Temperature and Salinity File Structure

The layer structure of the Atlantis temperature and salinity forcing files is the same as the initial conditions netCDF files.

The layers are in the following order:

Assuming z = 7, numwc = 6, numsed = 1

Box where numlayers = 6 (+ 1 sediment layer) data looks like:

layer 0, layer 1, layer 2, layer 3, layer 4, layer 5, layer 6, sediment 0

where layer 6 is the surface water column layer and layer 0 is the water column layer closest to the sediment.

Box where numlayer = 3 (+ 1 sediment layer) data looks like:

layer 0, layer 1, layer 2, 0, 0, 0, sediment 0

where layer 2 is the surface water column layer and layer 0 is the water column layer closest to the sediment.

Here is a sample of a section of a temperature file:

netcdf tempSmall {
dimensions: t = UNLIMITED ; // (6 currently) b = 132 ; z = 7 ;
variables: double t(t) ; t:units = “seconds since 1990-01-01 00:00:00 +10” ; t:dt = 43200. ; double temperature(t, b, z) ; temperature:FillValue = 0. ;
// global attributes: :title = “trivial” ; :geometry = “SEAP_14052012_aea.bgm” ; :parameters = “” ; :history = “Thu Oct  4 13:27:20 2012: ncks -d t,0,5 SEAP132_temp_1Year.nc tempSmall.nc” ; :NCO = “4.0.8” ;
data:
 t = 43200, 86400, 129600, 172800, 216000, 259200 ;
 temperature =
  24.543282, 24.420105, 24.420105, 24.420105, 24.420105, , 24.543282,
  15.066911, 15.066911, , , , , 15.066911,
  18.361917, 18.362057, 18.362057, 18.362057, , , 18.361917,
  18.188761, 18.223467, 18.223862, , , , 18.188761,
  17.655779, 17.689005, , , , , 17.655779,
  20.303896, 20.309582, , , , , 20.303896,
  18.210901, 17.923788, 17.917063, 17.917063, , , 18.210901,
  18.39819, 18.318493, 18.318493, 18.318493, 18.318493, , 18.39819,
  23.756937, 23.761934, 23.73678, 23.734312, 23.734312, 23.734312, 23.756937,