Box I.9 MATLAB plotting scripts
A series of MATLAB scrips are provided for basic spatial visualization of the results. These are;
plot2_biogem_i.m - plots a vertical meridional slice through the ocean, i.e., all cells have the same 'i' (longitudinal) coordinate value.
plot2_biogem_i_AVE.m - based on plot2_biogem_i.m but plots a slice constructed by averaging longitudinally over a supplied mask. Thus, if the mask is of the entire ocean (mask_worbe2_ALL.dat), the result is a global meridional cross-sectional mean. If the mask is just of a single basin such as the Atlantic (mask_worbe2_Atlantic.dat), the result is the Atlantic meridional cross-sectional mean. Masks can also be constructed that are only a single cell 'wide' longitunically, but which take a meandering path following an ocean transect (e.g., mask_worbe2_WOCE_P16.dat). The trivial usage would be to contruct a mask consisting of a vertical slice with equal 'i' - the result is then the same as plot2_biogem_i.m above. The mask is a 2D surface of model grid points. A value of '1' represent a vertical column of ocean cells to include, whereas a value '0' will exclude all cells in the water column at that particular grid point.
plot2_biogem_k.m - plots a horizontal slice through the ocean, i.e., all cells having the same 'k' (vertical) coordinate. Note that for the 8-layer version of c/b/c-goldstein, legal values for k range from 1 through 8, with k=8 representing the uppermost (surface layer).
plot2_biogem_k_INT.m - based on plot2_biogem_k.m but calculates the integrated water-column inventory to produce a 2D map. For bulk ocean tracers, the units are mol at each model grid point. Because the grid is an equal-area projection, it is simple to re-scale the plot to give inventory as mol m-2 (or uptake in mol m-2 yr-1). Note that you must use the *_ocnTOT_<ocn>.res data fields in the calculation (Box II.1).
plot2_biogem_opsi.m - plots the overturning streamfunction for Atlantic basin, Pacific basin, and global ocean (so don't be suprised when you get 3 figure windows). Units are Sv (unless you re-scale). Note that this particular script has no 'advanced' options (see Box II.6).
plot2_sedgem.m - plots the sediment surface. Similar in usage to plot2_biogem_i.m.