!-------------------------------------------------------------------------------
!-- INITIALIZATION PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/inipar
!-------------------------------------------------------------------------------
&initialization_parameters
!
!-- grid parameters
!-------------------------------------------------------------------------------
    nx                         = 899, ! Number of gridboxes in x-direction (nx+1)
    ny                         = 1007, ! Number of gridboxes in y-direction (ny+1)
    nz                         = 248, ! Number of gridboxes in z-direction (nz)

    dx                         = 30.0, ! Size of single gridbox in x-direction
    dy                         = 30.0, ! Size of single gridbox in y-direction
    dz                         = 12.0, ! Size of single gridbox in z-direction


    humidity                   = .TRUE.,
    passive_scalar             = .TRUE.,

!
!-- initialization
!-------------------------------------------------------------------------------
    initializing_actions       = 'interpolate_from_parent', ! initial conditions


    origin_date_time           = '2019-08-22 00:00:00 -5', !starting at midnight localtime, CDT,  and -5 from UTC
    topography                 = 'read_from_file',



!
!-- boundary conditions
!-------------------------------------------------------------------------------
    bc_pt_b                    = 'dirichlet',                                    ! dirichlet required for lsm / neumann required for surface_heatflux
    bc_uv_b                    = 'dirichlet',
    bc_q_b                     = 'dirichlet',                                    ! dirichlet required for lsm / neumann required for surface_heatflux
    bc_p_t                     = 'neumann',
    bc_p_b                     = 'neumann',
!

!-- numerics
!-------------------------------------------------------------------------------
    psolver                    = 'multigrid',   !Using non-cyclic lateral boundary conditions requires the multigrid method 
!                                                for solving the Poisson equation for the perturbation pressure.
    cycle_mg  = 'w',
    mg_cycles = 2,
    mg_switch_to_pe0_level = -1,

    turbulence_closure         = '1.5-order',
    
!-- PHYSICS -------------------------------------------------------------------

!   Not employed for testing, but later please replace by appropriate values to bring surface temperature into equilibrium - MS
!   Replaced with two day values taken from the HRRR data - SP
    spinup_time         = 158400., !  44:00 hours
    spinup_pt_mean      = 289.87,  
    spinup_pt_amplitude = 8.20,    
    dt_spinup           = 5.0,
    data_output_during_spinup = .F.,
    

/ ! end of initialization parameter namelist

!------------------------------------------------------------------------------
!-- LAND SURFACE MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/lsmpar
!------------------------------------------------------------------------------
&land_surface_parameters
!
!
    aero_resist_kray           = .T.,
    conserve_water_content     = .T.,
    min_soil_resistance        = 50.0,

    soil_moisture              =   0.1874 , 0.1882, 0.1896, 0.1908, 0.1917,0.1884 , 0.1720, 0.1613, ! from HRRR data
    soil_temperature           =   284.16, 284.72, 285.60, 286.42 ,287.16, 287.35, 286.66, 279.46,   ! from HRRR data
    deep_soil_temperature      = 283.42,

    surface_type               = 'netcdf',
    constant_roughness         = .T.,
!
! end of land surface model parameter namelist
/                                                                               

!------------------------------------------------------------------------------
!-- RADIATION MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/radpar
!------------------------------------------------------------------------------
&radiation_parameters
    dt_radiation               = 60.0,
    radiation_scheme           = 'external',
    radiation_interactions_on  = .T.,                                           !  interaction of radiation inside the canopy, i.e. grass
    rad_angular_discretization = .T.,
    raytrace_discrete_azims    = 10,
    raytrace_discrete_elevs    = 10,

    surface_reflections = .T.,

    nrefsteps = 2,
!
/                                                                               ! end of radiation model parameter namelist

!------------------------------------------------------------------------------
!-- PLANT CANOPY MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/plant_canopy_parameters
!------------------------------------------------------------------------------
&plant_canopy_parameters
    canopy_mode                 = 'read_from_file',      
    canopy_drag_coeff           = 0.15,
    plant_canopy_transpiration  = .T.,
/


!-------------------------------------------------------------------------------
!-- RUNTIME PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/d3par
!-------------------------------------------------------------------------------
&runtime_parameters
!
!-- run steering
!-------------------------------------------------------------------------------
    end_time                   = 158400, ! simulation time of the 3D model , 44.0h,
    dt_max                     = 0.6, !max timestep 
    restart_time               = 0.1, 

    create_disturbances        = .TRUE., ! randomly perturbate horiz. velocity
    dt_disturb                 = 150.0,  ! interval for random perturbations
    disturbance_energy_limit   = 0.01,   ! upper limit for perturbation energy

    data_output_2d_on_each_pe  = .TRUE., ! do 2D output on each MPI rank
    
    npex = 45,
    npey = 21,
    debug_output                 = .F.,

!
!-- data output
!-------------------------------------------------------------------------------
    netcdf_data_format         = 5,

    dt_run_control             = 0.0,    ! output interval for run control
    dt_data_output             = 1800.0,  ! output interval for general data, setting 30 mins
    dt_data_output_av          = 1800.0, ! output interval for averaged data, setting 30 mins
    dt_dopr                    = 900.0,  ! output interval for profile data, 10 mins

!
!-- In case you want to calculate TKE or fluxes from 3D output averaging_input need to be every timestep
    averaging_interval         = 1800.0,  ! averaging interval general data change this for longer/final runs**
    dt_averaging_input         = 0.001,  ! averaging general data sampling rate

    averaging_interval_pr      = 900.0, ! averaging interval profile data
    dt_averaging_input_pr      = 5.0,   ! averaging profile data sampling rate


    do3d_at_begin      = .T., 
    do2d_at_begin      = .T.,
!---- output data variables
!----not writing out any cross section data because we have 3D data          

    data_output                = 'u', 'v', 'w','e',               !----3D data of instantaneous velocities and SGS TKE  
                                 'u_av', 'v_av', 'w_av','e_av',   !----3D data of averaged velocities
                                 'uu_av', 'vv_av', 'ww_av',   !---only writing out avg values for TKE calculations   
                                 'uv_av','uw_av', 'vw_av',    !---only writing out avg values for TKE calculations   
                                 'theta', 'q','s',            !----3D data of instantaneous scalars
                                 'theta_av', 'q_av','s_av',   !----3D data of avg scalars
                                 'wtheta_av','wq_av','ws_av', !---only writing out av values for EC flux calculations
                                 'shf*_xy_av', 'qsws*_xy_av', 'ghf*_xy_av', 'rad_net*_xy_av','ssws*_xy_av',   !---surface cross sections
                                 'us*_xy_av','ol*_xy_av','t*_xy_av','tsurf*_xy_av',     !---surface cross sections
                                 'rad_lw_in*_xy_av', 'rad_lw_out*_xy_av', 'rad_sw_in*_xy_av', 'rad_sw_out*_xy_av',   !---surface cross sections
                                 'pcm_heatrate', 'pcm_heatrate_av',                   !---3D plant canopy  data
                                 'pcm_transpirationrate', 'pcm_transpirationrate_av', !---3D plant canopy  data
                                 'pcm_latentrate','pcm_latentrate_av', !---3D plant canopy  data
                                 'm_soil', 't_soil',                   !---2D soils   data
!                                 'lai*_xy_av', 'r_a*_xy_av', 'r_s*_xy_av',      !---2D plant   data

    data_output_pr             = 'wtheta', 'w"theta"', 'w*theta*',
                                 'wq','w"q"','w*q*',
                                 'ws','w"s"','w*s*',
                                 'w', 'w*2',
                                 '#u', 'u*2',  'wu',  'w*u*',  'w"u"',
                                 '#v', 'v*2',  'wv',  'w*v*',  'w"v"',
                                 '#theta','theta*2','#q','q*2','#s','s*2',
                                 'w*p*:dz','rh','rho',

    section_xy                 = 0, ! grid index for 2D XY cross sections


 / ! end of runtime parameter namelist

&virtual_flight_parameters

   flight_begin = 32400., ! 9hours to simulation start
   leg_mode = 'return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return',    !RF17&RF18
              'return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return','return',    !RF19&RF20


   flight_level = 400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,
                  400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,400.0, 100.0,


   rate_of_climb = 0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,
                   0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,

   speed_agl =     82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,
                   82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,82.31,

   x_start = 14850.,3180.,14970.,5160.,16470.,4920.,16830.,6930.,18450.,6810.,20100.,8250.,20190.,10320.,21960.,10260.,21720.,12030.,23700.,12510., !RF17&RF18 SE-NW
             3390.,14610.,3450.,16620.,5100.,16230.,5100.,17880.,6810.,17880.,8340.,19800.,8520.,21750.,10230.,21810.,10230.,23490.,12000.,23520.,  !RF19&RF20 SW-NE


   x_end  =  3180.,14850.,5160.,14970.,4920.,16470.,6930.,16830.,6810.,18450.,8250.,20100.,10320.,20190.,10260.,21960.,12030.,21720.,12510.,23700.,
             14610.,3390.,16620.,3450.,16230.,5100.,17880.,5100.,17880.,6810.,19800.,8340.,21750.,8520.,21810.,10230.,23490.,10230.,23520.,12000.,


   y_start = 1350.,23790.,1260.,24720.,2490.,24900.,2370.,25440.,3510.,25800.,4320.,27120.,4410.,27840.,5220.,27750.,5370.,28740.,6390.,28080.,
             6420.,28500.,6180.,27840.,5820.,27420.,5460.,26550.,4530.,26400.,3210.,25620.,3570.,24840.,2700.,25140.,2370.,23790.,1350.,24090.,

   y_end =   23790.,1350.,24720.,1260.,24900.,2490.,25440.,2370.,25800.,3510.,27120.,4320.,27840.,4410.,27750.,5220.,28740.,5370.,28080.,6390.,
             28500.,6420.,27840.,6180.,27420.,5820.,26550.,5460.,26400.,4530.,25620.,3210.,24840.,3570.,25140.,2700.,23790.,2370.,24090.,1350.,


/ ! end of virtual flight parameters

