Update particles_run call to allow accurate particle advection using … #785
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…u, v or uh, vh
The drifters package is able to run in 2 different modes: one where the particles are advected using u and v, and one where they are advected using uh and vh. When u and v are used (i.e. the drifters are advected using the resolved velocities only, with no sub-grd component), the particles package needs the layer thickness that is consistent with these velocities, so particles_run needs to be called before any subgrid scale parameterizations are applied. This was not implemented correctly in my last PR, and is corrected here.
The particles package also needs the correct timestep for particle advection. This is added here.