Utilities

We provide some utilities that may be useful.

Time step adaptation

We have added a few additional utilities which extend the capabilities of Oceananigans' time step wizard. For column models where there is no water velocity we have added functions to calculate the advection timescale from the biogeochemical model defined sinking velocities. This could be used by:

wizard = TimeStepWizard(cfl = 0.2, diffusive_cfl = 0.2, max_change = 2.0, min_change = 0.5, cell_advection_timescale = column_advection_timescale)
simulation.callbacks[:wizard] = Callback(wizard, IterationInterval(10))

Finally, sinking may be more limiting than the normal advective CFL conditions so, we have an additional cell advection timescale defined for 3D models:

wizard = TimeStepWizard(cfl = 0.6, diffusive_cfl = 0.5, max_change = 1.5, min_change = 0., cell_advection_timescale = sinking_advection_timescale)
simulation.callbacks[:wizard] = Callback(wizard, IterationInterval(10))

Negative tracer detection

As a temporary measure we have implemented a callback to either detect negative tracers and either scale a conserved group, force them back to zero, or throw an error. Please see the numerical implementations' page for details. This can be set up by:

negativity_protection = ScaleNegativeTracers((:P, :Z, :N))
biogeochemistry = Biogeochemistry(...; modifiers = negativity_protection)

You may also pass a scale factor for each component (e.g. in case they have different redfield ratios):

negativity_protection = ScaleNegativeTracers((:P, :Z, :N); scalefactors = (1, 1, 2))
biogeochemistry = Biogeochemistry(...; modifiers = negativity_protection)

Here you should carefully consider which tracers form a conserved group (if at all). If some tracers are in more than one group (e.g. plankton contain both nitrogen and carbon), give all of the groups to the same ScaleNegativeTracers so that they are all conserved:

negativity_protection = ScaleNegativeTracers((nitrogen = (N = 1, P = 1, Z = 1),
                                              carbon = (DIC = 1, P = 6.56, Z = 6.56)))
biogeochemistry = Biogeochemistry(...; modifiers = negativity_protection)

Separate ScaleNegativeTracers modifiers are applied one after the other, so each would change the totals of the others. The scale_negatives = true option of the models does this for the groups given by OceanBioME.conserved_tracers(biogeochemistry). Alternatively, force to zero by:

negativity_protection = ZeroNegativeTracers()
biogeochemistry = Biogeochemistry(...; modifiers = negativity_protection)

The latter optionally takes a named tuple of parameters that may include exclude, which can be a tuple of tracer names (Symbols) which are allowed to be negative.