Problem Setup
Each problem setup with a different initial e.g. temperature profile and bathymetry has its own subdirectory within Exec.
To create a new problem, create a new subdirectory and copy the following files from another subdirectory:
inputsamrvis.defaults(for visualization with AMRVis)
You may also copy the Exec/BlankProblem directory.
The files in Source/Prob contain a number of functions that set initial conditions (temperature, salinity, scalar, velocities),
as well as other variables like bathymetry, Coriolis forcing, and wind speed). Which of these routines is called is controlled
by Exec/REMORA_prob.cpp; if you introduce a new type of problem you will need to edit Exec/REMORA_prob.cpp and potentially add
new files in Source/Prob.
New problem-specific input parameters can be defined by reading in additional values with the ParmParse prefix remora.prob.
See the AMReX documentation on ParmParse for how to add parameters.
REMORA will call FillBoundary on the relevant variables after the functions called from REMORA_Prob.cpp.
This will fill the values in the ghost cells at interior grid-grid and periodic boundaries.
However, it will not do so at interior grid-grid boundaries that fall on non-periodic domain boundaries.
This is primarily a concern for variables such as bathymetry, which are not specified by boundary conditions, but still have well-defined values at boundaries.
By default, these functions will be evaluated at level 0 and interpolated to higher levels as needed for mesh refinement. If remora.hires_grid_level > 0, the analytic function for bathymetry is evaluated on level remora.hires_grid_level. Bathymetry on higher levels is interpoalted as usual. Bathymetry on lower levels is calculated by averaging down.