Atlantis NetCDF Structure

Depth Structure

The following image shows how the layer are ordered in the model:

Input NetCDF Structure

There should only be a single timestep in your initial conditions netCDF file.

The generate structure of the variable is as follows:

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.

Often the best way is to look at the dz or temperature variables.

Temperature example:

Temp =
15, 15, 15, 0, 0, 15,
15.75692, 18.54764, 18.55747, 0, 0, 11.8506063390378,
16.38466, 17.64911, 17.49957, 0, 0, 11.7739521098362,
15.66056, 17.34827, 17.31265, 0, 0, 11.5732538369471,
16.05924, 16.92816, 16.87717, 0, 0, 11.2929959545543,
5.152982, 11.85202, 17.02763, 19.01461, 19.83993, 0.327186732920063,
5.2956, 11.91765, 16.3935, 18.50452, 19.48259, 0.936462059214167,

here we have warmer water on the surface.

dz example:

dz =
50, 100, 50, 0, 0, 1,
50.0008980607395, 100.001016436064, 47.7364553552973, 0, 0, 1.00053608029592,
50.0000086311325, 100.000102219634, 47.7364088557938, 0, 0, 1.00030413305374,
50.0001889261175, 100.000163259489, 47.7364117489861, 0, 0, 1.0002832508735,
50.0000055516363, 100.000162982956, 47.736412622015, 0, 0, 1.00044724712438,
900.001395164631, 450.000766659147, 99.9983202606676, 99.9924801598264, 54.9264866944315, 1.00006563744724,
900.002145639133, 450.002999281262, 100.001327120773, 100.001968639764, 54.9424943328129, 1.00021997830258,

So we have the shallow layers near the surface and the deeper layers towards the sediment.

Output NetCDF structure

Each layer variable in the netcdf file contains data per box, layer. Data is written out every toutinc days.

The generate structure of the variable is as follows:

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:

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

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

If we look at the temperature and dz data again we see the difference, this is the same data at t = 0 of the model run.

Temp =
0, 0, 15, 15, 15, 15,
0, 0, 15.75692, 18.54764, 18.55747, 11.8506063390378,
0, 0, 16.38466, 17.64911, 17.49957, 11.7739521098362,
0, 0, 15.66056, 17.34827, 17.31265, 11.5732538369471,
0, 0, 16.05924, 16.92816, 16.87717, 11.2929959545543,
5.152982, 11.85202, 17.02763, 19.01461, 19.83993, 0.327186732920063,
5.2956, 11.91765, 16.3935, 18.50452, 19.48259, 0.936462059214167,

dz =
0, 0, 50, 100, 50, 1,
0, 0, 50.0008980607395, 100.001016436064, 47.7364553552973, 1.00053608029592,
0, 0, 50.0000086311325, 100.000102219634, 47.7364088557938, 1.00030413305374,
0, 0, 50.0001889261175, 100.000163259489, 47.7364117489861, 1.0002832508735,
0, 0, 50.0000055516363, 100.000162982956, 47.736412622015, 1.00044724712438,
900.001395164631, 450.000766659147, 99.9983202606676, 99.9924801598264, 54.9264866944315, 1.00006563744724,
900.002145639133, 450.002999281262, 100.001327120773, 100.001968639764, 54.9424943328129, 1.00021997830258,