mix/bmix.f90

The program bmix

Generally, the boundary conditions are necessary for the upper and lower boundaries as well as for maximal two vertical boundaries if lat $_{min} > -90.$ and/or lat $_{max} < 90.$ deg N was chosen. The update of the boundary conditions occurs after each time step $\Delta t$ . First, the APs in the highest, lowest and the vertical layers are replaced by the APs as defined in the initialization file. For the lowest layer, an orographically adjusted layer can be used (only in $\zeta$ -coordinates)

To take into account that the mixing ratios of the APs at the boundaries may change during the CLaMS run, a re-initialization procedure of these APs was implemented in bmix.f90. The informations necessary for the re-initialization are stored in the NetCDF files where the following names can be used:

chem_bound_0900K.nc- e.g. for the boundary condition at $\theta_{max}(\zeta_{max})=900$ K

chem_vert_25N.nc - e.g. for the vertical condition at lat $_{min}=25$ deg N

The mixing ratios in the horizontal and vertical files are stored as 2D fields [time $\times$ eqlat] or [time $\times$ theta/zeta], respectively. To create these files the Mainz-2D model or HALOE climatology can be used. In a similar way the variable TRACER can be re-initialized.

The options for the execution of bmix are set in the configuration file bmix.inp:

1) traj_JL0_3d_05030712_05030812.nc      ! trajectory file
2) bsp4                                  ! its directory
3) init_JL0_04112012.nc                  ! file for boundary conditions
4) bsp4                                  ! input directory  (wind files)
5) ECZ                                   ! Prefix of wind files (3 characters)
6) 340 1350  70 -70 ! boundaries (lower layer, upper layer, north vert., south vert.)
7) 50.                                   ! delta_theta
8) 1                                     ! interpolation from pos file? (0=no,1=lower boundary,2=upper boundary,3=both)
9) CH4  1  1  chem_bound_noaa_cmdl.nc    ! redefine species from boundary file:
   CH4  2  1  chem_bound_upper_bound.nc  ! species, boundary (1=lower,2=upper), 
   CO   1  1  chem_bound_noaa_cmdl.nc    ! replace/add (1/2), bound file
   CO2  1  1  boundfile2.nc              ! one line per species (0-50 lines)

Remarks:

Name of trajectory file: the prefix (e.g. JL0) and the end date (e.g. 05030812) specified in this filename are used to create the filenames for the pos file (input, created in mix) and the init file (output)
Directory used for input (pos file and bound file); the output file (init file) is also created in this directory.
File for boundary conditions
Input directory containing wind files
Prefix of wind files (3 characters)
Position of the boundaries: lower layer, upper layer, north vertical, south vertical
The first two values define the lower and upper layers which are replaced by bmix, i.e. all APs within these layers are replaced by the APs defined in the initialization file. E.g. $\zeta=340$ K (first value) means that all APs with $\zeta_{min}<\zeta<340$ , with $\zeta_{min}=\zeta_1-\Delta\zeta_1/2$ undergo this procedure ( $\zeta_i$ , $\Delta\zeta_i$ is the grid of layers, each of them with the thickness $\Delta\zeta_i$ ). If this boundary value (here $\zeta=340$ ) is within $\Delta\zeta_1$ , than bmix replaces this value by $\zeta_1+\Delta\zeta_1/2$ (so only an approximate value can be used). The same procedure is applied for the upper layer.
delta_theta or better $\Delta\zeta$ is the thickness of the orographic boundary layer. This procedure is applied only if $\Delta\zeta>0$ is set. In this case, the APs within the layer that follows the orography are replaced. Orography is defined by $\zeta_0(lon,lat)$ that is derived from the wind data as the lowest $\zeta$ level with valid pressure values. Then, the orographic layer is defined as the region with $\zeta_{min}<\zeta<\zeta_{min}+\Delta\zeta$ and $\zeta_{min}=max(\zeta_0, \zeta_1-\Delta\zeta_1/2)$ . Note that this procedure is carried out only in the region with $\zeta$ smaller than the definition of the lower boundary (here 340 K).
The vmr of all species on these APs are interpolated from all APs within the lower and/or upper boundary if this is specified in this line
The vmr of CO, CO, and CH can be also updated using the files provided by Climate Monitoring and Diagnostics Laboratory (CMDL) at NOAA (Globalview, Pieter.Tans@noaa.gov). These data can be converted from the original format to NetCDF using the sub-package cmdl stored in mix directory. This package creates an additional boundary layer file
- chem_bound_noaa_cmdl.nc
that overwrites the vmr values set by the orographic boundary layer.
This file or other additional boundary layer files can be specified in line 9 et seq.
There must be one line per species. Every line must contain the following specifications:
- the name of the species
- boundary (1=lower,2=upper)
- The values at the boundary are replaced with the interpolated values from boundfile (1)
  or the interpolated values from boundfile are added to the interpolated values from pos-file (2)
  If the option 2 is choosen, in line 8 "y" must be specified (interpolation from pos-file)
- the name of the bound file
The specifications in line 9 et seq. are optional.