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update docs to better reflect bcs and nudging #301

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update docs to better reflect bcs and nudging #301

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25 changes: 24 additions & 1 deletion Docs/sphinx_doc/BoundaryConditions.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ Boundary types for per-side or per-variable specification
+-------------+-----------+--------------------+---------------------+--------------------+---------------------+--------------------+--------------------+
| symmetry | N/A | reflect_odd | reflect_even | reflect_odd | reflect_even | reflect_even | reflect_even |
+-------------+-----------+--------------------+---------------------+--------------------+---------------------+--------------------+--------------------+
| clamped* | N/A | clamped | clamped | clamped | clamped | clamped | clamped |
| clamped* | Cla | clamped | clamped | clamped | clamped | clamped | clamped |
+-------------+-----------+--------------------+---------------------+--------------------+---------------------+--------------------+--------------------+

Boundary types for per-variable specification ONLY
Expand Down Expand Up @@ -191,3 +191,26 @@ It is important to note that external Dirichlet boundary data should be specifie
as the value on the face of the cell bounding the domain, even for cell-centered
state data.

.. _sec:nudging-options:

Nudging options
---------------

When using ``orlanski_nudg``, the nudging strength is specified by input parameters. Climatology nudging
has not yet been implemented.

+-------------------+-------------------------+-------------------+---------------+
| Parameter | Definition | Acceptable Values | Default |
+===================+=========================+===================+===============+
| **remora.tnudg** | Nudging timescale for | Positive real | 0.0 |
| | tracers in days | | |
+-------------------+-------------------------+-------------------+---------------+
| **remora.m3nudg** | Nudging timescale for | Positive real | 0.0 |
| | 3D momentum in days | | |
+-------------------+-------------------------+-------------------+---------------+
| **remora.obcfac** | Ratio between inflow | Positive real | 0.0 |
| | and outflow | | |
| | boundary conditions | | |
+-------------------+-------------------------+-------------------+---------------+


37 changes: 4 additions & 33 deletions Docs/sphinx_doc/Inputs.rst
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Expand Up @@ -63,44 +63,15 @@ Examples of Usage
Domain Boundary Conditions
==========================

.. _list-of-parameters-1:

List of Parameters
------------------

+---------------+---------------------------------+-------------------+-----------------------------+
| Parameter | Definition | Acceptable Values | Default |
+===============+=================================+===================+=============================+
| **xlo.type** | boundary type of xlo face | see below | must be set if not periodic |
+---------------+---------------------------------+-------------------+-----------------------------+
| **xhi.type** | boundary type of xhi face | see below | must be set if not periodic |
+---------------+---------------------------------+-------------------+-----------------------------+
| **ylo.type** | boundary type of ylo face | see below | must be set if not periodic |
+---------------+---------------------------------+-------------------+-----------------------------+
| **yhi.type** | boundary type of yhi face | see below | must be set if not periodic |
+---------------+---------------------------------+-------------------+-----------------------------+
| **zlo.type** | boundary type of zlo face | slipwall | must be set |
+---------------+---------------------------------+-------------------+-----------------------------+
| **zhi.type** | boundary type of zhi face | slipwall | must be set |
+---------------+---------------------------------+-------------------+-----------------------------+

Currently available type of boundary conditions are
``inflow``, ``outflow``, ``slipwall``, ``noslipwall``, or ``symmetry``
(Spelling of the type matters; capitalization does not.) Z-boundaries are always treated as the seafloor
and surface, and boundary type selection here will not affect program behavior. Domain boundary types
are specified on a per-side basis, rather than a per-variable basis. Inflow, outflow, etc

Usage examples can be found :ref:`here<sec:domainBCs>`.
Instructions for how to specify domain boundary conditions, with usage examples can be found in :ref:`Domain Boundary Conditions`<sec:domainBCs>`.

.. _icbc-parameters:

Imposing Boundary and Initial Conditions from NetCDF File
=========================================================

Grid, initial, and time-dependent boundary data can be specified using NetCDF files, as in ROMS. REMORA expects files in the same format as ROMS.
Currently, if one of these are specified in a file, they all must be. Boundary conditions are currently applied as Dirichelet conditions, as in the ROMS ``clamped`` boundary type. More sophisticated boundary conditions like nudging are a work in progress.

The ``outflow`` option must be selected for ``xlo.type``, ``xhi.type``, ``ylo.type``, and ``yhi.type`` to read the boundary data.
Grid, initial, and time-dependent boundary data can be specified using NetCDF files, as in ROMS. REMORA expects files in the same format as ROMS, in NetCDF classic format (32- or 64-bit).
Currently, if one of these are specified in a file, they all must be. Boundary condition options with NetCDF boundary data are equivalent to ROMS clamped, Chapman-Flather, and Orlanski + Nudging boundary conditions. Options and examples can be found in the section on :ref:`Domain Boundary Conditions`<sec:domainBCs>`.

List of Parameters
------------------
Expand All @@ -111,7 +82,7 @@ List of Parameters
+===========================+===============================+=============+==========================+
| **remora.ic_bc_type** | read initial, grid, and | | |
| | boundary data from NetCDF | true/false | false |
| | files | | is true |
| | files | | |
+---------------------------+-------------------------------+-------------+--------------------------+
| **remora.nc_init_file_0** | initial data NetCDF file name | string | must be set |
| | | | if ``remora.ic_bc_type`` |
Expand Down
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