README

Author:      Daniel Neumann
Institution: Institute of Coastal Research, Helmholtz-Zentrum Geesthacht
Contact:     daniel.neumann@hzg.de
Version:     1.0
Date:        2015-11-22


~~~ CONTENT ~~~
  (1) Get Input Data
        Which data was employed?
        How to get it?
        What considerations had to be taken?
  (2) Pre-process Input Data
        How was the data formatted/prepared in order to be read-in by the ssemis
         calculation tool described in (3).
        How was data of different sources merged?
        Instructions for employed pre-processing scripts
  (3) Calculate Sea Salt Emissions
        General ideas on the ssemis calculation tool
        How to run the tool
        Which modifications need to be made when you want to use it?
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~~~ (1) Get Input Data ~~~
 SP13: SST, SAL, U10m (RH or [TA, QV, DENS])
 OV14: SST, SAL, U10m, HS, CD/FV (RH or [TA, QV, DENS])
 
 SST: sea surface temperatur
 SAL: salinity
 U10m: 10 m wind speed
 HS: significant wave height
 CD: drag coefficient through waves
 FV: friction velocity at the sea surface
 RH: relative humidity
 TA: air temperature
 QV: water vapour mixing ratio
 DENS: air density
 
 
 SST: BSH data (North and Baltic Sea), ERA-Intrim Input Data (NCEP, remaining regions)
 SAL: BSH data (North and Baltic Sea), 35 g/kg in Atlantic, 37 g/kg in Mediterranean Sea, 18 g/kg (TODO) in Black Sea
 U10m: coastDatII COSMO-CLM (whole region) (doi: 10.1594/WDCC/coastDat-2_COSMO-CLM)
 HS: colastDatII WAM (North Sea) (see http://www.coastdat.de/data_all/hindcast2/index.php), ERA-Interim Wave Model (remaining regions)
 CD: colastDatII WAM (North Sea) (see http://www.coastdat.de/data_all/hindcast2/index.php), calculated from u10 (remaining regions)
 TA: see U10m
 QV: see U10m
 DENS: see U10m
 RH: calculated from TA, QV, and DENS


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~~~ (2) Pre-process Input Data ~~~
The input data were combined (coastDatII and ERA-Interim data) and interpolated
on this study's CMAQ grids (CD24 and CD72). For this purpose, mainly Climate
Data Operators (cdo) and netCDF operators (NCO) were used. Minor work was done
via R scripts. The exact scripts can be provided on request. One file of dummy 
input data formatted according to the CMAQ netCDF conventions is attached. Since
the employed input data belongs to thrid parties, no real input data can be
provided.

Included data
 - lon and lat coordinates of the CD24 and CD72 grids (netCDF)
    -- coords_CD24_ROWCOL.nc
    -- coords_CD72_ROWCOL.nc
 - cdo grid definition of the CD24 and CD72 grids (Text)
    -- griddef_CMAQ_CD24
    -- griddef_CMAQ_CD72
 - land-sea-mask applied to the data after interpolation (netCDF)
    -- LW_MASK_CD24.nc
    -- LW_MASK_CD72.nc
 - dummy input data in the CMAQ format for day 2008370 (4th Undecimber 2008)
    -- pub.neumannd.dummy_data.sea_salt.CD24.2008370.nc
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~~~ (3) Calculate Sea Salt Emissions ~~~
Overview over source code files
   -- ssemis_params:      parameters, directories, etc.
   -- ssemis_funs:        functions generally used independent of the emission
                           parameterisation
   -- ssemis_calc_sp13:   function with emission parameterisation suggested by
                           Spada et al. (2013)
   -- ssemis_calc_ov14:   function with emission parameterisation derived by
                           Ovadnevaite (2014); CURRENTLY NOT WORKING 
   -- ssemis_main_*:      main programms to source the R scripts and call the 
                           integration routines; can be started from command line
   -- ssemis_versioning:  contains version number

The ssemis_main* can be started from the command line. The following arguments 
can be set. If they are not set, standard values are used.

Argument Name   Variable in R   Description
GRID_NAME       GRID_NAME       CMAQ grid descriptions; choose 'CD24' or 'CD72'
TO              myDate          set end date (format: YYYYDDD)
FROM            myDate          set start date (format: YYYYDDD)
MODE            myMode          for experimenting between different types
                                    of integrations or different salinity
                                    dependences; better leave open
AERO            myAero          choose CMAQ aerosol mechanism version; the
                                    number of sea salt species was increased in
                                    AERO06 compared with AERO05; AERO05 is 
                                    assumed if nothing is defined here
CMAQ            myCMAQ          set CMAQ version; set 5.0 or leave blank
SURF            surfzone        special treatment of the surfzone (TRUE=yes);
                                only reasonable for SP13; OV14 ignores it

# example calls
Rscript ssemis_main_ovadnevaite.R --args GRID_NAME=CD24 FROM=2008370 TO=2008370 MODE=1 AERO=5 CMAQ=5.0 SURF=FALSE
Rscript ssemis_main_ovadnevaite.R --args FROM=2008370 TO=2008370 GRID_NAME=CD24
Rscript ssemis_main_spada.R --args FROM=2008370 TO=2008370 GRID_NAME=CD24


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