Index: palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d
===================================================================
--- palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d	(revision 4098)
+++ palm/trunk/TUTORIALS/cases/lsm_short/INPUT/lsm_short_p3d	(revision 4222)
@@ -1,115 +1,133 @@
+!-------------------------------------------------------------------------------
+!-- INITIALIZATION PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/inipar
+!-------------------------------------------------------------------------------
 &initialization_parameters
 !
 !-- grid parameters
-!------------------------------------------------------------------------------
-   nx                         = 39,
-   ny                         = 39,
-   nz                         = 80,
+!-------------------------------------------------------------------------------
+    nx                         = 39, ! Number of gridboxes in x-direction (nx+1)
+    ny                         = 39, ! Number of gridboxes in y-direction (ny+1)
+    nz                         = 80, ! Number of gridboxes in z-direction (nz)
 
-   dx                         = 50.0,
-   dy                         = 50.0,
-   dz                         = 25.0,
-
+    dx                         = 50.0, ! Size of single gridbox in x-direction
+    dy                         = 50.0, ! Size of single gridbox in y-direction
+    dz                         = 25.0, ! Size of single gridbox in z-direction
 !
 !-- initialization
 !------------------------------------------------------------------------------
-   initializing_actions       = 'set_constant_profiles',
+    initializing_actions       = 'set_constant_profiles', ! initial conditions
 
-   ug_surface                 = 0.0, ! free convection
-   vg_surface                 = 0.0,
+    ug_surface                 = 0.0, ! u-comp of geostrophic wind at surface
+    vg_surface                 = 0.0, ! v-comp of geostrophic wind at surface
 
-   pt_surface                 = 293.0,
-   pt_vertical_gradient       =    0.0,  2.0,
-   pt_vertical_gradient_level = 0.0,  800,
+    pt_surface                 = 293.0, ! initial surface potential temp
 
-   day_of_year_init           = 232, ! Aug 20
-   time_utc_init              = 39600.0, ! 11:00 UTC
-   
+    pt_vertical_gradient       = 0.0,
+                                 2.0, ! piecewise temp gradients
+    pt_vertical_gradient_level = 0.0,
+                                 800.0, ! height level of temp gradients
+
+    day_of_year_init           = 232,     ! Aug 20
+    time_utc_init              = 39600.0, ! 11:00 UTC
 !
 !-- boundary conditions
 !------------------------------------------------------------------------------
-   constant_flux_layer        = .TRUE.,
+    constant_flux_layer        = .TRUE., ! use a constant flux layer at 
+                                         ! the bottom boundary
 
-
-   bc_pt_b                    = 'dirichlet', ! required when using LSM
+    bc_pt_b                    = 'dirichlet', ! required when using LSM
 !
 !-- numerics
 !------------------------------------------------------------------------------
-   fft_method                 = 'temperton-algorithm', ! 'fftw' if available
-/
+    fft_method                 = 'temperton-algorithm', ! build-in fft method
 
+/ ! end of initialization parameter namelist
+
+!-------------------------------------------------------------------------------
+!-- RUNTIME PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/d3par
+!-------------------------------------------------------------------------------
 &runtime_parameters
 !
 !-- run steering
-!------------------------------------------------------------------------------
-   end_time                   = 7200.0, ! 2 h
+!-------------------------------------------------------------------------------
+    end_time                   = 7200.0, ! simulation time of the 3D model
 
-   create_disturbances        = .T.,
-   dt_disturb                 = 150.0,
-   disturbance_energy_limit   = 0.01,
+    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
 !
-!-- general output settings
-!------------------------------------------------------------------------------
-   netcdf_data_format         = 2, ! NetCDF3
-   dt_dots                    = 0.0,
-   dt_run_control             = 60.0,
-!
-!-- profile output settings
-!------------------------------------------------------------------------------
-   dt_dopr                    = 600.0,
-   averaging_interval_pr      = 600.0,
+!-- data output
+!-------------------------------------------------------------------------------
+    netcdf_data_format         = 2, ! use NetCDF3
 
-   data_output_pr             = '#u', '#v', '#theta',
-                                '#km', '#kh', '#l',
-                                'w', 'e', 'e*', 'p',
-                                'w"theta"', 'w*theta*', 'wtheta', 'w*e*', 
-                                'theta*2','u*2', 'v*2', 'w*2', 
-                                '#t_soil',
-!
-!-- 2D and 3D output settings
-!------------------------------------------------------------------------------
-   dt_do3d                    = 60.0,
-   dt_do2d_xy                 = 60.0,
+    dt_run_control             = 60.0,   ! output interval for run control
+    dt_data_output             = 900.0,  ! output interval for general data
+    dt_data_output_av          = 1800.0, ! output interval for averaged data
+    dt_dots                    = 0.0,    ! output interval for time-series data
+    dt_dopr                    = 600.0,  ! output interval for profile data
+    dt_do3d                    = 60.0,   ! output interval for 3d data
+    dt_do2d_xy                 = 60.0,   ! output interval for 2d-xy data
 
-   section_xy                 = 0, ! surface variables only 
+    data_output                = 'theta', 'w', 'u', 'v',
+                                 'us*_xy', 
+                                 'ghf*_xy', 'shf*_xy', 
+                                 'tsurf*_xy',
+                                 't_soil',    ! 2d and/ 
+                                              ! or 3d 
+                                              ! output 
 
-   data_output                = 'theta', 'w', 'u', 'v',
-                                'us*_xy', 
-                                'ghf*_xy', 'shf*_xy', 
-                                'tsurf*_xy',
-                                't_soil',
-/
+    data_output_pr             = '#u', '#v', '#theta',
+                                 '#km', '#kh', '#l',
+                                 'w', 'e', 'e*', 'p',
+                                 'w"theta"', 'w*theta*', 'wtheta', 'w*e*', 
+                                 'theta*2','u*2', 'v*2', 'w*2', 
+                                 '#t_soil',                        ! Profile 
+                                                                   ! output
 
+    section_xy                 = 0, ! grid index for 2D XY cross sections
+
+    averaging_interval         = 1800.0, ! averaging interval general data
+    dt_averaging_input         =    6.0, ! averaging general data sampling rate
+
+    averaging_interval_pr      = 600.0, ! averaging interval profile data
+    dt_averaging_input_pr      =   6.0, ! averaging profile data sampling rate
+
+/ ! end of runtime parameter namelist
+
+!-------------------------------------------------------------------------------
+!-- LAND-SURFACE PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/lsmpar
+!-------------------------------------------------------------------------------
 &land_surface_parameters
-!
-!-- soil setup
-!------------------------------------------------------------------------------
-   soil_type                  = 3,
-   soil_moisture              = 0.0,   0.0,   0.0,   0.0,
-                                0.0,   0.0,   0.0,   0.0,
-   soil_temperature           = 293,   293,   293,   293,
-                                293,   293,   293,   293,  
-   deep_soil_temperature      = 293, 
-!
-!-- boundary conditions
-!------------------------------------------------------------------------------
-   surface_type               = 'vegetation',
-   vegetation_type            = 1,
-/
+    soil_type                  = 3,  ! type to be used in soil model
+    soil_moisture              = 0.0,   0.0,   0.0,   0.0, ! moisture at every
+                                 0.0,   0.0,   0.0,   0.0, ! soil level
+    soil_temperature           = 293,   293,   293,   293, ! temperature at
+                                 293,   293,   293,   293, ! every soil level
+    deep_soil_temperature      = 293,  ! temperature of deep soil
 
+    surface_type               = 'vegetation',  ! surface classification
+    vegetation_type            = 1, ! vegetation to be used in surface model
+
+/ ! end of land-surface parameter namelist
+
+!-------------------------------------------------------------------------------
+!-- RADIATION PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/radpar
+!-------------------------------------------------------------------------------
 &radiation_parameters
-!
-!-- general setup
-!------------------------------------------------------------------------------
-   radiation_scheme           = 'clear-sky',
-   dt_radiation               = 20.0,
-/
+    radiation_scheme           = 'clear-sky', ! Radiation scheme to be used
+    dt_radiation               = 20.0, ! Time step of the radiation model
 
+/ ! end of radiation parameter namelist
+
+!-------------------------------------------------------------------------------
+!-- USER PARAMETER NAMELIST
+!   Documentation: https://palm.muk.uni-hannover.de/trac/wiki/doc/app/userpar
+!-------------------------------------------------------------------------------
 &user_parameters
-!
-!-- User-defined setup
-!------------------------------------------------------------------------------
+    data_output_user           = 'v_h', 'v_h_xy', ! user defined data output
 
-  data_output_user           = 'v_h', 'v_h_xy',
-  
-/
+/ ! end of user parameter namelist
