source: palm/trunk/SOURCE/init_3d_model.f90 @ 3608

!> @file init_3d_model.f90
!------------------------------------------------------------------------------!
! This file is part of the PALM model system.
!
! PALM is free software: you can redistribute it and/or modify it under the
! terms of the GNU General Public License as published by the Free Software
! Foundation, either version 3 of the License, or (at your option) any later
! version.
!
! PALM is distributed in the hope that it will be useful, but WITHOUT ANY
! WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
! A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
!
! You should have received a copy of the GNU General Public License along with
! PALM. If not, see <http://www.gnu.org/licenses/>.
!
! Copyright 1997-2018 Leibniz Universitaet Hannover
!------------------------------------------------------------------------------!
!
! Current revisions:
! ------------------
! 
! 
! Former revisions:
! -----------------
! $Id: init_3d_model.f90 3608 2018-12-07 12:59:57Z suehring $
! Bugfix in initialization of surfaces in cyclic-fill case
! 
! 3589 2018-11-30 15:09:51Z suehring
! Move the control parameter "salsa" from salsa_mod to control_parameters 
! (M. Kurppa)
! 
! 3582 2018-11-29 19:16:36Z suehring
! Bugfix in initialization of turbulence generator
! 
! 3569 2018-11-27 17:03:40Z kanani
! dom_dwd_user, Schrempf:
! Remove uv exposure model code, this is now part of biometeorology_mod,
! remove bio_init_arrays.
!
! 3547 2018-11-21 13:21:24Z suehring
! variables documented
! 
! 3525 2018-11-14 16:06:14Z kanani
! Changes related to clean-up of biometeorology (dom_dwd_user)
! 
! 3524 2018-11-14 13:36:44Z raasch
! preprocessor directive added to avoid the compiler to complain about unused
! variable
! 
! 3473 2018-10-30 20:50:15Z suehring
! Add virtual measurement module
! 
! 3472 2018-10-30 20:43:50Z suehring
! Add indoor model (kanani, srissman, tlang)
! 
! 3467 2018-10-30 19:05:21Z suehring
! Implementation of a new aerosol module salsa.
! 
! 3458 2018-10-30 14:51:23Z kanani
! from chemistry branch r3443, basit:
! bug fixed in sums and sums_l for chemistry profile output
! 
! 3448 2018-10-29 18:14:31Z kanani
! Add biometeorology
! 
! 3421 2018-10-24 18:39:32Z gronemeier
! Initialize surface data output
! 
! 3415 2018-10-24 11:57:50Z suehring
! Set bottom boundary condition for geostrophic wind components in inifor
! initialization
! 
! 3347 2018-10-15 14:21:08Z suehring
! - Separate offline nesting from large_scale_nudging_mod
! - Improve the synthetic turbulence generator
! 
! 3298 2018-10-02 12:21:11Z kanani
! Minor formatting (kanani)
! Added CALL to the chem_emissions module (Russo)
! 
! 3294 2018-10-01 02:37:10Z raasch
! allocate and set stokes drift velocity profiles
! 
! 3298 2018-10-02 12:21:11Z kanani
! Minor formatting (kanani)
! Added CALL to the chem_emissions module (Russo)
! 
! 3294 2018-10-01 02:37:10Z raasch
! changes concerning modularization of ocean option
! 
! 3289 2018-09-28 10:23:58Z suehring
! Introduce module parameter for number of inflow profiles
! 
! 3288 2018-09-28 10:23:08Z suehring
! Modularization of all bulk cloud physics code components
! 
! 3241 2018-09-12 15:02:00Z raasch
! unused variables removed
! 
! 3234 2018-09-07 13:46:58Z schwenkel
! The increase of dots_num in case of radiation or land surface model must 
! be done before user_init is called
! 
! 3183 2018-07-27 14:25:55Z suehring
! Revise Inifor initialization
! 
! 3182 2018-07-27 13:36:03Z suehring
! Added multi agent system
! 
! 3129 2018-07-16 07:45:13Z gronemeier
! Move initialization call for nudging and 1D/3D offline nesting. 
! Revise initialization with inifor data.
! 
! 3045 2018-05-28 07:55:41Z Giersch
! Error messages revised
! 
! 3045 2018-05-28 07:55:41Z Giersch
! Error messages revised
! 
! 3042 2018-05-25 10:44:37Z schwenkel
! Changed the name specific humidity to mixing ratio
! 
! 3040 2018-05-25 10:22:08Z schwenkel
! Add option to initialize warm air bubble close to surface
! 
! 3014 2018-05-09 08:42:38Z maronga
! Bugfix: initialization of ts_value missing
! 
! 3011 2018-05-07 14:38:42Z schwenkel
! removed redundant if statement
! 
! 3004 2018-04-27 12:33:25Z Giersch
! precipitation_rate removed
! 
! 2995 2018-04-19 12:13:16Z Giersch
! CALL radiation_control is not necessary during initialization because 
! calculation of radiative fluxes at model start is done in radiation_init 
! in any case 
! 
! 2977 2018-04-17 10:27:57Z kanani
! Implement changes from branch radiation (r2948-2971) with minor modifications
! (moh.hefny):
! - set radiation_interactions according to the existence of urban/land vertical
!   surfaces and trees to activiate RTM
! - set average_radiation to TRUE if RTM is activiated
! 
! 2938 2018-03-27 15:52:42Z suehring
! - Revise Inifor initialization for geostrophic wind components
! - Initialize synthetic turbulence generator in case of Inifor initialization  
!
! 2936 2018-03-27 14:49:27Z suehring
! Synchronize parent and child models after initialization.
! Remove obsolete masking of topography grid points for Runge-Kutta weighted
! tendency arrays.
! 
! 2920 2018-03-22 11:22:01Z kanani
! Add call for precalculating apparent solar positions (moh.hefny)
! 
! 2906 2018-03-19 08:56:40Z Giersch
! The variables read/write_svf_on_init have been removed. Instead ENVIRONMENT
! variables read/write_svf have been introduced. Location_message has been 
! added.
! 
! 2894 2018-03-15 09:17:58Z Giersch
! Renamed routines with respect to reading restart data, file 13 is closed in
! rrd_read_parts_of_global now
! 
! 2867 2018-03-09 09:40:23Z suehring
! Further bugfix concerning call of user_init. 
! 
! 2864 2018-03-08 11:57:45Z suehring
! Bugfix, move call of user_init in front of initialization of grid-point 
! arrays
! 
! 2817 2018-02-19 16:32:21Z knoop
! Preliminary gust module interface implemented
! 
! 2776 2018-01-31 10:44:42Z Giersch
! Variable use_synthetic_turbulence_generator has been abbreviated
! 
! 2766 2018-01-22 17:17:47Z kanani
! Removed preprocessor directive __chem
! 
! 2758 2018-01-17 12:55:21Z suehring
! In case of spinup of land- and urban-surface model, do not mask wind velocity
! at first computational grid level
! 
! 2746 2018-01-15 12:06:04Z suehring
! Move flag plant canopy to modules
! 
! 2718 2018-01-02 08:49:38Z maronga
! Corrected "Former revisions" section
! 
! 2705 2017-12-18 11:26:23Z maronga
! Bugfix for reading initial profiles from ls/nuding file
!
! 2701 2017-12-15 15:40:50Z suehring
! Changes from last commit documented
! 
! 2700 2017-12-15 14:12:35Z suehring
! Bugfix, missing initialization of surface attributes in case of 
! inifor-initialization branch
!
! 2698 2017-12-14 18:46:24Z suehring
! Bugfix in get_topography_top_index
!
! 2696 2017-12-14 17:12:51Z kanani
! Change in file header (GPL part)
! Implementation of uv exposure model (FK)
! Moved initialisation of diss, e, kh, km to turbulence_closure_mod (TG)
! Added chemical emissions (FK)
! Initialize masking arrays and number-of-grid-points arrays before initialize
! LSM, USM and radiation module 
! Initialization with inifor (MS)
! 
! 2618 2017-11-16 15:37:30Z suehring
! Reorder calls of init_surfaces.
! 
! 2564 2017-10-19 15:56:56Z Giersch
! Variable wind_turbine was added to control_parameters.
! 
! 2550 2017-10-16 17:12:01Z boeske
! Modifications to cyclic fill method and turbulence recycling method in case of
! complex terrain simulations
! 
! 2513 2017-10-04 09:24:39Z kanani
! Bugfix in storing initial scalar profile (wrong index)
! 
! 2350 2017-08-15 11:48:26Z kanani
! Bugfix in nopointer version
! 
! 2339 2017-08-07 13:55:26Z gronemeier
! corrected timestamp in header
! 
! 2338 2017-08-07 12:15:38Z gronemeier
! Modularize 1D model
! 
! 2329 2017-08-03 14:24:56Z knoop
! Removed temporary bugfix (r2327) as bug is properly resolved by this revision
! 
! 2327 2017-08-02 07:40:57Z maronga
! Temporary bugfix
! 
! 2320 2017-07-21 12:47:43Z suehring
! Modularize large-scale forcing and nudging
! 
! 2292 2017-06-20 09:51:42Z schwenkel
! Implementation of new microphysic scheme: cloud_scheme = 'morrison' 
! includes two more prognostic equations for cloud drop concentration (nc)  
! and cloud water content (qc). 
! 
! 2277 2017-06-12 10:47:51Z kanani
! Removed unused variable sums_up_fraction_l
! 
! 2270 2017-06-09 12:18:47Z maronga
! dots_num must be increased when LSM and/or radiation is used
! 
! 2259 2017-06-08 09:09:11Z gronemeier
! Implemented synthetic turbulence generator
!
! 2252 2017-06-07 09:35:37Z knoop
! rho_air now depending on surface_pressure even in Boussinesq mode
! 
! 2233 2017-05-30 18:08:54Z suehring
!
! 2232 2017-05-30 17:47:52Z suehring
! Adjustments to new topography and surface concept: 
!   - Modify passed parameters for disturb_field
!   - Topography representation via flags
!   - Remove unused arrays. 
!   - Move initialization of surface-related quantities to surface_mod
! 
! 2172 2017-03-08 15:55:25Z knoop
! Bugfix: moved parallel random generator initialization into its module
! 
! 2118 2017-01-17 16:38:49Z raasch
! OpenACC directives removed
! 
! 2037 2016-10-26 11:15:40Z knoop
! Anelastic approximation implemented
! 
! 2031 2016-10-21 15:11:58Z knoop
! renamed variable rho to rho_ocean
! 
! 2011 2016-09-19 17:29:57Z kanani
! Flag urban_surface is now defined in module control_parameters.
! 
! 2007 2016-08-24 15:47:17Z kanani
! Added support for urban surface model,
! adjusted location_message in case of plant_canopy
! 
! 2000 2016-08-20 18:09:15Z knoop
! Forced header and separation lines into 80 columns
! 
! 1992 2016-08-12 15:14:59Z suehring
! Initializaton of scalarflux at model top
! Bugfixes in initialization of surface and top salinity flux, top scalar and 
! humidity fluxes
! 
! 1960 2016-07-12 16:34:24Z suehring
! Separate humidity and passive scalar
! Increase dimension for mean_inflow_profiles
! Remove inadvertent write-statement
! Bugfix, large-scale forcing is still not implemented for passive scalars
!
! 1957 2016-07-07 10:43:48Z suehring
! flight module added
!
! 1920 2016-05-30 10:50:15Z suehring 
! Initialize us with very small number to avoid segmentation fault during 
! calculation of Obukhov length
!
! 1918 2016-05-27 14:35:57Z raasch
! intermediate_timestep_count is set 0 instead 1 for first call of pres,
! bugfix: initialization of local sum arrays are moved to the beginning of the
!         routine because otherwise results from pres are overwritten
!
! 1914 2016-05-26 14:44:07Z witha
! Added initialization of the wind turbine model
!
! 1878 2016-04-19 12:30:36Z hellstea
! The zeroth element of weight_pres removed as unnecessary
!
! 1849 2016-04-08 11:33:18Z hoffmann
! Adapted for modularization of microphysics.
! precipitation_amount, precipitation_rate, prr moved to arrays_3d.
! Initialization of nc_1d, nr_1d, pt_1d, qc_1d, qr_1d, q_1d moved to
! bcm_init.
!
! 1845 2016-04-08 08:29:13Z raasch
! nzb_2d replaced by nzb_u|v_inner
!
! 1833 2016-04-07 14:23:03Z raasch
! initialization of spectra quantities moved to spectra_mod
!
! 1831 2016-04-07 13:15:51Z hoffmann
! turbulence renamed collision_turbulence
!
! 1826 2016-04-07 12:01:39Z maronga
! Renamed radiation calls.
! Renamed canopy model calls.
! 
! 1822 2016-04-07 07:49:42Z hoffmann
! icloud_scheme replaced by microphysics_*
! 
! 1817 2016-04-06 15:44:20Z maronga
! Renamed lsm calls.
!
! 1815 2016-04-06 13:49:59Z raasch
! zero-settings for velocities inside topography re-activated (was deactivated
! in r1762)
!
! 1788 2016-03-10 11:01:04Z maronga
! Added z0q. 
! Syntax layout improved.
!
! 1783 2016-03-06 18:36:17Z raasch
! netcdf module name changed + related changes
!
! 1764 2016-02-28 12:45:19Z raasch
! bugfix: increase size of volume_flow_area_l and volume_flow_initial_l by 1
!
! 1762 2016-02-25 12:31:13Z hellstea
! Introduction of nested domain feature
!
! 1738 2015-12-18 13:56:05Z raasch
! calculate mean surface level height for each statistic region
!
! 1734 2015-12-02 12:17:12Z raasch
! no initial disturbances in case that the disturbance energy limit has been
! set zero
!
! 1707 2015-11-02 15:24:52Z maronga
! Bugfix: transfer of Richardson number from 1D model to Obukhov length caused
! devision by zero in neutral stratification
! 
! 1691 2015-10-26 16:17:44Z maronga
! Call to init_surface_layer added. rif is replaced by ol and zeta.
! 
! 1682 2015-10-07 23:56:08Z knoop
! Code annotations made doxygen readable
! 
! 1615 2015-07-08 18:49:19Z suehring
! Enable turbulent inflow for passive_scalar and humidity
!
! 1585 2015-04-30 07:05:52Z maronga
! Initialization of radiation code is now done after LSM initializtion
!
! 1575 2015-03-27 09:56:27Z raasch
! adjustments for psolver-queries
!
! 1551 2015-03-03 14:18:16Z maronga
! Allocation of land surface arrays is now done in the subroutine lsm_init_arrays,
! which is part of land_surface_model.
! 
! 1507 2014-12-10 12:14:18Z suehring
! Bugfix: set horizontal velocity components to zero inside topography
!
! 1496 2014-12-02 17:25:50Z maronga
! Added initialization of the land surface and radiation schemes
! 
! 1484 2014-10-21 10:53:05Z kanani
! Changes due to new module structure of the plant canopy model:
! canopy-related initialization (e.g. lad and canopy_heat_flux) moved to new 
! subroutine init_plant_canopy within the module plant_canopy_model_mod,
! call of subroutine init_plant_canopy added.
! 
! 1431 2014-07-15 14:47:17Z suehring
! var_d added, in order to normalize spectra.
! 
! 1429 2014-07-15 12:53:45Z knoop
! Ensemble run capability added to parallel random number generator
! 
! 1411 2014-05-16 18:01:51Z suehring
! Initial horizontal velocity profiles were not set to zero at the first vertical 
! grid level in case of non-cyclic lateral boundary conditions. 
! 
! 1406 2014-05-16 13:47:01Z raasch
! bugfix: setting of initial velocities at k=1 to zero not in case of a
! no-slip boundary condition for uv
! 
! 1402 2014-05-09 14:25:13Z raasch
! location messages modified
! 
! 1400 2014-05-09 14:03:54Z knoop
! Parallel random number generator added
! 
! 1384 2014-05-02 14:31:06Z raasch
! location messages added
! 
! 1361 2014-04-16 15:17:48Z hoffmann
! tend_* removed
! Bugfix: w_subs is not allocated anymore if it is already allocated
! 
! 1359 2014-04-11 17:15:14Z hoffmann
! module lpm_init_mod added to use statements, because lpm_init has become a 
! module
! 
! 1353 2014-04-08 15:21:23Z heinze
! REAL constants provided with KIND-attribute 
! 
! 1340 2014-03-25 19:45:13Z kanani
! REAL constants defined as wp-kind
!
! 1322 2014-03-20 16:38:49Z raasch
! REAL constants defined as wp-kind
! module interfaces removed
!
! 1320 2014-03-20 08:40:49Z raasch
! ONLY-attribute added to USE-statements,
! kind-parameters added to all INTEGER and REAL declaration statements, 
! kinds are defined in new module kinds, 
! revision history before 2012 removed,
! comment fields (!:) to be used for variable explanations added to
! all variable declaration statements 
! 
! 1316 2014-03-17 07:44:59Z heinze
! Bugfix: allocation of w_subs
!
! 1299 2014-03-06 13:15:21Z heinze
! Allocate w_subs due to extension of large scale subsidence in combination
! with large scale forcing data (LSF_DATA)
!
! 1241 2013-10-30 11:36:58Z heinze
! Overwrite initial profiles in case of nudging
! Inititialize shf and qsws in case of large_scale_forcing
!
! 1221 2013-09-10 08:59:13Z raasch
! +rflags_s_inner in copyin statement, use copyin for most arrays instead of
! copy
!
! 1212 2013-08-15 08:46:27Z raasch
! array tri is allocated and included in data copy statement
!
! 1195 2013-07-01 12:27:57Z heinze
! Bugfix: move allocation of ref_state to parin.f90 and read_var_list.f90
!
! 1179 2013-06-14 05:57:58Z raasch
! allocate and set ref_state to be used in buoyancy terms
!
! 1171 2013-05-30 11:27:45Z raasch
! diss array is allocated with full size if accelerator boards are used
!
! 1159 2013-05-21 11:58:22Z fricke
! -bc_lr_dirneu, bc_lr_neudir, bc_ns_dirneu, bc_ns_neudir
!
! 1153 2013-05-10 14:33:08Z raasch
! diss array is allocated with dummy elements even if it is not needed
! (required by PGI 13.4 / CUDA 5.0)
!
! 1115 2013-03-26 18:16:16Z hoffmann
! unused variables removed
!
! 1113 2013-03-10 02:48:14Z raasch
! openACC directive modified
!
! 1111 2013-03-08 23:54:10Z raasch
! openACC directives added for pres
! array diss allocated only if required
!
! 1092 2013-02-02 11:24:22Z raasch
! unused variables removed
!
! 1065 2012-11-22 17:42:36Z hoffmann
! allocation of diss (dissipation rate) in case of turbulence = .TRUE. added
!
! 1053 2012-11-13 17:11:03Z hoffmann
! allocation and initialisation of necessary data arrays for the two-moment 
! cloud physics scheme the two new prognostic equations (nr, qr):
! +dr, lambda_r, mu_r, sed_*, xr, *s, *sws, *swst, *, *_p, t*_m, *_1, *_2, *_3, 
! +tend_*, prr
!
! 1036 2012-10-22 13:43:42Z raasch
! code put under GPL (PALM 3.9)
!
! 1032 2012-10-21 13:03:21Z letzel
! save memory by not allocating pt_2 in case of neutral = .T.
!
! 1025 2012-10-07 16:04:41Z letzel
! bugfix: swap indices of mask for ghost boundaries
!
! 1015 2012-09-27 09:23:24Z raasch
! mask is set to zero for ghost boundaries
!
! 1010 2012-09-20 07:59:54Z raasch
! cpp switch __nopointer added for pointer free version
!
! 1003 2012-09-14 14:35:53Z raasch
! nxra,nyna, nzta replaced ny nxr, nyn, nzt
!
! 1001 2012-09-13 14:08:46Z raasch
! all actions concerning leapfrog scheme removed
!
! 996 2012-09-07 10:41:47Z raasch
! little reformatting
!
! 978 2012-08-09 08:28:32Z fricke
! outflow damping layer removed
! roughness length for scalar quantites z0h added
! damping zone for the potential temperatur in case of non-cyclic lateral
! boundaries added
! initialization of ptdf_x, ptdf_y
! initialization of c_u_m, c_u_m_l, c_v_m, c_v_m_l, c_w_m, c_w_m_l
!
! 849 2012-03-15 10:35:09Z raasch
! init_particles renamed lpm_init
!
! 825 2012-02-19 03:03:44Z raasch
! wang_collision_kernel renamed wang_kernel
!
! Revision 1.1  1998/03/09 16:22:22  raasch
! Initial revision
!
!
! Description:
! ------------
!> Allocation of arrays and initialization of the 3D model via
!> a) pre-run the 1D model
!> or
!> b) pre-set constant linear profiles
!> or
!> c) read values of a previous run
!------------------------------------------------------------------------------!
 SUBROUTINE init_3d_model


    USE advec_ws

    USE arrays_3d

    USE basic_constants_and_equations_mod,                                     &
        ONLY:  c_p, g, l_v, pi, r_d, exner_function, exner_function_invers,    &
               ideal_gas_law_rho, ideal_gas_law_rho_pt, barometric_formula

    USE biometeorology_mod,                                                    &
        ONLY:  bio_init

    USE bulk_cloud_model_mod,                                                  &
        ONLY:  bulk_cloud_model, bcm_init, bcm_init_arrays

    USE chem_emissions_mod,                                                    &
        ONLY:  chem_emissions_init

    USE chem_modules,                                                          &
        ONLY:  do_emis, max_pr_cs, nspec_out

    USE control_parameters

    USE flight_mod,                                                            &
        ONLY:  flight_init

    USE grid_variables,                                                        &
        ONLY:  dx, dy, ddx2_mg, ddy2_mg

    USE gust_mod,                                                              &
        ONLY:  gust_init, gust_init_arrays, gust_module_enabled

    USE indices

    USE indoor_model_mod,                                                      &
        ONLY:  im_init

    USE kinds

    USE land_surface_model_mod,                                                &
        ONLY:  lsm_init, lsm_init_arrays

    USE lpm_init_mod,                                                          &
        ONLY:  lpm_init
  
    USE lsf_nudging_mod,                                                       &
        ONLY:  lsf_init, ls_forcing_surf, nudge_init

    USE model_1d_mod,                                                          &
        ONLY:  init_1d_model, l1d, u1d, v1d

    USE multi_agent_system_mod,                                                &
        ONLY:  agents_active, mas_init

    USE netcdf_interface,                                                      &
        ONLY:  dots_max, dots_num, dots_unit, dots_label

    USE netcdf_data_input_mod,                                                 &
        ONLY:  chem_emis, chem_emis_att, init_3d,                              &
               netcdf_data_input_init_3d, netcdf_data_input_interpolate

    USE nesting_offl_mod,                                                      &
        ONLY:  nesting_offl_init

    USE ocean_mod,                                                             &
        ONLY:  ocean_init, ocean_init_arrays

    USE particle_attributes,                                                   &
        ONLY:  particle_advection

    USE pegrid

    USE plant_canopy_model_mod,                                                &
        ONLY:  pcm_init

#if defined( __parallel )
    USE pmc_interface,                                                         &
        ONLY:  nested_run
#endif

    USE radiation_model_mod,                                                   &
        ONLY:  average_radiation,                                              &
               radiation_init, radiation, radiation_scheme,                    &
               radiation_calc_svf, radiation_write_svf,                        &
               radiation_interaction, radiation_interactions,                  &
               radiation_interaction_init, radiation_read_svf,                 &
               radiation_presimulate_solar_pos, radiation_interactions_on
    
    USE random_function_mod 
    
    USE random_generator_parallel,                                             &
        ONLY:  init_parallel_random_generator
        
    USE read_restart_data_mod,                                                 &
        ONLY:  rrd_read_parts_of_global, rrd_local    
             
    USE salsa_mod,                                                             &
        ONLY:  salsa_init, salsa_init_arrays      
    
    USE statistics,                                                            &
        ONLY:  hom, hom_sum, mean_surface_level_height, pr_palm, rmask,        &
               statistic_regions, sums, sums_divnew_l, sums_divold_l, sums_l,  &
               sums_l_l, sums_wsts_bc_l, ts_value,                             &
               weight_pres, weight_substep

    USE synthetic_turbulence_generator_mod,                                    &
        ONLY:  parametrize_inflow_turbulence, stg_adjust, stg_init,            &
               use_syn_turb_gen
               
    USE surface_layer_fluxes_mod,                                              &
        ONLY:  init_surface_layer_fluxes

    USE surface_mod,                                                           &
        ONLY :  init_surface_arrays, init_surfaces, surf_def_h, surf_lsm_h,    &
                surf_usm_h, get_topography_top_index_ji, vertical_surfaces_exist
   
    USE surface_output_mod,                                                    &
        ONLY:  surface_output_init
   
    USE transpose_indices

    USE turbulence_closure_mod,                                                &
        ONLY:  tcm_init_arrays, tcm_init

    USE urban_surface_mod,                                                     &
        ONLY:  usm_init_urban_surface, usm_allocate_surface

    USE virtual_measurement_mod,                                               &
        ONLY:  vm_init

    USE wind_turbine_model_mod,                                                &
        ONLY:  wtm_init, wtm_init_arrays

    IMPLICIT NONE

    INTEGER(iwp) ::  i             !< grid index in x direction
    INTEGER(iwp) ::  ind_array(1)  !< dummy used to determine start index for external pressure forcing
    INTEGER(iwp) ::  j             !< grid index in y direction
    INTEGER(iwp) ::  k             !< grid index in z direction
    INTEGER(iwp) ::  k_surf        !< surface level index
    INTEGER(iwp) ::  m             !< index of surface element in surface data type
    INTEGER(iwp) ::  sr            !< index of statistic region

    INTEGER(iwp), DIMENSION(:), ALLOCATABLE   ::  ngp_2dh_l  !< toal number of horizontal grid points in statistical region on subdomain

    INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE ::  ngp_2dh_outer_l    !< number of horizontal non-wall bounded grid points on subdomain
    INTEGER(iwp), DIMENSION(:,:), ALLOCATABLE ::  ngp_2dh_s_inner_l  !< number of horizontal non-topography grid points on subdomain

    REAL(wp)     ::  t_surface !< air temperature at the surface

    REAL(wp), DIMENSION(:), ALLOCATABLE ::  init_l        !< dummy array used for averaging 3D data to obtain inital profiles 
    REAL(wp), DIMENSION(:), ALLOCATABLE ::  p_hydrostatic !< hydrostatic pressure

    INTEGER(iwp) ::  l       !< loop variable
    INTEGER(iwp) ::  nzt_l   !< index of top PE boundary for multigrid level
    REAL(wp) ::  dx_l !< grid spacing along x on different multigrid level
    REAL(wp) ::  dy_l !< grid spacing along y on different multigrid level

    REAL(wp), DIMENSION(1:3) ::  volume_flow_area_l     !< area of lateral and top model domain surface on local subdomain
    REAL(wp), DIMENSION(1:3) ::  volume_flow_initial_l  !< initial volume flow into model domain

    REAL(wp), DIMENSION(:), ALLOCATABLE ::  mean_surface_level_height_l !< mean surface level height on subdomain
    REAL(wp), DIMENSION(:), ALLOCATABLE ::  ngp_3d_inner_l    !< total number of non-topography grid points on subdomain
    REAL(wp), DIMENSION(:), ALLOCATABLE ::  ngp_3d_inner_tmp  !< total number of non-topography grid points

    INTEGER(iwp) ::  nz_u_shift   !< topography-top index on u-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_v_shift   !< topography-top index on v-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_w_shift   !< topography-top index on w-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_s_shift   !< topography-top index on scalar-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_u_shift_l !< topography-top index on u-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_v_shift_l !< topography-top index on v-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_w_shift_l !< topography-top index on w-grid, used to vertically shift initial profiles
    INTEGER(iwp) ::  nz_s_shift_l !< topography-top index on scalar-grid, used to vertically shift initial profiles

    CALL location_message( 'allocating arrays', .FALSE. )
!
!-- Allocate arrays
    ALLOCATE( mean_surface_level_height(0:statistic_regions),                  &
              mean_surface_level_height_l(0:statistic_regions),                &
              ngp_2dh(0:statistic_regions), ngp_2dh_l(0:statistic_regions),    &
              ngp_3d(0:statistic_regions),                                     &
              ngp_3d_inner(0:statistic_regions),                               &
              ngp_3d_inner_l(0:statistic_regions),                             &
              ngp_3d_inner_tmp(0:statistic_regions),                           &
              sums_divnew_l(0:statistic_regions),                              &
              sums_divold_l(0:statistic_regions) )
    ALLOCATE( dp_smooth_factor(nzb:nzt), rdf(nzb+1:nzt), rdf_sc(nzb+1:nzt) )
    ALLOCATE( ngp_2dh_outer(nzb:nzt+1,0:statistic_regions),                    &
              ngp_2dh_outer_l(nzb:nzt+1,0:statistic_regions),                  &
              ngp_2dh_s_inner(nzb:nzt+1,0:statistic_regions),                  &
              ngp_2dh_s_inner_l(nzb:nzt+1,0:statistic_regions),                &
              rmask(nysg:nyng,nxlg:nxrg,0:statistic_regions),                  &
              sums(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs),                   &
              sums_l(nzb:nzt+1,pr_palm+max_pr_user+max_pr_cs,0:threads_per_task-1),      &
              sums_l_l(nzb:nzt+1,0:statistic_regions,0:threads_per_task-1),    &
              sums_wsts_bc_l(nzb:nzt+1,0:statistic_regions),                   &
              ts_value(dots_max,0:statistic_regions) )
    ALLOCATE( ptdf_x(nxlg:nxrg), ptdf_y(nysg:nyng) )

    ALLOCATE( d(nzb+1:nzt,nys:nyn,nxl:nxr),                                    &
              p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                                &
              tend(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )

#if defined( __nopointer )
    ALLOCATE( pt(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                               &
              pt_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
              u(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                                &
              u_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              v(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                                &
              v_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              w(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                                &
              w_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              tpt_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                            &
              tu_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
              tv_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
              tw_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#else
    ALLOCATE( pt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
              pt_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
              u_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              u_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              u_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              v_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              v_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              v_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              w_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              w_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                              &
              w_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
    IF (  .NOT.  neutral )  THEN
       ALLOCATE( pt_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
    ENDIF
#endif

!
!-- Following array is required for perturbation pressure within the iterative
!-- pressure solvers. For the multistep schemes (Runge-Kutta), array p holds
!-- the weighted average of the substeps and cannot be used in the Poisson
!-- solver.
    IF ( psolver == 'sor' )  THEN
       ALLOCATE( p_loc(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
    ELSEIF ( psolver(1:9) == 'multigrid' )  THEN
!
!--    For performance reasons, multigrid is using one ghost layer only
       ALLOCATE( p_loc(nzb:nzt+1,nys-1:nyn+1,nxl-1:nxr+1) )
    ENDIF

!
!-- Array for storing constant coeffficients of the tridiagonal solver
    IF ( psolver == 'poisfft' )  THEN
       ALLOCATE( tri(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1,2) )
       ALLOCATE( tric(nxl_z:nxr_z,nys_z:nyn_z,0:nz-1) )
    ENDIF

    IF ( humidity )  THEN
!
!--    3D-humidity
#if defined( __nopointer )
       ALLOCATE( q(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
                 q_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 tq_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                          &
                 vpt(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#else
       ALLOCATE( q_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 q_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 q_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 vpt_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg) ) 
#endif

       IF ( cloud_droplets )  THEN
!
!--       Liquid water content, change in liquid water content
#if defined( __nopointer )
          ALLOCATE ( ql(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                        &
                     ql_c(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#else
          ALLOCATE ( ql_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                      &
                     ql_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#endif
!
!--       Real volume of particles (with weighting), volume of particles
          ALLOCATE ( ql_v(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                      &
                     ql_vp(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
       ENDIF

    ENDIF   
    
    IF ( passive_scalar )  THEN

!
!--    3D scalar arrays
#if defined( __nopointer )
       ALLOCATE( s(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                             &
                 s_p(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 ts_m(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#else
       ALLOCATE( s_1(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 s_2(nzb:nzt+1,nysg:nyng,nxlg:nxrg),                           &
                 s_3(nzb:nzt+1,nysg:nyng,nxlg:nxrg) )
#endif
    ENDIF

!
!-- Allocate and set 1d-profiles for Stokes drift velocity. It may be set to
!-- non-zero values later in ocean_init
    ALLOCATE( u_stokes_zu(nzb:nzt+1), u_stokes_zw(nzb:nzt+1),                  &
              v_stokes_zu(nzb:nzt+1), v_stokes_zw(nzb:nzt+1) )
    u_stokes_zu(:) = 0.0_wp
    u_stokes_zw(:) = 0.0_wp
    v_stokes_zu(:) = 0.0_wp
    v_stokes_zw(:) = 0.0_wp

!
!-- Allocation of anelastic and Boussinesq approximation specific arrays
    ALLOCATE( p_hydrostatic(nzb:nzt+1) )
    ALLOCATE( rho_air(nzb:nzt+1) )
    ALLOCATE( rho_air_zw(nzb:nzt+1) )
    ALLOCATE( drho_air(nzb:nzt+1) )
    ALLOCATE( drho_air_zw(nzb:nzt+1) )
!
!-- Density profile calculation for anelastic approximation
    t_surface = pt_surface * ( surface_pressure / 1000.0_wp )**( r_d / c_p )
    IF ( TRIM( approximation ) == 'anelastic' ) THEN
       DO  k = nzb, nzt+1
          p_hydrostatic(k)    = surface_pressure * 100.0_wp *                  &
                                ( 1 - ( g * zu(k) ) / ( c_p * t_surface )      &
                                )**( c_p / r_d )
          rho_air(k)          = ( p_hydrostatic(k) *                           &
                                  ( 100000.0_wp / p_hydrostatic(k)             &
                                  )**( r_d / c_p )                             &
                                ) / ( r_d * pt_init(k) )
       ENDDO
       DO  k = nzb, nzt
          rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
       ENDDO
       rho_air_zw(nzt+1)  = rho_air_zw(nzt)                                    &
                            + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt)  )
    ELSE
       DO  k = nzb, nzt+1
          p_hydrostatic(k)    = surface_pressure * 100.0_wp *                  &
                                ( 1 - ( g * zu(nzb) ) / ( c_p * t_surface )    &
                                )**( c_p / r_d )
          rho_air(k)          = ( p_hydrostatic(k) *                           &
                                  ( 100000.0_wp / p_hydrostatic(k)             &
                                  )**( r_d / c_p )                             &
                                ) / ( r_d * pt_init(nzb) )
       ENDDO
       DO  k = nzb, nzt
          rho_air_zw(k) = 0.5_wp * ( rho_air(k) + rho_air(k+1) )
       ENDDO
       rho_air_zw(nzt+1)  = rho_air_zw(nzt)                                    &
                            + 2.0_wp * ( rho_air(nzt+1) - rho_air_zw(nzt)  )
    ENDIF
!
!-- compute the inverse density array in order to avoid expencive divisions
    drho_air    = 1.0_wp / rho_air
    drho_air_zw = 1.0_wp / rho_air_zw

!
!-- Allocation of flux conversion arrays
    ALLOCATE( heatflux_input_conversion(nzb:nzt+1) )
    ALLOCATE( waterflux_input_conversion(nzb:nzt+1) )
    ALLOCATE( momentumflux_input_conversion(nzb:nzt+1) )
    ALLOCATE( heatflux_output_conversion(nzb:nzt+1) )
    ALLOCATE( waterflux_output_conversion(nzb:nzt+1) )
    ALLOCATE( momentumflux_output_conversion(nzb:nzt+1) )

!
!-- calculate flux conversion factors according to approximation and in-/output mode
    DO  k = nzb, nzt+1

        IF ( TRIM( flux_input_mode ) == 'kinematic' )  THEN
            heatflux_input_conversion(k)      = rho_air_zw(k)
            waterflux_input_conversion(k)     = rho_air_zw(k)
            momentumflux_input_conversion(k)  = rho_air_zw(k)
        ELSEIF ( TRIM( flux_input_mode ) == 'dynamic' ) THEN
            heatflux_input_conversion(k)      = 1.0_wp / c_p
            waterflux_input_conversion(k)     = 1.0_wp / l_v
            momentumflux_input_conversion(k)  = 1.0_wp
        ENDIF

        IF ( TRIM( flux_output_mode ) == 'kinematic' )  THEN
            heatflux_output_conversion(k)     = drho_air_zw(k)
            waterflux_output_conversion(k)    = drho_air_zw(k)
            momentumflux_output_conversion(k) = drho_air_zw(k)
        ELSEIF ( TRIM( flux_output_mode ) == 'dynamic' ) THEN
            heatflux_output_conversion(k)     = c_p
            waterflux_output_conversion(k)    = l_v
            momentumflux_output_conversion(k) = 1.0_wp
        ENDIF

        IF ( .NOT. humidity ) THEN
            waterflux_input_conversion(k)  = 1.0_wp
            waterflux_output_conversion(k) = 1.0_wp
        ENDIF

    ENDDO

!
!-- In case of multigrid method, compute grid lengths and grid factors for the
!-- grid levels with respective density on each grid
    IF ( psolver(1:9) == 'multigrid' )  THEN

       ALLOCATE( ddx2_mg(maximum_grid_level) )
       ALLOCATE( ddy2_mg(maximum_grid_level) )
       ALLOCATE( dzu_mg(nzb+1:nzt+1,maximum_grid_level) )
       ALLOCATE( dzw_mg(nzb+1:nzt+1,maximum_grid_level) )
       ALLOCATE( f1_mg(nzb+1:nzt,maximum_grid_level) )
       ALLOCATE( f2_mg(nzb+1:nzt,maximum_grid_level) )
       ALLOCATE( f3_mg(nzb+1:nzt,maximum_grid_level) )
       ALLOCATE( rho_air_mg(nzb:nzt+1,maximum_grid_level) )
       ALLOCATE( rho_air_zw_mg(nzb:nzt+1,maximum_grid_level) )

       dzu_mg(:,maximum_grid_level) = dzu
       rho_air_mg(:,maximum_grid_level) = rho_air
!       
!--    Next line to ensure an equally spaced grid. 
       dzu_mg(1,maximum_grid_level) = dzu(2)
       rho_air_mg(nzb,maximum_grid_level) = rho_air(nzb) +                     &
                                             (rho_air(nzb) - rho_air(nzb+1))

       dzw_mg(:,maximum_grid_level) = dzw
       rho_air_zw_mg(:,maximum_grid_level) = rho_air_zw
       nzt_l = nzt
       DO  l = maximum_grid_level-1, 1, -1
           dzu_mg(nzb+1,l) = 2.0_wp * dzu_mg(nzb+1,l+1)
           dzw_mg(nzb+1,l) = 2.0_wp * dzw_mg(nzb+1,l+1)
           rho_air_mg(nzb,l)    = rho_air_mg(nzb,l+1) + (rho_air_mg(nzb,l+1) - rho_air_mg(nzb+1,l+1))
           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))
           rho_air_mg(nzb+1,l)    = rho_air_mg(nzb+1,l+1)
           rho_air_zw_mg(nzb+1,l) = rho_air_zw_mg(nzb+1,l+1)
           nzt_l = nzt_l / 2
           DO  k = 2, nzt_l+1
              dzu_mg(k,l) = dzu_mg(2*k-2,l+1) + dzu_mg(2*k-1,l+1)
              dzw_mg(k,l) = dzw_mg(2*k-2,l+1) + dzw_mg(2*k-1,l+1)
              rho_air_mg(k,l)    = rho_air_mg(2*k-1,l+1)
              rho_air_zw_mg(k,l) = rho_air_zw_mg(2*k-1,l+1)
           ENDDO
       ENDDO

       nzt_l = nzt
       dx_l  = dx
       dy_l  = dy
       DO  l = maximum_grid_level, 1, -1
          ddx2_mg(l) = 1.0_wp / dx_l**2
          ddy2_mg(l) = 1.0_wp / dy_l**2
          DO  k = nzb+1, nzt_l
             f2_mg(k,l) = rho_air_zw_mg(k,l) / ( dzu_mg(k+1,l) * dzw_mg(k,l) )
             f3_mg(k,l) = rho_air_zw_mg(k-1,l) / ( dzu_mg(k,l)   * dzw_mg(k,l) )
             f1_mg(k,l) = 2.0_wp * ( ddx2_mg(l) + ddy2_mg(l) ) &
                          * rho_air_mg(k,l) + f2_mg(k,l) + f3_mg(k,l)
          ENDDO
          nzt_l = nzt_l / 2
          dx_l  = dx_l * 2.0_wp
          dy_l  = dy_l * 2.0_wp
       ENDDO

    ENDIF

!
!-- 1D-array for large scale subsidence velocity
    IF ( .NOT. ALLOCATED( w_subs ) )  THEN
       ALLOCATE ( w_subs(nzb:nzt+1) )
       w_subs = 0.0_wp
    ENDIF

!
!-- Arrays to store velocity data from t-dt and the phase speeds which
!-- are needed for radiation boundary conditions
    IF ( bc_radiation_l )  THEN
       ALLOCATE( u_m_l(nzb:nzt+1,nysg:nyng,1:2),                               &
                 v_m_l(nzb:nzt+1,nysg:nyng,0:1),                               &
                 w_m_l(nzb:nzt+1,nysg:nyng,0:1) )
    ENDIF
    IF ( bc_radiation_r )  THEN
       ALLOCATE( u_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx),                           &
                 v_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx),                           &
                 w_m_r(nzb:nzt+1,nysg:nyng,nx-1:nx) )
    ENDIF
    IF ( bc_radiation_l  .OR.  bc_radiation_r )  THEN
       ALLOCATE( c_u(nzb:nzt+1,nysg:nyng), c_v(nzb:nzt+1,nysg:nyng),           &
                 c_w(nzb:nzt+1,nysg:nyng) )
    ENDIF
    IF ( bc_radiation_s )  THEN
       ALLOCATE( u_m_s(nzb:nzt+1,0:1,nxlg:nxrg),                               &
                 v_m_s(nzb:nzt+1,1:2,nxlg:nxrg),                               &
                 w_m_s(nzb:nzt+1,0:1,nxlg:nxrg) )
    ENDIF
    IF ( bc_radiation_n )  THEN
       ALLOCATE( u_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg),                           &
                 v_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg),                           &
                 w_m_n(nzb:nzt+1,ny-1:ny,nxlg:nxrg) )
    ENDIF
    IF ( bc_radiation_s  .OR.  bc_radiation_n )  THEN
       ALLOCATE( c_u(nzb:nzt+1,nxlg:nxrg), c_v(nzb:nzt+1,nxlg:nxrg),           &
                 c_w(nzb:nzt+1,nxlg:nxrg) )
    ENDIF
    IF ( bc_radiation_l  .OR.  bc_radiation_r  .OR.  bc_radiation_s  .OR.      &
         bc_radiation_n )  THEN
       ALLOCATE( c_u_m_l(nzb:nzt+1), c_v_m_l(nzb:nzt+1), c_w_m_l(nzb:nzt+1) )                   
       ALLOCATE( c_u_m(nzb:nzt+1), c_v_m(nzb:nzt+1), c_w_m(nzb:nzt+1) )
    ENDIF


#if ! defined( __nopointer )
!
!-- Initial assignment of the pointers
    IF ( .NOT. neutral )  THEN
       pt => pt_1;  pt_p => pt_2;  tpt_m => pt_3
    ELSE
       pt => pt_1;  pt_p => pt_1;  tpt_m => pt_3
    ENDIF
    u  => u_1;   u_p  => u_2;   tu_m  => u_3
    v  => v_1;   v_p  => v_2;   tv_m  => v_3
    w  => w_1;   w_p  => w_2;   tw_m  => w_3

    IF ( humidity )  THEN
       q => q_1;  q_p => q_2;  tq_m => q_3
       vpt  => vpt_1
       IF ( cloud_droplets )  THEN
          ql   => ql_1
          ql_c => ql_2
       ENDIF
    ENDIF
    
    IF ( passive_scalar )  THEN
       s => s_1;  s_p => s_2;  ts_m => s_3
    ENDIF    
#endif

!
!-- Initialize arrays for turbulence closure
    CALL tcm_init_arrays
!
!-- Initialize surface arrays
    CALL init_surface_arrays
!
!-- Allocate arrays for other modules
    IF ( bulk_cloud_model    )  CALL bcm_init_arrays
    IF ( gust_module_enabled )  CALL gust_init_arrays
    IF ( land_surface        )  CALL lsm_init_arrays
    IF ( ocean_mode          )  CALL ocean_init_arrays
    IF ( salsa               )  CALL salsa_init_arrays
    IF ( wind_turbine        )  CALL wtm_init_arrays

!
!-- Initialize virtual flight measurements
    IF ( virtual_flight )  THEN
       CALL flight_init
    ENDIF


!
!-- Allocate arrays containing the RK coefficient for calculation of 
!-- perturbation pressure and turbulent fluxes. At this point values are
!-- set for pressure calculation during initialization (where no timestep
!-- is done). Further below the values needed within the timestep scheme
!-- will be set.
    ALLOCATE( weight_substep(1:intermediate_timestep_count_max),               &
              weight_pres(1:intermediate_timestep_count_max) )
    weight_substep = 1.0_wp
    weight_pres    = 1.0_wp
    intermediate_timestep_count = 0  ! needed when simulated_time = 0.0
       
    CALL location_message( 'finished', .TRUE. )

!
!-- Initialize time series
    ts_value = 0.0_wp

!
!-- Initialize local summation arrays for routine flow_statistics.
!-- This is necessary because they may not yet have been initialized when they
!-- are called from flow_statistics (or - depending on the chosen model run -
!-- are never initialized)
    sums_divnew_l      = 0.0_wp
    sums_divold_l      = 0.0_wp
    sums_l_l           = 0.0_wp
    sums_wsts_bc_l     = 0.0_wp
    
!
!-- Initialize model variables
    IF ( TRIM( initializing_actions ) /= 'read_restart_data'  .AND.            &
         TRIM( initializing_actions ) /= 'cyclic_fill' )  THEN
!
!--    Initialization with provided input data derived from larger-scale model
       IF ( INDEX( initializing_actions, 'inifor' ) /= 0 )  THEN
          CALL location_message( 'initializing with INIFOR', .FALSE. )
!
!--       Read initial 1D profiles or 3D data from NetCDF file, depending 
!--       on the provided level-of-detail. 
!--       At the moment, only u, v, w, pt and q are provided. 
          CALL netcdf_data_input_init_3d
!
!--       Please note, Inifor provides data from nzb+1 to nzt. 
!--       Bottom and top boundary conditions for Inifor profiles are already 
!--       set (just after reading), so that this is not necessary here.
!--       Depending on the provided level-of-detail, initial Inifor data is
!--       either stored on data type (lod=1), or directly on 3D arrays (lod=2). 
!--       In order to obtain also initial profiles in case of lod=2 (which 
!--       is required for e.g. damping), average over 3D data.
          IF( init_3d%lod_u == 1 )  THEN
             u_init = init_3d%u_init
          ELSEIF( init_3d%lod_u == 2 )  THEN 
             ALLOCATE( init_l(nzb:nzt+1) ) 
             DO  k = nzb, nzt+1
                init_l(k) = SUM( u(k,nys:nyn,nxl:nxr) )
             ENDDO
             init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )

#if defined( __parallel )
             CALL MPI_ALLREDUCE( init_l, u_init, nzt+1-nzb+1,                  &
                                 MPI_REAL, MPI_SUM, comm2d, ierr )
#else
             u_init = init_l
#endif
             DEALLOCATE( init_l )

          ENDIF
           
          IF( init_3d%lod_v == 1 )  THEN  
             v_init = init_3d%v_init
          ELSEIF( init_3d%lod_v == 2 )  THEN 
             ALLOCATE( init_l(nzb:nzt+1) ) 
             DO  k = nzb, nzt+1
                init_l(k) = SUM( v(k,nys:nyn,nxl:nxr) )
             ENDDO
             init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )

#if defined( __parallel )
             CALL MPI_ALLREDUCE( init_l, v_init, nzt+1-nzb+1,                  &
                                 MPI_REAL, MPI_SUM, comm2d, ierr )
#else
             v_init = init_l
#endif
             DEALLOCATE( init_l )
          ENDIF
          IF( .NOT. neutral )  THEN
             IF( init_3d%lod_pt == 1 )  THEN
                pt_init = init_3d%pt_init
             ELSEIF( init_3d%lod_pt == 2 )  THEN 
                ALLOCATE( init_l(nzb:nzt+1) ) 
                DO  k = nzb, nzt+1
                   init_l(k) = SUM( pt(k,nys:nyn,nxl:nxr) )
                ENDDO
                init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )

#if defined( __parallel )
                CALL MPI_ALLREDUCE( init_l, pt_init, nzt+1-nzb+1,               &
                                    MPI_REAL, MPI_SUM, comm2d, ierr )
#else
                pt_init = init_l
#endif
                DEALLOCATE( init_l )
             ENDIF
          ENDIF


          IF( humidity )  THEN
             IF( init_3d%lod_q == 1 )  THEN
                q_init = init_3d%q_init
             ELSEIF( init_3d%lod_q == 2 )  THEN 
                ALLOCATE( init_l(nzb:nzt+1) ) 
                DO  k = nzb, nzt+1
                   init_l(k) = SUM( q(k,nys:nyn,nxl:nxr) )
                ENDDO
                init_l = init_l / REAL( ( nx + 1 ) * ( ny + 1 ), KIND = wp )

#if defined( __parallel )
                CALL MPI_ALLREDUCE( init_l, q_init, nzt+1-nzb+1,               &
                                    MPI_REAL, MPI_SUM, comm2d, ierr )
#else
                q_init = init_l
#endif
                DEALLOCATE( init_l )
             ENDIF
          ENDIF

!
!--       Write initial profiles onto 3D arrays. Note, only in case of lod = 1, 
!--       for lod = 2 data is already on 3D arrays.   
          DO  i = nxlg, nxrg
             DO  j = nysg, nyng
                IF( init_3d%lod_u == 1 )  u(:,j,i) = u_init(:)
                IF( init_3d%lod_v == 1 )  v(:,j,i) = v_init(:)
                IF( .NOT. neutral  .AND.  init_3d%lod_pt == 1 )                &
                   pt(:,j,i) = pt_init(:)
                IF( humidity  .AND.  init_3d%lod_q == 1 )  q(:,j,i) = q_init(:)
             ENDDO
          ENDDO
!
!--       Exchange ghost points in case of level-of-detail = 2
          IF( init_3d%lod_u == 2 )   CALL exchange_horiz( u, nbgp )
          IF( init_3d%lod_v == 2 )   CALL exchange_horiz( v, nbgp )
          IF( init_3d%lod_w == 2 )   CALL exchange_horiz( w, nbgp )
          IF( .NOT. neutral  .AND.  init_3d%lod_pt == 2 )                      &
             CALL exchange_horiz( pt, nbgp )
          IF( humidity  .AND.  init_3d%lod_q == 2 )                            &
             CALL exchange_horiz( q, nbgp )
!
!--       Set geostrophic wind components.  
          IF ( init_3d%from_file_ug )  THEN
             ug(:) = init_3d%ug_init(:)
          ENDIF
          IF ( init_3d%from_file_vg )  THEN
             vg(:) = init_3d%vg_init(:)
          ENDIF
!
!--       Set bottom and top boundary condition for geostrophic wind
          ug(nzt+1) = ug(nzt)
          vg(nzt+1) = vg(nzt)
          ug(nzb)   = ug(nzb+1)
          vg(nzb)   = vg(nzb+1)
!
!--       Set inital w to 0
          w = 0.0_wp

          IF ( passive_scalar )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   s(:,j,i) = s_init
                ENDDO
             ENDDO
          ENDIF

!
!--       Set velocity components at non-atmospheric / oceanic grid points to 
!--       zero. 
          u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
          v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )
          w = MERGE( w, 0.0_wp, BTEST( wall_flags_0, 3 ) )
!
!--       Initialize surface variables, e.g. friction velocity, momentum 
!--       fluxes, etc. 
          CALL init_surfaces
!
!--       Initialize turbulence generator
          IF( use_syn_turb_gen )  CALL stg_init

          CALL location_message( 'finished', .TRUE. )
!
!--    Initialization via computed 1D-model profiles
       ELSEIF ( INDEX( initializing_actions, 'set_1d-model_profiles' ) /= 0 )  THEN

          CALL location_message( 'initializing with 1D model profiles', .FALSE. )
!
!--       Use solutions of the 1D model as initial profiles,
!--       start 1D model
          CALL init_1d_model
!
!--       Transfer initial profiles to the arrays of the 3D model
          DO  i = nxlg, nxrg
             DO  j = nysg, nyng
                pt(:,j,i) = pt_init
                u(:,j,i)  = u1d
                v(:,j,i)  = v1d
             ENDDO
          ENDDO

          IF ( humidity )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   q(:,j,i) = q_init
                ENDDO
             ENDDO
          ENDIF

          IF ( passive_scalar )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   s(:,j,i) = s_init
                ENDDO
             ENDDO   
          ENDIF
!
!--          Store initial profiles for output purposes etc.
          IF ( .NOT. constant_diffusion )  THEN
             hom(:,1,25,:) = SPREAD( l1d, 2, statistic_regions+1 )
          ENDIF
!
!--       Set velocities back to zero
          u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
          v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )         
!
!--       WARNING: The extra boundary conditions set after running the
!--       -------  1D model impose an error on the divergence one layer
!--                below the topography; need to correct later 
!--       ATTENTION: Provisional correction for Piacsek & Williams
!--       ---------  advection scheme: keep u and v zero one layer below
!--                  the topography.
          IF ( ibc_uv_b == 1 )  THEN
!
!--          Neumann condition
             DO  i = nxl-1, nxr+1
                DO  j = nys-1, nyn+1
                   u(nzb,j,i) = u(nzb+1,j,i)
                   v(nzb,j,i) = v(nzb+1,j,i)
                ENDDO
             ENDDO

          ENDIF
!
!--       Initialize surface variables, e.g. friction velocity, momentum 
!--       fluxes, etc. 
          CALL init_surfaces
!
!--       Initialize synthetic turbulence generator if required 
          IF( use_syn_turb_gen )  CALL stg_init

          CALL location_message( 'finished', .TRUE. )

       ELSEIF ( INDEX(initializing_actions, 'set_constant_profiles') /= 0 )    &
       THEN

          CALL location_message( 'initializing with constant profiles', .FALSE. )

!
!--       Use constructed initial profiles (velocity constant with height,
!--       temperature profile with constant gradient)
          DO  i = nxlg, nxrg
             DO  j = nysg, nyng
                pt(:,j,i) = pt_init
                u(:,j,i)  = u_init
                v(:,j,i)  = v_init
             ENDDO
          ENDDO
!
!--       Mask topography
          u = MERGE( u, 0.0_wp, BTEST( wall_flags_0, 1 ) )
          v = MERGE( v, 0.0_wp, BTEST( wall_flags_0, 2 ) )
!
!--       Set initial horizontal velocities at the lowest computational grid 
!--       levels to zero in order to avoid too small time steps caused by the 
!--       diffusion limit in the initial phase of a run (at k=1, dz/2 occurs
!--       in the limiting formula!). 
!--       Please note, in case land- or urban-surface model is used and a 
!--       spinup is applied, masking the lowest computational level is not 
!--       possible as MOST as well as energy-balance parametrizations will not 
!--       work with zero wind velocity. 
          IF ( ibc_uv_b /= 1  .AND.  .NOT.  spinup )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   DO  k = nzb, nzt
                      u(k,j,i) = MERGE( u(k,j,i), 0.0_wp,                      &
                                        BTEST( wall_flags_0(k,j,i), 20 ) )
                      v(k,j,i) = MERGE( v(k,j,i), 0.0_wp,                      &
                                        BTEST( wall_flags_0(k,j,i), 21 ) )
                   ENDDO
                ENDDO
             ENDDO
          ENDIF

          IF ( humidity )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   q(:,j,i) = q_init
                ENDDO
             ENDDO
          ENDIF
          
          IF ( passive_scalar )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   s(:,j,i) = s_init
                ENDDO
             ENDDO
          ENDIF

!
!--       Compute initial temperature field and other constants used in case
!--       of a sloping surface
          IF ( sloping_surface )  CALL init_slope
!
!--       Initialize surface variables, e.g. friction velocity, momentum 
!--       fluxes, etc. 
          CALL init_surfaces
!
!--       Initialize synthetic turbulence generator if required 
          IF( use_syn_turb_gen )  CALL stg_init
          
          CALL location_message( 'finished', .TRUE. )

       ELSEIF ( INDEX(initializing_actions, 'by_user') /= 0 )                  &
       THEN

          CALL location_message( 'initializing by user', .FALSE. )
!
!--       Pre-initialize surface variables, i.e. setting start- and end-indices
!--       at each (j,i)-location. Please note, this does not supersede 
!--       user-defined initialization of surface quantities. 
          CALL init_surfaces
!
!--       Initialization will completely be done by the user
          CALL user_init_3d_model

          CALL location_message( 'finished', .TRUE. )

       ENDIF

       CALL location_message( 'initializing statistics, boundary conditions, etc.', &
                              .FALSE. )

!
!--    Bottom boundary
       IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2  )  THEN
          u(nzb,:,:) = 0.0_wp
          v(nzb,:,:) = 0.0_wp
       ENDIF

!
!--    Apply channel flow boundary condition
       IF ( TRIM( bc_uv_t ) == 'dirichlet_0' )  THEN
          u(nzt+1,:,:) = 0.0_wp
          v(nzt+1,:,:) = 0.0_wp
       ENDIF

!
!--    Calculate virtual potential temperature
       IF ( humidity )  vpt = pt * ( 1.0_wp + 0.61_wp * q )

!
!--    Store initial profiles for output purposes etc.. Please note, in case of 
!--    initialization of u, v, w, pt, and q via output data derived from larger 
!--    scale models, data will not be horizontally homogeneous. Actually, a mean 
!--    profile should be calculated before.   
       hom(:,1,5,:) = SPREAD( u(:,nys,nxl), 2, statistic_regions+1 )
       hom(:,1,6,:) = SPREAD( v(:,nys,nxl), 2, statistic_regions+1 )
       IF ( ibc_uv_b == 0 .OR. ibc_uv_b == 2)  THEN
          hom(nzb,1,5,:) = 0.0_wp
          hom(nzb,1,6,:) = 0.0_wp
       ENDIF
       hom(:,1,7,:)  = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )

       IF ( humidity )  THEN
!
!--       Store initial profile of total water content, virtual potential
!--       temperature 
          hom(:,1,26,:) = SPREAD(   q(:,nys,nxl), 2, statistic_regions+1 )
          hom(:,1,29,:) = SPREAD( vpt(:,nys,nxl), 2, statistic_regions+1 )
!
!--       Store initial profile of mixing ratio and potential
!--       temperature
          IF ( bulk_cloud_model  .OR.  cloud_droplets ) THEN
             hom(:,1,27,:) = SPREAD(  q(:,nys,nxl), 2, statistic_regions+1 )
             hom(:,1,28,:) = SPREAD( pt(:,nys,nxl), 2, statistic_regions+1 )
          ENDIF
       ENDIF

!
!--    Store initial scalar profile
       IF ( passive_scalar )  THEN
          hom(:,1,121,:) = SPREAD(  s(:,nys,nxl), 2, statistic_regions+1 )
       ENDIF

!
!--    Initialize the random number generators (from numerical recipes)
       CALL random_function_ini
       
       IF ( random_generator == 'random-parallel' )  THEN
          CALL init_parallel_random_generator( nx, nys, nyn, nxl, nxr )
       ENDIF
!
!--    Set the reference state to be used in the buoyancy terms (for ocean runs
!--    the reference state will be set (overwritten) in init_ocean)
       IF ( use_single_reference_value )  THEN
          IF (  .NOT.  humidity )  THEN
             ref_state(:) = pt_reference
          ELSE
             ref_state(:) = vpt_reference
          ENDIF
       ELSE
          IF (  .NOT.  humidity )  THEN
             ref_state(:) = pt_init(:)
          ELSE
             ref_state(:) = vpt(:,nys,nxl)
          ENDIF
       ENDIF

!
!--    For the moment, vertical velocity is zero
       w = 0.0_wp

!
!--    Initialize array sums (must be defined in first call of pres)
       sums = 0.0_wp

!
!--    In case of iterative solvers, p must get an initial value
       IF ( psolver(1:9) == 'multigrid'  .OR.  psolver == 'sor' )  p = 0.0_wp
!
!--    Impose vortex with vertical axis on the initial velocity profile
       IF ( INDEX( initializing_actions, 'initialize_vortex' ) /= 0 )  THEN
          CALL init_rankine
       ENDIF

!
!--    Impose temperature anomaly (advection test only) or warm air bubble 
!--    close to surface
       IF ( INDEX( initializing_actions, 'initialize_ptanom' ) /= 0  .OR.  &
            INDEX( initializing_actions, 'initialize_bubble' ) /= 0  )  THEN
          CALL init_pt_anomaly
       ENDIF
       
!
!--    If required, change the surface temperature at the start of the 3D run
       IF ( pt_surface_initial_change /= 0.0_wp )  THEN
          pt(nzb,:,:) = pt(nzb,:,:) + pt_surface_initial_change
       ENDIF

!
!--    If required, change the surface humidity/scalar at the start of the 3D
!--    run
       IF ( humidity  .AND.  q_surface_initial_change /= 0.0_wp )              &
          q(nzb,:,:) = q(nzb,:,:) + q_surface_initial_change
          
       IF ( passive_scalar .AND.  s_surface_initial_change /= 0.0_wp )         &
          s(nzb,:,:) = s(nzb,:,:) + s_surface_initial_change
        

!
!--    Initialize old and new time levels.
       tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
       pt_p = pt; u_p = u; v_p = v; w_p = w

       IF ( humidity  )  THEN
          tq_m = 0.0_wp
          q_p = q
       ENDIF
       
       IF ( passive_scalar )  THEN
          ts_m = 0.0_wp
          s_p  = s
       ENDIF       

       CALL location_message( 'finished', .TRUE. )

    ELSEIF ( TRIM( initializing_actions ) == 'read_restart_data'  .OR.         &
             TRIM( initializing_actions ) == 'cyclic_fill' )                   &
    THEN

       CALL location_message( 'initializing in case of restart / cyclic_fill', &
                              .FALSE. )
!
!--    When reading data for cyclic fill of 3D prerun data files, read
!--    some of the global variables from the restart file which are required
!--    for initializing the inflow
       IF ( TRIM( initializing_actions ) == 'cyclic_fill' )  THEN

          DO  i = 0, io_blocks-1
             IF ( i == io_group )  THEN
                CALL rrd_read_parts_of_global
             ENDIF
#if defined( __parallel )
             CALL MPI_BARRIER( comm2d, ierr )
#endif
          ENDDO

       ENDIF

!
!--    Read processor specific binary data from restart file
       DO  i = 0, io_blocks-1
          IF ( i == io_group )  THEN
             CALL rrd_local
          ENDIF
#if defined( __parallel )
          CALL MPI_BARRIER( comm2d, ierr )
#endif
       ENDDO
!
!--    Initialize surface elements and its attributes, e.g. heat- and 
!--    momentumfluxes, roughness, scaling parameters. As number of surface 
!--    elements might be different between runs, e.g. in case of cyclic fill, 
!--    and not all surface elements are read, surface elements need to be 
!--    initialized before. 
!--    Please note, surfaces should be initialized after restart data is read,
!--    else, individual settings of surface parameters will be overwritten
!--    from data of precursor run. 
       CALL init_surfaces

!
!--    In case of complex terrain and cyclic fill method as initialization,
!--    shift initial data in the vertical direction for each point in the 
!--    x-y-plane depending on local surface height
       IF ( complex_terrain  .AND.                                             &
            TRIM( initializing_actions ) == 'cyclic_fill' )  THEN
          DO  i = nxlg, nxrg
             DO  j = nysg, nyng
                nz_u_shift = get_topography_top_index_ji( j, i, 'u' )
                nz_v_shift = get_topography_top_index_ji( j, i, 'v' )
                nz_w_shift = get_topography_top_index_ji( j, i, 'w' )
                nz_s_shift = get_topography_top_index_ji( j, i, 's' )

                u(nz_u_shift:nzt+1,j,i)  = u(0:nzt+1-nz_u_shift,j,i)                

                v(nz_v_shift:nzt+1,j,i)  = v(0:nzt+1-nz_v_shift,j,i)

                w(nz_w_shift:nzt+1,j,i)  = w(0:nzt+1-nz_w_shift,j,i)

                p(nz_s_shift:nzt+1,j,i)  =  p(0:nzt+1-nz_s_shift,j,i)
                pt(nz_s_shift:nzt+1,j,i) = pt(0:nzt+1-nz_s_shift,j,i)
             ENDDO
          ENDDO
       ENDIF

!
!--    Initialization of the turbulence recycling method
       IF ( TRIM( initializing_actions ) == 'cyclic_fill'  .AND.               &
            turbulent_inflow )  THEN
!
!--       First store the profiles to be used at the inflow.
!--       These profiles are the (temporally) and horizontally averaged vertical
!--       profiles from the prerun. Alternatively, prescribed profiles
!--       for u,v-components can be used.
          ALLOCATE( mean_inflow_profiles(nzb:nzt+1,1:num_mean_inflow_profiles) )

          IF ( use_prescribed_profile_data )  THEN
             mean_inflow_profiles(:,1) = u_init            ! u
             mean_inflow_profiles(:,2) = v_init            ! v
          ELSE
             mean_inflow_profiles(:,1) = hom_sum(:,1,0)    ! u
             mean_inflow_profiles(:,2) = hom_sum(:,2,0)    ! v
          ENDIF
          mean_inflow_profiles(:,4) = hom_sum(:,4,0)       ! pt
          IF ( humidity )                                                      &
             mean_inflow_profiles(:,6) = hom_sum(:,41,0)   ! q
          IF ( passive_scalar )                                                &
             mean_inflow_profiles(:,7) = hom_sum(:,115,0)   ! s
!
!--       In case of complex terrain, determine vertical displacement at inflow 
!--       boundary and adjust mean inflow profiles
          IF ( complex_terrain )  THEN
             IF ( nxlg <= 0 .AND. nxrg >= 0 .AND. nysg <= 0 .AND. nyng >= 0 )  THEN
                nz_u_shift_l = get_topography_top_index_ji( 0, 0, 'u' )
                nz_v_shift_l = get_topography_top_index_ji( 0, 0, 'v' )
                nz_w_shift_l = get_topography_top_index_ji( 0, 0, 'w' )
                nz_s_shift_l = get_topography_top_index_ji( 0, 0, 's' )
             ELSE
                nz_u_shift_l = 0
                nz_v_shift_l = 0
                nz_w_shift_l = 0
                nz_s_shift_l = 0
             ENDIF

#if defined( __parallel )
             CALL MPI_ALLREDUCE(nz_u_shift_l, nz_u_shift, 1, MPI_INTEGER,      &
                                MPI_MAX, comm2d, ierr)
             CALL MPI_ALLREDUCE(nz_v_shift_l, nz_v_shift, 1, MPI_INTEGER,      &
                                MPI_MAX, comm2d, ierr)
             CALL MPI_ALLREDUCE(nz_w_shift_l, nz_w_shift, 1, MPI_INTEGER,      & 
                                MPI_MAX, comm2d, ierr)
             CALL MPI_ALLREDUCE(nz_s_shift_l, nz_s_shift, 1, MPI_INTEGER,      &
                                MPI_MAX, comm2d, ierr)
#else
             nz_u_shift = nz_u_shift_l
             nz_v_shift = nz_v_shift_l
             nz_w_shift = nz_w_shift_l
             nz_s_shift = nz_s_shift_l
#endif

             mean_inflow_profiles(:,1) = 0.0_wp
             mean_inflow_profiles(nz_u_shift:nzt+1,1) = hom_sum(0:nzt+1-nz_u_shift,1,0)  ! u

             mean_inflow_profiles(:,2) = 0.0_wp
             mean_inflow_profiles(nz_v_shift:nzt+1,2) = hom_sum(0:nzt+1-nz_v_shift,2,0)  ! v

             mean_inflow_profiles(nz_s_shift:nzt+1,4) = hom_sum(0:nzt+1-nz_s_shift,4,0)  ! pt

          ENDIF

!
!--       If necessary, adjust the horizontal flow field to the prescribed
!--       profiles
          IF ( use_prescribed_profile_data )  THEN
             DO  i = nxlg, nxrg
                DO  j = nysg, nyng
                   DO  k = nzb, nzt+1
                      u(k,j,i) = u(k,j,i) - hom_sum(k,1,0) + u_init(k)
                      v(k,j,i) = v(k,j,i) - hom_sum(k,2,0) + v_init(k)
                   ENDDO
                ENDDO
             ENDDO
          ENDIF

!
!--       Use these mean profiles at the inflow (provided that Dirichlet
!--       conditions are used)
          IF ( bc_dirichlet_l )  THEN
             DO  j = nysg, nyng
                DO  k = nzb, nzt+1
                   u(k,j,nxlg:-1)  = mean_inflow_profiles(k,1)
                   v(k,j,nxlg:-1)  = mean_inflow_profiles(k,2)
                   w(k,j,nxlg:-1)  = 0.0_wp
                   pt(k,j,nxlg:-1) = mean_inflow_profiles(k,4)
                   IF ( humidity )                                             &
                      q(k,j,nxlg:-1)  = mean_inflow_profiles(k,6)
                   IF ( passive_scalar )                                       &
                      s(k,j,nxlg:-1)  = mean_inflow_profiles(k,7)                      
                ENDDO
             ENDDO
          ENDIF

!
!--       Calculate the damping factors to be used at the inflow. For a
!--       turbulent inflow the turbulent fluctuations have to be limited
!--       vertically because otherwise the turbulent inflow layer will grow
!--       in time.
          IF ( inflow_damping_height == 9999999.9_wp )  THEN
!
!--          Default: use the inversion height calculated by the prerun; if
!--          this is zero, inflow_damping_height must be explicitly
!--          specified.
             IF ( hom_sum(nzb+6,pr_palm,0) /= 0.0_wp )  THEN
                inflow_damping_height = hom_sum(nzb+6,pr_palm,0)
             ELSE
                WRITE( message_string, * ) 'inflow_damping_height must be ',   &
                     'explicitly specified because&the inversion height ',     &
                     'calculated by the prerun is zero.'
                CALL message( 'init_3d_model', 'PA0318', 1, 2, 0, 6, 0 )
             ENDIF

          ENDIF

          IF ( inflow_damping_width == 9999999.9_wp )  THEN
!
!--          Default for the transition range: one tenth of the undamped
!--          layer
             inflow_damping_width = 0.1_wp * inflow_damping_height

          ENDIF

          ALLOCATE( inflow_damping_factor(nzb:nzt+1) )

          DO  k = nzb, nzt+1

             IF ( zu(k) <= inflow_damping_height )  THEN
                inflow_damping_factor(k) = 1.0_wp
             ELSEIF ( zu(k) <= ( inflow_damping_height + inflow_damping_width ) )  THEN
                inflow_damping_factor(k) = 1.0_wp -                            &
                                           ( zu(k) - inflow_damping_height ) / &
                                           inflow_damping_width
             ELSE
                inflow_damping_factor(k) = 0.0_wp
             ENDIF

          ENDDO

       ENDIF

!
!--    Inside buildings set velocities back to zero
       IF ( TRIM( initializing_actions ) == 'cyclic_fill' .AND.                &
            topography /= 'flat' )  THEN
!
!--       Inside buildings set velocities back to zero.
!--       Other scalars (pt, q, s, p, sa, ...) are ignored at present,
!--       maybe revise later.
          DO  i = nxlg, nxrg
             DO  j = nysg, nyng
                DO  k = nzb, nzt
                   u(k,j,i)     = MERGE( u(k,j,i), 0.0_wp,                     &
                                         BTEST( wall_flags_0(k,j,i), 1 ) )
                   v(k,j,i)     = MERGE( v(k,j,i), 0.0_wp,                     &
                                         BTEST( wall_flags_0(k,j,i), 2 ) )
                   w(k,j,i)     = MERGE( w(k,j,i), 0.0_wp,                     &
                                         BTEST( wall_flags_0(k,j,i), 3 ) )
                ENDDO
             ENDDO
          ENDDO

       ENDIF

!
!--    Calculate initial temperature field and other constants used in case
!--    of a sloping surface
       IF ( sloping_surface )  CALL init_slope

!
!--    Initialize new time levels (only done in order to set boundary values
!--    including ghost points)
       pt_p = pt; u_p = u; v_p = v; w_p = w
       IF ( humidity )  THEN
          q_p = q
       ENDIF
       IF ( passive_scalar )  s_p  = s
!
!--    Allthough tendency arrays are set in prognostic_equations, they have
!--    have to be predefined here because they are used (but multiplied with 0)
!--    there before they are set. 
       tpt_m = 0.0_wp; tu_m = 0.0_wp; tv_m = 0.0_wp; tw_m = 0.0_wp
       IF ( humidity )  THEN
          tq_m = 0.0_wp
       ENDIF
       IF ( passive_scalar )  ts_m  = 0.0_wp
!
!--    Initialize synthetic turbulence generator in case of restart.
       IF ( TRIM( initializing_actions ) == 'read_restart_data'  .AND.         &
            use_syn_turb_gen )  CALL stg_init

       CALL location_message( 'finished', .TRUE. )

    ELSE
!
!--    Actually this part of the programm should not be reached
       message_string = 'unknown initializing problem'
       CALL message( 'init_3d_model', 'PA0193', 1, 2, 0, 6, 0 )
    ENDIF

!
!-- Initialize TKE, Kh and Km
    CALL tcm_init


    IF (  TRIM( initializing_actions ) /= 'read_restart_data' )  THEN
!
!--    Initialize old timelevels needed for radiation boundary conditions
       IF ( bc_radiation_l )  THEN
          u_m_l(:,:,:) = u(:,:,1:2)
          v_m_l(:,:,:) = v(:,:,0:1)
          w_m_l(:,:,:) = w(:,:,0:1)
       ENDIF
       IF ( bc_radiation_r )  THEN
          u_m_r(:,:,:) = u(:,:,nx-1:nx)
          v_m_r(:,:,:) = v(:,:,nx-1:nx)
          w_m_r(:,:,:) = w(:,:,nx-1:nx)
       ENDIF
       IF ( bc_radiation_s )  THEN
          u_m_s(:,:,:) = u(:,0:1,:)
          v_m_s(:,:,:) = v(:,1:2,:)
          w_m_s(:,:,:) = w(:,0:1,:)
       ENDIF
       IF ( bc_radiation_n )  THEN
          u_m_n(:,:,:) = u(:,ny-1:ny,:)
          v_m_n(:,:,:) = v(:,ny-1:ny,:)
          w_m_n(:,:,:) = w(:,ny-1:ny,:)
       ENDIF
       
    ENDIF

!
!-- Calculate the initial volume flow at the right and north boundary
    IF ( conserve_volume_flow )  THEN

       IF ( use_prescribed_profile_data )  THEN

          volume_flow_initial_l = 0.0_wp
          volume_flow_area_l    = 0.0_wp

          IF ( nxr == nx )  THEN
             DO  j = nys, nyn
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(1) = volume_flow_initial_l(1) +       &
                                              u_init(k) * dzw(k)               &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nxr), 1 )&
                                            )

                   volume_flow_area_l(1)    = volume_flow_area_l(1) + dzw(k)   &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nxr), 1 )&
                                            )
                ENDDO
             ENDDO
          ENDIF
          
          IF ( nyn == ny )  THEN
             DO  i = nxl, nxr
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(2) = volume_flow_initial_l(2) +       &
                                              v_init(k) * dzw(k)               &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,nyn,i), 2 )&
                                            )
                   volume_flow_area_l(2)    = volume_flow_area_l(2) + dzw(k)   &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,nyn,i), 2 )&
                                            )
                ENDDO
             ENDDO
          ENDIF

#if defined( __parallel )
          CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )
          CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1),      &
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )

#else
          volume_flow_initial = volume_flow_initial_l
          volume_flow_area    = volume_flow_area_l
#endif  

       ELSEIF ( TRIM( initializing_actions ) == 'cyclic_fill' )  THEN

          volume_flow_initial_l = 0.0_wp
          volume_flow_area_l    = 0.0_wp

          IF ( nxr == nx )  THEN
             DO  j = nys, nyn
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(1) = volume_flow_initial_l(1) +       &
                                              hom_sum(k,1,0) * dzw(k)          &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nx), 1 ) &
                                            )
                   volume_flow_area_l(1)    = volume_flow_area_l(1) + dzw(k)   &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nx), 1 ) &
                                            )
                ENDDO
             ENDDO
          ENDIF
          
          IF ( nyn == ny )  THEN
             DO  i = nxl, nxr
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(2) = volume_flow_initial_l(2) +       &
                                              hom_sum(k,2,0) * dzw(k)          &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,ny,i), 2 ) &
                                            )
                   volume_flow_area_l(2)    = volume_flow_area_l(2) + dzw(k)   &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,ny,i), 2 ) &
                                            )
                ENDDO
             ENDDO
          ENDIF

#if defined( __parallel )
          CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )
          CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1),      &
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )

#else
          volume_flow_initial = volume_flow_initial_l
          volume_flow_area    = volume_flow_area_l
#endif  

       ELSEIF ( TRIM( initializing_actions ) /= 'read_restart_data' )  THEN

          volume_flow_initial_l = 0.0_wp
          volume_flow_area_l    = 0.0_wp

          IF ( nxr == nx )  THEN
             DO  j = nys, nyn
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(1) = volume_flow_initial_l(1) +       &
                                              u(k,j,nx) * dzw(k)               &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nx), 1 ) &
                                            )
                   volume_flow_area_l(1)    = volume_flow_area_l(1) + dzw(k)   &
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,j,nx), 1 ) &
                                            )
                ENDDO
             ENDDO
          ENDIF
          
          IF ( nyn == ny )  THEN
             DO  i = nxl, nxr
                DO  k = nzb+1, nzt
                   volume_flow_initial_l(2) = volume_flow_initial_l(2) +       &
                                              v(k,ny,i) * dzw(k)               &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,ny,i), 2 ) &
                                            )
                   volume_flow_area_l(2)    = volume_flow_area_l(2) + dzw(k)   &        
                                     * MERGE( 1.0_wp, 0.0_wp,                  &
                                              BTEST( wall_flags_0(k,ny,i), 2 ) &
                                            )
                ENDDO
             ENDDO
          ENDIF

#if defined( __parallel )
          CALL MPI_ALLREDUCE( volume_flow_initial_l(1), volume_flow_initial(1),&
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )
          CALL MPI_ALLREDUCE( volume_flow_area_l(1), volume_flow_area(1),      &
                              2, MPI_REAL, MPI_SUM, comm2d, ierr )

#else
          volume_flow_initial = volume_flow_initial_l
          volume_flow_area    = volume_flow_area_l
#endif  

       ENDIF

!
!--    In case of 'bulk_velocity' mode, volume_flow_initial is calculated
!--    from u|v_bulk instead
       IF ( TRIM( conserve_volume_flow_mode ) == 'bulk_velocity' )  THEN
          volume_flow_initial(1) = u_bulk * volume_flow_area(1)
          volume_flow_initial(2) = v_bulk * volume_flow_area(2)
       ENDIF

    ENDIF
!
!-- Finally, if random_heatflux is set, disturb shf at horizontal
!-- surfaces. Actually, this should be done in surface_mod, where all other 
!-- initializations of surface quantities are done. However, this
!-- would create a ring dependency, hence, it is done here. Maybe delete
!-- disturb_heatflux and tranfer the respective code directly into the 
!-- initialization in surface_mod.         
    IF ( TRIM( initializing_actions ) /= 'read_restart_data'  .AND.            &
         TRIM( initializing_actions ) /= 'cyclic_fill' )  THEN
 
       IF ( use_surface_fluxes  .AND.  constant_heatflux  .AND.                &
            random_heatflux )  THEN
          IF ( surf_def_h(0)%ns >= 1 )  CALL disturb_heatflux( surf_def_h(0) )
          IF ( surf_lsm_h%ns    >= 1 )  CALL disturb_heatflux( surf_lsm_h    )
          IF ( surf_usm_h%ns    >= 1 )  CALL disturb_heatflux( surf_usm_h    )
       ENDIF
    ENDIF

!
!-- Before initializing further modules, compute total sum of active mask 
!-- grid points and the mean surface level height for each statistic region.
!-- ngp_2dh: number of grid points of a horizontal cross section through the
!--          total domain
!-- ngp_3d:  number of grid points of the total domain
    ngp_2dh_outer_l   = 0
    ngp_2dh_outer     = 0
    ngp_2dh_s_inner_l = 0
    ngp_2dh_s_inner   = 0
    ngp_2dh_l         = 0
    ngp_2dh           = 0
    ngp_3d_inner_l    = 0.0_wp
    ngp_3d_inner      = 0
    ngp_3d            = 0
    ngp_sums          = ( nz + 2 ) * ( pr_palm + max_pr_user )

    mean_surface_level_height   = 0.0_wp
    mean_surface_level_height_l = 0.0_wp
!
!-- Pre-set masks for regional statistics. Default is the total model domain.
!-- Ghost points are excluded because counting values at the ghost boundaries
!-- would bias the statistics
    rmask = 1.0_wp
    rmask(:,nxlg:nxl-1,:) = 0.0_wp;  rmask(:,nxr+1:nxrg,:) = 0.0_wp
    rmask(nysg:nys-1,:,:) = 0.0_wp;  rmask(nyn+1:nyng,:,:) = 0.0_wp

!
!-- Temporary solution to add LSM and radiation time series to the default
!-- output
    IF ( land_surface  .OR.  radiation )  THEN
       IF ( TRIM( radiation_scheme ) == 'rrtmg' )  THEN
          dots_num = dots_num + 15
       ELSE
          dots_num = dots_num + 11
       ENDIF
    ENDIF
!
!-- User-defined initializing actions
    CALL user_init
!
!-- To do: New concept for these non-topography grid points!
    DO  sr = 0, statistic_regions
       DO  i = nxl, nxr
          DO  j = nys, nyn
             IF ( rmask(j,i,sr) == 1.0_wp )  THEN
!
!--             All xy-grid points
                ngp_2dh_l(sr) = ngp_2dh_l(sr) + 1
!
!--             Determine mean surface-level height. In case of downward-
!--             facing walls are present, more than one surface level exist.
!--             In this case, use the lowest surface-level height. 
                IF ( surf_def_h(0)%start_index(j,i) <=                         &
                     surf_def_h(0)%end_index(j,i) )  THEN
                   m = surf_def_h(0)%start_index(j,i)
                   k = surf_def_h(0)%k(m)
                   mean_surface_level_height_l(sr) =                           &
                                       mean_surface_level_height_l(sr) + zw(k-1)
                ENDIF
                IF ( surf_lsm_h%start_index(j,i) <=                            &
                     surf_lsm_h%end_index(j,i) )  THEN
                   m = surf_lsm_h%start_index(j,i)
                   k = surf_lsm_h%k(m)
                   mean_surface_level_height_l(sr) =                           &
                                       mean_surface_level_height_l(sr) + zw(k-1)
                ENDIF
                IF ( surf_usm_h%start_index(j,i) <=                            &
                     surf_usm_h%end_index(j,i) )  THEN
                   m = surf_usm_h%start_index(j,i)
                   k = surf_usm_h%k(m)
                   mean_surface_level_height_l(sr) =                           &
                                       mean_surface_level_height_l(sr) + zw(k-1)
                ENDIF

                k_surf = k - 1

                DO  k = nzb, nzt+1
!
!--                xy-grid points above topography
                   ngp_2dh_outer_l(k,sr) = ngp_2dh_outer_l(k,sr)     +         &
                                  MERGE( 1, 0, BTEST( wall_flags_0(k,j,i), 24 ) )

                   ngp_2dh_s_inner_l(k,sr) = ngp_2dh_s_inner_l(k,sr) +         &
                                  MERGE( 1, 0, BTEST( wall_flags_0(k,j,i), 22 ) )

                ENDDO
!
!--             All grid points of the total domain above topography
                ngp_3d_inner_l(sr) = ngp_3d_inner_l(sr) + ( nz - k_surf + 2 )



             ENDIF
          ENDDO
       ENDDO
    ENDDO
!
!-- Initialize arrays encompassing number of grid-points in inner and outer
!-- domains, statistic regions, etc. Mainly used for horizontal averaging
!-- of turbulence statistics. Please note, user_init must be called before
!-- doing this.   
    sr = statistic_regions + 1
#if defined( __parallel )
    IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
    CALL MPI_ALLREDUCE( ngp_2dh_l(0), ngp_2dh(0), sr, MPI_INTEGER, MPI_SUM,    &
                        comm2d, ierr )
    IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
    CALL MPI_ALLREDUCE( ngp_2dh_outer_l(0,0), ngp_2dh_outer(0,0), (nz+2)*sr,   &
                        MPI_INTEGER, MPI_SUM, comm2d, ierr )
    IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
    CALL MPI_ALLREDUCE( ngp_2dh_s_inner_l(0,0), ngp_2dh_s_inner(0,0),          &
                        (nz+2)*sr, MPI_INTEGER, MPI_SUM, comm2d, ierr )
    IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
    CALL MPI_ALLREDUCE( ngp_3d_inner_l(0), ngp_3d_inner_tmp(0), sr, MPI_REAL,  &
                        MPI_SUM, comm2d, ierr )
    ngp_3d_inner = INT( ngp_3d_inner_tmp, KIND = SELECTED_INT_KIND( 18 ) )
    IF ( collective_wait )  CALL MPI_BARRIER( comm2d, ierr )
    CALL MPI_ALLREDUCE( mean_surface_level_height_l(0),                        &
                        mean_surface_level_height(0), sr, MPI_REAL,            &
                        MPI_SUM, comm2d, ierr )
    mean_surface_level_height = mean_surface_level_height / REAL( ngp_2dh )
#else
    ngp_2dh         = ngp_2dh_l
    ngp_2dh_outer   = ngp_2dh_outer_l
    ngp_2dh_s_inner = ngp_2dh_s_inner_l
    ngp_3d_inner    = INT( ngp_3d_inner_l, KIND = SELECTED_INT_KIND( 18 ) )
    mean_surface_level_height = mean_surface_level_height_l / REAL( ngp_2dh_l )
#endif

    ngp_3d = INT ( ngp_2dh, KIND = SELECTED_INT_KIND( 18 ) ) * &
             INT ( (nz + 2 ), KIND = SELECTED_INT_KIND( 18 ) )

!
!-- Set a lower limit of 1 in order to avoid zero divisions in flow_statistics,
!-- buoyancy, etc. A zero value will occur for cases where all grid points of
!-- the respective subdomain lie below the surface topography
    ngp_2dh_outer   = MAX( 1, ngp_2dh_outer(:,:)   ) 
    ngp_3d_inner    = MAX( INT(1, KIND = SELECTED_INT_KIND( 18 )),             &
                           ngp_3d_inner(:) )
    ngp_2dh_s_inner = MAX( 1, ngp_2dh_s_inner(:,:) ) 

    DEALLOCATE( mean_surface_level_height_l, ngp_2dh_l, ngp_2dh_outer_l,       &
                ngp_3d_inner_l, ngp_3d_inner_tmp )

!
!-- Initialize nudging if required
    IF ( nudging )  CALL nudge_init
!
!-- Initialize 1D large-scale forcing and nudging and read data from external
!-- ASCII file
    IF ( large_scale_forcing )  CALL lsf_init
!
!-- Initialize surface forcing corresponding to large-scale forcing. Therein, 
!-- initialize heat-fluxes, etc. via datatype. Revise it later!
    IF ( large_scale_forcing .AND. lsf_surf )  THEN
       IF ( use_surface_fluxes  .AND.  constant_heatflux )  THEN
          CALL ls_forcing_surf ( simulated_time )
       ENDIF
    ENDIF
!
!-- Initializae 3D offline nesting in COSMO model and read data from 
!-- external NetCDF file.
    IF ( nesting_offline )  CALL nesting_offl_init
!
!-- Initialize quantities for special advections schemes
    CALL init_advec

!
!-- Impose random perturbation on the horizontal velocity field and then
!-- remove the divergences from the velocity field at the initial stage
    IF ( create_disturbances  .AND.  disturbance_energy_limit /= 0.0_wp  .AND. &
         TRIM( initializing_actions ) /= 'read_restart_data'  .AND.            &
         TRIM( initializing_actions ) /= 'cyclic_fill' )  THEN

       CALL location_message( 'creating initial disturbances', .FALSE. )
       CALL disturb_field( 'u', tend, u )
       CALL disturb_field( 'v', tend, v )
       CALL location_message( 'finished', .TRUE. )

       CALL location_message( 'calling pressure solver', .FALSE. )
       n_sor = nsor_ini
       CALL pres
       n_sor = nsor
       CALL location_message( 'finished', .TRUE. )

    ENDIF

!
!-- If required, initialize quantities needed for the plant canopy model
    IF ( plant_canopy )  THEN
       CALL location_message( 'initializing plant canopy model', .FALSE. )    
       CALL pcm_init
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- If required, initialize dvrp-software
    IF ( dt_dvrp /= 9999999.9_wp )  CALL init_dvrp

!
!-- Initialize quantities needed for the ocean model
    IF ( ocean_mode )  CALL ocean_init

!
!-- Initialize quantities for handling cloud physics.
!-- This routine must be called before lpm_init, becaus otherwise,
!-- array d_exner, needed in data_output_dvrp (called by lpm_init) is not defined.
    IF ( .NOT. ocean_mode )  THEN

       ALLOCATE( hyp(nzb:nzt+1) )
       ALLOCATE( d_exner(nzb:nzt+1) )
       ALLOCATE( exner(nzb:nzt+1) )
       ALLOCATE( hyrho(nzb:nzt+1) )
!
!--    Check temperature in case of too large domain height
       DO  k = nzb, nzt+1
          IF ( ( pt_surface * exner_function(surface_pressure * 100.0_wp) - g/c_p * zu(k) ) < 0.0_wp )  THEN
             WRITE( message_string, * )  'absolute temperature < 0.0 at zu(', k, &
                                         ') = ', zu(k)
             CALL message( 'init_bulk_cloud_model', 'PA0142', 1, 2, 0, 6, 0 )
          ENDIF
       ENDDO

!
!--    Calculate vertical profile of the hydrostatic pressure (hyp)
       hyp    = barometric_formula(zu, pt_surface * exner_function(surface_pressure * 100.0_wp), surface_pressure * 100.0_wp)
       d_exner = exner_function_invers(hyp)
       exner = 1.0_wp / exner_function_invers(hyp)
       hyrho  = ideal_gas_law_rho_pt(hyp, pt_init)
!
!--    Compute reference density
       rho_surface = ideal_gas_law_rho(surface_pressure * 100.0_wp, pt_surface * exner_function(surface_pressure * 100.0_wp))

    ENDIF
!
!-- If required, initialize quantities needed for the microphysics module
    IF ( bulk_cloud_model )  THEN
       CALL bcm_init
    ENDIF

!
!-- If required, initialize particles
    IF ( particle_advection )  CALL lpm_init

!
!-- If required, initialize particles
    IF ( agents_active )  CALL mas_init

!
!-- If required, initialize quantities needed for the LSM
    IF ( land_surface )  THEN
       CALL location_message( 'initializing land surface model', .FALSE. )
       CALL lsm_init
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- If required, allocate USM and LSM surfaces
    IF ( urban_surface )  THEN
       CALL location_message( 'initializing and allocating urban surfaces', .FALSE. )
       CALL usm_allocate_surface
       CALL location_message( 'finished', .TRUE. )
    ENDIF
!
!-- If required, initialize urban surface model
    IF ( urban_surface )  THEN
       CALL location_message( 'initializing urban surface model', .FALSE. )
       CALL usm_init_urban_surface
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- Initialize surface layer (done after LSM as roughness length are required
!-- for initialization
    IF ( constant_flux_layer )  THEN
       CALL location_message( 'initializing surface layer', .FALSE. )
       CALL init_surface_layer_fluxes
       CALL location_message( 'finished', .TRUE. )
    ENDIF
!
!-- In case the synthetic turbulence generator does not have any information
!-- about the inflow turbulence, these information will be parametrized 
!-- depending on the initial atmospheric conditions and surface properties.
!-- Please note, within pre-determined time intervals these turbulence 
!-- information can be updated if desired. 
    IF ( use_syn_turb_gen  .AND.  parametrize_inflow_turbulence )              &
       CALL stg_adjust
!
!-- If required, set chemical emissions
!-- Initialize values of cssws according to chemistry emission values
    IF ( air_chemistry  .AND.  do_emis )  THEN
       CALL chem_emissions_init( chem_emis_att, chem_emis, nspec_out )
    ENDIF
!
!-- Initialize radiation processes
    IF ( radiation )  THEN
!
!--    Activate radiation_interactions according to the existence of vertical surfaces and/or trees.
!--    The namelist parameter radiation_interactions_on can override this behavior.
!--    (This check cannot be performed in check_parameters, because vertical_surfaces_exist is first set in 
!--    init_surface_arrays.)
       IF ( radiation_interactions_on )  THEN
          IF ( vertical_surfaces_exist  .OR.  plant_canopy )  THEN
             radiation_interactions    = .TRUE.
             average_radiation         = .TRUE.
          ELSE
             radiation_interactions_on = .FALSE.   !< reset namelist parameter: no interactions 
                                                   !< calculations necessary in case of flat surface
          ENDIF
       ELSEIF ( vertical_surfaces_exist  .OR.  plant_canopy )  THEN
          message_string = 'radiation_interactions_on is set to .FALSE. although '     // &
                           'vertical surfaces and/or trees exist. The model will run ' // &
                           'without RTM (no shadows, no radiation reflections)'
          CALL message( 'init_3d_model', 'PA0348', 0, 1, 0, 6, 0 )
       ENDIF
!
!--    If required, initialize radiation interactions between surfaces 
!--    via sky-view factors. This must be done before radiation is initialized.
       IF ( radiation_interactions )  CALL radiation_interaction_init

!
!--    Initialize radiation model
       CALL location_message( 'initializing radiation model', .FALSE. )
       CALL radiation_init
       CALL location_message( 'finished', .TRUE. )

!
!--    Find all discretized apparent solar positions for radiation interaction.
!--    This must be done after radiation_init.
       IF ( radiation_interactions )  CALL radiation_presimulate_solar_pos

!
!--    If required, read or calculate and write out the SVF 
       IF ( radiation_interactions .AND. read_svf)  THEN
!
!--       Read sky-view factors and further required data from file
          CALL location_message( '    Start reading SVF from file', .FALSE. )
          CALL radiation_read_svf()
          CALL location_message( '    Reading SVF from file has finished', .TRUE. )

       ELSEIF ( radiation_interactions .AND. .NOT. read_svf)  THEN
!
!--       calculate SFV and CSF
          CALL location_message( '    Start calculation of SVF', .FALSE. )
          CALL radiation_calc_svf()
          CALL location_message( '    Calculation of SVF has finished', .TRUE. )
       ENDIF

       IF ( radiation_interactions .AND. write_svf)  THEN
!
!--       Write svf, csf svfsurf and csfsurf data to file
          CALL location_message( '    Start writing SVF in file', .FALSE. )
          CALL radiation_write_svf()
          CALL location_message( '    Writing SVF in file has finished', .TRUE. )
       ENDIF

!
!--    Adjust radiative fluxes. In case of urban and land surfaces, also 
!--    call an initial interaction.
       IF ( radiation_interactions )  THEN
          CALL radiation_interaction
       ENDIF
    ENDIF
  
!
!-- If required, initialize quantities needed for the wind turbine model
    IF ( wind_turbine )  THEN
       CALL location_message( 'initializing wind turbine model', .FALSE. )
       CALL wtm_init
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- If required, initialize quantities needed in SALSA 
    IF ( salsa )  THEN
       CALL location_message( 'initializing SALSA model', .TRUE. )
       CALL salsa_init 
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- If required, initialize quantities needed for the gust module
    IF ( gust_module_enabled )  THEN
       CALL gust_init( dots_label, dots_unit, dots_num, dots_max )
    ENDIF
!
!-- Initialize surface data output
    IF ( surface_data_output )  THEN
       CALL surface_output_init
    ENDIF
!
!-- If virtual measurements should be taken, initialize all relevant 
!-- arrays and quantities.
    IF ( virtual_measurement )  CALL vm_init

!
!-- If required initialize biometeorology module
    IF ( biometeorology )  THEN
        CALL location_message( 'initializing biometeorology module', .FALSE. )
        CALL bio_init
        CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- If required, initialize indoor model
    IF ( indoor_model )  THEN
       CALL location_message( 'initializing indoor model', .FALSE. )
       CALL im_init
       CALL location_message( 'finished', .TRUE. )
    ENDIF

!
!-- Initialize the ws-scheme.    
    IF ( ws_scheme_sca .OR. ws_scheme_mom )  CALL ws_init

!
!-- Setting weighting factors for calculation of perturbation pressure 
!-- and turbulent quantities from the RK substeps
    IF ( TRIM(timestep_scheme) == 'runge-kutta-3' )  THEN      ! for RK3-method

       weight_substep(1) = 1._wp/6._wp
       weight_substep(2) = 3._wp/10._wp
       weight_substep(3) = 8._wp/15._wp

       weight_pres(1)    = 1._wp/3._wp
       weight_pres(2)    = 5._wp/12._wp
       weight_pres(3)    = 1._wp/4._wp

    ELSEIF ( TRIM(timestep_scheme) == 'runge-kutta-2' )  THEN  ! for RK2-method

       weight_substep(1) = 1._wp/2._wp
       weight_substep(2) = 1._wp/2._wp
          
       weight_pres(1)    = 1._wp/2._wp
       weight_pres(2)    = 1._wp/2._wp        

    ELSE                                     ! for Euler-method

       weight_substep(1) = 1.0_wp      
       weight_pres(1)    = 1.0_wp                   

    ENDIF

!
!-- Initialize Rayleigh damping factors
    rdf    = 0.0_wp
    rdf_sc = 0.0_wp
    IF ( rayleigh_damping_factor /= 0.0_wp )  THEN

       IF (  .NOT.  ocean_mode )  THEN
          DO  k = nzb+1, nzt
             IF ( zu(k) >= rayleigh_damping_height )  THEN
                rdf(k) = rayleigh_damping_factor *                             &
                      ( SIN( pi * 0.5_wp * ( zu(k) - rayleigh_damping_height ) &
                             / ( zu(nzt) - rayleigh_damping_height ) )         &
                      )**2
             ENDIF
          ENDDO
       ELSE
!
!--       In ocean mode, rayleigh damping is applied in the lower part of the
!--       model domain
          DO  k = nzt, nzb+1, -1
             IF ( zu(k) <= rayleigh_damping_height )  THEN
                rdf(k) = rayleigh_damping_factor *                             &
                      ( SIN( pi * 0.5_wp * ( rayleigh_damping_height - zu(k) ) &
                             / ( rayleigh_damping_height - zu(nzb+1) ) )       &
                      )**2
             ENDIF
          ENDDO
       ENDIF

    ENDIF
    IF ( scalar_rayleigh_damping )  rdf_sc = rdf

!
!-- Initialize the starting level and the vertical smoothing factor used for 
!-- the external pressure gradient
    dp_smooth_factor = 1.0_wp
    IF ( dp_external )  THEN
!
!--    Set the starting level dp_level_ind_b only if it has not been set before
!--    (e.g. in init_grid).
       IF ( dp_level_ind_b == 0 )  THEN
          ind_array = MINLOC( ABS( dp_level_b - zu ) )
          dp_level_ind_b = ind_array(1) - 1 + nzb 
                                        ! MINLOC uses lower array bound 1
       ENDIF
       IF ( dp_smooth )  THEN
          dp_smooth_factor(:dp_level_ind_b) = 0.0_wp
          DO  k = dp_level_ind_b+1, nzt
             dp_smooth_factor(k) = 0.5_wp * ( 1.0_wp + SIN( pi *               &
                        ( REAL( k - dp_level_ind_b, KIND=wp ) /                &
                          REAL( nzt - dp_level_ind_b, KIND=wp ) - 0.5_wp ) ) )
          ENDDO
       ENDIF
    ENDIF

!
!-- Initialize damping zone for the potential temperature in case of
!-- non-cyclic lateral boundaries. The damping zone has the maximum value 
!-- at the inflow boundary and decreases to zero at pt_damping_width.
    ptdf_x = 0.0_wp
    ptdf_y = 0.0_wp
    IF ( bc_lr_dirrad )  THEN
       DO  i = nxl, nxr
          IF ( ( i * dx ) < pt_damping_width )  THEN
             ptdf_x(i) = pt_damping_factor * ( SIN( pi * 0.5_wp *              &
                            REAL( pt_damping_width - i * dx, KIND=wp ) / (     &
                            REAL( pt_damping_width, KIND=wp ) ) ) )**2 
          ENDIF
       ENDDO
    ELSEIF ( bc_lr_raddir )  THEN
       DO  i = nxl, nxr
          IF ( ( i * dx ) > ( nx * dx - pt_damping_width ) )  THEN
             ptdf_x(i) = pt_damping_factor *                                   &
                         SIN( pi * 0.5_wp *                                    &
                                 ( ( i - nx ) * dx + pt_damping_width ) /      &
                                 REAL( pt_damping_width, KIND=wp ) )**2
          ENDIF
       ENDDO 
    ELSEIF ( bc_ns_dirrad )  THEN
       DO  j = nys, nyn
          IF ( ( j * dy ) > ( ny * dy - pt_damping_width ) )  THEN
             ptdf_y(j) = pt_damping_factor *                                   &
                         SIN( pi * 0.5_wp *                                    &
                                 ( ( j - ny ) * dy + pt_damping_width ) /      &
                                 REAL( pt_damping_width, KIND=wp ) )**2
          ENDIF
       ENDDO 
    ELSEIF ( bc_ns_raddir )  THEN
       DO  j = nys, nyn
          IF ( ( j * dy ) < pt_damping_width )  THEN
             ptdf_y(j) = pt_damping_factor *                                   &
                         SIN( pi * 0.5_wp *                                    &
                                ( pt_damping_width - j * dy ) /                &
                                REAL( pt_damping_width, KIND=wp ) )**2
          ENDIF
       ENDDO
    ENDIF
!
!-- Check if maximum number of allowed timeseries is exceeded
    IF ( dots_num > dots_max )  THEN
       WRITE( message_string, * ) 'number of time series quantities exceeds',  &
                                  ' its maximum of dots_max = ', dots_max,     &
                                  '&Please increase dots_max in modules.f90.'
       CALL message( 'init_3d_model', 'PA0194', 1, 2, 0, 6, 0 )    
    ENDIF

!
!-- Input binary data file is not needed anymore. This line must be placed
!-- after call of user_init!
    CALL close_file( 13 )
!
!-- In case of nesting, put an barrier to assure that all parent and child 
!-- domains finished initialization. 
#if defined( __parallel )
    IF ( nested_run )  CALL MPI_BARRIER( MPI_COMM_WORLD, ierr )
#endif


    CALL location_message( 'leaving init_3d_model', .TRUE. )

 END SUBROUTINE init_3d_model