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init_3d_model.f90 @ 4447

Last change on this file since 4447 was 4392, checked in by pavelkrc, 5 years ago

Merge branch resler (updated documentation, optional flux tracing, bugfix)

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/palm/branches/chemistry/SOURCE/init_3d_model.f90	2047-3190,3218-3297
/palm/branches/forwind/SOURCE/init_3d_model.f90	1564-1913
/palm/branches/mosaik_M2/init_3d_model.f90	2360-3471
/palm/branches/palm4u/SOURCE/init_3d_model.f90	2540-2692
/palm/branches/rans/SOURCE/init_3d_model.f90	2078-3128
/palm/branches/resler/SOURCE/init_3d_model.f90	2023-4391
/palm/branches/salsa/SOURCE/init_3d_model.f90	2503-3581

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1	!> @file init_3d_model.f90
2	!------------------------------------------------------------------------------!
3	! This file is part of the PALM model system.
4	!
5	! PALM is free software: you can redistribute it and/or modify it under the
6	! terms of the GNU General Public License as published by the Free Software
7	! Foundation, either version 3 of the License, or (at your option) any later
8	! version.
9	!
10	! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
11	! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
12	! A PARTICULAR PURPOSE. See the GNU General Public License for more details.
13	!
14	! You should have received a copy of the GNU General Public License along with
15	! PALM. If not, see <http://www.gnu.org/licenses/>.
16	!
17	! Copyright 1997-2020 Leibniz Universitaet Hannover
18	!------------------------------------------------------------------------------!
19	!
20	! Current revisions:
21	! ------------------
22	!
23	!
24	! Former revisions:
25	! -----------------
26	! $Id: init_3d_model.f90 4392 2020-01-31 16:14:57Z oliver.maas $
27	! Overwrite u_init, v_init, pt_init, q_init and s_init with hom for all
28	! cyclic_fill-cases, not only for turbulent_inflow = .TRUE.
29	!
30	! 4360 2020-01-07 11:25:50Z suehring
31	! Introduction of wall_flags_total_0, which currently sets bits based on static
32	! topography information used in wall_flags_static_0
33	!
34	! 4329 2019-12-10 15:46:36Z motisi
35	! Renamed wall_flags_0 to wall_flags_static_0
36	!
37	! 4286 2019-10-30 16:01:14Z resler
38	! implement new palm_date_time_mod
39	!
40	! 4223 2019-09-10 09:20:47Z gronemeier
41	! Deallocate temporary string array since it may be re-used to read different
42	! input data in other modules
43	!
44	! 4186 2019-08-23 16:06:14Z suehring
45	! Design change, use variables defined in netcdf_data_input_mod to read netcd
46	! variables rather than define local ones.
47	!
48	! 4185 2019-08-23 13:49:38Z oliver.maas
49	! For initializing_actions = ' cyclic_fill':
50	! Overwrite u_init, v_init, pt_init, q_init and s_init with the
51	! (temporally) and horizontally averaged vertical profiles from the end
52	! of the prerun, because these profiles shall be used as the basic state
53	! for the rayleigh damping and the pt_damping.
54	!
55	! 4182 2019-08-22 15:20:23Z scharf
56	! Corrected "Former revisions" section
57	!
58	! 4168 2019-08-16 13:50:17Z suehring
59	! Replace function get_topography_top_index by topo_top_ind
60	!
61	! 4151 2019-08-09 08:24:30Z suehring
62	! Add netcdf directive around input calls (fix for last commit)
63	!
64	! 4150 2019-08-08 20:00:47Z suehring
65	! Input of additional surface variables independent on land- or urban-surface
66	! model
67	!
68	! 4131 2019-08-02 11:06:18Z monakurppa
69	! Allocate sums and sums_l to allow profile output for salsa variables.
70	!
71	! 4130 2019-08-01 13:04:13Z suehring
72	! Effectively reduce 3D initialization to 1D initial profiles. This is because
73	! 3D initialization produces structures in the w-component that are correlated
74	! with the processor grid for some unknown reason
75	!
76	! 4090 2019-07-11 15:06:47Z Giersch
77	! Unused variables removed
78	!
79	! 4088 2019-07-11 13:57:56Z Giersch
80	! Pressure and density profile calculations revised using basic functions
81	!
82	! 4048 2019-06-21 21:00:21Z knoop
83	! Further modularization of particle code components
84	!
85	! 4017 2019-06-06 12:16:46Z schwenkel
86	! Convert most location messages to debug messages to reduce output in
87	! job logfile to a minimum
88	!
89	!
90	! unused variable removed
91	!
92	! 3937 2019-04-29 15:09:07Z suehring
93	! Move initialization of synthetic turbulence generator behind initialization
94	! of offline nesting. Remove call for stg_adjust, as this is now already done
95	! in stg_init.
96	!
97	! 3900 2019-04-16 15:17:43Z suehring
98	! Fix problem with LOD = 2 initialization
99	!
100	! 3885 2019-04-11 11:29:34Z kanani
101	! Changes related to global restructuring of location messages and introduction
102	! of additional debug messages
103	!
104	! 3849 2019-04-01 16:35:16Z knoop
105	! Move initialization of rmask before initializing user_init_arrays
106	!
107	! 3711 2019-01-31 13:44:26Z knoop
108	! Introduced module_interface_init_checks for post-init checks in modules
109	!
110	! 3700 2019-01-26 17:03:42Z knoop
111	! Some interface calls moved to module_interface + cleanup
112	!
113	! 3648 2019-01-02 16:35:46Z suehring
114	! Rename subroutines for surface-data output
115	!
116	! Revision 1.1 1998/03/09 16:22:22 raasch
117	! Initial revision
118	!
119	!
120	! Description:
121	! ------------
122	!> Allocation of arrays and initialization of the 3D model via
123	!> a) pre-run the 1D model
124	!> or
125	!> b) pre-set constant linear profiles
126	!> or
127	!> c) read values of a previous run
128	!------------------------------------------------------------------------------!
129	SUBROUTINE init_3d_model
130
131
132	USE advec_ws
133
134	USE arrays_3d
135
136	USE basic_constants_and_equations_mod, &
137	ONLY: c_p, g, l_v, pi, exner_function, exner_function_invers, &
138	ideal_gas_law_rho, ideal_gas_law_rho_pt, barometric_formula
139
140	USE bulk_cloud_model_mod, &
141	ONLY: bulk_cloud_model
142
143	USE chem_modules, &
144	ONLY: max_pr_cs ! ToDo: this dependency needs to be removed cause it is ugly #new_dom
145
146	USE control_parameters
147
148	USE grid_variables, &
149	ONLY: dx, dy, ddx2_mg, ddy2_mg
150
151	USE indices
152
153	USE kinds
154
155	USE lsf_nudging_mod, &
156	ONLY: ls_forcing_surf
157
158	USE model_1d_mod, &
159	ONLY: init_1d_model, l1d, u1d, v1d
160
161	USE module_interface, &
162	ONLY: module_interface_init_arrays, &
163	module_interface_init, &
164	module_interface_init_checks
165
166	USE multi_agent_system_mod, &
167	ONLY: agents_active, mas_init
168
169	USE netcdf_interface, &
170	ONLY: dots_max
171
172	USE netcdf_data_input_mod, &
173	ONLY: char_fill, &
174	check_existence, &
175	close_input_file, &
176	get_attribute, &
177	get_variable, &
178	init_3d, &
179	input_pids_static, &
180	inquire_num_variables, &
181	inquire_variable_names, &
182	input_file_static, &
183	netcdf_data_input_init_3d, &
184	num_var_pids, &
185	open_read_file, &
186	pids_id, &
187	real_2d, &
188	vars_pids
189
190	USE nesting_offl_mod, &
191	ONLY: nesting_offl_init
192
193	USE palm_date_time_mod, &
194	ONLY: set_reference_date_time
195
196	USE pegrid
197
198	#if defined( __parallel )
199	USE pmc_interface, &
200	ONLY: nested_run
201	#endif
202
203	USE random_function_mod
204
205	USE random_generator_parallel, &
206	ONLY: init_parallel_random_generator
207
208	USE read_restart_data_mod, &
209	ONLY: rrd_read_parts_of_global, rrd_local
210
211	USE statistics, &
212	ONLY: hom, hom_sum, mean_surface_level_height, pr_palm, rmask, &
213	statistic_regions, sums, sums_divnew_l, sums_divold_l, sums_l, &
214	sums_l_l, sums_wsts_bc_l, ts_value, &
215	weight_pres, weight_substep
216
217	USE synthetic_turbulence_generator_mod, &
218	ONLY: stg_init, use_syn_turb_gen
219
220	USE surface_layer_fluxes_mod, &
221	ONLY: init_surface_layer_fluxes
222
223	USE surface_mod, &
224	ONLY : init_single_surface_properties, &
225	init_surface_arrays, &
226	init_surfaces, &
227	surf_def_h, &
228	surf_def_v, &
229	surf_lsm_h, &
230	surf_usm_h
231
232	#if defined( _OPENACC )
233	USE surface_mod, &
234	ONLY : bc_h
235	#endif
236
237	USE surface_data_output_mod, &
238	ONLY: surface_data_output_init
239
240	USE transpose_indices
241
242	IMPLICIT NONE
243
244	INTEGER(iwp) :: i !< grid index in x direction
245	INTEGER(iwp) :: ind_array(1) !< dummy used to determine start index for external pressure forcing
246	INTEGER(iwp) :: j !< grid index in y direction
247	INTEGER(iwp) :: k !< grid index in z direction
248	INTEGER(iwp) :: k_surf !< surface level index
249	INTEGER(iwp) :: l !< running index over surface orientation
250	INTEGER(iwp) :: m !< index of surface element in surface data type
251	INTEGER(iwp) :: nz_u_shift !< topography-top index on u-grid, used to vertically shift initial profiles
252	INTEGER(iwp) :: nz_v_shift !< topography-top index on v-grid, used to vertically shift initial profiles
253	INTEGER(iwp) :: nz_w_shift !< topography-top index on w-grid, used to vertically shift initial profiles
254	INTEGER(iwp) :: nz_s_shift !< topography-top index on scalar-grid, used to vertically shift initial profiles
255	INTEGER(iwp) :: nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
256	INTEGER(iwp) :: nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
257	INTEGER(iwp) :: nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
258	INTEGER(iwp) :: nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles
259	INTEGER(iwp) :: nzt_l !< index of top PE boundary for multigrid level
260	INTEGER(iwp) :: sr !< index of statistic region
261
262	INTEGER(iwp), DIMENSION(:), ALLOCATABLE :: ngp_2dh_l !< toal number of horizontal grid points in statistical region on subdomain
263
264	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_outer_l !< number of horizontal non-wall bounded grid points on subdomain
265	INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE :: ngp_2dh_s_inner_l !< number of horizontal non-topography grid points on subdomain
266
267
268
269	REAL(wp), DIMENSION(:), ALLOCATABLE :: init_l !< dummy array used for averaging 3D data to obtain inital profiles
270	REAL(wp), DIMENSION(:), ALLOCATABLE :: p_hydrostatic !< hydrostatic pressure
271
272	REAL(wp) :: dx_l !< grid spacing along x on different multigrid level
273	REAL(wp) :: dy_l !< grid spacing along y on different multigrid level
274
275	REAL(wp), DIMENSION(1:3) :: volume_flow_area_l !< area of lateral and top model domain surface on local subdomain
276	REAL(wp), DIMENSION(1:3) :: volume_flow_initial_l !< initial volume flow into model domain
277
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
282	TYPE(real_2d) :: tmp_2d !< temporary variable to input additional surface-data from static file
283
284	CALL location_message( 'model initialization', 'start' )
285	!
286	!-- Set reference date-time
287	CALL set_reference_date_time( date_time_str=origin_date_time )
288
289	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'start' )
290	!
291	!-- Allocate arrays
292	ALLOCATE( mean_surface_level_height(0:statistic_regions), &
293	mean_surface_level_height_l(0:statistic_regions), &
294	ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions), &
295	ngp_3d(0:statistic_regions), &
296	ngp_3d_inner(0:statistic_regions), &
297	ngp_3d_inner_l(0:statistic_regions), &
298	ngp_3d_inner_tmp(0:statistic_regions), &
299	sums_divnew_l(0:statistic_regions), &
300	sums_divold_l(0:statistic_regions) )
301	ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
302	ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions), &
303	ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions), &
304	ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions), &
305	ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions), &
306	rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions), &
307	sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa), &
308	sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs+max_pr_salsa,0:threads_per_task-1), &
309	sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1), &
310	sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions) )
311	ALLOCATE( ts_value(dots_max,0:statistic_regions) )
312	ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )
313
314	ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr), &
315	p(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
316	tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
317
318	ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
319	pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
320	u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
321	u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
322	u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
323	v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
324	v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
325	v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
326	w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
327	w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
328	w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
329	IF ( .NOT. neutral ) THEN
330	ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
331	ENDIF
332	!
333	!-- Pre-set masks for regional statistics. Default is the total model domain.
334	!-- Ghost points are excluded because counting values at the ghost boundaries
335	!-- would bias the statistics
336	rmask = 1.0_wp
337	rmask(:,nxlg:nxl-1,:) = 0.0_wp; rmask(:,nxr+1:nxrg,:) = 0.0_wp
338	rmask(nysg:nys-1,:,:) = 0.0_wp; rmask(nyn+1:nyng,:,:) = 0.0_wp
339	!
340	!-- Following array is required for perturbation pressure within the iterative
341	!-- pressure solvers. For the multistep schemes (Runge-Kutta), array p holds
342	!-- the weighted average of the substeps and cannot be used in the Poisson
343	!-- solver.
344	IF ( psolver == 'sor' ) THEN
345	ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
346	ELSEIF ( psolver(1:9) == 'multigrid' ) THEN
347	!
348	!-- For performance reasons, multigrid is using one ghost layer only
349	ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
350	ENDIF
351
352	!
353	!-- Array for storing constant coeffficients of the tridiagonal solver
354	IF ( psolver == 'poisfft' ) THEN
355	ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
356	ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
357	ENDIF
358
359	IF ( humidity ) THEN
360	!
361	!-- 3D-humidity
362	ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
363	q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
364	q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
365	vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
366	ENDIF
367
368	IF ( passive_scalar ) THEN
369
370	!
371	!-- 3D scalar arrays
372	ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
373	s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg), &
374	s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
375
376	ENDIF
377
378	!
379	!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to
380	!-- non-zero values later in ocean_init
381	ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1), &
382	v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
383	u_stokes_zu(:) = 0.0_wp
384	u_stokes_zw(:) = 0.0_wp
385	v_stokes_zu(:) = 0.0_wp
386	v_stokes_zw(:) = 0.0_wp
387
388	!
389	!-- Allocation of anelastic and Boussinesq approximation specific arrays
390	ALLOCATE( p_hydrostatic(nzb:nzt+1) )
391	ALLOCATE( rho_air(nzb:nzt+1) )
392	ALLOCATE( rho_air_zw(nzb:nzt+1) )
393	ALLOCATE( drho_air(nzb:nzt+1) )
394	ALLOCATE( drho_air_zw(nzb:nzt+1) )
395	!
396	!-- Density profile calculation for anelastic and Boussinesq approximation
397	!-- In case of a Boussinesq approximation, a constant density is calculated
398	!-- mainly for output purposes. This density do not need to be considered
399	!-- in the model's system of equations.
400	IF ( TRIM( approximation ) == 'anelastic' ) THEN
401	DO k = nzb, nzt+1
402	p_hydrostatic(k) = barometric_formula(zu(k), pt_surface * &
403	exner_function(surface_pressure * 100.0_wp), &
404	surface_pressure * 100.0_wp)
405
406	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(k))
407	ENDDO
408
409	DO k = nzb, nzt
410	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
411	ENDDO
412
413	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
414	+ 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt) )
415
416	ELSE
417	DO k = nzb, nzt+1
418	p_hydrostatic(k) = barometric_formula(zu(nzb), pt_surface * &
419	exner_function(surface_pressure * 100.0_wp), &
420	surface_pressure * 100.0_wp)
421
422	rho_air(k) = ideal_gas_law_rho_pt(p_hydrostatic(k), pt_init(nzb))
423	ENDDO
424
425	DO k = nzb, nzt
426	rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
427	ENDDO
428
429	rho_air_zw(nzt+1) = rho_air_zw(nzt) &
430	+ 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
480	!-- grid levels with 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) + &
499	(rho_air(nzb) - rho_air(nzb+1))
500
501	dzw_mg(:,maximum_grid_level) = dzw
502	rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
503	nzt_l = nzt
504	DO l = maximum_grid_level-1, 1, -1
505	dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
506	dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
507	rho_air_mg(nzb,l) = rho_air_mg(nzb,l+1) + (rho_air_mg(nzb,l+1) - 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) - rho_air_zw_mg(nzb+1,l+1))
509	rho_air_mg(nzb+1,l) = rho_air_mg(nzb+1,l+1)
510	rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
511	nzt_l = nzt_l / 2
512	DO k = 2, nzt_l+1
513	dzu_mg(k,l) = dzu_mg(2k-2,l+1) + dzu_mg(2k-1,l+1)
514	dzw_mg(k,l) = dzw_mg(2k-2,l+1) + dzw_mg(2k-1,l+1)
515	rho_air_mg(k,l) = rho_air_mg(2*k-1,l+1)
516	rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
517	ENDDO
518	ENDDO
519
520	nzt_l = nzt
521	dx_l = dx
522	dy_l = dy
523	DO l = maximum_grid_level, 1, -1
524	ddx2_mg(l) = 1.0_wp / dx_l**2
525	ddy2_mg(l) = 1.0_wp / dy_l**2
526	DO k = nzb+1, nzt_l
527	f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
528	f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l) * dzw_mg(k,l) )
529	f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
530	* rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
531	ENDDO
532	nzt_l = nzt_l / 2
533	dx_l = dx_l * 2.0_wp
534	dy_l = dy_l * 2.0_wp
535	ENDDO
536
537	ENDIF
538
539	!
540	!-- 1D-array for large scale subsidence velocity
541	IF ( .NOT. ALLOCATED( w_subs ) ) THEN
542	ALLOCATE ( w_subs(nzb:nzt+1) )
543	w_subs = 0.0_wp
544	ENDIF
545
546	!
547	!-- Arrays to store velocity data from t-dt and the phase speeds which
548	!-- are needed for radiation boundary conditions
549	IF ( bc_radiation_l ) THEN
550	ALLOCATE( u_m_l(nzb:nzt+1,nysg:nyng,1:2), &
551	v_m_l(nzb:nzt+1,nysg:nyng,0:1), &
552	w_m_l(nzb:nzt+1,nysg:nyng,0:1) )
553	ENDIF
554	IF ( bc_radiation_r ) THEN
555	ALLOCATE( u_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
556	v_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx), &
557	w_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx) )
558	ENDIF
559	IF ( bc_radiation_l .OR. bc_radiation_r ) THEN
560	ALLOCATE( c_u(nzb:nzt+1,nysg:nyng), c_v(nzb:nzt+1,nysg:nyng), &
561	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), &
575	c_w(nzb:nzt+1,nxlg:nxrg) )
576	ENDIF
577	IF ( bc_radiation_l .OR. bc_radiation_r .OR. bc_radiation_s .OR. &
578	bc_radiation_n ) THEN
579	ALLOCATE( c_u_m_l(nzb:nzt+1), c_v_m_l(nzb:nzt+1), c_w_m_l(nzb:nzt+1) )
580	ALLOCATE( c_u_m(nzb:nzt+1), c_v_m(nzb:nzt+1), c_w_m(nzb:nzt+1) )
581	ENDIF
582
583	!
584	!-- Initial assignment of the pointers
585	IF ( .NOT. neutral ) THEN
586	pt => pt_1; pt_p => pt_2; tpt_m => pt_3
587	ELSE
588	pt => pt_1; pt_p => pt_1; tpt_m => pt_3
589	ENDIF
590	u => u_1; u_p => u_2; tu_m => u_3
591	v => v_1; v_p => v_2; tv_m => v_3
592	w => w_1; w_p => w_2; tw_m => w_3
593
594	IF ( humidity ) THEN
595	q => q_1; q_p => q_2; tq_m => q_3
596	vpt => vpt_1
597	ENDIF
598
599	IF ( passive_scalar ) THEN
600	s => s_1; s_p => s_2; ts_m => s_3
601	ENDIF
602
603	!
604	!-- Initialize surface arrays
605	CALL init_surface_arrays
606	!
607	!-- Allocate arrays for other modules
608	CALL module_interface_init_arrays
609
610
611	!
612	!-- Allocate arrays containing the RK coefficient for calculation of
613	!-- perturbation pressure and turbulent fluxes. At this point values are
614	!-- set for pressure calculation during initialization (where no timestep
615	!-- is done). Further below the values needed within the timestep scheme
616	!-- will be set.
617	ALLOCATE( weight_substep(1:intermediate_timestep_count_max), &
618	weight_pres(1:intermediate_timestep_count_max) )
619	weight_substep = 1.0_wp
620	weight_pres = 1.0_wp
621	intermediate_timestep_count = 0 ! needed when simulated_time = 0.0
622
623	IF ( debug_output ) CALL debug_message( 'allocating arrays', 'end' )
624
625	!
626	!-- Initialize time series
627	ts_value = 0.0_wp
628
629	!
630	!-- Initialize local summation arrays for routine flow_statistics.
631	!-- This is necessary because they may not yet have been initialized when they
632	!-- are called from flow_statistics (or - depending on the chosen model run -
633	!-- are never initialized)
634	sums_divnew_l = 0.0_wp
635	sums_divold_l = 0.0_wp
636	sums_l_l = 0.0_wp
637	sums_wsts_bc_l = 0.0_wp
638
639	!
640	!-- Initialize model variables
641	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
642	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
643	!
644	!-- Initialization with provided input data derived from larger-scale model
645	IF ( INDEX( initializing_actions, 'inifor' ) /= 0 ) THEN
646	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'start' )
647	!
648	!-- Read initial 1D profiles or 3D data from NetCDF file, depending
649	!-- on the provided level-of-detail.
650	!-- At the moment, only u, v, w, pt and q are provided.
651	CALL netcdf_data_input_init_3d
652	!
653	!-- Please note, Inifor provides data from nzb+1 to nzt.
654	!-- Bottom and top boundary conditions for Inifor profiles are already
655	!-- set (just after reading), so that this is not necessary here.
656	!-- Depending on the provided level-of-detail, initial Inifor data is
657	!-- either stored on data type (lod=1), or directly on 3D arrays (lod=2).
658	!-- In order to obtain also initial profiles in case of lod=2 (which
659	!-- is required for e.g. damping), average over 3D data.
660	IF( init_3d%lod_u == 1 ) THEN
661	u_init = init_3d%u_init
662	ELSEIF( init_3d%lod_u == 2 ) THEN
663	ALLOCATE( init_l(nzb:nzt+1) )
664	DO k = nzb, nzt+1
665	init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
666	ENDDO
667	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
668
669	#if defined( __parallel )
670	CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1, &
671	MPI_REAL, MPI_SUM, comm2d, ierr )
672	#else
673	u_init = init_l
674	#endif
675	DEALLOCATE( init_l )
676
677	ENDIF
678
679	IF( init_3d%lod_v == 1 ) THEN
680	v_init = init_3d%v_init
681	ELSEIF( init_3d%lod_v == 2 ) THEN
682	ALLOCATE( init_l(nzb:nzt+1) )
683	DO k = nzb, nzt+1
684	init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
685	ENDDO
686	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
687
688	#if defined( __parallel )
689	CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1, &
690	MPI_REAL, MPI_SUM, comm2d, ierr )
691	#else
692	v_init = init_l
693	#endif
694	DEALLOCATE( init_l )
695	ENDIF
696	IF( .NOT. neutral ) THEN
697	IF( init_3d%lod_pt == 1 ) THEN
698	pt_init = init_3d%pt_init
699	ELSEIF( init_3d%lod_pt == 2 ) THEN
700	ALLOCATE( init_l(nzb:nzt+1) )
701	DO k = nzb, nzt+1
702	init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
703	ENDDO
704	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
705
706	#if defined( __parallel )
707	CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1, &
708	MPI_REAL, MPI_SUM, comm2d, ierr )
709	#else
710	pt_init = init_l
711	#endif
712	DEALLOCATE( init_l )
713	ENDIF
714	ENDIF
715
716
717	IF( humidity ) THEN
718	IF( init_3d%lod_q == 1 ) THEN
719	q_init = init_3d%q_init
720	ELSEIF( init_3d%lod_q == 2 ) THEN
721	ALLOCATE( init_l(nzb:nzt+1) )
722	DO k = nzb, nzt+1
723	init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
724	ENDDO
725	init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )
726
727	#if defined( __parallel )
728	CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1, &
729	MPI_REAL, MPI_SUM, comm2d, ierr )
730	#else
731	q_init = init_l
732	#endif
733	DEALLOCATE( init_l )
734	ENDIF
735	ENDIF
736
737	!
738	!-- Write initial profiles onto 3D arrays.
739	!-- Work-around, 3D initialization of u,v,w creates artificial
740	!-- structures wich correlate with the processor grid. The reason
741	!-- for this is still unknown. To work-around this, 3D initialization
742	!-- will be effectively reduce to a 1D initialization where no such
743	!-- artificial structures appear.
744	DO i = nxlg, nxrg
745	DO j = nysg, nyng
746	IF( init_3d%lod_u == 1 .OR. init_3d%lod_u == 2 ) &
747	u(:,j,i) = u_init(:)
748	IF( init_3d%lod_v == 1 .OR. init_3d%lod_u == 2 ) &
749	v(:,j,i) = v_init(:)
750	IF( .NOT. neutral .AND. &
751	( init_3d%lod_pt == 1 .OR. init_3d%lod_pt == 2 ) ) &
752	pt(:,j,i) = pt_init(:)
753	IF( humidity .AND. &
754	( init_3d%lod_q == 1 .OR. init_3d%lod_q == 2 ) ) &
755	q(:,j,i) = q_init(:)
756	ENDDO
757	ENDDO
758	!
759	!-- Set geostrophic wind components.
760	IF ( init_3d%from_file_ug ) THEN
761	ug(:) = init_3d%ug_init(:)
762	ENDIF
763	IF ( init_3d%from_file_vg ) THEN
764	vg(:) = init_3d%vg_init(:)
765	ENDIF
766	!
767	!-- Set bottom and top boundary condition for geostrophic wind
768	ug(nzt+1) = ug(nzt)
769	vg(nzt+1) = vg(nzt)
770	ug(nzb) = ug(nzb+1)
771	vg(nzb) = vg(nzb+1)
772	!
773	!-- Set inital w to 0
774	w = 0.0_wp
775
776	IF ( passive_scalar ) THEN
777	DO i = nxlg, nxrg
778	DO j = nysg, nyng
779	s(:,j,i) = s_init
780	ENDDO
781	ENDDO
782	ENDIF
783
784	!
785	!-- Set velocity components at non-atmospheric / oceanic grid points to
786	!-- zero.
787	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
788	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
789	w = MERGE( w, 0.0_wp, BTEST( wall_flags_total_0, 3 ) )
790	!
791	!-- Initialize surface variables, e.g. friction velocity, momentum
792	!-- fluxes, etc.
793	CALL init_surfaces
794
795	IF ( debug_output ) CALL debug_message( 'initializing with INIFOR', 'end' )
796	!
797	!-- Initialization via computed 1D-model profiles
798	ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 ) THEN
799
800	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'start' )
801	!
802	!-- Use solutions of the 1D model as initial profiles,
803	!-- start 1D model
804	CALL init_1d_model
805	!
806	!-- Transfer initial profiles to the arrays of the 3D model
807	DO i = nxlg, nxrg
808	DO j = nysg, nyng
809	pt(:,j,i) = pt_init
810	u(:,j,i) = u1d
811	v(:,j,i) = v1d
812	ENDDO
813	ENDDO
814
815	IF ( humidity ) THEN
816	DO i = nxlg, nxrg
817	DO j = nysg, nyng
818	q(:,j,i) = q_init
819	ENDDO
820	ENDDO
821	ENDIF
822
823	IF ( passive_scalar ) THEN
824	DO i = nxlg, nxrg
825	DO j = nysg, nyng
826	s(:,j,i) = s_init
827	ENDDO
828	ENDDO
829	ENDIF
830	!
831	!-- Store initial profiles for output purposes etc.
832	IF ( .NOT. constant_diffusion ) THEN
833	hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
834	ENDIF
835	!
836	!-- Set velocities back to zero
837	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
838	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
839	!
840	!-- WARNING: The extra boundary conditions set after running the
841	!-- ------- 1D model impose an error on the divergence one layer
842	!-- below the topography; need to correct later
843	!-- ATTENTION: Provisional correction for Piacsek & Williams
844	!-- --------- advection scheme: keep u and v zero one layer below
845	!-- the topography.
846	IF ( ibc_uv_b == 1 ) THEN
847	!
848	!-- Neumann condition
849	DO i = nxl-1, nxr+1
850	DO j = nys-1, nyn+1
851	u(nzb,j,i) = u(nzb+1,j,i)
852	v(nzb,j,i) = v(nzb+1,j,i)
853	ENDDO
854	ENDDO
855
856	ENDIF
857	!
858	!-- Initialize surface variables, e.g. friction velocity, momentum
859	!-- fluxes, etc.
860	CALL init_surfaces
861
862	IF ( debug_output ) CALL debug_message( 'initializing with 1D model profiles', 'end' )
863
864	ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 ) &
865	THEN
866
867	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'start' )
868
869	!
870	!-- Use constructed initial profiles (velocity constant with height,
871	!-- temperature profile with constant gradient)
872	DO i = nxlg, nxrg
873	DO j = nysg, nyng
874	pt(:,j,i) = pt_init
875	u(:,j,i) = u_init
876	v(:,j,i) = v_init
877	ENDDO
878	ENDDO
879	!
880	!-- Mask topography
881	u = MERGE( u, 0.0_wp, BTEST( wall_flags_total_0, 1 ) )
882	v = MERGE( v, 0.0_wp, BTEST( wall_flags_total_0, 2 ) )
883	!
884	!-- Set initial horizontal velocities at the lowest computational grid
885	!-- levels to zero in order to avoid too small time steps caused by the
886	!-- diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
887	!-- in the limiting formula!).
888	!-- Please note, in case land- or urban-surface model is used and a
889	!-- spinup is applied, masking the lowest computational level is not
890	!-- possible as MOST as well as energy-balance parametrizations will not
891	!-- work with zero wind velocity.
892	IF ( ibc_uv_b /= 1 .AND. .NOT. spinup ) THEN
893	DO i = nxlg, nxrg
894	DO j = nysg, nyng
895	DO k = nzb, nzt
896	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
897	BTEST( wall_flags_total_0(k,j,i), 20 ) )
898	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
899	BTEST( wall_flags_total_0(k,j,i), 21 ) )
900	ENDDO
901	ENDDO
902	ENDDO
903	ENDIF
904
905	IF ( humidity ) THEN
906	DO i = nxlg, nxrg
907	DO j = nysg, nyng
908	q(:,j,i) = q_init
909	ENDDO
910	ENDDO
911	ENDIF
912
913	IF ( passive_scalar ) THEN
914	DO i = nxlg, nxrg
915	DO j = nysg, nyng
916	s(:,j,i) = s_init
917	ENDDO
918	ENDDO
919	ENDIF
920
921	!
922	!-- Compute initial temperature field and other constants used in case
923	!-- of a sloping surface
924	IF ( sloping_surface ) CALL init_slope
925	!
926	!-- Initialize surface variables, e.g. friction velocity, momentum
927	!-- fluxes, etc.
928	CALL init_surfaces
929
930	IF ( debug_output ) CALL debug_message( 'initializing with constant profiles', 'end' )
931
932	ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 ) &
933	THEN
934
935	IF ( debug_output ) CALL debug_message( 'initializing by user', 'start' )
936	!
937	!-- Pre-initialize surface variables, i.e. setting start- and end-indices
938	!-- at each (j,i)-location. Please note, this does not supersede
939	!-- user-defined initialization of surface quantities.
940	CALL init_surfaces
941	!
942	!-- Initialization will completely be done by the user
943	CALL user_init_3d_model
944
945	IF ( debug_output ) CALL debug_message( 'initializing by user', 'end' )
946
947	ENDIF
948
949	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'start' )
950
951	!
952	!-- Bottom boundary
953	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2 ) THEN
954	u(nzb,:,:) = 0.0_wp
955	v(nzb,:,:) = 0.0_wp
956	ENDIF
957
958	!
959	!-- Apply channel flow boundary condition
960	IF ( TRIM( bc_uv_t ) == 'dirichlet_0' ) THEN
961	u(nzt+1,:,:) = 0.0_wp
962	v(nzt+1,:,:) = 0.0_wp
963	ENDIF
964
965	!
966	!-- Calculate virtual potential temperature
967	IF ( humidity ) vpt = pt * ( 1.0_wp + 0.61_wp * q )
968
969	!
970	!-- Store initial profiles for output purposes etc.. Please note, in case of
971	!-- initialization of u, v, w, pt, and q via output data derived from larger
972	!-- scale models, data will not be horizontally homogeneous. Actually, a mean
973	!-- profile should be calculated before.
974	hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
975	hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
976	IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2) THEN
977	hom(nzb,1,5,:) = 0.0_wp
978	hom(nzb,1,6,:) = 0.0_wp
979	ENDIF
980	hom(:,1,7,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
981
982	IF ( humidity ) THEN
983	!
984	!-- Store initial profile of total water content, virtual potential
985	!-- temperature
986	hom(:,1,26,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
987	hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
988	!
989	!-- Store initial profile of mixing ratio and potential
990	!-- temperature
991	IF ( bulk_cloud_model .OR. cloud_droplets ) THEN
992	hom(:,1,27,:) = SPREAD( q(:,nys,nxl), 2, statistic_regions+1 )
993	hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
994	ENDIF
995	ENDIF
996
997	!
998	!-- Store initial scalar profile
999	IF ( passive_scalar ) THEN
1000	hom(:,1,121,:) = SPREAD( s(:,nys,nxl), 2, statistic_regions+1 )
1001	ENDIF
1002
1003	!
1004	!-- Initialize the random number generators (from numerical recipes)
1005	CALL random_function_ini
1006
1007	IF ( random_generator == 'random-parallel' ) THEN
1008	CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
1009	ENDIF
1010	!
1011	!-- Set the reference state to be used in the buoyancy terms (for ocean runs
1012	!-- the reference state will be set (overwritten) in init_ocean)
1013	IF ( use_single_reference_value ) THEN
1014	IF ( .NOT. humidity ) THEN
1015	ref_state(:) = pt_reference
1016	ELSE
1017	ref_state(:) = vpt_reference
1018	ENDIF
1019	ELSE
1020	IF ( .NOT. humidity ) THEN
1021	ref_state(:) = pt_init(:)
1022	ELSE
1023	ref_state(:) = vpt(:,nys,nxl)
1024	ENDIF
1025	ENDIF
1026
1027	!
1028	!-- For the moment, vertical velocity is zero
1029	w = 0.0_wp
1030
1031	!
1032	!-- Initialize array sums (must be defined in first call of pres)
1033	sums = 0.0_wp
1034
1035	!
1036	!-- In case of iterative solvers, p must get an initial value
1037	IF ( psolver(1:9) == 'multigrid' .OR. psolver == 'sor' ) p = 0.0_wp
1038	!
1039	!-- Impose vortex with vertical axis on the initial velocity profile
1040	IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 ) THEN
1041	CALL init_rankine
1042	ENDIF
1043
1044	!
1045	!-- Impose temperature anomaly (advection test only) or warm air bubble
1046	!-- close to surface
1047	IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0 .OR. &
1048	INDEX( initializing_actions, 'initialize_bubble' ) /= 0 ) THEN
1049	CALL init_pt_anomaly
1050	ENDIF
1051
1052	!
1053	!-- If required, change the surface temperature at the start of the 3D run
1054	IF ( pt_surface_initial_change /= 0.0_wp ) THEN
1055	pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
1056	ENDIF
1057
1058	!
1059	!-- If required, change the surface humidity/scalar at the start of the 3D
1060	!-- run
1061	IF ( humidity .AND. q_surface_initial_change /= 0.0_wp ) &
1062	q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
1063
1064	IF ( passive_scalar .AND. s_surface_initial_change /= 0.0_wp ) &
1065	s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
1066
1067
1068	!
1069	!-- Initialize old and new time levels.
1070	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1071	pt_p = pt; u_p = u; v_p = v; w_p = w
1072
1073	IF ( humidity ) THEN
1074	tq_m = 0.0_wp
1075	q_p = q
1076	ENDIF
1077
1078	IF ( passive_scalar ) THEN
1079	ts_m = 0.0_wp
1080	s_p = s
1081	ENDIF
1082
1083	IF ( debug_output ) CALL debug_message( 'initializing statistics, boundary conditions, etc.', 'end' )
1084
1085	ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data' .OR. &
1086	TRIM( initializing_actions ) == 'cyclic_fill' ) &
1087	THEN
1088
1089	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'start' )
1090	!
1091	!-- Initialize surface elements and its attributes, e.g. heat- and
1092	!-- momentumfluxes, roughness, scaling parameters. As number of surface
1093	!-- elements might be different between runs, e.g. in case of cyclic fill,
1094	!-- and not all surface elements are read, surface elements need to be
1095	!-- initialized before.
1096	!-- Please note, in case of cyclic fill, surfaces should be initialized
1097	!-- after restart data is read, else, individual settings of surface
1098	!-- parameters will be overwritten from data of precursor run, hence,
1099	!-- init_surfaces is called a second time after reading the restart data.
1100	CALL init_surfaces
1101	!
1102	!-- When reading data for cyclic fill of 3D prerun data files, read
1103	!-- some of the global variables from the restart file which are required
1104	!-- for initializing the inflow
1105	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1106
1107	DO i = 0, io_blocks-1
1108	IF ( i == io_group ) THEN
1109	CALL rrd_read_parts_of_global
1110	ENDIF
1111	#if defined( __parallel )
1112	CALL MPI_BARRIER( comm2d, ierr )
1113	#endif
1114	ENDDO
1115
1116	ENDIF
1117
1118	!
1119	!-- Read processor specific binary data from restart file
1120	DO i = 0, io_blocks-1
1121	IF ( i == io_group ) THEN
1122	CALL rrd_local
1123	ENDIF
1124	#if defined( __parallel )
1125	CALL MPI_BARRIER( comm2d, ierr )
1126	#endif
1127	ENDDO
1128
1129
1130	IF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1131
1132	!
1133	!-- In case of cyclic fill, call init_surfaces a second time, so that
1134	!-- surface properties such as heat fluxes are initialized as prescribed.
1135	CALL init_surfaces
1136
1137	!
1138	!-- Overwrite u_init, v_init, pt_init, q_init and s_init with the
1139	!-- horizontally mean (hom) vertical profiles from the end
1140	!-- of the prerun, because these profiles shall be used as the reference
1141	!-- state for the rayleigh damping and the pt_damping. This is especially
1142	!-- important for the use of large_scale_subsidence, because the
1143	!-- reference temperature in the free atmosphere changes in time.
1144	u_init(:) = hom_sum(:,1,0)
1145	v_init(:) = hom_sum(:,2,0)
1146	pt_init(:) = hom_sum(:,4,0)
1147	IF ( humidity ) &
1148	q_init(:) = hom_sum(:,41,0)
1149	IF ( passive_scalar ) &
1150	s_init(:) = hom_sum(:,115,0)
1151	ENDIF
1152	!
1153	!-- In case of complex terrain and cyclic fill method as initialization,
1154	!-- shift initial data in the vertical direction for each point in the
1155	!-- x-y-plane depending on local surface height
1156	IF ( complex_terrain .AND. &
1157	TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1158	DO i = nxlg, nxrg
1159	DO j = nysg, nyng
1160	nz_u_shift = topo_top_ind(j,i,1)
1161	nz_v_shift = topo_top_ind(j,i,2)
1162	nz_w_shift = topo_top_ind(j,i,3)
1163	nz_s_shift = topo_top_ind(j,i,0)
1164
1165	u(nz_u_shift:nzt+1,j,i) = u(0:nzt+1-nz_u_shift,j,i)
1166
1167	v(nz_v_shift:nzt+1,j,i) = v(0:nzt+1-nz_v_shift,j,i)
1168
1169	w(nz_w_shift:nzt+1,j,i) = w(0:nzt+1-nz_w_shift,j,i)
1170
1171	p(nz_s_shift:nzt+1,j,i) = p(0:nzt+1-nz_s_shift,j,i)
1172	pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
1173	ENDDO
1174	ENDDO
1175	ENDIF
1176	!
1177	!-- Initialization of the turbulence recycling method
1178	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1179	turbulent_inflow ) THEN
1180	!
1181	!-- First store the profiles to be used at the inflow.
1182	!-- These profiles are the (temporally) and horizontally averaged vertical
1183	!-- profiles from the prerun. Alternatively, prescribed profiles
1184	!-- for u,v-components can be used.
1185	ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )
1186
1187	IF ( use_prescribed_profile_data ) THEN
1188	mean_inflow_profiles(:,1) = u_init ! u
1189	mean_inflow_profiles(:,2) = v_init ! v
1190	ELSE
1191	mean_inflow_profiles(:,1) = hom_sum(:,1,0) ! u
1192	mean_inflow_profiles(:,2) = hom_sum(:,2,0) ! v
1193	ENDIF
1194	mean_inflow_profiles(:,4) = hom_sum(:,4,0) ! pt
1195	IF ( humidity ) &
1196	mean_inflow_profiles(:,6) = hom_sum(:,41,0) ! q
1197	IF ( passive_scalar ) &
1198	mean_inflow_profiles(:,7) = hom_sum(:,115,0) ! s
1199
1200	!
1201	!-- In case of complex terrain, determine vertical displacement at inflow
1202	!-- boundary and adjust mean inflow profiles
1203	IF ( complex_terrain ) THEN
1204	IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 ) THEN
1205	nz_u_shift_l = topo_top_ind(j,i,1)
1206	nz_v_shift_l = topo_top_ind(j,i,2)
1207	nz_w_shift_l = topo_top_ind(j,i,3)
1208	nz_s_shift_l = topo_top_ind(j,i,0)
1209	ELSE
1210	nz_u_shift_l = 0
1211	nz_v_shift_l = 0
1212	nz_w_shift_l = 0
1213	nz_s_shift_l = 0
1214	ENDIF
1215
1216	#if defined( __parallel )
1217	CALL MPI_ALLREDUCE(nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER, &
1218	MPI_MAX, comm2d, ierr)
1219	CALL MPI_ALLREDUCE(nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER, &
1220	MPI_MAX, comm2d, ierr)
1221	CALL MPI_ALLREDUCE(nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER, &
1222	MPI_MAX, comm2d, ierr)
1223	CALL MPI_ALLREDUCE(nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER, &
1224	MPI_MAX, comm2d, ierr)
1225	#else
1226	nz_u_shift = nz_u_shift_l
1227	nz_v_shift = nz_v_shift_l
1228	nz_w_shift = nz_w_shift_l
1229	nz_s_shift = nz_s_shift_l
1230	#endif
1231
1232	mean_inflow_profiles(:,1) = 0.0_wp
1233	mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0) ! u
1234
1235	mean_inflow_profiles(:,2) = 0.0_wp
1236	mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0) ! v
1237
1238	mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0) ! pt
1239
1240	ENDIF
1241
1242	!
1243	!-- If necessary, adjust the horizontal flow field to the prescribed
1244	!-- profiles
1245	IF ( use_prescribed_profile_data ) THEN
1246	DO i = nxlg, nxrg
1247	DO j = nysg, nyng
1248	DO k = nzb, nzt+1
1249	u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
1250	v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
1251	ENDDO
1252	ENDDO
1253	ENDDO
1254	ENDIF
1255
1256	!
1257	!-- Use these mean profiles at the inflow (provided that Dirichlet
1258	!-- conditions are used)
1259	IF ( bc_dirichlet_l ) THEN
1260	DO j = nysg, nyng
1261	DO k = nzb, nzt+1
1262	u(k,j,nxlg:-1) = mean_inflow_profiles(k,1)
1263	v(k,j,nxlg:-1) = mean_inflow_profiles(k,2)
1264	w(k,j,nxlg:-1) = 0.0_wp
1265	pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
1266	IF ( humidity ) &
1267	q(k,j,nxlg:-1) = mean_inflow_profiles(k,6)
1268	IF ( passive_scalar ) &
1269	s(k,j,nxlg:-1) = mean_inflow_profiles(k,7)
1270	ENDDO
1271	ENDDO
1272	ENDIF
1273
1274	!
1275	!-- Calculate the damping factors to be used at the inflow. For a
1276	!-- turbulent inflow the turbulent fluctuations have to be limited
1277	!-- vertically because otherwise the turbulent inflow layer will grow
1278	!-- in time.
1279	IF ( inflow_damping_height == 9999999.9_wp ) THEN
1280	!
1281	!-- Default: use the inversion height calculated by the prerun; if
1282	!-- this is zero, inflow_damping_height must be explicitly
1283	!-- specified.
1284	IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp ) THEN
1285	inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
1286	ELSE
1287	WRITE( message_string, * ) 'inflow_damping_height must be ', &
1288	'explicitly specified because&the inversion height ', &
1289	'calculated by the prerun is zero.'
1290	CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
1291	ENDIF
1292
1293	ENDIF
1294
1295	IF ( inflow_damping_width == 9999999.9_wp ) THEN
1296	!
1297	!-- Default for the transition range: one tenth of the undamped
1298	!-- layer
1299	inflow_damping_width = 0.1_wp * inflow_damping_height
1300
1301	ENDIF
1302
1303	ALLOCATE( inflow_damping_factor(nzb:nzt+1) )
1304
1305	DO k = nzb, nzt+1
1306
1307	IF ( zu(k) <= inflow_damping_height ) THEN
1308	inflow_damping_factor(k) = 1.0_wp
1309	ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) ) THEN
1310	inflow_damping_factor(k) = 1.0_wp - &
1311	( zu(k) - inflow_damping_height ) / &
1312	inflow_damping_width
1313	ELSE
1314	inflow_damping_factor(k) = 0.0_wp
1315	ENDIF
1316
1317	ENDDO
1318
1319	ENDIF
1320
1321	!
1322	!-- Inside buildings set velocities back to zero
1323	IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND. &
1324	topography /= 'flat' ) THEN
1325	!
1326	!-- Inside buildings set velocities back to zero.
1327	!-- Other scalars (pt, q, s, p, sa, ...) are ignored at present,
1328	!-- maybe revise later.
1329	DO i = nxlg, nxrg
1330	DO j = nysg, nyng
1331	DO k = nzb, nzt
1332	u(k,j,i) = MERGE( u(k,j,i), 0.0_wp, &
1333	BTEST( wall_flags_total_0(k,j,i), 1 ) )
1334	v(k,j,i) = MERGE( v(k,j,i), 0.0_wp, &
1335	BTEST( wall_flags_total_0(k,j,i), 2 ) )
1336	w(k,j,i) = MERGE( w(k,j,i), 0.0_wp, &
1337	BTEST( wall_flags_total_0(k,j,i), 3 ) )
1338	ENDDO
1339	ENDDO
1340	ENDDO
1341
1342	ENDIF
1343
1344	!
1345	!-- Calculate initial temperature field and other constants used in case
1346	!-- of a sloping surface
1347	IF ( sloping_surface ) CALL init_slope
1348
1349	!
1350	!-- Initialize new time levels (only done in order to set boundary values
1351	!-- including ghost points)
1352	pt_p = pt; u_p = u; v_p = v; w_p = w
1353	IF ( humidity ) THEN
1354	q_p = q
1355	ENDIF
1356	IF ( passive_scalar ) s_p = s
1357	!
1358	!-- Allthough tendency arrays are set in prognostic_equations, they have
1359	!-- have to be predefined here because they are used (but multiplied with 0)
1360	!-- there before they are set.
1361	tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
1362	IF ( humidity ) THEN
1363	tq_m = 0.0_wp
1364	ENDIF
1365	IF ( passive_scalar ) ts_m = 0.0_wp
1366
1367	IF ( debug_output ) CALL debug_message( 'initializing in case of restart / cyclic_fill', 'end' )
1368
1369	ELSE
1370	!
1371	!-- Actually this part of the programm should not be reached
1372	message_string = 'unknown initializing problem'
1373	CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
1374	ENDIF
1375
1376
1377	IF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1378	!
1379	!-- Initialize old timelevels needed for radiation boundary conditions
1380	IF ( bc_radiation_l ) THEN
1381	u_m_l(:,:,:) = u(:,:,1:2)
1382	v_m_l(:,:,:) = v(:,:,0:1)
1383	w_m_l(:,:,:) = w(:,:,0:1)
1384	ENDIF
1385	IF ( bc_radiation_r ) THEN
1386	u_m_r(:,:,:) = u(:,:,nx-1:nx)
1387	v_m_r(:,:,:) = v(:,:,nx-1:nx)
1388	w_m_r(:,:,:) = w(:,:,nx-1:nx)
1389	ENDIF
1390	IF ( bc_radiation_s ) THEN
1391	u_m_s(:,:,:) = u(:,0:1,:)
1392	v_m_s(:,:,:) = v(:,1:2,:)
1393	w_m_s(:,:,:) = w(:,0:1,:)
1394	ENDIF
1395	IF ( bc_radiation_n ) THEN
1396	u_m_n(:,:,:) = u(:,ny-1:ny,:)
1397	v_m_n(:,:,:) = v(:,ny-1:ny,:)
1398	w_m_n(:,:,:) = w(:,ny-1:ny,:)
1399	ENDIF
1400
1401	ENDIF
1402
1403	!
1404	!-- Calculate the initial volume flow at the right and north boundary
1405	IF ( conserve_volume_flow ) THEN
1406
1407	IF ( use_prescribed_profile_data ) THEN
1408
1409	volume_flow_initial_l = 0.0_wp
1410	volume_flow_area_l = 0.0_wp
1411
1412	IF ( nxr == nx ) THEN
1413	DO j = nys, nyn
1414	DO k = nzb+1, nzt
1415	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1416	u_init(k) * dzw(k) &
1417	* MERGE( 1.0_wp, 0.0_wp, &
1418	BTEST( wall_flags_total_0(k,j,nxr), 1 )&
1419	)
1420
1421	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1422	* MERGE( 1.0_wp, 0.0_wp, &
1423	BTEST( wall_flags_total_0(k,j,nxr), 1 )&
1424	)
1425	ENDDO
1426	ENDDO
1427	ENDIF
1428
1429	IF ( nyn == ny ) THEN
1430	DO i = nxl, nxr
1431	DO k = nzb+1, nzt
1432	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1433	v_init(k) * dzw(k) &
1434	* MERGE( 1.0_wp, 0.0_wp, &
1435	BTEST( wall_flags_total_0(k,nyn,i), 2 )&
1436	)
1437	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1438	* MERGE( 1.0_wp, 0.0_wp, &
1439	BTEST( wall_flags_total_0(k,nyn,i), 2 )&
1440	)
1441	ENDDO
1442	ENDDO
1443	ENDIF
1444
1445	#if defined( __parallel )
1446	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1447	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1448	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1449	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1450
1451	#else
1452	volume_flow_initial = volume_flow_initial_l
1453	volume_flow_area = volume_flow_area_l
1454	#endif
1455
1456	ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' ) THEN
1457
1458	volume_flow_initial_l = 0.0_wp
1459	volume_flow_area_l = 0.0_wp
1460
1461	IF ( nxr == nx ) THEN
1462	DO j = nys, nyn
1463	DO k = nzb+1, nzt
1464	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1465	hom_sum(k,1,0) * dzw(k) &
1466	* MERGE( 1.0_wp, 0.0_wp, &
1467	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1468	)
1469	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1470	* MERGE( 1.0_wp, 0.0_wp, &
1471	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1472	)
1473	ENDDO
1474	ENDDO
1475	ENDIF
1476
1477	IF ( nyn == ny ) THEN
1478	DO i = nxl, nxr
1479	DO k = nzb+1, nzt
1480	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1481	hom_sum(k,2,0) * dzw(k) &
1482	* MERGE( 1.0_wp, 0.0_wp, &
1483	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1484	)
1485	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1486	* MERGE( 1.0_wp, 0.0_wp, &
1487	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1488	)
1489	ENDDO
1490	ENDDO
1491	ENDIF
1492
1493	#if defined( __parallel )
1494	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1495	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1496	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1497	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1498
1499	#else
1500	volume_flow_initial = volume_flow_initial_l
1501	volume_flow_area = volume_flow_area_l
1502	#endif
1503
1504	ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' ) THEN
1505
1506	volume_flow_initial_l = 0.0_wp
1507	volume_flow_area_l = 0.0_wp
1508
1509	IF ( nxr == nx ) THEN
1510	DO j = nys, nyn
1511	DO k = nzb+1, nzt
1512	volume_flow_initial_l(1) = volume_flow_initial_l(1) + &
1513	u(k,j,nx) * dzw(k) &
1514	* MERGE( 1.0_wp, 0.0_wp, &
1515	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1516	)
1517	volume_flow_area_l(1) = volume_flow_area_l(1) + dzw(k) &
1518	* MERGE( 1.0_wp, 0.0_wp, &
1519	BTEST( wall_flags_total_0(k,j,nx), 1 ) &
1520	)
1521	ENDDO
1522	ENDDO
1523	ENDIF
1524
1525	IF ( nyn == ny ) THEN
1526	DO i = nxl, nxr
1527	DO k = nzb+1, nzt
1528	volume_flow_initial_l(2) = volume_flow_initial_l(2) + &
1529	v(k,ny,i) * dzw(k) &
1530	* MERGE( 1.0_wp, 0.0_wp, &
1531	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1532	)
1533	volume_flow_area_l(2) = volume_flow_area_l(2) + dzw(k) &
1534	* MERGE( 1.0_wp, 0.0_wp, &
1535	BTEST( wall_flags_total_0(k,ny,i), 2 ) &
1536	)
1537	ENDDO
1538	ENDDO
1539	ENDIF
1540
1541	#if defined( __parallel )
1542	CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
1543	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1544	CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1), &
1545	2, MPI_REAL, MPI_SUM, comm2d, ierr )
1546
1547	#else
1548	volume_flow_initial = volume_flow_initial_l
1549	volume_flow_area = volume_flow_area_l
1550	#endif
1551
1552	ENDIF
1553
1554	!
1555	!-- In case of 'bulk_velocity' mode, volume_flow_initial is calculated
1556	!-- from u\|v_bulk instead
1557	IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' ) THEN
1558	volume_flow_initial(1) = u_bulk * volume_flow_area(1)
1559	volume_flow_initial(2) = v_bulk * volume_flow_area(2)
1560	ENDIF
1561
1562	ENDIF
1563	!
1564	!-- In the following, surface properties can be further initialized with
1565	!-- input from static driver file.
1566	!-- At the moment this affects only default surfaces. For example,
1567	!-- roughness length or sensible / latent heat fluxes can be initialized
1568	!-- heterogeneously for default surfaces. Therefore, a generic routine
1569	!-- from netcdf_data_input_mod is called to read a 2D array.
1570	IF ( input_pids_static ) THEN
1571	!
1572	!-- Allocate memory for possible static input
1573	ALLOCATE( tmp_2d%var(nys:nyn,nxl:nxr) )
1574	tmp_2d%var = 0.0_wp
1575	!
1576	!-- Open the static input file
1577	#if defined( __netcdf )
1578	CALL open_read_file( TRIM( input_file_static ) // &
1579	TRIM( coupling_char ), &
1580	pids_id )
1581
1582	CALL inquire_num_variables( pids_id, num_var_pids )
1583	!
1584	!-- Allocate memory to store variable names and read them
1585	ALLOCATE( vars_pids(1:num_var_pids) )
1586	CALL inquire_variable_names( pids_id, vars_pids )
1587	!
1588	!-- Input roughness length.
1589	IF ( check_existence( vars_pids, 'z0' ) ) THEN
1590	!
1591	!-- Read _FillValue attribute
1592	CALL get_attribute( pids_id, char_fill, tmp_2d%fill, &
1593	.FALSE., 'z0' )
1594	!
1595	!-- Read variable
1596	CALL get_variable( pids_id, 'z0', tmp_2d%var, &
1597	nxl, nxr, nys, nyn )
1598	!
1599	!-- Initialize roughness length. Note, z0 will be only initialized at
1600	!-- default-type surfaces. At natural or urban z0 is implicitly
1601	!-- initialized bythe respective parameter lists.
1602	!-- Initialize horizontal surface elements.
1603	CALL init_single_surface_properties( surf_def_h(0)%z0, &
1604	tmp_2d%var, &
1605	surf_def_h(0)%ns, &
1606	tmp_2d%fill, &
1607	surf_def_h(0)%i, &
1608	surf_def_h(0)%j )
1609	!
1610	!-- Initialize roughness also at vertical surface elements.
1611	!-- Note, the actual 2D input arrays are only defined on the
1612	!-- subdomain. Therefore, pass the index arrays with their respective
1613	!-- offset values.
1614	DO l = 0, 3
1615	CALL init_single_surface_properties( &
1616	surf_def_v(l)%z0, &
1617	tmp_2d%var, &
1618	surf_def_v(l)%ns, &
1619	tmp_2d%fill, &
1620	surf_def_v(l)%i + surf_def_v(l)%ioff, &
1621	surf_def_v(l)%j + surf_def_v(l)%joff )
1622	ENDDO
1623
1624	ENDIF
1625	!
1626	!-- Additional variables, e.g. shf, qsws, etc, can be initialized the
1627	!-- same way.
1628
1629	!
1630	!-- Finally, close the input file and deallocate temporary arrays
1631	DEALLOCATE( vars_pids )
1632
1633	CALL close_input_file( pids_id )
1634	#endif
1635	DEALLOCATE( tmp_2d%var )
1636	ENDIF
1637	!
1638	!-- Finally, if random_heatflux is set, disturb shf at horizontal
1639	!-- surfaces. Actually, this should be done in surface_mod, where all other
1640	!-- initializations of surface quantities are done. However, this
1641	!-- would create a ring dependency, hence, it is done here. Maybe delete
1642	!-- disturb_heatflux and tranfer the respective code directly into the
1643	!-- initialization in surface_mod.
1644	IF ( TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1645	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1646
1647	IF ( use_surface_fluxes .AND. constant_heatflux .AND. &
1648	random_heatflux ) THEN
1649	IF ( surf_def_h(0)%ns >= 1 ) CALL disturb_heatflux( surf_def_h(0) )
1650	IF ( surf_lsm_h%ns >= 1 ) CALL disturb_heatflux( surf_lsm_h )
1651	IF ( surf_usm_h%ns >= 1 ) CALL disturb_heatflux( surf_usm_h )
1652	ENDIF
1653	ENDIF
1654
1655	!
1656	!-- Compute total sum of grid points and the mean surface level height for each
1657	!-- statistic region. These are mainly used for horizontal averaging of
1658	!-- turbulence statistics.
1659	!-- ngp_2dh: number of grid points of a horizontal cross section through the
1660	!-- respective statistic region
1661	!-- ngp_3d: number of grid points of the respective statistic region
1662	ngp_2dh_outer_l = 0
1663	ngp_2dh_outer = 0
1664	ngp_2dh_s_inner_l = 0
1665	ngp_2dh_s_inner = 0
1666	ngp_2dh_l = 0
1667	ngp_2dh = 0
1668	ngp_3d_inner_l = 0.0_wp
1669	ngp_3d_inner = 0
1670	ngp_3d = 0
1671	ngp_sums = ( nz + 2 ) * ( pr_palm + max_pr_user )
1672
1673	mean_surface_level_height = 0.0_wp
1674	mean_surface_level_height_l = 0.0_wp
1675	!
1676	!-- To do: New concept for these non-topography grid points!
1677	DO sr = 0, statistic_regions
1678	DO i = nxl, nxr
1679	DO j = nys, nyn
1680	IF ( rmask(j,i,sr) == 1.0_wp ) THEN
1681	!
1682	!-- All xy-grid points
1683	ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
1684	!
1685	!-- Determine mean surface-level height. In case of downward-
1686	!-- facing walls are present, more than one surface level exist.
1687	!-- In this case, use the lowest surface-level height.
1688	IF ( surf_def_h(0)%start_index(j,i) <= &
1689	surf_def_h(0)%end_index(j,i) ) THEN
1690	m = surf_def_h(0)%start_index(j,i)
1691	k = surf_def_h(0)%k(m)
1692	mean_surface_level_height_l(sr) = &
1693	mean_surface_level_height_l(sr) + zw(k-1)
1694	ENDIF
1695	IF ( surf_lsm_h%start_index(j,i) <= &
1696	surf_lsm_h%end_index(j,i) ) THEN
1697	m = surf_lsm_h%start_index(j,i)
1698	k = surf_lsm_h%k(m)
1699	mean_surface_level_height_l(sr) = &
1700	mean_surface_level_height_l(sr) + zw(k-1)
1701	ENDIF
1702	IF ( surf_usm_h%start_index(j,i) <= &
1703	surf_usm_h%end_index(j,i) ) THEN
1704	m = surf_usm_h%start_index(j,i)
1705	k = surf_usm_h%k(m)
1706	mean_surface_level_height_l(sr) = &
1707	mean_surface_level_height_l(sr) + zw(k-1)
1708	ENDIF
1709
1710	k_surf = k - 1
1711
1712	DO k = nzb, nzt+1
1713	!
1714	!-- xy-grid points above topography
1715	ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr) + &
1716	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 24 ) )
1717
1718	ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) + &
1719	MERGE( 1, 0, BTEST( wall_flags_total_0(k,j,i), 22 ) )
1720
1721	ENDDO
1722	!
1723	!-- All grid points of the total domain above topography
1724	ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )
1725
1726
1727
1728	ENDIF
1729	ENDDO
1730	ENDDO
1731	ENDDO
1732
1733	sr = statistic_regions + 1
1734	#if defined( __parallel )
1735	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1736	CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM, &
1737	comm2d, ierr )
1738	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1739	CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr, &
1740	MPI_INTEGER, MPI_SUM, comm2d, ierr )
1741	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1742	CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0), &
1743	(nz+2)*sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
1744	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1745	CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL, &
1746	MPI_SUM, comm2d, ierr )
1747	ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
1748	IF ( collective_wait ) CALL MPI_BARRIER( comm2d, ierr )
1749	CALL MPI_ALLREDUCE( mean_surface_level_height_l(0), &
1750	mean_surface_level_height(0), sr, MPI_REAL, &
1751	MPI_SUM, comm2d, ierr )
1752	mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
1753	#else
1754	ngp_2dh = ngp_2dh_l
1755	ngp_2dh_outer = ngp_2dh_outer_l
1756	ngp_2dh_s_inner = ngp_2dh_s_inner_l
1757	ngp_3d_inner = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
1758	mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
1759	#endif
1760
1761	ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
1762	INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )
1763
1764	!
1765	!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics,
1766	!-- buoyancy, etc. A zero value will occur for cases where all grid points of
1767	!-- the respective subdomain lie below the surface topography
1768	ngp_2dh_outer = MAX( 1, ngp_2dh_outer(:,:) )
1769	ngp_3d_inner = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )), &
1770	ngp_3d_inner(:) )
1771	ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) )
1772
1773	DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l, &
1774	ngp_3d_inner_l, ngp_3d_inner_tmp )
1775	!
1776	!-- Initialize surface forcing corresponding to large-scale forcing. Therein,
1777	!-- initialize heat-fluxes, etc. via datatype. Revise it later!
1778	IF ( large_scale_forcing .AND. lsf_surf ) THEN
1779	IF ( use_surface_fluxes .AND. constant_heatflux ) THEN
1780	CALL ls_forcing_surf ( simulated_time )
1781	ENDIF
1782	ENDIF
1783	!
1784	!-- Initializae 3D offline nesting in COSMO model and read data from
1785	!-- external NetCDF file.
1786	IF ( nesting_offline ) CALL nesting_offl_init
1787	!
1788	!-- Initialize quantities for special advections schemes
1789	CALL init_advec
1790
1791	!
1792	!-- Impose random perturbation on the horizontal velocity field and then
1793	!-- remove the divergences from the velocity field at the initial stage
1794	IF ( create_disturbances .AND. disturbance_energy_limit /= 0.0_wp .AND. &
1795	TRIM( initializing_actions ) /= 'read_restart_data' .AND. &
1796	TRIM( initializing_actions ) /= 'cyclic_fill' ) THEN
1797
1798	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'start' )
1799	!
1800	!-- Needed for both disturb_field and pres
1801	!$ACC DATA &
1802	!$ACC CREATE(tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1803	!$ACC COPY(u(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1804	!$ACC COPY(v(nzb:nzt+1,nysg:nyng,nxlg:nxrg))
1805
1806	CALL disturb_field( 'u', tend, u )
1807	CALL disturb_field( 'v', tend, v )
1808
1809	!$ACC DATA &
1810	!$ACC CREATE(d(nzb+1:nzt,nys:nyn,nxl:nxr)) &
1811	!$ACC COPY(w(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1812	!$ACC COPY(p(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1813	!$ACC COPYIN(rho_air(nzb:nzt+1), rho_air_zw(nzb:nzt+1)) &
1814	!$ACC COPYIN(ddzu(1:nzt+1), ddzw(1:nzt+1)) &
1815	!$ACC COPYIN(wall_flags_total_0(nzb:nzt+1,nysg:nyng,nxlg:nxrg)) &
1816	!$ACC COPYIN(bc_h(0:1)) &
1817	!$ACC COPYIN(bc_h(0)%i(1:bc_h(0)%ns)) &
1818	!$ACC COPYIN(bc_h(0)%j(1:bc_h(0)%ns)) &
1819	!$ACC COPYIN(bc_h(0)%k(1:bc_h(0)%ns)) &
1820	!$ACC COPYIN(bc_h(1)%i(1:bc_h(1)%ns)) &
1821	!$ACC COPYIN(bc_h(1)%j(1:bc_h(1)%ns)) &
1822	!$ACC COPYIN(bc_h(1)%k(1:bc_h(1)%ns))
1823
1824	n_sor = nsor_ini
1825	CALL pres
1826	n_sor = nsor
1827
1828	!$ACC END DATA
1829	!$ACC END DATA
1830
1831	IF ( debug_output ) CALL debug_message( 'creating disturbances + applying pressure solver', 'end' )
1832
1833	ENDIF
1834
1835	IF ( .NOT. ocean_mode ) THEN
1836
1837	ALLOCATE( hyp(nzb:nzt+1) )
1838	ALLOCATE( d_exner(nzb:nzt+1) )
1839	ALLOCATE( exner(nzb:nzt+1) )
1840	ALLOCATE( hyrho(nzb:nzt+1) )
1841	!
1842	!-- Check temperature in case of too large domain height
1843	DO k = nzb, nzt+1
1844	IF ( ( pt_surface * exner_function(surface_pressure * 100.0_wp) - g/c_p * zu(k) ) < 0.0_wp ) THEN
1845	WRITE( message_string, * ) 'absolute temperature < 0.0 at zu(', k, &
1846	') = ', zu(k)
1847	CALL message( 'init_3d_model', 'PA0142', 1, 2, 0, 6, 0 )
1848	ENDIF
1849	ENDDO
1850
1851	!
1852	!-- Calculate vertical profile of the hydrostatic pressure (hyp)
1853	hyp = barometric_formula(zu, pt_surface * exner_function(surface_pressure * 100.0_wp), surface_pressure * 100.0_wp)
1854	d_exner = exner_function_invers(hyp)
1855	exner = 1.0_wp / exner_function_invers(hyp)
1856	hyrho = ideal_gas_law_rho_pt(hyp, pt_init)
1857	!
1858	!-- Compute reference density
1859	rho_surface = ideal_gas_law_rho(surface_pressure * 100.0_wp, pt_surface * exner_function(surface_pressure * 100.0_wp))
1860
1861	ENDIF
1862
1863	!
1864	!-- If required, initialize particles
1865	IF ( agents_active ) CALL mas_init
1866	!
1867	!-- Initialization of synthetic turbulence generator
1868	IF ( use_syn_turb_gen ) CALL stg_init
1869	!
1870	!-- Initializing actions for all other modules
1871	CALL module_interface_init
1872	!
1873	!-- Initialize surface layer (done after LSM as roughness length are required
1874	!-- for initialization
1875	IF ( constant_flux_layer ) CALL init_surface_layer_fluxes
1876	!
1877	!-- Initialize surface data output
1878	IF ( surface_output ) CALL surface_data_output_init
1879	!
1880	!-- Initialize the ws-scheme.
1881	IF ( ws_scheme_sca .OR. ws_scheme_mom ) CALL ws_init
1882	!
1883	!-- Perform post-initializing checks for all other modules
1884	CALL module_interface_init_checks
1885
1886	!
1887	!-- Setting weighting factors for calculation of perturbation pressure
1888	!-- and turbulent quantities from the RK substeps
1889	IF ( TRIM(timestep_scheme) == 'runge-kutta-3' ) THEN ! for RK3-method
1890
1891	weight_substep(1) = 1._wp/6._wp
1892	weight_substep(2) = 3._wp/10._wp
1893	weight_substep(3) = 8._wp/15._wp
1894
1895	weight_pres(1) = 1._wp/3._wp
1896	weight_pres(2) = 5._wp/12._wp
1897	weight_pres(3) = 1._wp/4._wp
1898
1899	ELSEIF ( TRIM(timestep_scheme) == 'runge-kutta-2' ) THEN ! for RK2-method
1900
1901	weight_substep(1) = 1._wp/2._wp
1902	weight_substep(2) = 1._wp/2._wp
1903
1904	weight_pres(1) = 1._wp/2._wp
1905	weight_pres(2) = 1._wp/2._wp
1906
1907	ELSE ! for Euler-method
1908
1909	weight_substep(1) = 1.0_wp
1910	weight_pres(1) = 1.0_wp
1911
1912	ENDIF
1913
1914	!
1915	!-- Initialize Rayleigh damping factors
1916	rdf = 0.0_wp
1917	rdf_sc = 0.0_wp
1918	IF ( rayleigh_damping_factor /= 0.0_wp ) THEN
1919
1920	IF ( .NOT. ocean_mode ) THEN
1921	DO k = nzb+1, nzt
1922	IF ( zu(k) >= rayleigh_damping_height ) THEN
1923	rdf(k) = rayleigh_damping_factor * &
1924	( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
1925	/ ( zu(nzt) - rayleigh_damping_height ) ) &
1926	)**2
1927	ENDIF
1928	ENDDO
1929	ELSE
1930	!
1931	!-- In ocean mode, rayleigh damping is applied in the lower part of the
1932	!-- model domain
1933	DO k = nzt, nzb+1, -1
1934	IF ( zu(k) <= rayleigh_damping_height ) THEN
1935	rdf(k) = rayleigh_damping_factor * &
1936	( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
1937	/ ( rayleigh_damping_height - zu(nzb+1) ) ) &
1938	)**2
1939	ENDIF
1940	ENDDO
1941	ENDIF
1942
1943	ENDIF
1944	IF ( scalar_rayleigh_damping ) rdf_sc = rdf
1945
1946	!
1947	!-- Initialize the starting level and the vertical smoothing factor used for
1948	!-- the external pressure gradient
1949	dp_smooth_factor = 1.0_wp
1950	IF ( dp_external ) THEN
1951	!
1952	!-- Set the starting level dp_level_ind_b only if it has not been set before
1953	!-- (e.g. in init_grid).
1954	IF ( dp_level_ind_b == 0 ) THEN
1955	ind_array = MINLOC( ABS( dp_level_b - zu ) )
1956	dp_level_ind_b = ind_array(1) - 1 + nzb
1957	! MINLOC uses lower array bound 1
1958	ENDIF
1959	IF ( dp_smooth ) THEN
1960	dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
1961	DO k = dp_level_ind_b+1, nzt
1962	dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi * &
1963	( REAL( k - dp_level_ind_b, KIND=wp ) / &
1964	REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
1965	ENDDO
1966	ENDIF
1967	ENDIF
1968
1969	!
1970	!-- Initialize damping zone for the potential temperature in case of
1971	!-- non-cyclic lateral boundaries. The damping zone has the maximum value
1972	!-- at the inflow boundary and decreases to zero at pt_damping_width.
1973	ptdf_x = 0.0_wp
1974	ptdf_y = 0.0_wp
1975	IF ( bc_lr_dirrad ) THEN
1976	DO i = nxl, nxr
1977	IF ( ( i * dx ) < pt_damping_width ) THEN
1978	ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp * &
1979	REAL( pt_damping_width - i * dx, KIND=wp ) / ( &
1980	REAL( pt_damping_width, KIND=wp ) ) ) )**2
1981	ENDIF
1982	ENDDO
1983	ELSEIF ( bc_lr_raddir ) THEN
1984	DO i = nxl, nxr
1985	IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) ) THEN
1986	ptdf_x(i) = pt_damping_factor * &
1987	SIN( pi * 0.5_wp * &
1988	( ( i - nx ) * dx + pt_damping_width ) / &
1989	REAL( pt_damping_width, KIND=wp ) )**2
1990	ENDIF
1991	ENDDO
1992	ELSEIF ( bc_ns_dirrad ) THEN
1993	DO j = nys, nyn
1994	IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) ) THEN
1995	ptdf_y(j) = pt_damping_factor * &
1996	SIN( pi * 0.5_wp * &
1997	( ( j - ny ) * dy + pt_damping_width ) / &
1998	REAL( pt_damping_width, KIND=wp ) )**2
1999	ENDIF
2000	ENDDO
2001	ELSEIF ( bc_ns_raddir ) THEN
2002	DO j = nys, nyn
2003	IF ( ( j * dy ) < pt_damping_width ) THEN
2004	ptdf_y(j) = pt_damping_factor * &
2005	SIN( pi * 0.5_wp * &
2006	( pt_damping_width - j * dy ) / &
2007	REAL( pt_damping_width, KIND=wp ) )**2
2008	ENDIF
2009	ENDDO
2010	ENDIF
2011
2012	!
2013	!-- Input binary data file is not needed anymore. This line must be placed
2014	!-- after call of user_init!
2015	CALL close_file( 13 )
2016	!
2017	!-- In case of nesting, put an barrier to assure that all parent and child
2018	!-- domains finished initialization.
2019	#if defined( __parallel )
2020	IF ( nested_run ) CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
2021	#endif
2022
2023
2024	CALL location_message( 'model initialization', 'finished' )
2025
2026	END SUBROUTINE init_3d_model

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