Merge pull request seahorce-scidac#237 from hklion/setup_docs_fillbou…

…ndary

add a paragraph to ProblemSetup about FillBoundary

Docs/sphinx_doc/ProblemSetup.rst

@@ -17,3 +17,5 @@ Each problem setup with a different initial e.g. temperature profile and bathyme
 * ``amrvis.defaults`` (for visualization with AMRVis)
 
 The file ``prob.cpp`` contains a number of functions that set the initial temperature profile, as well as surface stress, mixing coefficients, and bathymetry. New problem-specific input parameters can be defined by adding a variable to the ``ProbParm`` class in ``prob.H``, and reading in the value in ``amrex_probinit`` in ``prob.cpp``. See the AMReX documentation on `ParmParse <https://amrex-codes.github.io/amrex/docs_html/Basics.html#parmparse>`_ for how to add parameters.
+
+REMORA will call ``FillBoundary`` on the relevant variables after the functions in ``prob.cpp`` are called. This will fill the values in the `ghost cells <https://amrex-codes.github.io/amrex/docs_html/Basics.html#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.