersch
29	! Add possibility to initialize surface flux of passive scalar via static driver
30	!
31	! 4783 2020-11-13 13:58:45Z raasch
32	! bugfix for reading restart data with MPI-I/O (does not work with blockwise I/O)
33	!
34	! 4680 2020-09-16 10:20:34Z gronemeier
35	! Add option to fix date or time of the simulation
36	!
37	! 4671 2020-09-09 20:27:58Z pavelkrc
38	! Implementation of downward facing USM and LSM surfaces
39	!
40	! 4648 2020-08-25 07:52:08Z raasch
41	! file re-formatted to follow the PALM coding standard
42	!
43	! 4548 2020-05-28 19:36:45Z suehring
44	! Bugfix, move call for lsf_forcing_surf after lsf_init is called
45	!
46	! 4514 2020-04-30 16:29:59Z suehring
47	! Add possibility to initialize surface sensible and latent heat fluxes via a static driver.
48	!
49	! 4493 2020-04-10 09:49:43Z pavelkrc
50	! Overwrite u_init, v_init, pt_init, q_init and s_init with hom for all cyclic_fill-cases, not only
51	! for turbulent_inflow = .TRUE.
52	!
53	! 4360 2020-01-07 11:25:50Z suehring
54	! Introduction of wall_flags_total_0, which currently sets bits based on static topography
55	! information used in wall_flags_static_0
56	!
57	! 4329 2019-12-10 15:46:36Z motisi
58	! Renamed wall_flags_0 to wall_flags_static_0
59	!
60	! 4286 2019-10-30 16:01:14Z resler
61	! implement new palm_date_time_mod
62	!
63	! 4223 2019-09-10 09:20:47Z gronemeier
64	! Deallocate temporary string array since it may be re-used to read different input data in other
65	! modules
66	!
67	! 4186 2019-08-23 16:06:14Z suehring
68	! Design change, use variables defined in netcdf_data_input_mod to read netcd variables rather than
69	! define local ones.
70	!
71	! 4185 2019-08-23 13:49:38Z oliver.maas
72	! For initializing_actions = ' cyclic_fill':
73	! Overwrite u_init, v_init, pt_init, q_init and s_init with the (temporally) and horizontally
74	! averaged vertical profiles from the end of the prerun, because these profiles shall be used as the
75	! basic state for the rayleigh damping and the pt_damping.
76	!
77	! 4182 2019-08-22 15:20:23Z scharf
78	! Corrected "Former revisions" section
79	!
80	! 4168 2019-08-16 13:50:17Z suehring
81	! Replace function get_topography_top_index by topo_top_ind
82	!
83	! 4151 2019-08-09 08:24:30Z suehring
84	! Add netcdf directive around input calls (fix for last commit)
85	!
86	! 4150 2019-08-08 20:00:47Z suehring
87	! Input of additional surface variables independent on land- or urban-surface model
88	!
89	! 4131 2019-08-02 11:06:18Z monakurppa
90	! Allocate sums and sums_l to allow profile output for salsa variables.
91	!
92	! 4130 2019-08-01 13:04:13Z suehring
93	! Effectively reduce 3D initialization to 1D initial profiles. This is because 3D initialization
94	! produces structures in the w-component that are correlated with the processor grid for some
95	! unknown reason
96	!
97	! 4090 2019-07-11 15:06:47Z Giersch
98	! Unused variables removed
99	!
100	! 4088 2019-07-11 13:57:56Z Giersch
101	! Pressure and density profile calculations revised using basic functions
102	!
103	! 4048 2019-06-21 21:00:21Z knoop
104	! Further modularization of particle code components
105	!
106	! 4017 2019-06-06 12:16:46Z schwenkel
107	! Convert most location messages to debug messages to reduce output in job logfile to a minimum
108	!
109	! unused variable removed
110	!
111	! 3937 2019-04-29 15:09:07Z suehring
112	! Move initialization of synthetic turbulence generator behind initialization of offline nesting.
113	! Remove call for stg_adjust, as this is now already done in stg_init.
114	!
115	! 3900 2019-04-16 15:17:43Z suehring
116	! Fix problem with LOD = 2 initialization
117	!
118	! 3885 2019-04-11 11:29:34Z kanani
119	! Changes related to global restructuring of location messages and introduction of additional debug
120	! messages
121	!
122	! 3849 2019-04-01 16:35:16Z knoop
123	! Move initialization of rmask before initializing user_init_arrays
124	!
125	! 3711 2019-01-31 13:44:26Z knoop
126	! Introduced module_interface_init_checks for post-init checks in modules
127	!
128	! 3700 2019-01-26 17:03:42Z knoop
129	! Some interface calls moved to module_interface + cleanup
130	!
131	! 3648 2019-01-02 16:35:46Z suehring
132	! Rename subroutines for surface-data output
133	!
134	! Revision 1.1 1998/03/09 16:22:22 raasch
135	! Initial revision
136	!
137	!
138	! Description:
139	! ------------
140	!> Allocation of arrays and initialization of the 3D model via
141	!> a) pre-run the 1D model
142	!> or
143	!> b) pre-set constant linear profiles
144	!> or
145	!> c) read values of a previous run
146	!--------------------------------------------------------------------------------------------------!
147	SUBROUTINE init_3d_model
148
149
150	USE advec_ws
151
152	USE arrays_3d
153
154	USE basic_constants_and_equations_mod, &
155	ONLY: barometric_formula, c_p, exner_function, exner_function_invers, g, &
156	ideal_gas_law_rho, ideal_gas_law_rho_pt, l_v, pi
157
158	USE bulk_cloud_model_mod, &
159	ONLY: bulk_cloud_model
160
161	USE chem_modules, &
162	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
163
164	USE control_parameters
165
166	USE grid_variables, &
167	ONLY: dx, dy, ddx2_mg, ddy2_mg
168
169	USE indices
170
171	USE kinds
172
173	USE lsf_nudging_mod, &
174	ONLY: ls_forcing_surf
175
176	USE model_1d_mod, &
177	ONLY: init_1d_model, l1d, u1d, v1d
178
179	USE module_interface, &
180	ONLY: module_interface_init_arrays, &
181	module_interface_init, &
182	module_interface_init_checks
183
184	USE multi_agent_system_mod, &
185	ONLY: agents_active, mas_init
186
187	USE netcdf_interface, &
188	ONLY: dots_max
189
190	USE netcdf_data_input_mod, &
191	ONLY: char_fill, &
192	check_existence, &
193	close_input_file, &
194	get_attribute, &
195	get_variable, &
196	init_3d, &
197	input_pids_static, &
198	inquire_num_variables, &
199	inquire_variable_names, &
200	input_file_static, &
201	netcdf_data_input_init_3d, &
202	num_var_pids, &
203	open_read_file, &
204	pids_id, &
205	real_2d, &
206	vars_pids
207
208	USE nesting_offl_mod, &
209	ONLY: nesting_offl_init
210
211	USE palm_date_time_mod, &
212	ONLY: init_date_time
213
214	USE pegrid
215
216	#if defined( __parallel )
217	USE pmc_interface, &
218	ONLY: nested_run
219	#endif
220
221	USE random_function_mod
222
223	USE random_generator_parallel, &
224	ONLY: init_parallel_random_generator
225
226	USE read_restart_data_mod, &
227	ONLY: rrd_local, rrd_read_parts_of_global
228
229	USE statistics, &
230	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, statistic_regions, sums, &
231	sums_divnew_l, sums_divold_l, sums_l, sums_l_l, sums_wsts_bc_l, ts_value, &
232	weight_pres, weight_substep
233
234	USE synthetic_turbulence_generator_mod, &
235	ONLY: stg_init, use_syn_turb_gen
236
237	USE surface_layer_fluxes_mod, &
238	ONLY: init_surface_layer_fluxes
239
240	USE surface_mod, &
241	ONLY : init_single_surface_properties, &
242	init_surface_arrays, &
243	init_surfaces, &
244	surf_def_h, &
245	surf_def_v, &
246	surf_lsm_h, &
247	surf_usm_h
248
249	#if defined( _OPENACC )
250	USE surface_mod, &
251	ONLY : bc_h
252	#endif
253
254	USE surface_data_output_mod, &
255	ONLY: surface_data_output_init
256
257	USE transpose_indices
258
259
260	IMPLICIT NONE
261
262	INTEGER(iwp) :: i !< grid index in x direction
263	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
264	INTEGER(iwp) :: j !< grid index in y direction
265	INTEGER(iwp) :: k !< grid index in z direction
266	INTEGER(iwp) :: k_surf !< surface level index
267	INTEGER(iwp) :: l !< running index over surface orientation
268	INTEGER(iwp) :: m !< index of surface element in surface data type
269	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
270	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
271	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
272	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
273	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
274	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
275	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
276	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
277	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
278	INTEGER(iwp) :: sr !< index of statistic region
279
280	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on
281	!< subdomain
282
283	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on
284	!< subdomain
285	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on
286	!< subdomain
287
288	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
289	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
290
291	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain
292	!< inital profiles
293	REAL(wp), DIMENSION(:), ALLOCATABLE :: mean_surface_level_height_l !< mean surface level height on subdomain
294	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_l !< total number of non-topography grid points on subdomain
295	REAL(wp), DIMENSION(:), ALLOCATABLE :: ngp_3d_inner_tmp !< total number of non-topography grid points
296	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
297
298	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
299	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
300
301	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
302
303	CALL location_message( 'model initialization', 'start' )
304	!
305	!-- Set reference date-time
306	CALL init_date_time( date_time_str=origin_date_time, &
307	use_fixed_date=use_fixed_date, &
308	use_fixed_time=use_fixed_time )
309
310	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
311	!
312	!-- Allocate arrays
313	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
314	mean_surface_level_height_l(0:statistic_regions), &
315	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
316	ngp_3d(0:statistic_regions), &
317	ngp_3d_inner(0:statistic_regions), &
318	ngp_3d_inner_l(0:statistic_regions), &
319	ngp_3d_inner_tmp(0:statistic_regions), &
320	sums_divnew_l(0:statistic_regions), &
321	sums_divold_l(0:statistic_regions) )
322	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
323	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
324	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
325	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
326	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
327	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
328	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
329	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
330	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
331	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
332	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
333	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
334
335	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
336	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
337	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
338
339	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
340	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
341	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
342	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
343	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
344	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
345	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
346	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
347	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
348	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
349	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
350	IF ( .NOT. neutral ) THEN
351	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
352	ENDIF
353	!
354	!-- Pre-set masks for regional statistics. Default is the total model domain.
355	!-- Ghost points are excluded because counting values at the ghost boundaries would bias the
356	!-- statistics.
357	rmask = 1.0_wp
358	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
359	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
360	!
361	!-- Following array is required for perturbation pressure within the iterative pressure solvers. For
362	!-- the multistep schemes (Runge-Kutta), array p holds the weighted average of the substeps and
363	!-- cannot be used in the Poisson solver.
364	IF ( psolver == 'sor' ) THEN
365	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
366	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
367	!
368	!-- For performance reasons, multigrid is using one ghost layer only
369	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
370	ENDIF
371
372	!
373	!-- Array for storing constant coeffficients of the tridiagonal solver
374	IF ( psolver == 'poisfft' ) THEN
375	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
376	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
377	ENDIF
378
379	IF ( humidity ) THEN
380	!
381	!-- 3D-humidity
382	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
383	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
384	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
385	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
386	ENDIF
387
388	IF ( passive_scalar ) THEN
389
390	!
391	!-- 3D scalar arrays
392	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
393	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
394	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
395
396	ENDIF
397
398	!
399	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to non-zero values later
400	!-- in ocean_init.
401	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
402	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
403	u_stokes_zu(:) = 0.0_wp
404	u_stokes_zw(:) = 0.0_wp
405	v_stokes_zu(:) = 0.0_wp
406	v_stokes_zw(:) = 0.0_wp
407
408	!
409	!-- Allocation of anelastic and Boussinesq approximation specific arrays
410	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
411	ALLOCATE( rho_air(nzb:nzt+1) )
412	ALLOCATE( rho_air_zw(nzb:nzt+1) )
413	ALLOCATE( drho_air(nzb:nzt+1) )
414	ALLOCATE( drho_air_zw(nzb:nzt+1) )
415	!
416	!-- Density profile calculation for anelastic and Boussinesq approximation.
417	!-- In case of a Boussinesq approximation, a constant density is calculated mainly for output
418	!-- purposes. This density does not need to be considered in the model's system of equations.
419	IF ( TRIM( approximation ) == 'anelastic' ) THEN
420	DO k = nzb, nzt+1
421	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
422	exner_function(surface_pressure * 100.0_wp), &
423	surface_pressure * 100.0_wp)
424
425	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
426	ENDDO
427
428	DO k = nzb, nzt
429	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
430	ENDDO
431
432	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
433
434	ELSE
435	DO k = nzb, nzt+1
436	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
437	exner_function(surface_pressure * 100.0_wp), &
438	surface_pressure * 100.0_wp)
439
440	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
441	ENDDO
442
443	DO k = nzb, nzt
444	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
445	ENDDO
446
447	rho_air_zw(nzt+1) = rho_air_zw(nzt) + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
448
449	ENDIF
450	!
451	!-- Compute the inverse density array in order to avoid expencive divisions
452	drho_air = 1.0_wp / rho_air
453	drho_air_zw = 1.0_wp / rho_air_zw
454
455	!
456	!-- Allocation of flux conversion arrays
457	ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
458	ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
459	ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
460	ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
461	ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
462	ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )
463
464	!
465	!-- Calculate flux conversion factors according to approximation and in-/output mode
466	DO k = nzb, nzt+1
467
468	IF ( TRIM( flux_input_mode ) == 'kinematic' ) THEN
469	heatflux_input_conversion(k) = rho_air_zw(k)
470	waterflux_input_conversion(k) = rho_air_zw(k)
471	momentumflux_input_conversion(k) = rho_air_zw(k)
472	ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
473	heatflux_input_conversion(k) = 1.0_wp / c_p
474	waterflux_input_conversion(k) = 1.0_wp / l_v
475	momentumflux_input_conversion(k) = 1.0_wp
476	ENDIF
477
478	IF ( TRIM( flux_output_mode ) == 'kinematic' ) THEN
479	heatflux_output_conversion(k) = drho_air_zw(k)
480	waterflux_output_conversion(k) = drho_air_zw(k)
481	momentumflux_output_conversion(k) = drho_air_zw(k)
482	ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
483	heatflux_output_conversion(k) = c_p
484	waterflux_output_conversion(k) = l_v
485	momentumflux_output_conversion(k) = 1.0_wp
486	ENDIF
487
488	IF ( .NOT. humidity ) THEN
489	waterflux_input_conversion(k) = 1.0_wp
490	waterflux_output_conversion(k) = 1.0_wp
491	ENDIF
492
493	ENDDO
494
495	!
496	!-- In case of multigrid method, compute grid lengths and grid factors for the grid levels with
497	!-- respective density on each grid.
498	IF ( psolver(1:9) == 'multigrid' ) THEN
499
500	ALLOCATE( ddx2_mg(maximum_grid_level) )
501	ALLOCATE( ddy2_mg(maximum_grid_level) )
502	ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
503	ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
504	ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
505	ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
506	ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
507	ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
508	ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )
509
510	dzu_mg(:,maximum_grid_level) = dzu
511	rho_air_mg(:,maximum_grid_level) = rho_air
512	!
513	!-- Next line to ensure an equally spaced grid.
514	dzu_mg(1,maximum_grid_level) = dzu(2)
515	rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) + (rho_air(nzb) - rho_air(nzb+1))
516
517	dzw_mg(:,maximum_grid_level) = dzw
518	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
519	nzt_l = nzt
520	DO l = maximum_grid_level-1, 1, -1
521	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
522	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
523	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + ( rho_air_mg(nzb,l+1) - &
524	rho_air_mg(nzb+1,l+1) )
525	rho_air_zw_mg(nzb,l) = rho_air_zw_mg(nzb,l+1) + ( rho_air_zw_mg(nzb,l+1) - &
526	rho_air_zw_mg(nzb+1,l+1) )
527	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
528	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
529	nzt_l = nzt_l / 2
530	DO k = 2, nzt_l+1
531	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
532	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
533	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
534	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
535	ENDDO
536	ENDDO
537
538	nzt_l = nzt
539	dx_l = dx
540	dy_l = dy
541	DO l = maximum_grid_level, 1, -1
542	ddx2_mg(l) = 1.0_wp / dx_l**2
543	ddy2_mg(l) = 1.0_wp / dy_l**2
544	DO k = nzb+1, nzt_l
545	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
546	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
547	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
548	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
549	ENDDO
550	nzt_l = nzt_l / 2
551	dx_l = dx_l * 2.0_wp
552	dy_l = dy_l * 2.0_wp
553	ENDDO
554
555	ENDIF
556
557	!
558	!-- 1D-array for large scale subsidence velocity
559	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
560	ALLOCATE ( w_subs(nzb:nzt+1) )
561	w_subs = 0.0_wp
562	ENDIF
563
564	!
565	!-- Initial assignment of the pointers
566	IF ( .NOT. neutral ) THEN
567	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
568	ELSE
569	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
570	ENDIF
571	u => u_1; u_p => u_2; tu_m => u_3
572	v => v_1; v_p => v_2; tv_m => v_3
573	w => w_1; w_p => w_2; tw_m => w_3
574
575	IF ( humidity ) THEN
576	q => q_1; q_p => q_2; tq_m => q_3
577	vpt => vpt_1
578	ENDIF
579
580	IF ( passive_scalar ) THEN
581	s => s_1; s_p => s_2; ts_m => s_3
582	ENDIF
583
584	!
585	!-- Initialize surface arrays
586	CALL init_surface_arrays
587	!
588	!-- Allocate arrays for other modules
589	CALL module_interface_init_arrays
590
591
592	!
593	!-- Allocate arrays containing the RK coefficient for calculation of perturbation pressure and
594	!-- turbulent fluxes. At this point values are set for pressure calculation during initialization
595	!-- (where no timestep is done). Further below the values needed within the timestep scheme will be
596	!-- set.
597	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
598	weight_pres(1:intermediate_timestep_count_max) )
599	weight_substep = 1.0_wp
600	weight_pres = 1.0_wp
601	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
602
603	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
604
605	!
606	!-- Initialize time series
607	ts_value = 0.0_wp
608
609	!
610	!-- Initialize local summation arrays for routine flow_statistics.
611	!-- This is necessary because they may not yet have been initialized when they are called from
612	!-- flow_statistics (or - depending on the chosen model run - are never initialized)
613	sums_divnew_l = 0.0_wp
614	sums_divold_l = 0.0_wp
615	sums_l_l = 0.0_wp
616	sums_wsts_bc_l = 0.0_wp
617
618	!
619	!-- Initialize model variables
620	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
621	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
622	!
623	!-- Initialization with provided input data derived from larger-scale model
624	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
625	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
626	!
627	!-- Read initial 1D profiles or 3D data from NetCDF file, depending on the provided
628	!-- level-of-detail.
629	!-- At the moment, only u, v, w, pt and q are provided.
630	CALL netcdf_data_input_init_3d
631	!
632	!-- Please note, Inifor provides data from nzb+1 to nzt.
633	!-- Bottom and top boundary conditions for Inifor profiles are already set (just after
634	!-- reading), so that this is not necessary here.
635	!-- Depending on the provided level-of-detail, initial Inifor data is either stored on data
636	!-- type (lod=1), or directly on 3D arrays (lod=2).
637	!-- In order to obtain also initial profiles in case of lod=2 (which is required for e.g.
638	!-- damping), average over 3D data.
639	IF( init_3d%lod_u == 1 ) THEN
640	u_init = init_3d%u_init
641	ELSEIF( init_3d%lod_u == 2 ) THEN
642	ALLOCATE( init_l(nzb:nzt+1) )
643	DO k = nzb, nzt+1
644	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
645	ENDDO
646	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
647
648	#if defined( __parallel )
649	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
650	#else
651	u_init = init_l
652	#endif
653	DEALLOCATE( init_l )
654
655	ENDIF
656
657	IF( init_3d%lod_v == 1 ) THEN
658	v_init = init_3d%v_init
659	ELSEIF( init_3d%lod_v == 2 ) THEN
660	ALLOCATE( init_l(nzb:nzt+1) )
661	DO k = nzb, nzt+1
662	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
663	ENDDO
664	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
665
666	#if defined( __parallel )
667	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
668	#else
669	v_init = init_l
670	#endif
671	DEALLOCATE( init_l )
672	ENDIF
673	IF( .NOT. neutral ) THEN
674	IF( init_3d%lod_pt == 1 ) THEN
675	pt_init = init_3d%pt_init
676	ELSEIF( init_3d%lod_pt == 2 ) THEN
677	ALLOCATE( init_l(nzb:nzt+1) )
678	DO k = nzb, nzt+1
679	init_l(k) = SUM( pt(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, pt_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
685	#else
686	pt_init = init_l
687	#endif
688	DEALLOCATE( init_l )
689	ENDIF
690	ENDIF
691
692
693	IF( humidity ) THEN
694	IF( init_3d%lod_q == 1 ) THEN
695	q_init = init_3d%q_init
696	ELSEIF( init_3d%lod_q == 2 ) THEN
697	ALLOCATE( init_l(nzb:nzt+1) )
698	DO k = nzb, nzt+1
699	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
700	ENDDO
701	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
702
703	#if defined( __parallel )
704	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, MPI_REAL, MPI_SUM, comm2d, ierr )
705	#else
706	q_init = init_l
707	#endif
708	DEALLOCATE( init_l )
709	ENDIF
710	ENDIF
711
712	!
713	!-- Write initial profiles onto 3D arrays.
714	!-- Work-around, 3D initialization of u,v,w creates artificial structures which correlate with
715	!-- the processor grid. The reason for this is still unknown. To work-around this, 3D
716	!-- initialization will be effectively reduce to a 1D initialization where no such artificial
717	!-- structures appear.
718	DO i = nxlg, nxrg
719	DO j = nysg, nyng
720	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) u(:,j,i) = u_init(:)
721	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) v(:,j,i) = v_init(:)
722	IF( .NOT. neutral .AND. ( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
723	pt(:,j,i) = pt_init(:)
724	IF( humidity .AND. ( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
725	q(:,j,i) = q_init(:)
726	ENDDO
727	ENDDO
728	!
729	!-- Set geostrophic wind components.
730	IF ( init_3d%from_file_ug ) THEN
731	ug(:) = init_3d%ug_init(:)
732	ENDIF
733	IF ( init_3d%from_file_vg ) THEN
734	vg(:) = init_3d%vg_init(:)
735	ENDIF
736	!
737	!-- Set bottom and top boundary condition for geostrophic wind
738	ug(nzt+1) = ug(nzt)
739	vg(nzt+1) = vg(nzt)
740	ug(nzb) = ug(nzb+1)
741	vg(nzb) = vg(nzb+1)
742	!
743	!-- Set inital w to 0
744	w = 0.0_wp
745
746	IF ( passive_scalar ) THEN
747	DO i = nxlg, nxrg
748	DO j = nysg, nyng
749	s(:,j,i) = s_init
750	ENDDO
751	ENDDO
752	ENDIF
753
754	!
755	!-- Set velocity components at non-atmospheric / oceanic grid points to zero.
756	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
757	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
758	w = MERGE( w, 0.0_wp, BTEST( wall_flags_total_0, 3 ) )
759	!
760	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
761	CALL init_surfaces
762
763	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
764	!
765	!-- Initialization via computed 1D-model profiles
766	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
767
768	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
769	!
770	!-- Use solutions of the 1D model as initial profiles,
771	!-- start 1D model
772	CALL init_1d_model
773	!
774	!-- Transfer initial profiles to the arrays of the 3D model
775	DO i = nxlg, nxrg
776	DO j = nysg, nyng
777	pt(:,j,i) = pt_init
778	u(:,j,i) = u1d
779	v(:,j,i) = v1d
780	ENDDO
781	ENDDO
782
783	IF ( humidity ) THEN
784	DO i = nxlg, nxrg
785	DO j = nysg, nyng
786	q(:,j,i) = q_init
787	ENDDO
788	ENDDO
789	ENDIF
790
791	IF ( passive_scalar ) THEN
792	DO i = nxlg, nxrg
793	DO j = nysg, nyng
794	s(:,j,i) = s_init
795	ENDDO
796	ENDDO
797	ENDIF
798	!
799	!-- Store initial profiles for output purposes etc.
800	IF ( .NOT. constant_diffusion ) THEN
801	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
802	ENDIF
803	!
804	!-- Set velocities back to zero
805	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
806	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
807	!
808	!-- WARNING: The extra boundary conditions set after running the 1D model impose an error on
809	!-- -------- the divergence one layer below the topography; need to correct later
810	!-- ATTENTION: Provisional correction for Piacsek & Williams advection scheme: keep u and v
811	!-- ---------- zero one layer below the topography.
812	IF ( ibc_uv_b == 1 ) THEN
813	!
814	!-- Neumann condition
815	DO i = nxl-1, nxr+1
816	DO j = nys-1, nyn+1
817	u(nzb,j,i) = u(nzb+1,j,i)
818	v(nzb,j,i) = v(nzb+1,j,i)
819	ENDDO
820	ENDDO
821
822	ENDIF
823	!
824	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
825	CALL init_surfaces
826
827	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
828
829	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) THEN
830
831	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
832
833	!
834	!-- Use constructed initial profiles (velocity constant with height, temperature profile with
835	!-- constant gradient)
836	DO i = nxlg, nxrg
837	DO j = nysg, nyng
838	pt(:,j,i) = pt_init
839	u(:,j,i) = u_init
840	v(:,j,i) = v_init
841	ENDDO
842	ENDDO
843	!
844	!-- Mask topography
845	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
846	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
847	!
848	!-- Set initial horizontal velocities at the lowest computational grid levels to zero in order
849	!-- to avoid too small time steps caused by the diffusion limit in the initial phase of a run
850	!-- (at k=1, dz/2 occurs in the limiting formula!).
851	!-- Please note, in case land- or urban-surface model is used and a spinup is applied, masking
852	!-- the lowest computational level is not possible as MOST as well as energy-balance
853	!-- parametrizations will not work with zero wind velocity.
854	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
855	DO i = nxlg, nxrg
856	DO j = nysg, nyng
857	DO k = nzb, nzt
858	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 20 ) )
859	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 21 ) )
860	ENDDO
861	ENDDO
862	ENDDO
863	ENDIF
864
865	IF ( humidity ) THEN
866	DO i = nxlg, nxrg
867	DO j = nysg, nyng
868	q(:,j,i) = q_init
869	ENDDO
870	ENDDO
871	ENDIF
872
873	IF ( passive_scalar ) THEN
874	DO i = nxlg, nxrg
875	DO j = nysg, nyng
876	s(:,j,i) = s_init
877	ENDDO
878	ENDDO
879	ENDIF
880
881	!
882	!-- Compute initial temperature field and other constants used in case of a sloping surface.
883	IF ( sloping_surface ) CALL init_slope
884	!
885	!-- Initialize surface variables, e.g. friction velocity, momentum fluxes, etc.
886	CALL init_surfaces
887
888	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
889
890	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) THEN
891
892	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
893	!
894	!-- Pre-initialize surface variables, i.e. setting start- and end-indices at each
895	!-- (j,i)-location. Please note, this does not supersede user-defined initialization of
896	!-- surface quantities.
897	CALL init_surfaces
898	!
899	!-- Initialization will completely be done by the user
900	CALL user_init_3d_model
901
902	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
903
904	ENDIF
905
906	IF ( debug_output ) THEN
907	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
908	ENDIF
909
910	!
911	!-- Bottom boundary
912	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
913	u(nzb,:,:) = 0.0_wp
914	v(nzb,:,:) = 0.0_wp
915	ENDIF
916
917	!
918	!-- Apply channel flow boundary condition
919	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
920	u(nzt+1,:,:) = 0.0_wp
921	v(nzt+1,:,:) = 0.0_wp
922	ENDIF
923
924	!
925	!-- Calculate virtual potential temperature
926	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
927
928	!
929	!-- Store initial profiles for output purposes etc.. Please note, in case of initialization of u,
930	!-- v, w, pt, and q via output data derived from larger scale models, data will not be
931	!-- horizontally homogeneous. Actually, a mean profile should be calculated before.
932	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
933	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
934	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
935	hom(nzb,1,5,:) = 0.0_wp
936	hom(nzb,1,6,:) = 0.0_wp
937	ENDIF
938	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
939
940	IF ( humidity ) THEN
941	!
942	!-- Store initial profile of total water content, virtual potential temperature
943	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
944	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
945	!
946	!-- Store initial profile of mixing ratio and potential temperature
947	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
948	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
949	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
950	ENDIF
951	ENDIF
952
953	!
954	!-- Store initial scalar profile
955	IF ( passive_scalar ) THEN
956	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
957	ENDIF
958
959	!
960	!-- Initialize the random number generators (from numerical recipes)
961	CALL random_function_ini
962
963	IF ( random_generator == 'random-parallel' ) THEN
964	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
965	ENDIF
966	!
967	!-- Set the reference state to be used in the buoyancy terms (for ocean runs the reference state
968	!-- will be set (overwritten) in init_ocean).
969	IF ( use_single_reference_value ) THEN
970	IF ( .NOT. humidity ) THEN
971	ref_state(:) = pt_reference
972	ELSE
973	ref_state(:) = vpt_reference
974	ENDIF
975	ELSE
976	IF ( .NOT. humidity ) THEN
977	ref_state(:) = pt_init(:)
978	ELSE
979	ref_state(:) = vpt(:,nys,nxl)
980	ENDIF
981	ENDIF
982
983	!
984	!-- For the moment, vertical velocity is zero
985	w = 0.0_wp
986
987	!
988	!-- Initialize array sums (must be defined in first call of pres)
989	sums = 0.0_wp
990
991	!
992	!-- In case of iterative solvers, p must get an initial value
993	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
994	!
995	!-- Impose vortex with vertical axis on the initial velocity profile
996	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
997	CALL init_rankine
998	ENDIF
999
1000	!
1001	!-- Impose temperature anomaly (advection test only) or warm air bubble close to surface.
1002	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1003	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1004	CALL init_pt_anomaly
1005	ENDIF
1006
1007	!
1008	!-- If required, change the surface temperature at the start of the 3D run
1009	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1010	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1011	ENDIF
1012
1013	!
1014	!-- If required, change the surface humidity/scalar at the start of the 3D
1015	!-- run
1016	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1017	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1018
1019	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1020	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1021
1022
1023	!
1024	!-- Initialize old and new time levels.
1025	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1026	pt_p = pt; u_p = u; v_p = v; w_p = w
1027
1028	IF ( humidity ) THEN
1029	tq_m = 0.0_wp
1030	q_p = q
1031	ENDIF
1032
1033	IF ( passive_scalar ) THEN
1034	ts_m = 0.0_wp
1035	s_p = s
1036	ENDIF
1037
1038	IF ( debug_output ) THEN
1039	CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1040	ENDIF
1041
1042	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1043	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1044	THEN
1045
1046	IF ( debug_output ) THEN
1047	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1048	ENDIF
1049	!
1050	!-- Initialize surface elements and its attributes, e.g. heat- and momentumfluxes, roughness,
1051	!-- scaling parameters. As number of surface elements might be different between runs, e.g. in
1052	!-- case of cyclic fill, and not all surface elements are read, surface elements need to be
1053	!-- initialized before.
1054	!-- Please note, in case of cyclic fill, surfaces should be initialized after restart data is
1055	!-- read, else, individual settings of surface parameters will be overwritten from data of
1056	!-- precursor run, hence, init_surfaces is called a second time after reading the restart data.
1057	CALL init_surfaces
1058	!
1059	!-- When reading data for cyclic fill of 3D prerun data files, read some of the global variables
1060	!-- from the restart file which are required for initializing the inflow
1061	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1062
1063	!
1064	!-- Blockwise I/O does not work together with MPI-I/O
1065	IF ( restart_data_format_input(1:3) == 'mpi' ) THEN
1066	CALL rrd_read_parts_of_global
1067	ELSE
1068	DO i = 0, io_blocks-1
1069	IF ( i == io_group ) THEN
1070	CALL rrd_read_parts_of_global
1071	ENDIF
1072	#if defined( __parallel )
1073	CALL MPI_BARRIER( comm2d, ierr )
1074	#endif
1075	ENDDO
1076	ENDIF
1077
1078	ENDIF
1079
1080	!
1081	!-- Read processor specific binary data from restart file.
1082	!-- Blockwise I/O does not work together with MPI-I/O
1083	IF ( restart_data_format_input(1:3) == 'mpi' ) THEN
1084	CALL rrd_local
1085	ELSE
1086	DO i = 0, io_blocks-1
1087	IF ( i == io_group ) THEN
1088	CALL rrd_local
1089	ENDIF
1090	#if defined( __parallel )
1091	CALL MPI_BARRIER( comm2d, ierr )
1092	#endif
1093	ENDDO
1094	ENDIF
1095
1096
1097	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1098
1099	!
1100	!-- In case of cyclic fill, call init_surfaces a second time, so that surface properties such
1101	!-- as heat fluxes are initialized as prescribed.
1102	CALL init_surfaces
1103
1104	!
1105	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the horizontally mean (hom)
1106	!-- vertical profiles from the end of the prerun, because these profiles shall be used as the
1107	!-- reference state for the rayleigh damping and the pt_damping. This is especially important
1108	!-- for the use of large_scale_subsidence, because the reference temperature in the free
1109	!-- atmosphere changes in time.
1110	u_init(:) = hom_sum(:,1,0)
1111	v_init(:) = hom_sum(:,2,0)
1112	pt_init(:) = hom_sum(:,4,0)
1113	IF ( humidity ) q_init(:) = hom_sum(:,41,0)
1114	IF ( passive_scalar ) s_init(:) = hom_sum(:,115,0)
1115	ENDIF
1116	!
1117	!-- In case of complex terrain and cyclic fill method as initialization, shift initial data in
1118	!-- the vertical direction for each point in the x-y-plane depending on local surface height.
1119	IF ( complex_terrain .AND. TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1120	DO i = nxlg, nxrg
1121	DO j = nysg, nyng
1122	nz_u_shift = topo_top_ind(j,i,1)
1123	nz_v_shift = topo_top_ind(j,i,2)
1124	nz_w_shift = topo_top_ind(j,i,3)
1125	nz_s_shift = topo_top_ind(j,i,0)
1126
1127	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1128
1129	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1130
1131	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1132
1133	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1134	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1135	ENDDO
1136	ENDDO
1137	ENDIF
1138	!
1139	!-- Initialization of the turbulence recycling method
1140	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. turbulent_inflow ) THEN
1141	!
1142	!-- First store the profiles to be used at the inflow.
1143	!-- These profiles are the (temporally) and horizontally averaged vertical profiles from the
1144	!-- prerun. Alternatively, prescribed profiles for u,v-components can be used.
1145	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1146
1147	IF ( use_prescribed_profile_data ) THEN
1148	mean_inflow_profiles(:,1) = u_init ! u
1149	mean_inflow_profiles(:,2) = v_init ! v
1150	ELSE
1151	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1152	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1153	ENDIF
1154	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1155	IF ( humidity ) mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1156	IF ( passive_scalar ) mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1157
1158	!
1159	!-- In case of complex terrain, determine vertical displacement at inflow boundary and adjust
1160	!-- mean inflow profiles
1161	IF ( complex_terrain ) THEN
1162	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1163	nz_u_shift_l = topo_top_ind(j,i,1)
1164	nz_v_shift_l = topo_top_ind(j,i,2)
1165	nz_w_shift_l = topo_top_ind(j,i,3)
1166	nz_s_shift_l = topo_top_ind(j,i,0)
1167	ELSE
1168	nz_u_shift_l = 0
1169	nz_v_shift_l = 0
1170	nz_w_shift_l = 0
1171	nz_s_shift_l = 0
1172	ENDIF
1173
1174	#if defined( __parallel )
1175	CALL MPI_ALLREDUCE( nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1176	CALL MPI_ALLREDUCE( nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1177	CALL MPI_ALLREDUCE( nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1178	CALL MPI_ALLREDUCE( nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, MPI_MAX, comm2d, ierr )
1179	#else
1180	nz_u_shift = nz_u_shift_l
1181	nz_v_shift = nz_v_shift_l
1182	nz_w_shift = nz_w_shift_l
1183	nz_s_shift = nz_s_shift_l
1184	#endif
1185
1186	mean_inflow_profiles(:,1) = 0.0_wp
1187	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1188
1189	mean_inflow_profiles(:,2) = 0.0_wp
1190	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1191
1192	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1193
1194	ENDIF
1195
1196	!
1197	!-- If necessary, adjust the horizontal flow field to the prescribed profiles
1198	IF ( use_prescribed_profile_data ) THEN
1199	DO i = nxlg, nxrg
1200	DO j = nysg, nyng
1201	DO k = nzb, nzt+1
1202	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1203	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1204	ENDDO
1205	ENDDO
1206	ENDDO
1207	ENDIF
1208
1209	!
1210	!-- Use these mean profiles at the inflow (provided that Dirichlet conditions are used)
1211	IF ( bc_dirichlet_l ) THEN
1212	DO j = nysg, nyng
1213	DO k = nzb, nzt+1
1214	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1215	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1216	w(k,j,nxlg:-1) = 0.0_wp
1217	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1218	IF ( humidity ) q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1219	IF ( passive_scalar ) s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1220	ENDDO
1221	ENDDO
1222	ENDIF
1223
1224	!
1225	!-- Calculate the damping factors to be used at the inflow. For a turbulent inflow the
1226	!-- turbulent fluctuations have to be limited vertically because otherwise the turbulent
1227	!-- inflow layer will grow in time.
1228	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1229	!
1230	!-- Default: use the inversion height calculated by the prerun; if this is zero,
1231	!-- inflow_damping_height must be explicitly specified.
1232	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1233	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1234	ELSE
1235	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1236	'explicitly specified because&the inversion height ', &
1237	'calculated by the prerun is zero.'
1238	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1239	ENDIF
1240
1241	ENDIF
1242
1243	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1244	!
1245	!-- Default for the transition range: one tenth of the undamped layer
1246	inflow_damping_width = 0.1_wp * inflow_damping_height
1247
1248	ENDIF
1249
1250	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1251
1252	DO k = nzb, nzt+1
1253
1254	IF ( zu(k) <= inflow_damping_height ) THEN
1255	inflow_damping_factor(k) = 1.0_wp
1256	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1257	inflow_damping_factor(k) = 1.0_wp - &
1258	( zu(k) - inflow_damping_height ) / inflow_damping_width
1259	ELSE
1260	inflow_damping_factor(k) = 0.0_wp
1261	ENDIF
1262
1263	ENDDO
1264
1265	ENDIF
1266
1267	!
1268	!-- Inside buildings set velocities back to zero
1269	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. topography /= 'flat' ) THEN
1270	!
1271	!-- Inside buildings set velocities back to zero.
1272	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1273	!-- maybe revise later.
1274	DO i = nxlg, nxrg
1275	DO j = nysg, nyng
1276	DO k = nzb, nzt
1277	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 1 ) )
1278	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 2 ) )
1279	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, BTEST( wall_flags_total_0(k,j,i), 3 ) )
1280	ENDDO
1281	ENDDO
1282	ENDDO
1283
1284	ENDIF
1285
1286	!
1287	!-- Calculate initial temperature field and other constants used in case of a sloping surface
1288	IF ( sloping_surface ) CALL init_slope
1289
1290	!
1291	!-- Initialize new time levels (only done in order to set boundary values including ghost points)
1292	pt_p = pt; u_p = u; v_p = v; w_p = w
1293	IF ( humidity ) THEN
1294	q_p = q
1295	ENDIF
1296	IF ( passive_scalar ) s_p = s
1297	!
1298	!-- Allthough tendency arrays are set in prognostic_equations, they have have to be predefined
1299	!-- here because they are used (but multiplied with 0) there before they are set.
1300	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1301	IF ( humidity ) THEN
1302	tq_m = 0.0_wp
1303	ENDIF
1304	IF ( passive_scalar ) ts_m = 0.0_wp
1305
1306	IF ( debug_output ) THEN
1307	CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1308	ENDIF
1309
1310	ELSE
1311	!
1312	!-- Actually this part of the programm should not be reached
1313	message_string = 'unknown initializing problem'
1314	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1315	ENDIF
1316
1317	!
1318	!-- Calculate the initial volume flow at the right and north boundary
1319	IF ( conserve_volume_flow ) THEN
1320
1321	IF ( use_prescribed_profile_data ) THEN
1322
1323	volume_flow_initial_l = 0.0_wp
1324	volume_flow_area_l = 0.0_wp
1325
1326	IF ( nxr == nx ) THEN
1327	DO j = nys, nyn
1328	DO k = nzb+1, nzt
1329	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1330	u_init(k) * dzw(k) &
1331	* MERGE( 1.0_wp, 0.0_wp, &
1332	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1333	)
1334
1335	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1336	* MERGE( 1.0_wp, 0.0_wp, &
1337	BTEST( wall_flags_total_0(k,j,nxr), 1 ) &
1338	)
1339	ENDDO
1340	ENDDO
1341	ENDIF
1342
1343	IF ( nyn == ny ) THEN
1344	DO i = nxl, nxr
1345	DO k = nzb+1, nzt
1346	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1347	v_init(k) * dzw(k) &
1348	* MERGE( 1.0_wp, 0.0_wp, &
1349	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1350	)
1351	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1352	* MERGE( 1.0_wp, 0.0_wp, &
1353	BTEST( wall_flags_total_0(k,nyn,i), 2 ) &
1354	)
1355	ENDDO
1356	ENDDO
1357	ENDIF
1358
1359	#if defined( __parallel )
1360	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1361	MPI_SUM, comm2d, ierr )
1362	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1363	comm2d, ierr )
1364
1365	#else
1366	volume_flow_initial = volume_flow_initial_l
1367	volume_flow_area = volume_flow_area_l
1368	#endif
1369
1370	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1371
1372	volume_flow_initial_l = 0.0_wp
1373	volume_flow_area_l = 0.0_wp
1374
1375	IF ( nxr == nx ) THEN
1376	DO j = nys, nyn
1377	DO k = nzb+1, nzt
1378	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1379	hom_sum(k,1,0) * dzw(k) &
1380	* MERGE( 1.0_wp, 0.0_wp, &
1381	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1382	)
1383	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1384	* MERGE( 1.0_wp, 0.0_wp, &
1385	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1386	)
1387	ENDDO
1388	ENDDO
1389	ENDIF
1390
1391	IF ( nyn == ny ) THEN
1392	DO i = nxl, nxr
1393	DO k = nzb+1, nzt
1394	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1395	hom_sum(k,2,0) * dzw(k) &
1396	* MERGE( 1.0_wp, 0.0_wp, &
1397	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1398	)
1399	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1400	* MERGE( 1.0_wp, 0.0_wp, &
1401	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1402	)
1403	ENDDO
1404	ENDDO
1405	ENDIF
1406
1407	#if defined( __parallel )
1408	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1409	MPI_SUM, comm2d, ierr )
1410	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1411	comm2d, ierr )
1412
1413	#else
1414	volume_flow_initial = volume_flow_initial_l
1415	volume_flow_area = volume_flow_area_l
1416	#endif
1417
1418	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1419
1420	volume_flow_initial_l = 0.0_wp
1421	volume_flow_area_l = 0.0_wp
1422
1423	IF ( nxr == nx ) THEN
1424	DO j = nys, nyn
1425	DO k = nzb+1, nzt
1426	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1427	u(k,j,nx) * dzw(k) &
1428	* MERGE( 1.0_wp, 0.0_wp, &
1429	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1430	)
1431	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1432	* MERGE( 1.0_wp, 0.0_wp, &
1433	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1434	)
1435	ENDDO
1436	ENDDO
1437	ENDIF
1438
1439	IF ( nyn == ny ) THEN
1440	DO i = nxl, nxr
1441	DO k = nzb+1, nzt
1442	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1443	v(k,ny,i) * dzw(k) &
1444	* MERGE( 1.0_wp, 0.0_wp, &
1445	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1446	)
1447	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1448	* MERGE( 1.0_wp, 0.0_wp, &
1449	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1450	)
1451	ENDDO
1452	ENDDO
1453	ENDIF
1454
1455	#if defined( __parallel )
1456	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1), 2, MPI_REAL, &
1457	MPI_SUM, comm2d, ierr )
1458	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), 2, MPI_REAL, MPI_SUM, &
1459	comm2d, ierr )
1460
1461	#else
1462	volume_flow_initial = volume_flow_initial_l
1463	volume_flow_area = volume_flow_area_l
1464	#endif
1465
1466	ENDIF
1467
1468	!
1469	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated from u\|v_bulk instead
1470	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1471	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1472	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1473	ENDIF
1474
1475	ENDIF
1476	!
1477	!-- In the following, surface properties can be further initialized with input from static driver
1478	!-- file.
1479	!-- At the moment this affects only default surfaces. For example, roughness length or sensible /
1480	!-- latent heat fluxes can be initialized heterogeneously for default surfaces. Therefore, a generic
1481	!-- routine from netcdf_data_input_mod is called to read a 2D array.
1482	IF ( input_pids_static ) THEN
1483	!
1484	!-- Allocate memory for possible static input
1485	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1486	tmp_2d%var = 0.0_wp
1487	!
1488	!-- Open the static input file
1489	#if defined( __netcdf )
1490	CALL open_read_file( TRIM( input_file_static ) // &
1491	TRIM( coupling_char ), pids_id )
1492
1493	CALL inquire_num_variables( pids_id, num_var_pids )
1494	!
1495	!-- Allocate memory to store variable names and read them
1496	ALLOCATE( vars_pids(1:num_var_pids) )
1497	CALL inquire_variable_names( pids_id, vars_pids )
1498	!
1499	!-- Input roughness length.
1500	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1501	!
1502	!-- Read _FillValue attribute
1503	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'z0' )
1504	!
1505	!-- Read variable
1506	CALL get_variable( pids_id, 'z0', tmp_2d%var, nxl, nxr, nys, nyn )
1507	!
1508	!-- Initialize roughness length. Note, z0 will be only initialized at default-type surfaces.
1509	!-- At natural or urban z0 is implicitly initialized by the respective parameter lists.
1510	!-- Initialize horizontal surface elements.
1511	CALL init_single_surface_properties( surf_def_h(0)%z0, tmp_2d%var, surf_def_h(0)%ns, &
1512	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1513	!
1514	!-- Initialize roughness also at vertical surface elements.
1515	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1516	!-- index arrays with their respective offset values.
1517	DO l = 0, 3
1518	CALL init_single_surface_properties( surf_def_v(l)%z0, tmp_2d%var, surf_def_v(l)%ns, &
1519	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1520	surf_def_v(l)%j+surf_def_v(l)%joff )
1521	ENDDO
1522
1523	ENDIF
1524	!
1525	!-- Input surface sensible heat flux.
1526	IF ( check_existence( vars_pids, 'shf' ) ) THEN
1527	!
1528	!-- Read _FillValue attribute
1529	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'shf' )
1530	!
1531	!-- Read variable
1532	CALL get_variable( pids_id, 'shf', tmp_2d%var, nxl, nxr, nys, nyn )
1533	!
1534	!-- Initialize heat flux. Note, shf will be only initialized at default-type surfaces. At
1535	!-- natural or urban shf is implicitly initialized by the respective parameter lists.
1536	!-- Initialize horizontal surface elements.
1537	CALL init_single_surface_properties( surf_def_h(0)%shf, tmp_2d%var, surf_def_h(0)%ns, &
1538	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1539	!
1540	!-- Initialize heat flux also at vertical surface elements.
1541	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1542	!-- index arrays with their respective offset values.
1543	DO l = 0, 3
1544	CALL init_single_surface_properties( surf_def_v(l)%shf, tmp_2d%var, surf_def_v(l)%ns, &
1545	tmp_2d%fill, surf_def_v(l)%i+surf_def_v(l)%ioff, &
1546	surf_def_v(l)%j+surf_def_v(l)%joff )
1547	ENDDO
1548
1549	ENDIF
1550	!
1551	!-- Input surface latent heat flux.
1552	IF ( humidity ) THEN
1553	IF ( check_existence( vars_pids, 'qsws' ) ) THEN
1554	!
1555	!-- Read _FillValue attribute
1556	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'qsws' )
1557	!
1558	!-- Read variable
1559	CALL get_variable( pids_id, 'qsws', tmp_2d%var, nxl, nxr, nys, nyn )
1560	!
1561	!-- Initialize latent heat flux. Note, qsws will be only initialized at default-type surfaces.
1562	!-- At natural or urban qsws is implicitly initialized by the respective parameter lists.
1563	!-- Initialize horizontal surface elements.
1564	CALL init_single_surface_properties( surf_def_h(0)%qsws, tmp_2d%var, surf_def_h(0)%ns,&
1565	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1566	!
1567	!-- Initialize latent heat flux also at vertical surface elements.
1568	!-- Note, the actual 2D input arrays are only defined on the subdomain. Therefore, pass the
1569	!-- index arrays with their respective offset values.
1570	DO l = 0, 3
1571	CALL init_single_surface_properties( surf_def_v(l)%qsws, tmp_2d%var, &
1572	surf_def_v(l)%ns, tmp_2d%fill, &
1573	surf_def_v(l)%i+surf_def_v(l)%ioff, &
1574	surf_def_v(l)%j+surf_def_v(l)%joff )
1575	ENDDO
1576
1577	ENDIF
1578	ENDIF
1579	!
1580	!-- Input passive scalar flux.
1581	IF ( passive_scalar ) THEN
1582	IF ( check_existence( vars_pids, 'ssws' ) ) THEN
1583	!
1584	!-- Read _FillValue attribute
1585	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, .FALSE., 'ssws' )
1586	!
1587	!-- Read variable
1588	CALL get_variable( pids_id, 'ssws', tmp_2d%var, nxl, nxr, nys, nyn )
1589	!
1590	!-- Initialize passive scalar flux. Initialize horizontal surface elements.
1591	CALL init_single_surface_properties( surf_def_h(0)%ssws, tmp_2d%var, surf_def_h(0)%ns,&
1592	tmp_2d%fill, surf_def_h(0)%i, surf_def_h(0)%j )
1593
1594	DO l = 0, 3
1595	CALL init_single_surface_properties( surf_def_v(l)%ssws, tmp_2d%var, &
1596	surf_def_v(l)%ns, tmp_2d%fill, &
1597	surf_def_v(l)%i+surf_def_v(l)%ioff, &
1598	surf_def_v(l)%j+surf_def_v(l)%joff )
1599	ENDDO
1600
1601	ENDIF
1602	ENDIF
1603	!
1604	!-- Additional variables, can be initialized the
1605	!-- same way.
1606
1607	!
1608	!-- Finally, close the input file and deallocate temporary arrays
1609	DEALLOCATE( vars_pids )
1610
1611	CALL close_input_file( pids_id )
1612	#endif
1613	DEALLOCATE( tmp_2d%var )
1614	ENDIF
1615	!
1616	!-- Finally, if random_heatflux is set, disturb shf at horizontal surfaces. Actually, this should be
1617	!-- done in surface_mod, where all other initializations of surface quantities are done. However,
1618	!-- this would create a ring dependency, hence, it is done here. Maybe delete disturb_heatflux and
1619	!-- tranfer the respective code directly into the initialization in surface_mod.
1620	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1621	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1622
1623	IF ( use_surface_fluxes .AND. constant_heatflux .AND. random_heatflux ) THEN
1624	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1625	IF ( surf_lsm_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h(0) )
1626	IF ( surf_usm_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_usm_h(0) )
1627	ENDIF
1628	ENDIF
1629
1630	!
1631	!-- Compute total sum of grid points and the mean surface level height for each statistic region.
1632	!-- These are mainly used for horizontal averaging of turbulence statistics.
1633	!-- ngp_2dh: number of grid points of a horizontal cross section through the respective statistic
1634	!-- region
1635	!-- ngp_3d: number of grid points of the respective statistic region
1636	ngp_2dh_outer_l = 0
1637	ngp_2dh_outer = 0
1638	ngp_2dh_s_inner_l = 0
1639	ngp_2dh_s_inner = 0
1640	ngp_2dh_l = 0
1641	ngp_2dh = 0
1642	ngp_3d_inner_l = 0.0_wp
1643	ngp_3d_inner = 0
1644	ngp_3d = 0
1645	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1646
1647	mean_surface_level_height = 0.0_wp
1648	mean_surface_level_height_l = 0.0_wp
1649	!
1650	!-- To do: New concept for these non-topography grid points!
1651	DO sr = 0, statistic_regions
1652	DO i = nxl, nxr
1653	DO j = nys, nyn
1654	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1655	!
1656	!-- All xy-grid points
1657	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1658	!
1659	!-- Determine mean surface-level height. In case of downward-facing walls are present,
1660	!-- more than one surface level exist.
1661	!-- In this case, use the lowest surface-level height.
1662	IF ( surf_def_h(0)%start_index(j,i) <= surf_def_h(0)%end_index(j,i) ) THEN
1663	m = surf_def_h(0)%start_index(j,i)
1664	k = surf_def_h(0)%k(m)
1665	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1666	ENDIF
1667	IF ( surf_lsm_h(0)%start_index(j,i) <= surf_lsm_h(0)%end_index(j,i) ) THEN
1668	m = surf_lsm_h(0)%start_index(j,i)
1669	k = surf_lsm_h(0)%k(m)
1670	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1671	ENDIF
1672	IF ( surf_usm_h(0)%start_index(j,i) <= surf_usm_h(0)%end_index(j,i) ) THEN
1673	m = surf_usm_h(0)%start_index(j,i)
1674	k = surf_usm_h(0)%k(m)
1675	mean_surface_level_height_l(sr) = mean_surface_level_height_l(sr) + zw(k-1)
1676	ENDIF
1677
1678	k_surf = k - 1
1679
1680	DO k = nzb, nzt+1
1681	!
1682	!-- xy-grid points above topography
1683	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1684	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 24 ) )
1685
1686	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1687	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 22 ) )
1688
1689	ENDDO
1690	!
1691	!-- All grid points of the total domain above topography
1692	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1693
1694
1695
1696	ENDIF
1697	ENDDO
1698	ENDDO
1699	ENDDO
1700
1701	sr = statistic_regions + 1
1702	#if defined( __parallel )
1703	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1704	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1705	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1706	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, MPI_INTEGER, MPI_SUM, &
1707	comm2d, ierr )
1708	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1709	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), (nz+2)*sr, MPI_INTEGER, &
1710	MPI_SUM, comm2d, ierr )
1711	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1712	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, MPI_SUM, comm2d, &
1713	ierr )
1714	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1715	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1716	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), mean_surface_level_height(0), sr, MPI_REAL,&
1717	MPI_SUM, comm2d, ierr )
1718	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1719	#else
1720	ngp_2dh = ngp_2dh_l
1721	ngp_2dh_outer = ngp_2dh_outer_l
1722	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1723	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1724	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1725	#endif
1726
1727	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1728	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1729
1730	!
1731	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics, buoyancy, etc. A
1732	!-- zero value will occur for cases where all grid points of the respective subdomain lie below the
1733	!-- surface topography
1734	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1735	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), ngp_3d_inner(:) )
1736	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1737
1738	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, ngp_3d_inner_l, &
1739	ngp_3d_inner_tmp )
1740
1741	!
1742	!-- Initializae 3D offline nesting in COSMO model and read data from
1743	!-- external NetCDF file.
1744	IF ( nesting_offline ) CALL nesting_offl_init
1745	!
1746	!-- Initialize quantities for special advections schemes
1747	CALL init_advec
1748
1749	!
1750	!-- Impose random perturbation on the horizontal velocity field and then
1751	!-- remove the divergences from the velocity field at the initial stage
1752	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1753	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1754	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1755
1756	IF ( debug_output ) THEN
1757	CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1758	ENDIF
1759	!
1760	!-- Needed for both disturb_field and pres
1761	!$ACC DATA &
1762	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1763	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1764	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1765
1766	CALL disturb_field( 'u', tend, u )
1767	CALL disturb_field( 'v', tend, v )
1768
1769	!$ACC DATA &
1770	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1771	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1772	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1773	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1774	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1775	!$ACC COPYIN(wall_flags_total_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1776	!$ACC COPYIN(bc_h(0:1)) &
1777	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1778	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1779	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1780	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1781	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1782	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1783
1784	n_sor = nsor_ini
1785	CALL pres
1786	n_sor = nsor
1787
1788	!$ACC END DATA
1789	!$ACC END DATA
1790
1791	IF ( debug_output ) THEN
1792	CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1793	ENDIF
1794
1795	ENDIF
1796
1797	IF ( .NOT. ocean_mode ) THEN
1798
1799	ALLOCATE( hyp(nzb:nzt+1) )
1800	ALLOCATE( d_exner(nzb:nzt+1) )
1801	ALLOCATE( exner(nzb:nzt+1) )
1802	ALLOCATE( hyrho(nzb:nzt+1) )
1803	!
1804	!-- Check temperature in case of too large domain height
1805	DO k = nzb, nzt+1
1806	IF ( ( pt_surface * exner_function( surface_pressure * 100.0_wp ) - g/c_p * zu(k) ) &
1807	< 0.0_wp ) THEN
1808	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, ') = ', zu(k)
1809	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1810	ENDIF
1811	ENDDO
1812
1813	!
1814	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1815	hyp = barometric_formula( zu, pt_surface * exner_function( surface_pressure * 100.0_wp ),&
1816	surface_pressure * 100.0_wp )
1817	d_exner = exner_function_invers( hyp )
1818	exner = 1.0_wp / exner_function_invers( hyp )
1819	hyrho = ideal_gas_law_rho_pt( hyp, pt_init )
1820	!
1821	!-- Compute reference density
1822	rho_surface = ideal_gas_law_rho( surface_pressure * 100.0_wp, &
1823	pt_surface * exner_function( surface_pressure * 100.0_wp ) )
1824
1825	ENDIF
1826
1827	!
1828	!-- If required, initialize particles
1829	IF ( agents_active ) CALL mas_init
1830	!
1831	!-- Initialization of synthetic turbulence generator
1832	IF ( use_syn_turb_gen ) CALL stg_init
1833	!
1834	!-- Initializing actions for all other modules
1835	CALL module_interface_init
1836	!
1837	!-- Initialize surface layer (done after LSM as roughness length are required for initialization
1838	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1839	!
1840	!-- Initialize surface data output
1841	IF ( surface_output ) CALL surface_data_output_init
1842	!
1843	!-- Initialize the ws-scheme.
1844	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1845	!
1846	!-- Perform post-initializing checks for all other modules
1847	CALL module_interface_init_checks
1848
1849	!
1850	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1851	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1852	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1853	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1854	CALL ls_forcing_surf( simulated_time )
1855	ENDIF
1856	ENDIF
1857	!
1858	!-- Setting weighting factors for calculation of perturbation pressure and turbulent quantities from
1859	!-- the RK substeps.
1860	IF ( TRIM( timestep_scheme ) == 'runge-kutta-3' ) THEN ! for RK3-method
1861
1862	weight_substep(1) = 1._wp/6._wp
1863	weight_substep(2) = 3._wp/10._wp
1864	weight_substep(3) = 8._wp/15._wp
1865
1866	weight_pres(1) = 1._wp/3._wp
1867	weight_pres(2) = 5._wp/12._wp
1868	weight_pres(3) = 1._wp/4._wp
1869
1870	ELSEIF ( TRIM( timestep_scheme ) == 'runge-kutta-2' ) THEN ! for RK2-method
1871
1872	weight_substep(1) = 1._wp/2._wp
1873	weight_substep(2) = 1._wp/2._wp
1874
1875	weight_pres(1) = 1._wp/2._wp
1876	weight_pres(2) = 1._wp/2._wp
1877
1878	ELSE ! for Euler-method
1879
1880	weight_substep(1) = 1.0_wp
1881	weight_pres(1) = 1.0_wp
1882
1883	ENDIF
1884
1885	!
1886	!-- Initialize Rayleigh damping factors
1887	rdf = 0.0_wp
1888	rdf_sc = 0.0_wp
1889	IF ( rayleigh_damping_factor /= 0.0_wp ) THEN
1890
1891	IF ( .NOT. ocean_mode ) THEN
1892	DO k = nzb+1, nzt
1893	IF ( zu(k) >= rayleigh_damping_height ) THEN
1894	rdf(k) = rayleigh_damping_factor * &
1895	( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
1896	/ ( zu(nzt) - rayleigh_damping_height ) ) &
1897	)**2
1898	ENDIF
1899	ENDDO
1900	ELSE
1901	!
1902	!-- In ocean mode, rayleigh damping is applied in the lower part of the model domain
1903	DO k = nzt, nzb+1, -1
1904	IF ( zu(k) <= rayleigh_damping_height ) THEN
1905	rdf(k) = rayleigh_damping_factor * &
1906	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1907	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1908	)**2
1909	ENDIF
1910	ENDDO
1911	ENDIF
1912
1913	ENDIF
1914	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1915
1916	!
1917	!-- Initialize the starting level and the vertical smoothing factor used for the external pressure
1918	!-- gradient
1919	dp_smooth_factor = 1.0_wp
1920	IF ( dp_external ) THEN
1921	!
1922	!-- Set the starting level dp_level_ind_b only if it has not been set before (e.g. in init_grid).
1923	IF ( dp_level_ind_b == 0 ) THEN
1924	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1925	dp_level_ind_b = ind_array(1) - 1 + nzb
1926	! MINLOC uses lower array bound 1
1927	ENDIF
1928	IF ( dp_smooth ) THEN
1929	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1930	DO k = dp_level_ind_b+1, nzt
1931	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1932	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1933	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1934	ENDDO
1935	ENDIF
1936	ENDIF
1937
1938	!
1939	!-- Initialize damping zone for the potential temperature in case of non-cyclic lateral boundaries.
1940	!-- The damping zone has the maximum value at the inflow boundary and decreases to zero at
1941	!-- pt_damping_width.
1942	ptdf_x = 0.0_wp
1943	ptdf_y = 0.0_wp
1944	IF ( bc_lr_dirrad ) THEN
1945	DO i = nxl, nxr
1946	IF ( ( i * dx ) < pt_damping_width ) THEN
1947	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1948	REAL( pt_damping_width - i * dx, KIND=wp ) / &
1949	REAL( pt_damping_width, KIND=wp ) ) )**2
1950	ENDIF
1951	ENDDO
1952	ELSEIF ( bc_lr_raddir ) THEN
1953	DO i = nxl, nxr
1954	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1955	ptdf_x(i) = pt_damping_factor * SIN( pi * 0.5_wp * &
1956	( ( i - nx ) * dx + pt_damping_width ) / &
1957	REAL( pt_damping_width, KIND=wp ) )**2
1958	ENDIF
1959	ENDDO
1960	ELSEIF ( bc_ns_dirrad ) THEN
1961	DO j = nys, nyn
1962	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1963	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1964	( ( j - ny ) * dy + pt_damping_width ) / &
1965	REAL( pt_damping_width, KIND=wp ) )**2
1966	ENDIF
1967	ENDDO
1968	ELSEIF ( bc_ns_raddir ) THEN
1969	DO j = nys, nyn
1970	IF ( ( j * dy ) < pt_damping_width ) THEN
1971	ptdf_y(j) = pt_damping_factor * SIN( pi * 0.5_wp * &
1972	( pt_damping_width - j * dy ) / &
1973	REAL( pt_damping_width, KIND=wp ) )**2
1974	ENDIF
1975	ENDDO
1976	ENDIF
1977
1978	!
1979	!-- Input binary data file is not needed anymore. This line must be placed after call of user_init!
1980	CALL close_file( 13 )
1981	!
1982	!-- In case of nesting, put an barrier to assure that all parent and child domains finished
1983	!-- initialization.
1984	#if defined( __parallel )
1985	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
1986	#endif
1987
1988
1989	CALL location_message( 'model initialization', 'finished' )
1990
1991	END SUBROUTINE init_3d_model

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