source: palm/trunk/TUTORIALS/cases/chem_phstatp_lod2/INPUT/chem_phstatp_lod2_p3d

!------------------------------------------------------------------------------
!-- INITIALIZATION PARAMETER NAMELIST
!-- Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/inipar
!------------------------------------------------------------------------------
 &initialization_parameters
!
!-- model grid
!--------------------------------------
    nx = 35,
    ny = 35,
    nz = 80,

    dx = 10.0,
    dy = 10.0,
    dz = 10.0,

    dz_stretch_level = 1200.0, dz_stretch_factor = 1.02, dz_max = 60.0,


!-- pressure solver
!--------------------------------------
!   fft_method =  'fftw',

      psolver = 'multigrid',
      cycle_mg  = 'w',
      mg_cycles = 2,
      mg_switch_to_pe0_level = -1,

!
!-- initial and boundary conditions
!--------------------------------------
    initializing_actions = 'set_constant_profiles',  ! options: 'set_constant_profiles', or 'inifor', 
                                                     ! or both, e.g. 'inifor set_constant_profiles'
    constant_flux_layer = .T.,
!
!-- wind speed
!--------------------------------------
     ug_surface = 1.0,
     vg_surface = 0.0,
!
!-- temperature
!--------------------------------------
    pt_surface = 290.0,
    bc_pt_b    = 'dirichlet',
    pt_vertical_gradient      = 0.1, 1.0,     !pt gradient/100m K
    pt_vertical_gradient_level= 0.0, 500.0,   !height (m) at which pt gradient is effective
!
!-- humidity
!--------------------------------------
    humidity   = .T.,
    q_surface  = 0.001,
    bc_q_b     = 'dirichlet',
!
!-- time
!--------------------------------------
    origin_date_time     = '2017-07-31 06:00:00 +00'
!
!-- wall/soil spinup
!--------------------------------------
     spinup_time         = 86400.0,         ! 24h wall/soil spinup
     spinup_pt_mean      = 290.0,
     spinup_pt_amplitude = 20.0,
     dt_spinup           = 120.0,           ! time step during spinup
     data_output_during_spinup = .F.,       ! set .T. if you want output
!
!-- building topology
!--------------------------------------
    topography = 'read_from_file',

/
!------------------------------------------------------------------------------
!-- RUNTIME PARAMETER NAMELIST
!-- Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/d3par
!------------------------------------------------------------------------------
 &runtime_parameters
!
!-- run time
!--------------------------------------
    end_time                =  7200.,
    termination_time_needed =  600.0,   
!
!-- processor topology
!--------------------------------------
!    npex = 6,
!    npey = 6,
!
!-- 2d/3d output
!--------------------------------------
    do3d_at_begin         = .T.,
    do2d_at_begin         = .T.,
    dt_data_output        = 300.0, 
    dt_data_output_av     = 600.0,
    dt_do2d_xy            = 600.0,
    section_xy            = 0,
    averaging_interval    = 600.0,

     
    data_output = 'theta', 'q', 'u', 'v', 'w','e',
                   't_soil', 'm_soil',
                   'tsurf*_xy', 'shf*_xy', 'qsws*_xy', 'ghf*_xy',
                   'rad_net*_xy', 'us*_xy', 't*_xy', 'r_a*_xy', 'm_liq*_xy',
                   'kc_NO2','kc_O3','kc_NO', 'kc_PM10',
                   'theta_av', 'q_av', 'u_av', 'v_av', 'w_av','e_av',
                   'tsurf*_xy_av', 'shf*_xy_av', 'qsws*_xy_av', 'ghf*_xy_av',
                   'kc_NO2_av','kc_O3_av','kc_NO_av', 'kc_PM10_av',
!
! Masked output - here for first layer above ground 
   mask_k_over_surface(1,:) = 0,          ! 1. layer above surface (terrain following)
   dt_domask        = 60.,                ! time interval for masked output
   data_output_masks(1,:) = 'u', 'v', 'kc_NO', 'kc_NO2', 'kc_O3', 'kc_PM10',
!
!-- timeseries output
!--------------------------------------
    dt_run_control =   0.0,
    dt_dots        =   60.0,
!
!-- profile output
!--------------------------------------
    skip_time_dopr        =   0.0,
    dt_dopr               =  600.0,
    averaging_interval_pr =  600.0,
    dt_averaging_input_pr =  600.0,

    data_output_pr = 'e', 'e*',
                     '#u', 'w"u"', 'w*u*', 'wu', 'u*2', 
                     '#v', 'w"v"', 'w*v*', 'wv', 'v*2',
                     'w',  'w*2',
                     '#theta', 'w"theta"', 'w*theta*','wtheta', 'theta*2',
                     'kc_NO2','kc_O3','kc_NO',
 /

!-------------------------------------------------------------------------------
!-- RADIATION MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/radpar
!-------------------------------------------------------------------------------
 &radiation_parameters
    radiation_scheme =  'clear-sky',    !'clear-sky', 'rrtmg',
    dt_radiation     = 60.0,

    albedo_type      = 5,
    constant_albedo  = .F.,

    surface_reflections = .T.,
    nrefsteps = 5,

 / ! end of radiation_parameters namelist

!------------------------------------------------------------------------------
!-- URBAN SURFACE MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/usmpar
!------------------------------------------------------------------------------
 &urban_surface_parameters

 / ! end of urban_surface_parameters namelist


!------------------------------------------------------------------------------
!-- LAND SURFACE MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/lsmpar
!------------------------------------------------------------------------------
 &land_surface_parameters
    vegetation_type = 2,
    soil_type       = 3,

    root_fraction = 0.49, 0.26, 0.25, 0.0, 0.0, 0.0, 0.0, 0.0,
    soil_moisture = 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3, 0.3,
    soil_temperature = 289., 289., 291., 292., 292., 290., 288., 287.,
    deep_soil_temperature = 285.,

    aero_resist_kray       = .T.,
    constant_roughness     = .T.,
    conserve_water_content = .T.,
 / ! end of land_surface_parameters namelist


!------------------------------------------------------------------------------
!-- PLANT CANOPY MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/canpar
!------------------------------------------------------------------------------
 &plant_canopy_parameters
    canopy_mode = 'read_from_file',
    canopy_drag_coeff = 0.3,
 / ! end of plant_canopy_parameters namelist

!------------------------------------------------------------------------------
!-- CHEMISTRY MODEL PARAMETER NAMELIST
!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/chempar
!------------------------------------------------------------------------------
 &chemistry_parameters

    chem_gasphase_on           = .TRUE.,
    chem_mechanism             = "phstatp", 
    deposition_dry             = .TRUE.,
    photolysis_scheme          = 'simple',

! initial profiles
    cs_name                    = 'O3',  'NO',  'NO2',   'PM10',
    cs_surface                 = 0.025, 0.000, 0.010,    2.0e-09,       !units- chem spcs in ppm, and PM10 in ug/m**2

    cs_profile(1,:)            = 0.025, 0.040, 0.050, 
    cs_profile(2,:)            = 0.000, 0.000,
    cs_profile(3,:)            = 0.010, 0.002,
    cs_profile(4,:)            = 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 2.0e-09, 1.0e-09,

    cs_heights(1,:)            = 0.0,  305.0,  495.0,
    cs_heights(2,:)            = 0.0,   295.0,
    cs_heights(3,:)            = 0.0,   295.0,
    cs_heights(4,:)            = 0.0,   15.0,   15.0,   45.0,  65.0,  85.0, 105.0, 125.0, 155.0,  185.0, 295.0,

! Emissions
    emissions_anthropogenic    = .TRUE.,
    emiss_lod                  = 2,                 ! 0 "PARAMETERIZED", 1 "DEFAULT", 2 "PRE-PROCESSED",
    emiss_read_legacy_mode      = .FALSE.
! Parameters for parameterized traffic emissions

! Bottom and top boundary conditions (lateral BCs are cyclic, which is the default)
    bc_cs_b                    = 'neumann',
    bc_cs_t                    = 'neumann',

! Parameters chemistry solver (see KPP description)
    icntrl(3)                  = 1,    ! solver ros2
    icntrl(4)                  = 500,  ! max number of chem-substeps
    rcntrl(3)                  = 0.1,  ! Hstart, starting value for the integration step size

 / ! end of chemistry_parameters namelist