The yourcase_input.nc file

Building the yourcase_input.nc

Each MicroHH experiment requires a NetCDF file with the initial vertical profiles, and optionally input for model components like e.g. large-scale forcings, boundary conditions, and/or radiation. The different input options are divided over different NetCDF groups.

Each input file should, as a bare minimum, specify the height of the full model levels:

Variable	Dims	Unit	Description
z	[z]	m	Height of the full model levels

The tables below show an overview of the input options. If a wildcard * is used, variables (with units @) can be filled in according to the description.

Warning

If a variable required by the model is not present in the NetCDF file, the profile is filled with zero’s, and a warning is printed by the model.

init group

The init group provides the initial vertical profiles of the prognostic variables, and optionally (non time dependent) large scale forcings like the geostrophic wind components, subsidence velocity, source terms, or nudging profiles. See Large-scale forcings [force] for details on the different options.

Variable	Dims	Unit	Description
*	[z]	@	Initial profile of any prognostic variable
*_ls	[z]	@ s-1	Source term of any prognostic variable (if swls=1 and swtimedep_ls=0)
*_nudge	[z]	@	Nudging target of any prognostic variable (if swnudge=1 and swtimedep_nudge=0)
u_geo	[z]	m s-1	Zonal component geostrophic wind (if swlspres=geo and swtimedep_geo=0)
u_geo	[z]	m s-1)	Meridional component geostrophic wind (if swlspres=geo and swtimedep_geo=0)
w_ls	[z]	m s-1	Subsidence velocity (if swwls=1 and swtimedep_wls=0)
nudgefac	[z]	s	Nudging time scale (if swnudge=1)

timedep group

The timedep group specifies the time dependent surface boundary conditions and/or large scale forcings.

Variable	Dims	Unit	Description
time_surface	[time_surface]	s	Input time of surface boundary conditions
*_sbot	[time_surface]	note 1	Surface boundary conditions of prognostic scalar variables
p_bot	[time_surface]	Pa	Surface pressure
time_ls	[time_ls]	s	Input time of large scale forcings
*_ls	[time_ls, z]	@ s-1	Source term of any prognostic variable (if swls=1 and swtimedep_ls=1)
*_nudge	[time_ls, z]	@	Nudging target of any prognostic variable (if swnudge=1 and swtimedep_nudge=1)
u_geo	[time_ls, z]	m s-1	Zonal component geostrophic wind (if swlspres=geo and swtimedep_geo=1)
u_geo	[time_ls, z]	m s-1	Meridional component geostrophic wind (if swlspres=geo and swtimedep_geo=1)
w_ls	[time_ls, z]	m s-1	Subsidence velocity (if swwls=1 and swtimedep_wls=1)

Note 1: the units of the scalar boundary conditions (BCs) depend on the boundary conditions used: @ for Dirichlet BCs, @ m s-1 for flux BCs, and @ m-1 for Neuman BCs.

radiation group

The radiation group defines background profiles, used by RRTMGP to calculate the radiation boundary conditions at the top of the LES domain. The input is specified at full (dimension lay) and half (dimension lev) pressure levels, and typically should extend to the top of the atmosphere (TOA).

Variable	Dims	Unit	Description
p_lay	[lay]	Pa	Full level pressure
p_lev	[lev]	Pa	Half level pressure
z_lay	[lay]	m	Full level height
z_lev	[lev]	m	Half level height
t_lay	[lay]	K	Full level absolute temperature
t_lev	[lev]	K	Half level absolute temperature
h2o	[lay]	??	Water vapour mixing ratio ??
co2	[lay]	ppm	Carbon dioxide mixing ratio
ch4	[lay]	ppb	Methane mixing ratio
n2o	[lay]	ppb	Nitrous oxide mixing ratio
n2	[lay]	??	Dinitrogen mixing ratio
o2	[lay]	??	Oxygen mixing ratio
o3	[lay]	??	Ozone mixing ratio

Example input NetCDF file

The code snippet below illustrates how to create a NetCDF input file with Python.

import netCDF4 as nc4
import numpy as np

# Vertical dimension and coordinates
ktot = 64
dz = 40.
z = np.arange(dz/2, ktot*dz, dz)

# Initial profiles
thl = 280. + 0.006*z
u = np.ones(ktot)*5
u_geo = np.ones(ktot)*5

# Time dependent surface boundary condition
time_surface = np.linspace(0, 43200, 128)

# Surface potential temperature flux (cosine with max 0.2 K m s-1)
thl_sbot = (1-np.cos(2*np.pi*time_surface/43200))/2*0.2

# Save all the input data to NetCDF
nc_file = nc4.Dataset('mycase_input.nc', mode='w', datamodel='NETCDF4', clobber=False)

def add_variable(nc_group, name, dims, data):
    """ Help function for adding a new variable """
    var = nc_group.createVariable(name, 'f8', dims)
    var[:] = data

# Create dimension and variable of vertical grid in main group:
nc_file.createDimension('z', ktot)
add_variable(nc_file, 'z', ('z'), z)

# Create a group called `init` for the initial profiles:
nc_group_init = nc_file.createGroup('init')
add_variable(nc_group_init, 'thl', ('z'), thl)
add_variable(nc_group_init, 'u', ('z'), u)
add_variable(nc_group_init, 'u_geo', ('z'), u_geo)

# Create a group called `timedep` for the time dependent variables:
nc_group_timedep = nc_file.createGroup('timedep')
nc_group_timedep.createDimension('time_surface', time_surface.size)
add_variable(nc_group_timedep, 'time_surface', ('time_surface'), time_surface)
add_variable(nc_group_timedep, 'thl_sbot', ('time_surface'), thl_sbot)

nc_file.close()

This results in a NetCDF file mycase_input.nc:

netcdf mycase_input {
dimensions:
        z = 64 ;
variables:
        double z(z) ;

group: init {
  variables:
        double thl(z) ;
        double u(z) ;
        double u_geo(z) ;
  } // group init

group: timedep {
  dimensions:
        time_surface = 128 ;
  variables:
        double time_surface(time_surface) ;
        double thl_sbot(time_surface) ;
  } // group timedep
}