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8679f9097b Jeff* .. _sub_phys_pkg_obcs:
                 
                 OBCS: Open boundary conditions for regional modeling
                 ----------------------------------------------------
                 
bd45a18e71 Mart* Authors:
025afa4065 Jeff* Alistair Adcroft, Patrick Heimbach, Samar Katiwala, Martin Losch
8679f9097b Jeff* 
                 .. _ssub_pkg_obcs_intro:
                 
                 Introduction
                 ++++++++++++
                 
3ceb1ce0a9 Jeff* The OBCS-package (:filelink:`pkg/obcs`) is fundamental to regional ocean modeling with the
bd45a18e71 Mart* MITgcm, but there are so many details to be considered in regional
                 ocean modeling that this package cannot accommodate all imaginable and
                 possible options. Therefore, for a regional simulation with very
                 particular details it is recommended to familiarize oneself not only
3ceb1ce0a9 Jeff* with the compile-time and run-time options of this package, but also with
bd45a18e71 Mart* the code itself. In many cases it will be necessary to adapt the
                 obcs-code (in particular :filelink:`S/R OBCS_CALC
                 <pkg/obcs/obcs_calc.F>`) to the application in question; in these cases
3ceb1ce0a9 Jeff* :filelink:`pkg/obcs` (together with the :filelink:`pkg/rbcs`, see
bd45a18e71 Mart* :numref:`sub_phys_pkg_rbcs`) is a very useful infrastructure for
                 implementing special regional models.
8679f9097b Jeff* 
                 .. _ssub_pkg_obcs_config_compiling:
                 
                 OBCS configuration and compiling
                 ++++++++++++++++++++++++++++++++
                 
3ceb1ce0a9 Jeff* As with all MITgcm packages, OBCS can be turned on or off
                 at compile-time
8679f9097b Jeff* 
bf89a37abc Phob*  - using the :code:`packages.conf` file by adding :code:`obcs` to it
8679f9097b Jeff*  - or using :code:`genmake2` adding :code:`-enable=obcs` or :code:`-disable=obcs` switches
                  - *Required packages and CPP options:*
                 
025afa4065 Jeff*    - Two alternatives are available for prescribing open boundary values, which differ in the way how OB's are treated in time:
8679f9097b Jeff* 
3ceb1ce0a9 Jeff*      - Simple time-management (e.g., constant in time, or cyclic with fixed frequency) is provided through :filelink:`S/R OBCS_FIELDS_LOAD <pkg/obcs/obcs_fields_load.F>`
                      - More sophisticated 'real-time' (i.e. calendar time) management is available through :filelink:`S/R OBCS_PRESCRIBE_READ <pkg/obcs/obcs_prescribe_read.F>`
                    - The latter case requires packages :filelink:`pkg/cal` and :filelink:`pkg/exf` to be enabled.
8679f9097b Jeff* 
3ceb1ce0a9 Jeff* Parts of the OBCS code can be enabled or disabled at compile-time
8679f9097b Jeff* via CPP preprocessor flags. These options are set in
0d16355195 Oliv* :filelink:`OBCS_OPTIONS.h <pkg/obcs/OBCS_OPTIONS.h>`.
                 :numref:`tab_phys_pkg_obcs_cpp_opts` summarizes these options.
8679f9097b Jeff* 
                 
bf89a37abc Phob* .. tabularcolumns:: |\Y{.475}|\Y{.1}|\Y{.45}|
8679f9097b Jeff* 
0d16355195 Oliv* .. table:: CPP flags for the obcs package
                    :name: tab_phys_pkg_obcs_cpp_opts
                 
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | CPP option               | Default | Description                                                                                              |
                    +==========================+=========+==========================================================================================================+
                    | ALLOW_OBCS_NORTH         | #define | enable Northern OB                                                                                       |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_SOUTH         | #define | enable Southern OB                                                                                       |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_EAST          | #define | enable Eastern OB                                                                                        |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_WEST          | #define | enable Western OB                                                                                        |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_PRESCRIBE     | #define | enable code for prescribing OB's                                                                         |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_SPONGE        | #undef  | enable sponge layer code                                                                                 |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_BALANCE       | #define | enable code for balancing transports through OB's                                                        |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_ORLANSKI           | #define | enable Orlanski radiation conditions at OB's                                                             |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_STEVENS       | #undef  | enable Stevens (1990) boundary conditions at OB's (currently NOT implemented for ptracers)               |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_SEAICE_SPONGE | #undef  | Include hooks to sponge layer treatment of pkg/seaice variables                                          |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
                    | ALLOW_OBCS_TIDES         | #undef  | Add tidal contributions to normal OB flow (At the moment tidal forcing is applied only to "normal" flow) |
                    +--------------------------+---------+----------------------------------------------------------------------------------------------------------+
8679f9097b Jeff* 
                 
                 .. _pkg_obcs_runtime:
                 
                 Run-time parameters
                 +++++++++++++++++++
                 
                 
3ceb1ce0a9 Jeff* Run-time parameters are set in files :code:`data.pkg`, :code:`data.obcs`, and
                 :code:`data.exf` if 'real-time' prescription is requested
                 (i.e., :filelink:`pkg/exf` enabled). These parameter files are
                 read in S/Rs :filelink:`PACKAGES_READPARMS <model/src/packages_readparms.F>`,
                 :filelink:`OBCS_READPARMS <pkg/obcs/obcs_readparms.F>`, and
                 :filelink:`EXF_READPARMS <pkg/exf/exf_readparms.F>`, respectively.
                 Run-time parameters may be broken into three categories:
bd45a18e71 Mart* 
bf89a37abc Phob*  #. switching on/off the package at runtime
                  #. OBCS package flags and parameters
                  #. additional timing flags in :code:`data.exf` if selected.
8679f9097b Jeff* 
                 
                 Enabling the package
                 ####################
                 
                 The OBCS package is switched on at runtime by setting
bf89a37abc Phob* :varlink:`useOBCS` = :code:`.TRUE.` in :code:`data.pkg`.
8679f9097b Jeff* 
                 Package flags and parameters
                 ############################
                 
0d16355195 Oliv* :numref:`tab_phys_pkg_obcs_runtime_flags` summarizes the
bf89a37abc Phob* runtime flags that are set in :code:`data.obcs` and
8679f9097b Jeff* their default values.
                 
                 
654ec02869 Phob* .. tabularcolumns:: |\X{1}{3}|c|\X{1}{2}|
8679f9097b Jeff* 
0d16355195 Oliv* .. table:: OBCS runtime parameters
                    :name: tab_phys_pkg_obcs_runtime_flags
                 
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    |         Flag/parameter         |    default    |                                             Description                                             |
                    +================================+===============+=====================================================================================================+
                    | :varlink:`OB_Jnorth`           | 0             | Nx-vector of J-indices (w.r.t. Ny) of Northern OB at each I-position (w.r.t. Nx)                    |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`OB_Jsouth`           | 0             | Nx-vector of J-indices (w.r.t. Ny) of Southern OB at each I-position (w.r.t. Nx)                    |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`OB_Ieast`            | 0             | Ny-vector of I-indices (w.r.t. Nx) of Eastern OB at each J-position (w.r.t. Ny)                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`OB_Iwest`            | 0             | Ny-vector of I-indices (w.r.t. Nx) of Western OB at each J-position (w.r.t. Ny)                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useOBCSprescribe`    | FALSE         |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useOBCSsponge`       | FALSE         |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useOBCSbalance`      | FALSE         |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`OBCS_balanceFacN`,   | 1             | Factor(s) determining the details of the balancing code                                             |
                    | :varlink:`OBCS_balanceFacS`,   |               |                                                                                                     |
                    | :varlink:`OBCS_balanceFacE`,   |               |                                                                                                     |
                    | :varlink:`OBCS_balanceFacW`    |               |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`OBCSbalanceSurf`     | FALSE         | include surface mass flux in balance                                                                |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useOrlanskiNorth`,   | FALSE         | Turn on Orlanski boundary conditions for individual boundary.                                       |
                    | :varlink:`useOrlanskiSouth`,   |               |                                                                                                     |
                    | :varlink:`useOrlanskiEast`,    |               |                                                                                                     |
                    | :varlink:`useOrlanskiWest`     |               |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useStevensNorth`,    | FALSE         | Turn on Stevens boundary conditions for individual boundary                                         |
                    | :varlink:`useStevensSouth`,    |               |                                                                                                     |
                    | :varlink:`useStevensEast`,     |               |                                                                                                     |
                    | :varlink:`useStevensWest`      |               |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | OB\ **Xy**\ File               | :kbd:`' '`    | File name of OB field:                                                                              |
                    |                                |               |                                                                                                     |
                    |                                |               | **X**: **N**\ (orth), **S**\ (outh), **E**\ (ast), **W**\(est)                                      |
                    |                                |               |                                                                                                     |
                    |                                |               | **y**: **t**\(emperature), **s**\ (salinity), **eta** (sea surface height),                         |
                    |                                |               | **u**\ (-velocity),  **v**\(-velocity), **w**\ (-velocity),                                         |
                    |                                |               | **a** (seaice area), **h** (sea ice thickness), **sn** (snow thickness), **sl** (sea ice salinity ) |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | **Orlanski Parameters**        | *OBCS_PARM02* |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`cvelTimeScale`       | 2000.0        | Averaging period for phase speed (seconds)                                                          |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`CMAX`                | 0.45          | Maximum allowable phase speed-CFL for AB-II (m/s)                                                   |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`CFIX`                | 0.8           | Fixed boundary phase speed (m/s)                                                                    |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useFixedCEast`       | FALSE         |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useFixedCWest`       | FALSE         |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | **Sponge layer parameters**    | *OBCS_PARM03* |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`spongeThickness`     | 0             | sponge layer thickness (in grid points)                                                             |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`Urelaxobcsinner`     | 0.0           | relaxation time scale at the innermost sponge layer point of a meridional OB (s)                    |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`Vrelaxobcsinner`     | 0.0           | relaxation time scale at the innermost sponge layer point of a zonal OB (s)                         |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`Urelaxobcsbound`     | 0.0           | relaxation time scale at the outermost sponge layer point of a meridional OB (s)                    |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`Vrelaxobcsbound`     | 0.0           | relaxation time scale at the outermost sponge layer point of a zonal OB (s)                         |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | **Stevens parameters**         | *OBCS_PARM04* |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`TrelaxStevens`       | 0             | Relaxation time scale for temperature/salinity (s)                                                  |
                    | :varlink:`SrelaxStevens`       |               |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useStevensPhaseVel`  | TRUE          |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
                    | :varlink:`useStevensAdvection` | TRUE          |                                                                                                     |
                    +--------------------------------+---------------+-----------------------------------------------------------------------------------------------------+
8679f9097b Jeff* 
                 
                 .. _ssub_phys_pkg_obcs_defining_open_boundaries:
                 
                 Defining open boundary positions
                 ++++++++++++++++++++++++++++++++
                 
bd45a18e71 Mart* There are up to four open boundaries (OBs): Northern, Southern, Eastern, and
8679f9097b Jeff* Western. All OB locations are specified by their absolute meridional
025afa4065 Jeff* (Northern/Southern) or zonal (Eastern/Western) indices. Thus, for each
bf89a37abc Phob* zonal position :math:`i=1\ldots N_x` a meridional index :math:`j`
025afa4065 Jeff* specifies the Northern/Southern OB position, and for each meridional
bf89a37abc Phob* position :math:`j=1\ldots N_y` a zonal index :math:`i` specifies the
8679f9097b Jeff* Eastern/Western OB position. For Northern/Southern OB this defines an
bd45a18e71 Mart* :math:`N_x`-dimensional “row” array :varlink:`OB_Jnorth`\(Nx) /
                 :varlink:`OB_Jsouth`\ (Nx) and an :math:`N_y`-dimenisonal “column”
                 array :varlink:`OB_Ieast`\(Ny) / :varlink:`OB_Iwest`\(Ny). Positions
8679f9097b Jeff* determined in this way allows Northern/Southern OBs to be at variable
bf89a37abc Phob* :math:`j` (or :math:`y`) positions and Eastern/Western OBs at variable
                 :math:`i` (or :math:`x`) positions. Here indices refer to tracer points
3ceb1ce0a9 Jeff* on the C-grid. A zero (0) element in ``OB_I...`` / ``OB_J...`` means there is no corresponding OB in that column/row.
                 By default all elements in ``OB_I...`` / ``OB_J...`` are zero. For a Northern/Southern OB, the OB V-point is to the South/North.
                 For an Eastern/Western OB, the OB U-point is to the West/East. For example
bf89a37abc Phob* 
                 
                 :code:`OB_Jnorth(3)=34`  means that:
bd45a18e71 Mart*   - :code:`T(3,34)`  is a an OB point
025afa4065 Jeff*   - :code:`U(3,34)`  is a an OB point
                   - :code:`V(3,34)`  is a an OB point
bd45a18e71 Mart* :code:`OB_Jsouth(3)=1`  means that:
                   - :code:`T(3,1)`  is a an OB point
                   - :code:`U(3,1)`  is a an OB point
                   - :code:`V(3,2)`  is a an OB point
                 :code:`OB_Ieast(10)=69`   means that:
                   - :code:`T(69,10)`  is a an OB point
                   - :code:`U(69,10)`  is a an OB point
                   - :code:`V(69,10)`  is a an OB point
                 :code:`OB_Iwest(10)=1`   means that:
                   - :code:`T(1,10)`  is a an OB point
                   - :code:`U(2,10)`  is a an OB point
025afa4065 Jeff*   - :code:`V(1,10)`  is a an OB point
bf89a37abc Phob* 
                 
3ceb1ce0a9 Jeff* For convenience, negative values for :varlink:`OB_Jnorth` / :varlink:`OB_Ieast` refer to points relative to the
                 Northern/Eastern edges of the model, e.g. ``OB_Jnorth(3)=-1`` means that the point ``(3,Ny)`` is a northern OB
                 and ``OB_Ieast(3)=-5`` means that the point ``(3,Nx-5)`` is an eastern OB.
bd45a18e71 Mart* 
8679f9097b Jeff* 
bd45a18e71 Mart* Simple examples
                 ###############
8679f9097b Jeff* 
3ceb1ce0a9 Jeff* For a model grid with :math:`N_x \times N_y = 120 \times 144` horizontal grid points with four open boundaries
                 along the four edges of the domain, the simplest way of specifying the boundary points:
8679f9097b Jeff* 
                 ::
                 
025afa4065 Jeff*       OB_Ieast = 144*-1,
                     # or OB_Ieast = 144*120,
                       OB_Iwest = 144*1,
                       OB_Jnorth = 120*-1,
                     # or OB_Jnorth = 120*144,
                       OB_Jsouth = 120*1,
8679f9097b Jeff* 
3ceb1ce0a9 Jeff* When the boundaries are in single rows or columns as in the above example, the same can be achieved with
                 the convenient parameters :varlink:`OB_singleJnorth` / :varlink:`OB_singleJsouth` / :varlink:`OB_singleIeast` / :varlink:`OB_singleIwest`:
bd45a18e71 Mart* 
                 ::
                 
                       OB_singleIeast  = -1,
                       OB_singleIwest  =  1,
                       OB_singleJnorth = -1,
                       OB_singleJsouth =  1,
                 
bf89a37abc Phob* If only the first 50 grid points of the southern boundary are
8679f9097b Jeff* boundary points:
                 
                 ::
                 
025afa4065 Jeff*       OB_Jsouth(1:50) = 50*1,
8679f9097b Jeff* 
bd45a18e71 Mart* A more complex example
                 ######################
aec20833e6 dram* 
bd45a18e71 Mart* Open boundaries are not restricted to single rows or columns. Each OB
                 can be distributed in different rows and columns resulting
                 in OBs consisting of the combination of different types of
3ceb1ce0a9 Jeff* open boundaries (i.e., N, S, E and W). :numref:`fig_obcsexample` displays
bd45a18e71 Mart* such an OB located on the left-bottom corner of a domain.
                 Note there are five boundary points defined by southern and
                 western boundaries. In particular, there are five southern
aec20833e6 dram* boundary (blue lines) and two western boundaries points (red lines).
bd45a18e71 Mart* For the boundary displayed in :numref:`fig_obcsexample` and the
                 same dimensions as in the previous example (i.e. :math:`120 \times 144` grid points),
aec20833e6 dram* the namelist looks like this:
                 
                 ::
                 
bd45a18e71 Mart*       OB_Iwest  = 1*0,1*5,142*0,
                       OB_Jsouth = 2*3,3*2,115*0,
aec20833e6 dram* 
                 .. figure:: figs/obcsexample.*
                     :width: 70%
                     :align: center
                     :alt: Example boundary
                     :name: fig_obcsexample
                 
bd45a18e71 Mart*     Example boundary with more than one row. The dark grey, light grey,
                     and white boxes are points outside the domain, OB points, and ocean points,
aec20833e6 dram*     respectively. The black dots mark the OB index to write into the namelist.
                 
7e0367ac08 Jeff* For an even more complicated open boundary geometry, e.g., delimiting a concave interior domain
                 (:varlink:`OB_Ieast` :math:`\leq` :varlink:`OB_Iwest`), one might need to also specify the
                 interior domain through an additional input file :varlink:`insideOBmaskFile` for the interior
                 mask (:math:`=1` inside, :math:`=0` outside).
                 
bd45a18e71 Mart* .. _ssub_phys_pkg_obcs_equations:
                 
8679f9097b Jeff* Equations and key routines
                 ++++++++++++++++++++++++++
                 
bf89a37abc Phob* :filelink:`OBCS\_READPARMS <pkg/obcs/obcs_readparms.F>`:
                 ########################################################
8679f9097b Jeff* 
025afa4065 Jeff* Set OB positions through arrays OB\_Jnorth(Nx), OB\_Jsouth(Nx),
                 OB\_Ieast(Ny), OB\_Iwest(Ny) and runtime flags (see Table
0d16355195 Oliv* :numref:`tab_phys_pkg_obcs_runtime_flags`).
8679f9097b Jeff* 
bf89a37abc Phob* :filelink:`OBCS\_CALC <pkg/obcs/obcs_calc.F>`:
                 ##############################################
8679f9097b Jeff* 
                 Top-level routine for filling values to be applied at OB for
025afa4065 Jeff* :math:`T,S,U,V,\eta` into corresponding “slice” arrays :math:`(x,z)`
bd45a18e71 Mart* :math:`(y,z)` for each OB: ``OB[N/S/E/W][t/s/u/v]``; e.g. for the
                 salinity array at the Southern OB, the array name is
                 :varlink:`OBSs`. Values filled are either
8679f9097b Jeff* 
025afa4065 Jeff* -  constant vertical :math:`T,S` profiles as specified in file data
bf380c1040 Mart*    (:varlink:`tRef`\ (Nr), :varlink:`sRef`\ (Nr)) with zero velocities
                    :math:`U,V`
8679f9097b Jeff* 
025afa4065 Jeff* -  :math:`T,S,U,V` values determined via Orlanski radiation conditions
bf89a37abc Phob*    (see below)
8679f9097b Jeff* 
                 -  prescribed time-constant or time-varying fields (see below).
                 
bd45a18e71 Mart* -  prescribed boundary fields to compute Stevens boundary
8679f9097b Jeff*    conditions.
                 
                 
bf89a37abc Phob* :filelink:`ORLANSKI <pkg/obcs/ORLANSKI.h>`:
                 ###########################################
8679f9097b Jeff* 
bf380c1040 Mart* Orlanski radiation conditions :cite:`orl:76` examples can be found in
c1f7a487c0 Jeff* example configurations :filelink:`verification/dome` and
                 :filelink:`verification/tutorial_plume_on_slope`
                 (as described in detail in :numref:`tutorial_plume_on_slope`).
8679f9097b Jeff* 
                 
bf89a37abc Phob* :filelink:`OBCS\_PRESCRIBE\_READ <pkg/obcs/obcs\_prescibe\_read.F>`:
                 ####################################################################
8679f9097b Jeff* 
                 
bd45a18e71 Mart* When :varlink:`useOBCSprescribe` = ``.TRUE.`` the model tries to read
025afa4065 Jeff* temperature, salinity, u- and v-velocities from files specified in the
bd45a18e71 Mart* runtime parameters ``OB[N/S/E/W][t/s/u/v]File``. These files are
025afa4065 Jeff* the usual IEEE, big-endian files with dimensions of a section along an
8679f9097b Jeff* open boundary:
                 
                 -  For North/South boundary files the dimensions are
025afa4065 Jeff*    :math:`(N_x\times N_r\times\mbox{time levels})`, for East/West
8679f9097b Jeff*    boundary files the dimensions are
                    :math:`(N_y\times N_r\times\mbox{time levels})`.
                 
                 -  If a non-linear free surface is used
025afa4065 Jeff*    (:numref:`nonlinear-freesurface`), additional files
3ceb1ce0a9 Jeff*    ``OB[N/S/E/W]etaFile`` for the sea surface height :math:`\eta` with
8679f9097b Jeff*    dimension :math:`(N_{x/y}\times\mbox{time levels})` may be specified.
                 
                 - If non-hydrostatic dynamics are used
025afa4065 Jeff*   (:numref:`non-hydrostatic`), additional files
3ceb1ce0a9 Jeff*   ``OB[N/S/E/W]wFile`` for the vertical velocity :math:`w` with
8679f9097b Jeff*   dimensions :math:`(N_{x/y}\times N_r\times\mbox{time levels})` can be
                   specified.
                 
bd45a18e71 Mart* - If :varlink:`useSEAICE` = ``.TRUE.`` then additional files
                   ``OB[N/S/E/W][a,h,sl,sn,uice,vice]`` for sea ice area, thickness
                   (:varlink:`HEFF`), seaice salinity, snow and ice velocities
8679f9097b Jeff*   :math:`(N_{x/y}\times\mbox{time levels})` can be specified.
                 
3ceb1ce0a9 Jeff* As in :filelink:`external_fields_load.F
                 <model/src/external_fields_load.F>` or as done in :filelink:`pkg/exf`,
                 the code reads two time levels for each
bd45a18e71 Mart* variable, e.g., :varlink:`OBNu0` and :varlink:`OBNu1`, and
                 interpolates linearly between these time levels to obtain the value
3ceb1ce0a9 Jeff* :varlink:`OBNu` at the current model time (step). When
                 :filelink:`pkg/exf` is used, the time levels are
bd45a18e71 Mart* controlled for each boundary separately in the same way as the
3ceb1ce0a9 Jeff* :filelink:`pkg/exf` fields in ``data.exf``, namelist
                 ``EXF_NML_OBCS``. The run-time flags follow the above naming
bd45a18e71 Mart* conventions, e.g., for the western boundary the corresponding flags
3ceb1ce0a9 Jeff* are :varlink:`OBCSWstartdate1`, :varlink:`OBCSWstartdate2` and
                 :varlink:`OBCSWperiod`. Sea-ice boundary values are controlled
bd45a18e71 Mart* separately with :varlink:`siobWstartdate1`, :varlink:`siobWstartdate2`
3ceb1ce0a9 Jeff* and :varlink:`siobWperiod`.  When :filelink:`pkg/exf`
bd45a18e71 Mart* is not used the time levels are controlled by the runtime flags
                 :varlink:`externForcingPeriod` and :varlink:`externForcingCycle` in
                 ``data``; see :filelink:`verification/exp4/input/data` for an example.
8679f9097b Jeff* 
                 
bf89a37abc Phob* :filelink:`OBCS\_CALC\_STEVENS <pkg/obcs/obcs_calc_stevens.F>`:
                 ###############################################################
8679f9097b Jeff* 
                 The boundary conditions following :cite:`stevens:90` require the
                 vertically averaged normal velocity (originally specified as a stream
                 function along the open boundary) :math:`\bar{u}_{ob}` and the tracer fields
                 :math:`\chi_{ob}` (note: passive tracers are currently not implemented and
bf89a37abc Phob* the code stops when package :ref:`ptracers <sub_phys_pkg_ptracers>` is used together with this
                 option). Currently the code vertically averages the normal velocity
025afa4065 Jeff* as specified in :code:`OB[E,W]u` or :code:`OB[N,S]v`. From these
8679f9097b Jeff* prescribed values the code computes the boundary values for the next
025afa4065 Jeff* timestep :math:`n+1` as follows (as an example, we use the notation for an
8679f9097b Jeff* eastern or western boundary):
                 
                 
025afa4065 Jeff* -  :math:`u^{n+1}(y,z) = \bar{u}_{ob}(y) + (u')^{n}(y,z)` where
8679f9097b Jeff*    :math:`(u')^{n}` is the deviation from the vertically averaged
                    velocity at timestep :math:`n` on the boundary. :math:`(u')^{n}` is
                    computed in the previous time step :math:`n` from the intermediate
025afa4065 Jeff*    velocity :math:`u^*` prior to the correction step (see
3ceb1ce0a9 Jeff*    :numref:`time_stepping` equation :eq:`ustar-backward-free-surface`). (This velocity is not
025afa4065 Jeff*    available at the beginning of the next time step :math:`n+1`, when
3ceb1ce0a9 Jeff*    S/Rs :filelink:`OBCS_CALC <pkg/obcs/obcs_calc.F>` and :filelink:`OBCS_CALC_STEVENS <pkg/obcs/obcs_calc_stevens.F>`
                    are called, therefore it needs to
                    be saved in :filelink:`S/R DYNAMICS <model/src/dynamics.F>` by
                    calling :filelink:`S/R OBCS_SAVE_UV_N <pkg/obcs/obcs_save_uv_n.F>` and also
8679f9097b Jeff*    stored in a separate restart files
                    ``pickup_stevens[N/S/E/W].${iteration}.data``)
                 
025afa4065 Jeff* -  If :math:`u^{n+1}` is directed into the model domain, the boudary
8679f9097b Jeff*    value for tracer :math:`\chi` is restored to the prescribed values:
                 
                    .. math::
                 
bd45a18e71 Mart*       \chi^{n+1} = \chi^{n} + \frac{\Delta{t}}{\tau_\chi} (\chi_{ob} -
bf89a37abc Phob*         \chi^{n})
8679f9097b Jeff* 
bd45a18e71 Mart*    where :math:`\tau_\chi` is the relaxation time scale (either
3ceb1ce0a9 Jeff*    :varlink:`TrelaxStevens` or :varlink:`SrelaxStevens`). The new
bd45a18e71 Mart*    :math:`\chi^{n+1}` is then subject to the advection by
                    :math:`u^{n+1}`.
8679f9097b Jeff* 
025afa4065 Jeff* -  If :math:`u^{n+1}` is directed out of the model domain, the tracer
8679f9097b Jeff*    :math:`\chi^{n+1}` on the boundary at timestep :math:`n+1` is
025afa4065 Jeff*    estimated from advection out of the domain with :math:`u^{n+1}+c`,
8679f9097b Jeff*    where :math:`c` is a phase velocity estimated as
bd45a18e71 Mart*    :math:`\frac{1}{2} \frac{\partial\chi}{\partial{t}}/
                    \frac{\partial\chi}{\partial{x}}`.
8679f9097b Jeff*    The numerical scheme is (as an example for an eastern boundary):
                 
                    .. math::
                 
bd45a18e71 Mart*       \chi_{i_{b},j,k}^{n+1} =   \chi_{i_{b},j,k}^{n} + \Delta{t}
025afa4065 Jeff*         (u^{n+1}+c)_{i_{b},j,k}\frac{\chi_{i_{b},j,k}^{n}
bd45a18e71 Mart*           - \chi_{i_{b}-1,j,k}^{n}}{\Delta{x}_{i_{b}j}^{C}}
                             \mbox{ if }u_{i_{b}jk}^{n+1}>0
8679f9097b Jeff* 
bd45a18e71 Mart*    where :math:`i_{b}` is the boundary index.  For test purposes, the
                    phase velocity contribution or the entire advection can be turned
                    off by setting the corresponding parameters
                    :varlink:`useStevensPhaseVel` and :varlink:`useStevensAdvection` to
                    ``.FALSE.``.
8679f9097b Jeff* 
                 See :cite:`stevens:90` for details. With this boundary condition
025afa4065 Jeff* specifying the exact net transport across the open boundary is simple,
bd45a18e71 Mart* so that balancing the flow with (:filelink:`S/R OBCS_BALANCE_FLOW
                 <pkg/obcs/obcs_balance_flow.F>` see next paragraph) is usually not
                 necessary.
8679f9097b Jeff* 
0ccc7e686c Mart* Special cases where the current implementation is not complete:
                 
bd45a18e71 Mart* - When you use the non-linear free surface option (parameter :varlink:`nonlinFreeSurf` > 1), the current implementation just assumes that the gradient normal to the open boundary is zero (:math:`\frac{\partial\eta}{\partial{n}} = 0`). Although this is inconsistent with geostrophic dynamics and the possibility to specify a non-zero tangent velocity together with Stevens BCs for normal velocities, it seems to work. Recommendation: Always specify zero tangential velocities with Stevens BCs.
0ccc7e686c Mart* 
bd45a18e71 Mart* - There is no code for passive tracers, just a commented template in :filelink:`S/R OBCS_CALC_STEVENS <pkg/obcs/obcs_calc_stevens.F>`. This means that passive tracers can be specified independently and are fluxed with the velocities that the Stevens BCs compute, but without the restoring term.
0ccc7e686c Mart* 
025afa4065 Jeff* - There are no specific Stevens BCs for sea ice, e.g., :ref:`pkg/seaice <sub_phys_pkg_seaice>`. The model uses the default boundary conditions for the sea ice packages.
0ccc7e686c Mart* 
bf89a37abc Phob* :filelink:`OBCS\_BALANCE\_FLOW <pkg/obcs/obcs_balance_flow.F>`:
                 ###############################################################
8679f9097b Jeff* 
3ceb1ce0a9 Jeff* When turned on (CPP option :varlink:`ALLOW_OBCS_BALANCE` defined in
bd45a18e71 Mart* :filelink:`OBCS_OPTIONS.h <pkg/obcs/OBCS_OPTIONS.h>` and
                 :varlink:`useOBCSbalance` set to ``.TRUE.`` in
                 ``data.obcs/OBCS_PARM01``), this routine balances the net flow across
                 the open boundaries. By default the net flow across the boundaries is
                 computed and all normal velocities on boundaries are adjusted to
                 obtain zero net inflow.
8679f9097b Jeff* 
                 This behavior can be controlled with the runtime flags
bd45a18e71 Mart* :varlink:`OBCS_balanceFacN`, :varlink:`OBCS_balanceFacS`,
                 :varlink:`OBCS_balanceFacE`, and :varlink:`OBCS_balanceFacW`. The
                 values of these flags determine how the net inflow is redistributed as
                 small correction velocities between the individual sections. A value
3ceb1ce0a9 Jeff* -1 balances an individual boundary, values >0 determine
bd45a18e71 Mart* the relative size of the correction. For example, the values
                 
                 ::
8679f9097b Jeff* 
bd45a18e71 Mart*    OBCS_balanceFacE = 1.,
                    OBCS_balanceFacW = -1.,
                    OBCS_balanceFacN = 2.,
                    OBCS_balanceFacS = 0.,
8679f9097b Jeff* 
                 
                 make the model
                 
bd45a18e71 Mart* -  correct Western :varlink:`OBWu` by substracting a uniform velocity to ensure zero net
8679f9097b Jeff*    transport through the Western open boundary;
                 
025afa4065 Jeff* -  correct Eastern and Northern normal flow, with the Northern velocity
                    correction two times larger than the Eastern correction, but *not*
                    the Southern normal flow, to ensure that the total inflow through
                    East, Northern, and Southern open boundary is balanced.
8679f9097b Jeff* 
                 
                 The old method of balancing the net flow for all sections individually
                 can be recovered by setting all flags to -1. Then the normal velocities
025afa4065 Jeff* across each of the four boundaries are modified separately, so that the
                 net volume transport across *each* boundary is zero. For example, for
                 the western boundary at :math:`i=i_{b}`, the modified velocity is:
8679f9097b Jeff* 
                 .. math::
                 
025afa4065 Jeff*    u(y,z) - \int_{\mbox{western boundary}}u dy dz \approx OBNu(j k) - \sum_{j k}
                    OBNu(j k) h_{w}(i_{b} j k)\Delta{y_G(i_{b} j)}\Delta{z(k)}.
8679f9097b Jeff* 
025afa4065 Jeff* This also ensures a net total inflow of zero through all boundaries, but
                 this combination of flags is *not* useful if you want to simulate, for example,
8679f9097b Jeff* a sector of the Southern Ocean with a strong ACC entering through the
025afa4065 Jeff* western and leaving through the eastern boundary, because the value of
3ceb1ce0a9 Jeff* -1 for these flags will make sure that the strong inflow is removed.
                 Clearly, global balancing with ``OBCS_balanceFacE/W/N/S`` :math:`\ge 0`
abfe198bce Mart* is the preferred method.
                 
bd45a18e71 Mart* Setting runtime parameter :varlink:`OBCSbalanceSurf` to ``TRUE.``, the
                 surface mass flux contribution, say, from surface freshwater flux
                 :varlink:`EmPmR` is included in the balancing scheme.
8679f9097b Jeff* 
                 
                 OBCS\_APPLY\_*:
                 ###############
                 
                 
bf89a37abc Phob* :filelink:`OBCS\_SPONGE <pkg/obcs/obcs_sponge.F>`:
                 ##################################################
8679f9097b Jeff* 
af61e5eb16 Mart* The sponge layer code (turned on with CPP option :varlink:`ALLOW_OBCS_SPONGE`
                 and run-time parameter :varlink:`useOBCSsponge`) adds a relaxation term to the
                 right-hand-side of the momentum and tracer equations. The variables are relaxed
                 towards the boundary values with a relaxation time scale that increases
8679f9097b Jeff* linearly with distance from the boundary
                 
                 .. math::
                 
bd45a18e71 Mart*    G_{\chi}^{\mbox{(sponge)}} =
8679f9097b Jeff*    - \frac{\chi - [( L - \delta{L} ) \chi_{BC} + \delta{L}\chi]/L}
bd45a18e71 Mart*    {[(L-\delta{L})\tau_{b}+\delta{L}\tau_{i}]/L}
8679f9097b Jeff*    = - \frac{\chi - [( 1 - l ) \chi_{BC} + l\chi]}
                    {[(1-l)\tau_{b}+l\tau_{i}]}
                 
025afa4065 Jeff* where :math:`\chi` is the model variable (U/V/T/S) in the interior,
af61e5eb16 Mart* :math:`\chi_{BC}` the boundary value, :math:`L` the thickness of the sponge
                 layer (runtime parameter :varlink:`spongeThickness` in number of grid points),
                 :math:`\delta{L}\in[0,L]` (:math:`\frac{\delta{L}}{L}=l\in[0,1]`) the distance
                 from the boundary (also in grid points), and :math:`\tau_{b}` (runtime
                 parameters :varlink:`Urelaxobcsbound` and :varlink:`Vrelaxobcsbound`) and
bd45a18e71 Mart* :math:`\tau_{i}` (runtime parameters :varlink:`Urelaxobcsinner` and
af61e5eb16 Mart* :varlink:`Vrelaxobcsinner`) the relaxation time scales on the boundary and at
                 the interior termination of the sponge layer. The parameters
                 :varlink:`Urelaxobcsbound` and :varlink:`Urelaxobcsinner` set the relaxation
                 time scales for the Eastern and Western boundaries, :varlink:`Vrelaxobcsbound`
                 and :varlink:`Vrelaxobcsinner` for the Northern and Southern boundaries.
8679f9097b Jeff* 
                 
                 OB's with nonlinear free surface
                 ################################
                 
0ccc7e686c Mart* OB's with sea ice
                 #################
                 
af61e5eb16 Mart* Simple Dirichlet boundary conditions for sea ice parameters can be specified in
                 anology to the ocean variables via filenames ``OB[N/S/E/W][a/h/sl/sn/u/v]File``
                 (sea ice concentration, cell averaged sea ice thickness, salinity, cell
                 averaged snow thickness, ice drift components). With CPP-flag
                 :varlink:`ALLOW_OBCS_SEAICE_SPONGE` and runtime flags
                 :varlink:`useSeaiceSponge`, :varlink:`seaiceSpongeThickness`, and
                 ``[A/H/SL/SN]relaxobcs[inner/bound]`` are available in analogy to the sponge
                 parameters for the ocean variables.
                 
                 Neumann boundary conditions :math:`\frac{\partial\phi}{\partial{n}}=0` for all
                 sea ice variables can be applied with runtime flag
                 :varlink:`SEAICEuseNeumannBC`, which overrides the input files for the
                 Dirichlet values.
                 
                 Defining CPP-flag :varlink:`OBCS_SEAICE_SMOOTH_EDGE` allows to smooth the
                 tracer sea-ice variables near the edges.
                 
0ccc7e686c Mart* 
8679f9097b Jeff* .. _ssub_phys_pkg_obcs_flowchart:
                 
                 Flow chart
                 ++++++++++
                 
                 
                 ::
                 
                 
                     C     !CALLING SEQUENCE:
af61e5eb16 Mart*     C    [...]
                     C    | |-MAIN_DO_LOOP    :: Open-AD case: Main timestepping loop routine
                     C    | \                    otherwise: just call FORWARD_STEP
                     C    | |
                     C/\  | |-FORWARD_STEP        :: Step forward a time-step ( AT LAST !!! )
                     C    [...]
                     C/\  | | |-DO_OCEANIC_PHYS   :: Oceanic (& seaice) physics computation
                     C/\  | | | |
                     C/\  | | | |-OBCS_CALC       :: Open boundary. package (see pkg/obcs).
                     C/\  | | | |
                     C    [...]
                     C/\  | | | |-SEAICE_MODEL          :: pkg/seaice
                     C/\  | | | | |-SEAICE_DYNSOLVER    :: pkg/seaice
                     C/\  | | | | | |-OBCS_APPLY_UVICE  :: apply uIce/vIce boudnary conditions
                     C/\  | | | | |-OBCS_ADJUST_UVICE   :: (Only for OBCS_UVICE_OLD)
                     C/\  | | | | |-SEAICE_GROWTH
                     C/\  | | | | |-SEAICE_APPLY_SEAICE :: add OBCS for scalar variables
                     C    [...]
                     C/\  | | |-THERMODYNAMICS         :: theta, salt + tracer equations driver.
                     C/\  | | | |                         (synchronous time-stepping case)
                     C    [...]
                     C/\  | | | |-TEMP_INTEGRATE       :: Step forward Prognostic Eq for Temperature.
                     C/\  | | | |
                     C/\  | | | |-SALT_INTEGRATE       :: Step forward Prognostic Eq for Salinity.
                     C/\  | | | |                         same sequence of calls as in TEMP_INTEGRATE
                     C/\  | | | |
                     C/\  | | | |-PTRACERS_INTEGRATE   :: Integrate other tracer(s) (see pkg/ptracers).
                     C/\  | | | | |                     same sequence of calls as in TEMP_INTEGRATE
                     C/\  | | | | |-OBCS_APPLY_PTRACER :: Open boundary package for pTracers
                     C/\  | | | |
                     C/\  | | | |-OBCS_APPLY_TS        :: Open boundary package (see pkg/obcs ).
                     C/\  | | |
                     C    [...]
                     C/\  | | |
                     C/\  | | |-DYNAMICS       :: Momentum equations driver.
                     C/\  | | | |
                     C    [...]
                     C/\  | | | |-OBCS_APPLY_UV    :: Apply Open bndary Conditions to provisional U,V
                     C    [...]
                     C/\  | | |-MOMENTUM_CORRECTION_STEP :: Finalise momentum stepping
                     C    [...]
                     C/\  | | | |-OBCS_APPLY_UV       :: Open boundary package (see pkg/obcs).
                 
8679f9097b Jeff* 
                 
                 .. _ssub_phys_pkg_obcs_diagnostics:
                 
                 OBCS diagnostics
                 ++++++++++++++++
                 
af61e5eb16 Mart* Diagnostics output is available via the diagnostics package (see
                 :numref:`sub_outp_pkg_diagnostics`). Currently there are no OBCS-specific
                 diagnostics available.
8679f9097b Jeff* 
                 
bf89a37abc Phob* .. _ssub_phys_pkg_obcs_experiments:
8679f9097b Jeff* 
bf89a37abc Phob* Experiments and tutorials that use obcs
                 +++++++++++++++++++++++++++++++++++++++
8679f9097b Jeff* 
025afa4065 Jeff* In the directory :filelink:`verification` the following experiments use
3ceb1ce0a9 Jeff* :filelink:`pkg/obcs`:
8679f9097b Jeff* 
                 
025afa4065 Jeff* -  :filelink:`exp4 <verification/exp4>`: box with 4 open boundaries, simulating flow over a Gaussian bump
bf89a37abc Phob*    based on  also tests Stevens-boundary conditions;
8679f9097b Jeff* 
bf89a37abc Phob* -  :filelink:`dome <verification/dome>`: based on the project “Dynamics of Overflow Mixing and Entrainment”
3ceb1ce0a9 Jeff*    uses Orlanski-BCs;
8679f9097b Jeff* 
3ceb1ce0a9 Jeff* -  :filelink:`internal_wave <verification/internal_wave>`: uses a heavily modified :filelink:`S/R OBCS_CALC <verification/internal_wave/code/obcs_calc.F>`
8679f9097b Jeff* 
bf89a37abc Phob* -  :filelink:`seaice_obcs <verification/seaice_obcs>`: simple example who to use the sea-ice related code based on :filelink:`lab_sea <verification/lab_sea>`;
8679f9097b Jeff* 
bf1e6e69d5 Mart* -  Tutorial :ref:`tutorial_plume_on_slope`: uses Orlanski-BCs.

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