source: NEMO/trunk/doc/latex/NEMO/subfiles/chap_SBC.tex @ 11577

Last change on this file since 11577 was 11577, checked in by nicolasmartin, 13 months ago

New LaTeX commands \nam and \np to mention namelist content
(Partial commit to serve as a backup before other large edits)
In order to benefit of the syntax highlighting and to have a simpler syntax for
citing namelist block (\nam) and parameter (\np) with an optional variable assignment (\forcode{…}),
at this time the only viable solution I found is to require a double marker for
what it looks like the same item:

  1. Marker with the real name: 'tra_adv' block or 'ln_flx' parameter
  2. Marker with underscore character escaping: 'tra\_adv' block or 'ln\_flx' parameter

Despite many searches and attempts, I did not find a workaround to edit on-the-fly one or
the other marker.
In fact, the problem is on one side that the LaTeX index interprets '_' as a switch for lowering like
in math mode while on the other hand the backslash is considered for Pygments as a typo in Fortran
(red box).

For instance, \nam and \np have as of now the aforementioned 2 mandatory arguments in
the previous order (between braces) + an optional argument for \np when the parameter is defined
(between brackets at the first position):

  • \nam: LaTeX code in the \nam{tra_adv}{tra\_adv} → PDF ' in the &namtra_adv (namelist X.X) ' with syntax highlighting, the hyperlink and the index entry
  • \np: LaTeX code \np[=.true.]{ln_flx}{ln\_flx} → PDF ln_flux=.true. with syntax highlighting for the whole string and the entry in the 'parameters' index
File size: 99.0 KB
5% ================================================================
6% Chapter —— Surface Boundary Condition (SBC, SAS, ISF, ICB)
7% ================================================================
8\chapter{Surface Boundary Condition (SBC, SAS, ISF, ICB)}
17  \nlst{namsbc}
18  \caption{\forcode{&namsbc}}
19  \label{lst:namsbc}
23The ocean needs seven fields as surface boundary condition:
27  the two components of the surface ocean stress $\left( {\tau_u \;,\;\tau_v} \right)$
29  the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$
31  the surface freshwater budget $\left( {\textit{emp}} \right)$
33  the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$
35  the atmospheric pressure at the ocean surface $\left( p_a \right)$
38Four different ways are available to provide the seven fields to the ocean. They are controlled by
39namelist \nam{sbc} variables:
43  a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.} with four possible bulk algorithms),
45  a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
47  a coupled or mixed forced/coupled formulation (exchanges with a atmospheric model via the OASIS coupler),
48(\np{ln_cpl}{ln\_cpl} or \np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.}),
50  a user defined formulation (\np{ln_usr}{ln\_usr}\forcode{=.true.}).
53The frequency at which the forcing fields have to be updated is given by the \np{nn_fsbc}{nn\_fsbc} namelist parameter.
55When the fields are supplied from data files (bulk, flux and mixed formulations),
56the input fields do not need to be supplied on the model grid.
57Instead, a file of coordinates and weights can be supplied to map the data from the input fields grid to
58the model points (so called "Interpolation on the Fly", see \autoref{subsec:SBC_iof}).
59If the "Interpolation on the Fly" option is used, input data belonging to land points (in the native grid)
60should be masked or filled to avoid spurious results in proximity of the coasts, as
61large sea-land gradients characterize most of the atmospheric variables.
63In addition, the resulting fields can be further modified using several namelist options.
64These options control:
68  the rotation of vector components supplied relative to an east-north coordinate system onto
69  the local grid directions in the model,
71  the use of a land/sea mask for input fields (\np{nn_lsm}{nn\_lsm}\forcode{=.true.}),
73  the addition of a surface restoring term to observed SST and/or SSS (\np{ln_ssr}{ln\_ssr}\forcode{=.true.}),
75  the modification of fluxes below ice-covered areas (using climatological ice-cover or a sea-ice model)
76  (\np{nn_ice}{nn\_ice}\forcode{=0..3}),
78  the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln_rnf}{ln\_rnf}\forcode{=.true.}),
80  the addition of ice-shelf melting as lateral inflow (parameterisation) or
81  as fluxes applied at the land-ice ocean interface (\np{ln_isf}{ln\_isf}\forcode{=.true.}),
83  the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift
84  (\np{nn_fwb}{nn\_fwb}\forcode{=0..2}),
86  the transformation of the solar radiation (if provided as daily mean) into an analytical diurnal cycle
87  (\np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.}),
89  the activation of wave effects from an external wave model  (\np{ln_wave}{ln\_wave}\forcode{=.true.}),
91  a neutral drag coefficient is read from an external wave model (\np{ln_cdgw}{ln\_cdgw}\forcode{=.true.}),
93  the Stokes drift from an external wave model is accounted for (\np{ln_sdw}{ln\_sdw}\forcode{=.true.}),
95  the choice of the Stokes drift profile parameterization (\np{nn_sdrift}{nn\_sdrift}\forcode{=0..2}),
97  the surface stress given to the ocean is modified by surface waves (\np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}),
99  the surface stress given to the ocean is read from an external wave model (\np{ln_tauw}{ln\_tauw}\forcode{=.true.}),
101  the Stokes-Coriolis term is included (\np{ln_stcor}{ln\_stcor}\forcode{=.true.}),
103  the light penetration in the ocean (\np{ln_traqsr}{ln\_traqsr}\forcode{=.true.} with namelist \nam{tra_qsr}{tra\_qsr}),
105  the atmospheric surface pressure gradient effect on ocean and ice dynamics (\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.} with namelist \nam{sbc_apr}{sbc\_apr}),
107  the effect of sea-ice pressure on the ocean (\np{ln_ice_embd}{ln\_ice\_embd}\forcode{=.true.}).
110In this chapter, we first discuss where the surface boundary conditions appear in the model equations.
111Then we present the three ways of providing the surface boundary conditions,
112followed by the description of the atmospheric pressure and the river runoff.
113Next, the scheme for interpolation on the fly is described.
114Finally, the different options that further modify the fluxes applied to the ocean are discussed.
115One of these is modification by icebergs (see \autoref{sec:SBC_ICB_icebergs}),
116which act as drifting sources of fresh water.
117Another example of modification is that due to the ice shelf melting/freezing (see \autoref{sec:SBC_isf}),
118which provides additional sources of fresh water.
122% ================================================================
123% Surface boundary condition for the ocean
124% ================================================================
125\section{Surface boundary condition for the ocean}
128The surface ocean stress is the stress exerted by the wind and the sea-ice on the ocean.
129It is applied in \mdl{dynzdf} module as a surface boundary condition of the computation of
130the momentum vertical mixing trend (see \autoref{eq:DYN_zdf_sbc} in \autoref{sec:DYN_zdf}).
131As such, it has to be provided as a 2D vector interpolated onto the horizontal velocity ocean mesh,
132\ie\ resolved onto the model (\textbf{i},\textbf{j}) direction at $u$- and $v$-points.
134The surface heat flux is decomposed into two parts, a non solar and a solar heat flux,
135$Q_{ns}$ and $Q_{sr}$, respectively.
136The former is the non penetrative part of the heat flux
137(\ie\ the sum of sensible, latent and long wave heat fluxes plus
138the heat content of the mass exchange between the ocean and sea-ice).
139It is applied in \mdl{trasbc} module as a surface boundary condition trend of
140the first level temperature time evolution equation
141(see \autoref{eq:TRA_sbc} and \autoref{eq:TRA_sbc_lin} in \autoref{subsec:TRA_sbc}).
142The latter is the penetrative part of the heat flux.
143It is applied as a 3D trend of the temperature equation (\mdl{traqsr} module) when
145The way the light penetrates inside the water column is generally a sum of decreasing exponentials
146(see \autoref{subsec:TRA_qsr}).
148The surface freshwater budget is provided by the \textit{emp} field.
149It represents the mass flux exchanged with the atmosphere (evaporation minus precipitation) and
150possibly with the sea-ice and ice shelves (freezing minus melting of ice).
151It affects the ocean in two different ways:
152$(i)$  it changes the volume of the ocean, and therefore appears in the sea surface height equation as      %GS: autoref ssh equation to be added
153a volume flux, and
154$(ii)$ it changes the surface temperature and salinity through the heat and salt contents of
155the mass exchanged with atmosphere, sea-ice and ice shelves.
158%\colorbox{yellow}{Miss: }
160%A extensive description of all namsbc namelist (parameter that have to be
163%Especially the \np{nn_fsbc}{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
164%ssv) \ie\ information required by flux computation or sea-ice
166%\mdl{sbc\_oce} containt the definition in memory of the 7 fields (6+runoff), add
167%a word on runoff: included in surface bc or add as lateral obc{\ldots}.
169%Sbcmod manage the ``providing'' (fourniture) to the ocean the 7 fields
171%Fluxes update only each nf\_sbc time step (namsbc) explain relation
172%between nf\_sbc and nf\_ice, do we define nf\_blk??? ? only one
175%Explain here all the namlist namsbc variable{\ldots}.
177% explain : use or not of surface currents
179%\colorbox{yellow}{End Miss }
181The ocean model provides, at each time step, to the surface module (\mdl{sbcmod})
182the surface currents, temperature and salinity.
183These variables are averaged over \np{nn_fsbc}{nn\_fsbc} time-step (\autoref{tab:SBC_ssm}), and
184these averaged fields are used to compute the surface fluxes at the frequency of \np{nn_fsbc}{nn\_fsbc} time-steps.
189  \centering
190  \begin{tabular}{|l|l|l|l|}
191    \hline
192    Variable description                           & Model variable  & Units  & point                 \\
193    \hline
194    i-component of the surface current & ssu\_m               & $m.s^{-1}$     & U     \\
195    \hline
196    j-component of the surface current & ssv\_m               & $m.s^{-1}$     & V     \\
197    \hline
198    Sea surface temperature                  & sst\_m               & \r{}$K$              & T     \\\hline
199    Sea surface salinty                         & sss\_m               & $psu$              & T     \\   \hline
200  \end{tabular}
201  \caption[Ocean variables provided to the surface module)]{
202    Ocean variables provided to the surface module (\texttt{SBC}).
203    The variable are averaged over \protect\np{nn_fsbc}{nn\_fsbc} time-step,
204    \ie\ the frequency of computation of surface fluxes.}
205  \label{tab:SBC_ssm}
209%\colorbox{yellow}{Penser a} mettre dans le restant l'info nn\_fsbc ET nn\_fsbc*rdt de sorte de reinitialiser la moyenne si on change la frequence ou le pdt
213% ================================================================
214%       Input Data
215% ================================================================
216\section{Input data generic interface}
219A generic interface has been introduced to manage the way input data
220(2D or 3D fields, like surface forcing or ocean T and S) are specified in \NEMO.
221This task is achieved by \mdl{fldread}.
222The module is designed with four main objectives in mind:
225  optionally provide a time interpolation of the input data every specified model time-step, whatever their input frequency is,
226  and according to the different calendars available in the model.
228  optionally provide an on-the-fly space interpolation from the native input data grid to the model grid.
230  make the run duration independent from the period cover by the input files.
232  provide a simple user interface and a rather simple developer interface by
233  limiting the number of prerequisite informations.
236As a result, the user has only to fill in for each variable a structure in the namelist file to
237define the input data file and variable names, the frequency of the data (in hours or months),
238whether its is climatological data or not, the period covered by the input file (one year, month, week or day),
239and three additional parameters for the on-the-fly interpolation.
240When adding a new input variable, the developer has to add the associated structure in the namelist,
241read this information by mirroring the namelist read in \rou{sbc\_blk\_init} for example,
242and simply call \rou{fld\_read} to obtain the desired input field at the model time-step and grid points.
244The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature
245(see \autoref{subsec:SBC_fldread}), the period it cover is one year, month, week or day, and,
246if on-the-fly interpolation is used, a file of weights must be supplied (see \autoref{subsec:SBC_iof}).
248Note that when an input data is archived on a disc which is accessible directly from the workspace where
249the code is executed, then the user can set the \np{cn_dir}{cn\_dir} to the pathway leading to the data.
250By default, the data are assumed to be in the same directory as the executable, so that cn\_dir='./'.
253% -------------------------------------------------------------------------------------------------------------
254% Input Data specification (\mdl{fldread})
255% -------------------------------------------------------------------------------------------------------------
256\subsection[Input data specification (\textit{fldread.F90})]{Input data specification (\protect\mdl{fldread})}
259The structure associated with an input variable contains the following information:
261!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
262!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
266\item[File name]:
267  the stem name of the NetCDF file to be opened.
268  This stem will be completed automatically by the model, with the addition of a '.nc' at its end and
269  by date information and possibly a prefix (when using AGRIF).
270  \autoref{tab:SBC_fldread} provides the resulting file name in all possible cases according to
271  whether it is a climatological file or not, and to the open/close frequency (see below for definition).
274  \begin{table}[htbp]
275    \centering
276    \begin{tabular}{|l|c|c|c|}
277      \hline
278                                  &  daily or weekLL     &  monthly           &  yearly        \\
279      \hline
280      \np{clim}{clim}\forcode{=.false.} &  fn\  &  fn\   &  fn\  \\
281      \hline
282      \np{clim}{clim}\forcode{=.true.}  &  not possible        &  fn\_m??.nc        &  fn            \\
283      \hline
284    \end{tabular}
285    \caption[Naming nomenclature for climatological or interannual input file]{
286      Naming nomenclature for climatological or interannual input file,
287      as a function of the open/close frequency.
288      The stem name is assumed to be 'fn'.
289      For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week
290      (\ie\ 'sun','sat','fri','thu','wed','tue','mon').
291      The 'YYYY', 'MM' and 'DD' should be replaced by the actual year/month/day,
292      always coded with 4 or 2 digits.
293      Note that (1) in mpp, if the file is split over each subdomain,
294      the suffix '.nc' is replaced by '\',
295      where 'PPPP' is the process number coded with 4 digits;
296      (2) when using AGRIF, the prefix '\_N' is added to files, where 'N' is the child grid number.
297    }
298    \label{tab:SBC_fldread}
299  \end{table}
303\item[Record frequency]:
304  the frequency of the records contained in the input file.
305  Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative
306  (for example -1 for monthly forcing or -12 for annual forcing).
307  Note that this frequency must REALLY be an integer and not a real.
308  On some computers, setting it to '24.' can be interpreted as 240!
310\item[Variable name]:
311  the name of the variable to be read in the input NetCDF file.
313\item[Time interpolation]:
314  a logical to activate, or not, the time interpolation.
315  If set to 'false', the forcing will have a steplike shape remaining constant during each forcing period.
316  For example, when using a daily forcing without time interpolation, the forcing remaining constant from
317  00h00'00'' to 23h59'59".
318  If set to 'true', the forcing will have a broken line shape.
319  Records are assumed to be dated at the middle of the forcing period.
320  For example, when using a daily forcing with time interpolation,
321  linear interpolation will be performed between mid-day of two consecutive days.
323\item[Climatological forcing]:
324  a logical to specify if a input file contains climatological forcing which can be cycle in time,
325  or an interannual forcing which will requires additional files if
326  the period covered by the simulation exceeds the one of the file.
327  See the above file naming strategy which impacts the expected name of the file to be opened.
329\item[Open/close frequency]:
330  the frequency at which forcing files must be opened/closed.
331  Four cases are coded:
332  'daily', 'weekLLL' (with 'LLL' the first 3 letters of the first day of the week), 'monthly' and 'yearly' which
333  means the forcing files will contain data for one day, one week, one month or one year.
334  Files are assumed to contain data from the beginning of the open/close period.
335  For example, the first record of a yearly file containing daily data is Jan 1st even if
336  the experiment is not starting at the beginning of the year.
339  'weights filename', 'pairing rotation' and 'land/sea mask' are associated with
340  on-the-fly interpolation which is described in \autoref{subsec:SBC_iof}.
344Additional remarks:\\
345(1) The time interpolation is a simple linear interpolation between two consecutive records of the input data.
346The only tricky point is therefore to specify the date at which we need to do the interpolation and
347the date of the records read in the input files.
348Following \citet{leclair.madec_OM09}, the date of a time step is set at the middle of the time step.
349For example, for an experiment starting at 0h00'00" with a one-hour time-step,
350a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
351However, for forcing data related to the surface module,
352values are not needed at every time-step but at every \np{nn_fsbc}{nn\_fsbc} time-step.
353For example with \np{nn_fsbc}{nn\_fsbc}\forcode{=3}, the surface module will be called at time-steps 1, 4, 7, etc.
354The date used for the time interpolation is thus redefined to the middle of \np{nn_fsbc}{nn\_fsbc} time-step period.
355In the previous example, this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\
356(2) For code readablility and maintenance issues, we don't take into account the NetCDF input file calendar.
357The calendar associated with the forcing field is build according to the information provided by
358user in the record frequency, the open/close frequency and the type of temporal interpolation.
359For example, the first record of a yearly file containing daily data that will be interpolated in time is assumed to
360start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\
361(3) If a time interpolation is requested, the code will pick up the needed data in the previous (next) file when
362interpolating data with the first (last) record of the open/close period.
363For example, if the input file specifications are ''yearly, containing daily data to be interpolated in time'',
364the values given by the code between 00h00'00" and 11h59'59" on Jan 1st will be interpolated values between
365Dec 31st 12h00'00" and Jan 1st 12h00'00".
366If the forcing is climatological, Dec and Jan will be keep-up from the same year.
367However, if the forcing is not climatological, at the end of
368the open/close period, the code will automatically close the current file and open the next one.
369Note that, if the experiment is starting (ending) at the beginning (end) of
370an open/close period, we do accept that the previous (next) file is not existing.
371In this case, the time interpolation will be performed between two identical values.
372For example, when starting an experiment on Jan 1st of year Y with yearly files and daily data to be interpolated,
373we do accept that the file related to year Y-1 is not existing.
374The value of Jan 1st will be used as the missing one for Dec 31st of year Y-1.
375If the file of year Y-1 exists, the code will read its last record.
376Therefore, this file can contain only one record corresponding to Dec 31st,
377a useful feature for user considering that it is too heavy to manipulate the complete file for year Y-1.
380% -------------------------------------------------------------------------------------------------------------
381% Interpolation on the Fly
382% -------------------------------------------------------------------------------------------------------------
383\subsection{Interpolation on-the-fly}
386Interpolation on the Fly allows the user to supply input files required for the surface forcing on
387grids other than the model grid.
388To do this, he or she must supply, in addition to the source data file(s), a file of weights to be used to
389interpolate from the data grid to the model grid.
390The original development of this code used the SCRIP package
391(freely available \href{}{here} under a copyright agreement).
392In principle, any package such as CDO can be used to generate the weights, but the variables in
393the input weights file must have the same names and meanings as assumed by the model.
394Two methods are currently available: bilinear and bicubic interpolations.
395Prior to the interpolation, providing a land/sea mask file, the user can decide to remove land points from
396the input file and substitute the corresponding values with the average of the 8 neighbouring points in
397the native external grid.
398Only "sea points" are considered for the averaging.
399The land/sea mask file must be provided in the structure associated with the input variable.
400The netcdf land/sea mask variable name must be 'LSM' and must have the same horizontal and vertical dimensions as
401the associated variables and should be equal to 1 over land and 0 elsewhere.
402The procedure can be recursively applied by setting nn\_lsm > 1 in namsbc namelist.
403Note that nn\_lsm=0 forces the code to not apply the procedure, even if a land/sea mask file is supplied.
406% -------------------------------------------------------------------------------------------------------------
407% Bilinear interpolation
408% -------------------------------------------------------------------------------------------------------------
409\subsubsection{Bilinear interpolation}
412The input weights file in this case has two sets of variables:
413src01, src02, src03, src04 and wgt01, wgt02, wgt03, wgt04.
414The "src" variables correspond to the point in the input grid to which the weight "wgt" is applied.
415Each src value is an integer corresponding to the index of a point in the input grid when
416written as a one dimensional array.
417For example, for an input grid of size 5x10, point (3,2) is referenced as point 8, since (2-1)*5+3=8.
418There are four of each variable because bilinear interpolation uses the four points defining
419the grid box containing the point to be interpolated.
420All of these arrays are on the model grid, so that values src01(i,j) and wgt01(i,j) are used to
421generate a value for point (i,j) in the model.
423Symbolically, the algorithm used is:
425  f_{m}(i,j) = f_{m}(i,j) + \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}
427where function idx() transforms a one dimensional index src(k) into a two dimensional index,
428and wgt(1) corresponds to variable "wgt01" for example.
431% -------------------------------------------------------------------------------------------------------------
432% Bicubic interpolation
433% -------------------------------------------------------------------------------------------------------------
434\subsubsection{Bicubic interpolation}
437Again, there are two sets of variables: "src" and "wgt".
438But in this case, there are 16 of each.
439The symbolic algorithm used to calculate values on the model grid is now:
442  \begin{split}
443    f_{m}(i,j) =  f_{m}(i,j) +& \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}
444    +  \sum_{k=5 }^{8 } {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\
445    +& \sum_{k=9 }^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} }
446    +  \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} }
447  \end{split}
449The gradients here are taken with respect to the horizontal indices and not distances since
450the spatial dependency has been included into the weights.
453% -------------------------------------------------------------------------------------------------------------
454% Implementation
455% -------------------------------------------------------------------------------------------------------------
459To activate this option, a non-empty string should be supplied in
460the weights filename column of the relevant namelist;
461if this is left as an empty string no action is taken.
462In the model, weights files are read in and stored in a structured type (WGT) in the fldread module,
463as and when they are first required.
464This initialisation procedure determines whether the input data grid should be treated as cyclical or not by
465inspecting a global attribute stored in the weights input file.
466This attribute must be called "ew\_wrap" and be of integer type.
467If it is negative, the input non-model grid is assumed to be not cyclic.
468If zero or greater, then the value represents the number of columns that overlap.
469$E.g.$ if the input grid has columns at longitudes 0, 1, 2, .... , 359, then ew\_wrap should be set to 0;
470if longitudes are 0.5, 2.5, .... , 358.5, 360.5, 362.5, ew\_wrap should be 2.
471If the model does not find attribute ew\_wrap, then a value of -999 is assumed.
472In this case, the \rou{fld\_read} routine defaults ew\_wrap to value 0 and
473therefore the grid is assumed to be cyclic with no overlapping columns.
474(In fact, this only matters when bicubic interpolation is required.)
475Note that no testing is done to check the validity in the model,
476since there is no way of knowing the name used for the longitude variable,
477so it is up to the user to make sure his or her data is correctly represented.
479Next the routine reads in the weights.
480Bicubic interpolation is assumed if it finds a variable with name "src05", otherwise bilinear interpolation is used.
481The WGT structure includes dynamic arrays both for the storage of the weights (on the model grid),
482and when required, for reading in the variable to be interpolated (on the input data grid).
483The size of the input data array is determined by examining the values in the "src" arrays to
484find the minimum and maximum i and j values required.
485Since bicubic interpolation requires the calculation of gradients at each point on the grid,
486the corresponding arrays are dimensioned with a halo of width one grid point all the way around.
487When the array of points from the data file is adjacent to an edge of the data grid,
488the halo is either a copy of the row/column next to it (non-cyclical case),
489or is a copy of one from the first few columns on the opposite side of the grid (cyclical case).
492% -------------------------------------------------------------------------------------------------------------
493% Limitations
494% -------------------------------------------------------------------------------------------------------------
500  The case where input data grids are not logically rectangular (irregular grid case) has not been tested.
502  This code is not guaranteed to produce positive definite answers from positive definite inputs when
503  a bicubic interpolation method is used.
505  The cyclic condition is only applied on left and right columns, and not to top and bottom rows.
507  The gradients across the ends of a cyclical grid assume that the grid spacing between
508  the two columns involved are consistent with the weights used.
510  Neither interpolation scheme is conservative. (There is a conservative scheme available in SCRIP,
511  but this has not been implemented.)
517% to be completed
518A set of utilities to create a weights file for a rectilinear input grid is available
519(see the directory NEMOGCM/TOOLS/WEIGHTS).
522% -------------------------------------------------------------------------------------------------------------
523% Standalone Surface Boundary Condition Scheme
524% -------------------------------------------------------------------------------------------------------------
525\subsection{Standalone surface boundary condition scheme (SAS)}
531  \nlst{namsbc_sas}
532  \caption{\forcode{&namsbc_sas}}
533  \label{lst:namsbc_sas}
537In some circumstances, it may be useful to avoid calculating the 3D temperature,
538salinity and velocity fields and simply read them in from a previous run or receive them from OASIS.
539For example:
543  Multiple runs of the model are required in code development to
544  see the effect of different algorithms in the bulk formulae.
546  The effect of different parameter sets in the ice model is to be examined.
548  Development of sea-ice algorithms or parameterizations.
550  Spinup of the iceberg floats
552  Ocean/sea-ice simulation with both models running in parallel (\np{ln_mixcpl}{ln\_mixcpl}\forcode{=.true.})
555The Standalone Surface scheme provides this capacity.
556Its options are defined through the \nam{sbc_sas}{sbc\_sas} namelist variables.
557A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM.
558However, no namelist parameters need be changed from the settings of the previous run (except perhaps nn\_date0).
559In this configuration, a few routines in the standard model are overriden by new versions.
560Routines replaced are:
564  \mdl{nemogcm}:
565  This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (\mdl{step}).
566  Since the ocean state is not calculated all associated initialisations have been removed.
568  \mdl{step}:
569  The main time stepping routine now only needs to call the sbc routine (and a few utility functions).
571  \mdl{sbcmod}:
572  This has been cut down and now only calculates surface forcing and the ice model required.
573  New surface modules that can function when only the surface level of the ocean state is defined can also be added
574  (\eg\ icebergs).
576  \mdl{daymod}:
577  No ocean restarts are read or written (though the ice model restarts are retained),
578  so calls to restart functions have been removed.
579  This also means that the calendar cannot be controlled by time in a restart file,
580  so the user must check that nn\_date0 in the model namelist is correct for his or her purposes.
582  \mdl{stpctl}:
583  Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module.
585  \mdl{diawri}:
586  All 3D data have been removed from the output.
587  The surface temperature, salinity and velocity components (which have been read in) are written along with
588  relevant forcing and ice data.
591One new routine has been added:
595  \mdl{sbcsas}:
596  This module initialises the input files needed for reading temperature, salinity and
597  velocity arrays at the surface.
598  These filenames are supplied in namelist namsbc\_sas.
599  Unfortunately, because of limitations with the \mdl{iom} module,
600  the full 3D fields from the mean files have to be read in and interpolated in time,
601  before using just the top level.
602  Since fldread is used to read in the data, Interpolation on the Fly may be used to change input data resolution.
606The user can also choose in the \nam{sbc_sas}{sbc\_sas} namelist to read the mean (nn\_fsbc time-step) fraction of solar net radiation absorbed in the 1st T level using
607 (\np{ln_flx}{ln\_flx}\forcode{=.true.}) and to provide 3D oceanic velocities instead of 2D ones (\np{ln_flx}{ln\_flx}\forcode{=.true.}). In that last case, only the 1st level will be read in.
611% ================================================================
612% Flux formulation
613% ================================================================
614\section[Flux formulation (\textit{sbcflx.F90})]{Flux formulation (\protect\mdl{sbcflx})}
619  \nlst{namsbc_flx}
620  \caption{\forcode{&namsbc_flx}}
621  \label{lst:namsbc_flx}
625In the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
626the surface boundary condition fields are directly read from input files.
627The user has to define in the namelist \nam{sbc_flx}{sbc\_flx} the name of the file,
628the name of the variable read in the file, the time frequency at which it is given (in hours),
629and a logical setting whether a time interpolation to the model time step is required for this field.
630See \autoref{subsec:SBC_fldread} for a more detailed description of the parameters.
632Note that in general, a flux formulation is used in associated with a restoring term to observed SST and/or SSS.
633See \autoref{subsec:SBC_ssr} for its specification.
637% ================================================================
638% Bulk formulation
639% ================================================================
640\section[Bulk formulation (\textit{sbcblk.F90})]{Bulk formulation (\protect\mdl{sbcblk})}
645  \nlst{namsbc_blk}
646  \caption{\forcode{&namsbc_blk}}
647  \label{lst:namsbc_blk}
651In the bulk formulation, the surface boundary condition fields are computed with bulk formulae using atmospheric fields
652and ocean (and sea-ice) variables averaged over \np{nn_fsbc}{nn\_fsbc} time-step.
654The atmospheric fields used depend on the bulk formulae used.
655In forced mode, when a sea-ice model is used, a specific bulk formulation is used.
656Therefore, different bulk formulae are used for the turbulent fluxes computation
657over the ocean and over sea-ice surface.
658For the ocean, four bulk formulations are available thanks to the \href{}{Aerobulk} package (\citet{brodeau.barnier.ea_JPO16}):
659the NCAR (formerly named CORE), COARE 3.0, COARE 3.5 and ECMWF bulk formulae.
660The choice is made by setting to true one of the following namelist variable:
661 \np{ln_NCAR}{ln\_NCAR}, \np{ln_COARE_3p0}{ln\_COARE\_3p0}\np{ln_COARE_3p5}{ln\_COARE\_3p5} and  \np{ln_ECMWF}{ln\_ECMWF}.
662For sea-ice, three possibilities can be selected:
663a constant transfer coefficient (1.4e-3; default value), \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}), and \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}) parameterizations
665Common options are defined through the \nam{sbc_blk}{sbc\_blk} namelist variables.
666The required 9 input fields are:
670  \centering
671  \begin{tabular}{|l|c|c|c|}
672    \hline
673    Variable description                 & Model variable & Units              & point \\
674    \hline
675    i-component of the 10m air velocity  & utau           & $m.s^{-1}$         & T     \\
676    \hline
677    j-component of the 10m air velocity  & vtau           & $m.s^{-1}$         & T     \\
678    \hline
679    10m air temperature                  & tair           & \r{}$K$            & T     \\
680    \hline
681    Specific humidity                    & humi           & \%                 & T     \\
682    \hline
683    Incoming long wave radiation         & qlw            & $W.m^{-2}$         & T     \\
684    \hline
685    Incoming short wave radiation        & qsr            & $W.m^{-2}$         & T     \\
686    \hline
687    Total precipitation (liquid + solid) & precip         & $Kg.m^{-2}.s^{-1}$ & T     \\
688    \hline
689    Solid precipitation                  & snow           & $Kg.m^{-2}.s^{-1}$ & T     \\
690    \hline
691    Mean sea-level pressure              & slp            & $hPa$              & T     \\
692    \hline
693    \end{tabular}
694  \label{tab:SBC_BULK}
698Note that the air velocity is provided at a tracer ocean point, not at a velocity ocean point ($u$- and $v$-points).
699It is simpler and faster (less fields to be read), but it is not the recommended method when
700the ocean grid size is the same or larger than the one of the input atmospheric fields.
702The \np{sn_wndi}{sn\_wndi}, \np{sn_wndj}{sn\_wndj}, \np{sn_qsr}{sn\_qsr}, \np{sn_qlw}{sn\_qlw}, \np{sn_tair}{sn\_tair}, \np{sn_humi}{sn\_humi}, \np{sn_prec}{sn\_prec},
703\np{sn_snow}{sn\_snow}, \np{sn_tdif}{sn\_tdif} parameters describe the fields and the way they have to be used
704(spatial and temporal interpolations).
706\np{cn_dir}{cn\_dir} is the directory of location of bulk files
707\np{ln_taudif}{ln\_taudif} is the flag to specify if we use Hight Frequency (HF) tau information (.true.) or not (.false.)
708\np{rn_zqt}{rn\_zqt}: is the height of humidity and temperature measurements (m)
709\np{rn_zu}{rn\_zu}: is the height of wind measurements (m)
711Three multiplicative factors are available:
712\np{rn_pfac}{rn\_pfac} and \np{rn_efac}{rn\_efac} allow to adjust (if necessary) the global freshwater budget by
713increasing/reducing the precipitations (total and snow) and or evaporation, respectively.
714The third one,\np{rn_vfac}{rn\_vfac}, control to which extend the ice/ocean velocities are taken into account in
715the calculation of surface wind stress.
716Its range must be between zero and one, and it is recommended to set it to 0 at low-resolution (ORCA2 configuration).
718As for the flux formulation, information about the input data required by the model is provided in
719the namsbc\_blk namelist (see \autoref{subsec:SBC_fldread}).
722% -------------------------------------------------------------------------------------------------------------
723%        Ocean-Atmosphere Bulk formulae
724% -------------------------------------------------------------------------------------------------------------
725\subsection[Ocean-Atmosphere Bulk formulae (\textit{sbcblk\_algo\_coare.F90, sbcblk\_algo\_coare3p5.F90, sbcblk\_algo\_ecmwf.F90, sbcblk\_algo\_ncar.F90})]{Ocean-Atmosphere Bulk formulae (\mdl{sbcblk\_algo\_coare}, \mdl{sbcblk\_algo\_coare3p5}, \mdl{sbcblk\_algo\_ecmwf}, \mdl{sbcblk\_algo\_ncar})}
728Four different bulk algorithms are available to compute surface turbulent momentum and heat fluxes over the ocean.
729COARE 3.0, COARE 3.5 and ECMWF schemes mainly differ by their roughness lenghts computation and consequently
730their neutral transfer coefficients relationships with neutral wind.
733  NCAR (\np{ln_NCAR}{ln\_NCAR}\forcode{=.true.}):
734  The NCAR bulk formulae have been developed by \citet{large.yeager_rpt04}.
735  They have been designed to handle the NCAR forcing, a mixture of NCEP reanalysis and satellite data.
736  They use an inertial dissipative method to compute the turbulent transfer coefficients
737  (momentum, sensible heat and evaporation) from the 10m wind speed, air temperature and specific humidity.
738  This \citet{large.yeager_rpt04} dataset is available through
739  the \href{}{GFDL web site}.
740  Note that substituting ERA40 to NCEP reanalysis fields does not require changes in the bulk formulea themself.
741  This is the so-called DRAKKAR Forcing Set (DFS) \citep{brodeau.barnier.ea_OM10}.
743  COARE 3.0 (\np{ln_COARE_3p0}{ln\_COARE\_3p0}\forcode{=.true.}):
744  See \citet{fairall.bradley.ea_JC03} for more details
746  COARE 3.5 (\np{ln_COARE_3p5}{ln\_COARE\_3p5}\forcode{=.true.}):
747  See \citet{edson.jampana.ea_JPO13} for more details
749  ECMWF (\np{ln_ECMWF}{ln\_ECMWF}\forcode{=.true.}):
750  Based on \href{}{IFS (Cy31)} implementation and documentation.
751  Surface roughness lengths needed for the Obukhov length are computed following \citet{beljaars_QJRMS95}.
754% -------------------------------------------------------------------------------------------------------------
755%        Ice-Atmosphere Bulk formulae
756% -------------------------------------------------------------------------------------------------------------
757\subsection{Ice-Atmosphere Bulk formulae}
760Surface turbulent fluxes between sea-ice and the atmosphere can be computed in three different ways:
764  Constant value (\np{constant value}{constant\ value}\forcode{ Cd_ice = 1.4e-3 }):
765  default constant value used for momentum and heat neutral transfer coefficients
767  \citet{lupkes.gryanik.ea_JGR12} (\np{ln_Cd_L12}{ln\_Cd\_L12}\forcode{=.true.}):
768  This scheme adds a dependency on edges at leads, melt ponds and flows
769  of the constant neutral air-ice drag. After some approximations,
770  this can be resumed to a dependency on ice concentration (A).
771  This drag coefficient has a parabolic shape (as a function of ice concentration)
772  starting at 1.5e-3 for A=0, reaching 1.97e-3 for A=0.5 and going down 1.4e-3 for A=1.
773  It is theoretically applicable to all ice conditions (not only MIZ).
775  \citet{lupkes.gryanik_JGR15} (\np{ln_Cd_L15}{ln\_Cd\_L15}\forcode{=.true.}):
776  Alternative turbulent transfer coefficients formulation between sea-ice
777  and atmosphere with distinct momentum and heat coefficients depending
778  on sea-ice concentration and atmospheric stability (no melt-ponds effect for now).
779  The parameterization is adapted from ECHAM6 atmospheric model.
780  Compared to Lupkes2012 scheme, it considers specific skin and form drags
781  to compute neutral transfer coefficients for both heat and momentum fluxes.
782  Atmospheric stability effect on transfer coefficient is also taken into account.
787% ================================================================
788% Coupled formulation
789% ================================================================
790\section[Coupled formulation (\textit{sbccpl.F90})]{Coupled formulation (\protect\mdl{sbccpl})}
795  \nlst{namsbc_cpl}
796  \caption{\forcode{&namsbc_cpl}}
797  \label{lst:namsbc_cpl}
801In the coupled formulation of the surface boundary condition,
802the fluxes are provided by the OASIS coupler at a frequency which is defined in the OASIS coupler namelist,
803while sea and ice surface temperature, ocean and ice albedo, and ocean currents are sent to
804the atmospheric component.
806A generalised coupled interface has been developed.
807It is currently interfaced with OASIS-3-MCT versions 1 to 4 (\key{oasis3}).
808An additional specific CPP key (\key{oa3mct\_v1v2}) is needed for OASIS-3-MCT versions 1 and 2.
809It has been successfully used to interface \NEMO\ to most of the European atmospheric GCM
810(ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz), as well as to \href{}{WRF}
811(Weather Research and Forecasting Model).
813When PISCES biogeochemical model (\key{top}) is also used in the coupled system,
814the whole carbon cycle is computed.
815In this case, CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system
816(and need to be activated in \nam{sbc_cpl}{sbc\_cpl} ).
818The namelist above allows control of various aspects of the coupling fields (particularly for vectors) and
819now allows for any coupling fields to have multiple sea ice categories (as required by LIM3 and CICE).
820When indicating a multi-category coupling field in \nam{sbc_cpl}{sbc\_cpl}, the number of categories will be determined by
821the number used in the sea ice model.
822In some limited cases, it may be possible to specify single category coupling fields even when
823the sea ice model is running with multiple categories -
824in this case, the user should examine the code to be sure the assumptions made are satisfactory.
825In cases where this is definitely not possible, the model should abort with an error message.
829% ================================================================
830%        Atmospheric pressure
831% ================================================================
832\section[Atmospheric pressure (\textit{sbcapr.F90})]{Atmospheric pressure (\protect\mdl{sbcapr})}
837  \nlst{namsbc_apr}
838  \caption{\forcode{&namsbc_apr}}
839  \label{lst:namsbc_apr}
843The optional atmospheric pressure can be used to force ocean and ice dynamics
844(\np{ln_apr_dyn}{ln\_apr\_dyn}\forcode{=.true.}, \nam{sbc} namelist).
845The input atmospheric forcing defined via \np{sn_apr}{sn\_apr} structure (\nam{sbc_apr}{sbc\_apr} namelist)
846can be interpolated in time to the model time step, and even in space when the interpolation on-the-fly is used.
847When used to force the dynamics, the atmospheric pressure is further transformed into
848an equivalent inverse barometer sea surface height, $\eta_{ib}$, using:
850  % \label{eq:SBC_ssh_ib}
851  \eta_{ib} = -  \frac{1}{g\,\rho_o}  \left( P_{atm} - P_o \right)
853where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure.
854A value of $101,000~N/m^2$ is used unless \np{ln_ref_apr}{ln\_ref\_apr} is set to true.
855In this case, $P_o$ is set to the value of $P_{atm}$ averaged over the ocean domain,
856\ie\ the mean value of $\eta_{ib}$ is kept to zero at all time steps.
858The gradient of $\eta_{ib}$ is added to the RHS of the ocean momentum equation (see \mdl{dynspg} for the ocean).
859For sea-ice, the sea surface height, $\eta_m$, which is provided to the sea ice model is set to $\eta - \eta_{ib}$
860(see \mdl{sbcssr} module).
861$\eta_{ib}$ can be written in the output.
862This can simplify altimetry data and model comparison as
863inverse barometer sea surface height is usually removed from these date prior to their distribution.
865When using time-splitting and BDY package for open boundaries conditions,
866the equivalent inverse barometer sea surface height $\eta_{ib}$ can be added to BDY ssh data:
867\np{ln_apr_obc}{ln\_apr\_obc}  might be set to true.
871% ================================================================
872%        Surface Tides Forcing
873% ================================================================
874\section[Surface tides (\textit{sbctide.F90})]{Surface tides (\protect\mdl{sbctide})}
880  \nlst{nam_tide}
881  \caption{\forcode{&nam_tide}}
882  \label{lst:nam_tide}
886The tidal forcing, generated by the gravity forces of the Earth-Moon and Earth-Sun sytems,
887is activated if \np{ln_tide}{ln\_tide} and \np{ln_tide_pot}{ln\_tide\_pot} are both set to \forcode{.true.} in \nam{_tide}{\_tide}.
888This translates as an additional barotropic force in the momentum \autoref{eq:MB_PE_dyn} such that:
890  % \label{eq:SBC_PE_dyn_tides}
891  \frac{\partial {\mathrm {\mathbf U}}_h }{\partial t}= ...
892  +g\nabla (\Pi_{eq} + \Pi_{sal})
894where $\Pi_{eq}$ stands for the equilibrium tidal forcing and
895$\Pi_{sal}$ is a self-attraction and loading term (SAL).
897The equilibrium tidal forcing is expressed as a sum over a subset of
898constituents chosen from the set of available tidal constituents
899defined in file \hf{SBC/tide} (this comprises the tidal
900constituents \textit{M2, N2, 2N2, S2, K2, K1, O1, Q1, P1, M4, Mf, Mm,
901  Msqm, Mtm, S1, MU2, NU2, L2}, and \textit{T2}). Individual
902constituents are selected by including their names in the array
903\np{clname}{clname} in \nam{_tide}{\_tide} (e.g., \np{clname}{clname}\forcode{(1)='M2', }
904\np{clname}{clname}\forcode{(2)='S2'} to select solely the tidal consituents \textit{M2}
905and \textit{S2}). Optionally, when \np{ln_tide_ramp}{ln\_tide\_ramp} is set to
906\forcode{.true.}, the equilibrium tidal forcing can be ramped up
907linearly from zero during the initial \np{rdttideramp}{rdttideramp} days of the
908model run.
910The SAL term should in principle be computed online as it depends on
911the model tidal prediction itself (see \citet{arbic.garner.ea_DSR04} for a
912discussion about the practical implementation of this term).
913Nevertheless, the complex calculations involved would make this
914computationally too expensive. Here, two options are available:
915$\Pi_{sal}$ generated by an external model can be read in
916(\np{ln_read_load}{ln\_read\_load}\forcode{ =.true.}), or a ``scalar approximation'' can be
917used (\np{ln_scal_load}{ln\_scal\_load}\forcode{ =.true.}). In the latter case
919  \Pi_{sal} = \beta \eta,
921where $\beta$ (\np{rn_scal_load}{rn\_scal\_load} with a default value of 0.094) is a
922spatially constant scalar, often chosen to minimize tidal prediction
923errors. Setting both \np{ln_read_load}{ln\_read\_load} and \np{ln_scal_load}{ln\_scal\_load} to
924\forcode{.false.} removes the SAL contribution.
928% ================================================================
929%        River runoffs
930% ================================================================
931\section[River runoffs (\textit{sbcrnf.F90})]{River runoffs (\protect\mdl{sbcrnf})}
936  \nlst{namsbc_rnf}
937  \caption{\forcode{&namsbc_rnf}}
938  \label{lst:namsbc_rnf}
942%River runoff generally enters the ocean at a nonzero depth rather than through the surface.
943%Many models, however, have traditionally inserted river runoff to the top model cell.
944%This was the case in \NEMO\ prior to the version 3.3. The switch toward a input of runoff
945%throughout a nonzero depth has been motivated by the numerical and physical problems
946%that arise when the top grid cells are of the order of one meter. This situation is common in
947%coastal modelling and becomes more and more often open ocean and climate modelling
948%\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
949%required to properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}. see also \autoref{fig:SBC_dcy}.}.
952%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the
953%\mdl{tra\_sbc} module.  We decided to separate them throughout the code, so that the variable
954%\textit{emp} represented solely evaporation minus precipitation fluxes, and a new 2d variable
955%rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with
956%emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use
957%emp or emps and the changes made are below:
961River runoff generally enters the ocean at a nonzero depth rather than through the surface.
962Many models, however, have traditionally inserted river runoff to the top model cell.
963This was the case in \NEMO\ prior to the version 3.3,
964and was combined with an option to increase vertical mixing near the river mouth.
966However, with this method numerical and physical problems arise when the top grid cells are of the order of one meter.
967This situation is common in coastal modelling and is becoming more common in open ocean and climate modelling
969  At least a top cells thickness of 1~meter and a 3 hours forcing frequency are required to
970  properly represent the diurnal cycle \citep{bernie.woolnough.ea_JC05}.
971  see also \autoref{fig:SBC_dcy}.}.
973As such from V~3.3 onwards it is possible to add river runoff through a non-zero depth,
974and for the temperature and salinity of the river to effect the surrounding ocean.
975The user is able to specify, in a NetCDF input file, the temperature and salinity of the river,
976along with the depth (in metres) which the river should be added to.
978Namelist variables in \nam{sbc_rnf}{sbc\_rnf}, \np{ln_rnf_depth}{ln\_rnf\_depth}, \np{ln_rnf_sal}{ln\_rnf\_sal} and
979\np{ln_rnf_temp}{ln\_rnf\_temp} control whether the river attributes (depth, salinity and temperature) are read in and used.
980If these are set as false the river is added to the surface box only, assumed to be fresh (0~psu),
981and/or taken as surface temperature respectively.
983The runoff value and attributes are read in in sbcrnf.
984For temperature -999 is taken as missing data and the river temperature is taken to
985be the surface temperatue at the river point.
986For the depth parameter a value of -1 means the river is added to the surface box only,
987and a value of -999 means the river is added through the entire water column.
988After being read in the temperature and salinity variables are multiplied by the amount of runoff
989(converted into m/s) to give the heat and salt content of the river runoff.
990After the user specified depth is read ini,
991the number of grid boxes this corresponds to is calculated and stored in the variable \np{nz_rnf}{nz\_rnf}.
992The variable \textit{h\_dep} is then calculated to be the depth (in metres) of
993the bottom of the lowest box the river water is being added to
994(\ie\ the total depth that river water is being added to in the model).
996The mass/volume addition due to the river runoff is, at each relevant depth level, added to
997the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divhor}).
998This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux.
999The sea surface height is calculated using the sum of the horizontal divergence terms,
1000and so the river runoff indirectly forces an increase in sea surface height.
1002The \textit{hdivn} terms are used in the tracer advection modules to force vertical velocities.
1003This causes a mass of water, equal to the amount of runoff, to be moved into the box above.
1004The heat and salt content of the river runoff is not included in this step,
1005and so the tracer concentrations are diluted as water of ocean temperature and salinity is moved upward out of
1006the box and replaced by the same volume of river water with no corresponding heat and salt addition.
1008For the linear free surface case, at the surface box the tracer advection causes a flux of water
1009(of equal volume to the runoff) through the sea surface out of the domain,
1010which causes a salt and heat flux out of the model.
1011As such the volume of water does not change, but the water is diluted.
1013For the non-linear free surface case, no flux is allowed through the surface.
1014Instead in the surface box (as well as water moving up from the boxes below) a volume of runoff water is added with
1015no corresponding heat and salt addition and so as happens in the lower boxes there is a dilution effect.
1016(The runoff addition to the top box along with the water being moved up through
1017boxes below means the surface box has a large increase in volume, whilst all other boxes remain the same size)
1019In trasbc the addition of heat and salt due to the river runoff is added.
1020This is done in the same way for both vvl and non-vvl.
1021The temperature and salinity are increased through the specified depth according to
1022the heat and salt content of the river.
1024In the non-linear free surface case (vvl),
1025near the end of the time step the change in sea surface height is redistrubuted through the grid boxes,
1026so that the original ratios of grid box heights are restored.
1027In doing this water is moved into boxes below, throughout the water column,
1028so the large volume addition to the surface box is spread between all the grid boxes.
1030It is also possible for runnoff to be specified as a negative value for modelling flow through straits,
1031\ie\ modelling the Baltic flow in and out of the North Sea.
1032When the flow is out of the domain there is no change in temperature and salinity,
1033regardless of the namelist options used,
1034as the ocean water leaving the domain removes heat and salt (at the same concentration) with it.
1037%\colorbox{yellow}{Nevertheless, Pb of vertical resolution and 3D input : increase vertical mixing near river mouths to mimic a 3D river
1039%All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.}
1041%\colorbox{yellow}{river mouths{\ldots}}
1043%IF( ln_rnf ) THEN                                     ! increase diffusivity at rivers mouths
1044%        DO jk = 2, nkrnf   ;   avt(:,:,jk) = avt(:,:,jk) + rn_avt_rnf * rnfmsk(:,:)   ;   END DO
1047%\gmcomment{  word doc of runoffs:
1049%In the current \NEMO\ setup river runoff is added to emp fluxes, these are then applied at just the sea surface as a volume change (in the variable volume case this is a literal volume change, and in the linear free surface case the free surface is moved) and a salt flux due to the concentration/dilution effect.  There is also an option to increase vertical mixing near river mouths; this gives the effect of having a 3d river.  All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.
1050%Our aim was to code the option to specify the temperature and salinity of river runoff, (as well as the amount), along with the depth that the river water will affect.  This would make it possible to model low salinity outflow, such as the Baltic, and would allow the ocean temperature to be affected by river runoff.
1052%The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between.
1054%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the tra_sbc module.  We decided to separate them throughout the code, so that the variable emp represented solely evaporation minus precipitation fluxes, and a new 2d variable rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use emp or emps and the changes made are below:
1058% ================================================================
1059%        Ice shelf melting
1060% ================================================================
1061\section[Ice shelf melting (\textit{sbcisf.F90})]{Ice shelf melting (\protect\mdl{sbcisf})}
1066  \nlst{namsbc_isf}
1067  \caption{\forcode{&namsbc_isf}}
1068  \label{lst:namsbc_isf}
1072The namelist variable in \nam{sbc}, \np{nn_isf}{nn\_isf}, controls the ice shelf representation.
1073Description and result of sensitivity test to \np{nn_isf}{nn\_isf} are presented in \citet{mathiot.jenkins.ea_GMD17}.
1074The different options are illustrated in \autoref{fig:SBC_isf}.
1078  \item[\np{nn_isf}{nn\_isf}\forcode{=1}]:
1079  The ice shelf cavity is represented (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
1080  The fwf and heat flux are depending of the local water properties.
1082  Two different bulk formulae are available:
1084   \begin{description}
1085   \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=1}]:
1086     The melt rate is based on a balance between the upward ocean heat flux and
1087     the latent heat flux at the ice shelf base. A complete description is available in \citet{hunter_rpt06}.
1088   \item[\np{nn_isfblk}{nn\_isfblk}\forcode{=2}]:
1089     The melt rate and the heat flux are based on a 3 equations formulation
1090     (a heat flux budget at the ice base, a salt flux budget at the ice base and a linearised freezing point temperature equation).
1091     A complete description is available in \citet{jenkins_JGR91}.
1092   \end{description}
1094     Temperature and salinity used to compute the melt are the average temperature in the top boundary layer \citet{losch_JGR08}.
1095     Its thickness is defined by \np{rn_hisf_tbl}{rn\_hisf\_tbl}.
1096     The fluxes and friction velocity are computed using the mean temperature, salinity and velocity in the the first \np{rn_hisf_tbl}{rn\_hisf\_tbl} m.
1097     Then, the fluxes are spread over the same thickness (ie over one or several cells).
1098     If \np{rn_hisf_tbl}{rn\_hisf\_tbl} larger than top $e_{3}t$, there is no more feedback between the freezing point at the interface and the the top cell temperature.
1099     This can lead to super-cool temperature in the top cell under melting condition.
1100     If \np{rn_hisf_tbl}{rn\_hisf\_tbl} smaller than top $e_{3}t$, the top boundary layer thickness is set to the top cell thickness.\\
1102     Each melt bulk formula depends on a exchange coeficient ($\Gamma^{T,S}$) between the ocean and the ice.
1103     There are 3 different ways to compute the exchange coeficient:
1104   \begin{description}
1105        \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=0}]:
1106     The salt and heat exchange coefficients are constant and defined by \np{rn_gammas0}{rn\_gammas0} and \np{rn_gammat0}{rn\_gammat0}.
1107     \begin{gather*}
1108       % \label{eq:SBC_isf_gamma_iso}
1109       \gamma^{T} = rn\_gammat0 \\
1110       \gamma^{S} = rn\_gammas0
1111     \end{gather*}
1112     This is the recommended formulation for ISOMIP.
1113   \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=1}]:
1114     The salt and heat exchange coefficients are velocity dependent and defined as
1115     \begin{gather*}
1116       \gamma^{T} = rn\_gammat0 \times u_{*} \\
1117       \gamma^{S} = rn\_gammas0 \times u_{*}
1118     \end{gather*}
1119     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters).
1120     See \citet{jenkins.nicholls.ea_JPO10} for all the details on this formulation. It is the recommended formulation for realistic application.
1121   \item[\np{nn_gammablk}{nn\_gammablk}\forcode{=2}]:
1122     The salt and heat exchange coefficients are velocity and stability dependent and defined as:
1124\gamma^{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}
1126     where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn_hisf_tbl}{rn\_hisf\_tbl} meters),
1127     $\Gamma_{Turb}$ the contribution of the ocean stability and
1128     $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
1129     See \citet{holland.jenkins_JPO99} for all the details on this formulation.
1130     This formulation has not been extensively tested in \NEMO\ (not recommended).
1131   \end{description}
1132  \item[\np{nn_isf}{nn\_isf}\forcode{=2}]:
1133   The ice shelf cavity is not represented.
1134   The fwf and heat flux are computed using the \citet{beckmann.goosse_OM03} parameterisation of isf melting.
1135   The fluxes are distributed along the ice shelf edge between the depth of the average grounding line (GL)
1136   (\np{sn_depmax_isf}{sn\_depmax\_isf}) and the base of the ice shelf along the calving front
1137   (\np{sn_depmin_isf}{sn\_depmin\_isf}) as in (\np{nn_isf}{nn\_isf}\forcode{=3}).
1138   The effective melting length (\np{sn_Leff_isf}{sn\_Leff\_isf}) is read from a file.
1139  \item[\np{nn_isf}{nn\_isf}\forcode{=3}]:
1140   The ice shelf cavity is not represented.
1141   The fwf (\np{sn_rnfisf}{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between
1142   the depth of the average grounding line (GL) (\np{sn_depmax_isf}{sn\_depmax\_isf}) and
1143   the base of the ice shelf along the calving front (\np{sn_depmin_isf}{sn\_depmin\_isf}).
1144   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
1145  \item[\np{nn_isf}{nn\_isf}\forcode{=4}]:
1146   The ice shelf cavity is opened (\np{ln_isfcav}{ln\_isfcav}\forcode{=.true.} needed).
1147   However, the fwf is not computed but specified from file \np{sn_fwfisf}{sn\_fwfisf}).
1148   The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
1149   As in \np{nn_isf}{nn\_isf}\forcode{=1}, the fluxes are spread over the top boundary layer thickness (\np{rn_hisf_tbl}{rn\_hisf\_tbl})\\
1152$\bullet$ \np{nn_isf}{nn\_isf}\forcode{=1} and \np{nn_isf}{nn\_isf}\forcode{=2} compute a melt rate based on
1153the water mass properties, ocean velocities and depth.
1154This flux is thus highly dependent of the model resolution (horizontal and vertical),
1155realism of the water masses onto the shelf ...\\
1157$\bullet$ \np{nn_isf}{nn\_isf}\forcode{=3} and \np{nn_isf}{nn\_isf}\forcode{=4} read the melt rate from a file.
1158You have total control of the fwf forcing.
1159This can be useful if the water masses on the shelf are not realistic or
1160the resolution (horizontal/vertical) are too coarse to have realistic melting or
1161for studies where you need to control your heat and fw input.\\
1163The ice shelf melt is implemented as a volume flux as for the runoff.
1164The fw addition due to the ice shelf melting is, at each relevant depth level, added to
1165the horizontal divergence (\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divhor}.
1166See the runoff section \autoref{sec:SBC_rnf} for all the details about the divergence correction.\\
1170  \centering
1171  \includegraphics[width=0.66\textwidth]{Fig_SBC_isf}
1172  \caption[Ice shelf location and fresh water flux definition]{
1173    Illustration of the location where the fwf is injected and
1174    whether or not the fwf is interactif or not depending of \protect\np{nn_isf}{nn\_isf}.}
1175  \label{fig:SBC_isf}
1181% ================================================================
1182%        Ice sheet coupling
1183% ================================================================
1184\section{Ice sheet coupling}
1189  \nlst{namsbc_iscpl}
1190  \caption{\forcode{&namsbc_iscpl}}
1191  \label{lst:namsbc_iscpl}
1195Ice sheet/ocean coupling is done through file exchange at the restart step.
1196At each restart step:
1199\item[Step 1]: the ice sheet model send a new bathymetry and ice shelf draft netcdf file.
1200\item[Step 2]: a new file is built using the DOMAINcfg tools.
1201\item[Step 3]: \NEMO\ run for a specific period and output the average melt rate over the period.
1202\item[Step 4]: the ice sheet model run using the melt rate outputed in step 4.
1203\item[Step 5]: go back to 1.
1206If \np{ln_iscpl}{ln\_iscpl}\forcode{=.true.}, the isf draft is assume to be different at each restart step with
1207potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
1208The wetting and drying scheme applied on the restart is very simple and described below for the 6 different possible cases:
1211\item[Thin a cell down]:
1212  T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant
1213  ($bt_b=bt_n$).
1214\item[Enlarge  a cell]:
1215  See case "Thin a cell down"
1216\item[Dry a cell]:
1217  mask, T/S, U/V and ssh are set to 0.
1218  Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$).
1219\item[Wet a cell]:
1220  mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0.
1221  If no neighbours, T/S is extrapolated from old top cell value.
1222  If no neighbours along i,j and k (both previous test failed), T/S/U/V/ssh and mask are set to 0.
1223\item[Dry a column]:
1224   mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0.
1225\item[Wet a column]:
1226  set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0.
1227  If no neighbour, T/S/U/V and mask set to 0.
1230Furthermore, as the before and now fields are not compatible (modification of the geometry),
1231the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.\\
1233The horizontal extrapolation to fill new cell with realistic value is called \np{nn_drown}{nn\_drown} times.
1234It means that if the grounding line retreat by more than \np{nn_drown}{nn\_drown} cells between 2 coupling steps,
1235the code will be unable to fill all the new wet cells properly.
1236The default number is set up for the MISOMIP idealised experiments.
1237This coupling procedure is able to take into account grounding line and calving front migration.
1238However, it is a non-conservative processe.
1239This could lead to a trend in heat/salt content and volume.\\
1241In order to remove the trend and keep the conservation level as close to 0 as possible,
1242a simple conservation scheme is available with \np{ln_hsb}{ln\_hsb}\forcode{=.true.}.
1243The heat/salt/vol. gain/loss is diagnosed, as well as the location.
1244A correction increment is computed and apply each time step during the next \np{rn_fiscpl}{rn\_fiscpl} time steps.
1245For safety, it is advised to set \np{rn_fiscpl}{rn\_fiscpl} equal to the coupling period (smallest increment possible).
1246The corrective increment is apply into the cell itself (if it is a wet cell), the neigbouring cells or the closest wet cell (if the cell is now dry).
1250% ================================================================
1251%        Handling of icebergs
1252% ================================================================
1253\section{Handling of icebergs (ICB)}
1258  \nlst{namberg}
1259  \caption{\forcode{&namberg}}
1260  \label{lst:namberg}
1264Icebergs are modelled as lagrangian particles in \NEMO\ \citep{marsh.ivchenko.ea_GMD15}.
1265Their physical behaviour is controlled by equations as described in \citet{martin.adcroft_OM10} ).
1266(Note that the authors kindly provided a copy of their code to act as a basis for implementation in \NEMO).
1267Icebergs are initially spawned into one of ten classes which have specific mass and thickness as
1268described in the \nam{berg} namelist: \np{rn_initial_mass}{rn\_initial\_mass} and \np{rn_initial_thickness}{rn\_initial\_thickness}.
1269Each class has an associated scaling (\np{rn_mass_scaling}{rn\_mass\_scaling}),
1270which is an integer representing how many icebergs of this class are being described as one lagrangian point
1271(this reduces the numerical problem of tracking every single iceberg).
1272They are enabled by setting \np{ln_icebergs}{ln\_icebergs}\forcode{=.true.}.
1274Two initialisation schemes are possible.
1277  In this scheme, the value of \np{nn_test_icebergs}{nn\_test\_icebergs} represents the class of iceberg to generate
1278  (so between 1 and 10), and \np{nn_test_icebergs}{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of
1279  which an iceberg is generated at the beginning of the run.
1280  (Note that this happens each time the timestep equals \np{nn_nit000}{nn\_nit000}.)
1281  \np{nn_test_icebergs}{nn\_test\_icebergs} is defined by four numbers in \np{nn_test_box}{nn\_test\_box} representing the corners of
1282  the geographical box: lonmin,lonmax,latmin,latmax
1284  In this scheme, the model reads a calving file supplied in the \np{sn_icb}{sn\_icb} parameter.
1285  This should be a file with a field on the configuration grid (typically ORCA)
1286  representing ice accumulation rate at each model point.
1287  These should be ocean points adjacent to land where icebergs are known to calve.
1288  Most points in this input grid are going to have value zero.
1289  When the model runs, ice is accumulated at each grid point which has a non-zero source term.
1290  At each time step, a test is performed to see if there is enough ice mass to
1291  calve an iceberg of each class in order (1 to 10).
1292  Note that this is the initial mass multiplied by the number each particle represents (\ie\ the scaling).
1293  If there is enough ice, a new iceberg is spawned and the total available ice reduced accordingly.
1296Icebergs are influenced by wind, waves and currents, bottom melt and erosion.
1297The latter act to disintegrate the iceberg.
1298This is either all melted freshwater,
1299or (if \np{rn_bits_erosion_fraction}{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits
1300which are assumed to propagate with their larger parent and thus delay fluxing into the ocean.
1301Melt water (and other variables on the configuration grid) are written into the main \NEMO\ model output files.
1303Extensive diagnostics can be produced.
1304Separate output files are maintained for human-readable iceberg information.
1305A separate file is produced for each processor (independent of \np{ln_ctl}{ln\_ctl}).
1306The amount of information is controlled by two integer parameters:
1308\item[\np{nn_verbose_level}{nn\_verbose\_level}] takes a value between one and four and
1309  represents an increasing number of points in the code at which variables are written,
1310  and an increasing level of obscurity.
1311\item[\np{nn_verbose_write}{nn\_verbose\_write}] is the number of timesteps between writes
1314Iceberg trajectories can also be written out and this is enabled by setting \np{nn_sample_rate}{nn\_sample\_rate}~$>$~0.
1315A non-zero value represents how many timesteps between writes of information into the output file.
1316These output files are in NETCDF format.
1317When \key{mpp\_mpi} is defined, each output file contains only those icebergs in the corresponding processor.
1318Trajectory points are written out in the order of their parent iceberg in the model's "linked list" of icebergs.
1319So care is needed to recreate data for individual icebergs,
1320since its trajectory data may be spread across multiple files.
1324% =============================================================================================================
1325%        Interactions with waves (sbcwave.F90, ln_wave)
1326% =============================================================================================================
1327\section[Interactions with waves (\textit{sbcwave.F90}, \forcode{ln_wave})]{Interactions with waves (\protect\mdl{sbcwave}, \protect\np{ln_wave}{ln\_wave})}
1332  \nlst{namsbc_wave}
1333  \caption{\forcode{&namsbc_wave}}
1334  \label{lst:namsbc_wave}
1338Ocean waves represent the interface between the ocean and the atmosphere, so \NEMO\ is extended to incorporate
1339physical processes related to ocean surface waves, namely the surface stress modified by growth and
1340dissipation of the oceanic wave field, the Stokes-Coriolis force and the Stokes drift impact on mass and
1341tracer advection; moreover the neutral surface drag coefficient from a wave model can be used to evaluate
1342the wind stress.
1344Physical processes related to ocean surface waves can be accounted by setting the logical variable
1345\np{ln_wave}{ln\_wave}\forcode{=.true.} in \nam{sbc} namelist. In addition, specific flags accounting for
1346different processes should be activated as explained in the following sections.
1348Wave fields can be provided either in forced or coupled mode:
1350\item[forced mode]: wave fields should be defined through the \nam{sbc_wave}{sbc\_wave} namelist
1351for external data names, locations, frequency, interpolation and all the miscellanous options allowed by
1352Input Data generic Interface (see \autoref{sec:SBC_input}).
1353\item[coupled mode]: \NEMO\ and an external wave model can be coupled by setting \np{ln_cpl}{ln\_cpl} \forcode{= .true.}
1354in \nam{sbc} namelist and filling the \nam{sbc_cpl}{sbc\_cpl} namelist.
1358% ----------------------------------------------------------------
1359% Neutral drag coefficient from wave model (ln_cdgw)
1361% ----------------------------------------------------------------
1362\subsection[Neutral drag coefficient from wave model (\forcode{ln_cdgw})]{Neutral drag coefficient from wave model (\protect\np{ln_cdgw}{ln\_cdgw})}
1365The neutral surface drag coefficient provided from an external data source (\ie\ a wave model),
1366can be used by setting the logical variable \np{ln_cdgw}{ln\_cdgw} \forcode{= .true.} in \nam{sbc} namelist.
1367Then using the routine \rou{sbcblk\_algo\_ncar} and starting from the neutral drag coefficent provided,
1368the drag coefficient is computed according to the stable/unstable conditions of the
1369air-sea interface following \citet{large.yeager_rpt04}.
1372% ----------------------------------------------------------------
1373% 3D Stokes Drift (ln_sdw, nn_sdrift)
1374% ----------------------------------------------------------------
1375\subsection[3D Stokes Drift (\forcode{ln_sdw} \& \forcode{nn_sdrift})]{3D Stokes Drift (\protect\np{ln_sdw}{ln\_sdw} \& \np{nn_sdrift}{nn\_sdrift})}
1378The Stokes drift is a wave driven mechanism of mass and momentum transport \citep{stokes_ibk09}.
1379It is defined as the difference between the average velocity of a fluid parcel (Lagrangian velocity)
1380and the current measured at a fixed point (Eulerian velocity).
1381As waves travel, the water particles that make up the waves travel in orbital motions but
1382without a closed path. Their movement is enhanced at the top of the orbit and slowed slightly
1383at the bottom, so the result is a net forward motion of water particles, referred to as the Stokes drift.
1384An accurate evaluation of the Stokes drift and the inclusion of related processes may lead to improved
1385representation of surface physics in ocean general circulation models. %GS: reference needed
1386The Stokes drift velocity $\mathbf{U}_{st}$ in deep water can be computed from the wave spectrum and may be written as:
1389  % \label{eq:SBC_wave_sdw}
1390  \mathbf{U}_{st} = \frac{16{\pi^3}} {g}
1391  \int_0^\infty \int_{-\pi}^{\pi} (cos{\theta},sin{\theta}) {f^3}
1392  \mathrm{S}(f,\theta) \mathrm{e}^{2kz}\,\mathrm{d}\theta {d}f
1395where: ${\theta}$ is the wave direction, $f$ is the wave intrinsic frequency,
1396$\mathrm{S}($f$,\theta)$ is the 2D frequency-direction spectrum,
1397$k$ is the mean wavenumber defined as:
1398$k=\frac{2\pi}{\lambda}$ (being $\lambda$ the wavelength). \\
1400In order to evaluate the Stokes drift in a realistic ocean wave field, the wave spectral shape is required
1401and its computation quickly becomes expensive as the 2D spectrum must be integrated for each vertical level.
1402To simplify, it is customary to use approximations to the full Stokes profile.
1403Three possible parameterizations for the calculation for the approximate Stokes drift velocity profile
1404are included in the code through the \np{nn_sdrift}{nn\_sdrift} parameter once provided the surface Stokes drift
1405$\mathbf{U}_{st |_{z=0}}$ which is evaluated by an external wave model that accurately reproduces the wave spectra
1406and makes possible the estimation of the surface Stokes drift for random directional waves in
1407realistic wave conditions:
1410\item[\np{nn_sdrift}{nn\_sdrift} = 0]: exponential integral profile parameterization proposed by
1414  % \label{eq:SBC_wave_sdw_0a}
1415  \mathbf{U}_{st} \cong \mathbf{U}_{st |_{z=0}} \frac{\mathrm{e}^{-2k_ez}} {1-8k_ez}
1418where $k_e$ is the effective wave number which depends on the Stokes transport $T_{st}$ defined as follows:
1421  % \label{eq:SBC_wave_sdw_0b}
1422  k_e = \frac{|\mathbf{U}_{\\right|_{z=0}}|} {|T_{st}|}
1423  \quad \text{and }\
1424  T_{st} = \frac{1}{16} \bar{\omega} H_s^2
1427where $H_s$ is the significant wave height and $\omega$ is the wave frequency.
1429\item[\np{nn_sdrift}{nn\_sdrift} = 1]: velocity profile based on the Phillips spectrum which is considered to be a
1430reasonable estimate of the part of the spectrum mostly contributing to the Stokes drift velocity near the surface
1434  % \label{eq:SBC_wave_sdw_1}
1435  \mathbf{U}_{st} \cong \mathbf{U}_{st |_{z=0}} \Big[exp(2k_pz)-\beta \sqrt{-2 \pi k_pz}
1436  \textit{ erf } \Big(\sqrt{-2 k_pz}\Big)\Big]
1439where $erf$ is the complementary error function and $k_p$ is the peak wavenumber.
1441\item[\np{nn_sdrift}{nn\_sdrift} = 2]: velocity profile based on the Phillips spectrum as for \np{nn_sdrift}{nn\_sdrift} = 1
1442but using the wave frequency from a wave model.
1446The Stokes drift enters the wave-averaged momentum equation, as well as the tracer advection equations
1447and its effect on the evolution of the sea-surface height ${\eta}$ is considered as follows:
1450  % \label{eq:SBC_wave_eta_sdw}
1451  \frac{\partial{\eta}}{\partial{t}} =
1452  -\nabla_h \int_{-H}^{\eta} (\mathbf{U} + \mathbf{U}_{st}) dz
1455The tracer advection equation is also modified in order for Eulerian ocean models to properly account
1456for unresolved wave effect. The divergence of the wave tracer flux equals the mean tracer advection
1457that is induced by the three-dimensional Stokes velocity.
1458The advective equation for a tracer $c$ combining the effects of the mean current and sea surface waves
1459can be formulated as follows:
1462  % \label{eq:SBC_wave_tra_sdw}
1463  \frac{\partial{c}}{\partial{t}} =
1464  - (\mathbf{U} + \mathbf{U}_{st}) \cdot \nabla{c}
1468% ----------------------------------------------------------------
1469% Stokes-Coriolis term (ln_stcor)
1470% ----------------------------------------------------------------
1471\subsection[Stokes-Coriolis term (\forcode{ln_stcor})]{Stokes-Coriolis term (\protect\np{ln_stcor}{ln\_stcor})}
1474In a rotating ocean, waves exert a wave-induced stress on the mean ocean circulation which results
1475in a force equal to $\mathbf{U}_{st}$×$f$, where $f$ is the Coriolis parameter.
1476This additional force may have impact on the Ekman turning of the surface current.
1477In order to include this term, once evaluated the Stokes drift (using one of the 3 possible
1478approximations described in \autoref{subsec:SBC_wave_sdw}),
1479\np{ln_stcor}{ln\_stcor}\forcode{=.true.} has to be set.
1482% ----------------------------------------------------------------
1483% Waves modified stress (ln_tauwoc, ln_tauw)
1484% ----------------------------------------------------------------
1485\subsection[Wave modified stress (\forcode{ln_tauwoc} \& \forcode{ln_tauw})]{Wave modified sress (\protect\np{ln_tauwoc}{ln\_tauwoc} \& \np{ln_tauw}{ln\_tauw})}
1488The surface stress felt by the ocean is the atmospheric stress minus the net stress going
1489into the waves \citep{janssen.breivik.ea_rpt13}. Therefore, when waves are growing, momentum and energy is spent and is not
1490available for forcing the mean circulation, while in the opposite case of a decaying sea
1491state, more momentum is available for forcing the ocean.
1492Only when the sea state is in equilibrium, the ocean is forced by the atmospheric stress,
1493but in practice, an equilibrium sea state is a fairly rare event.
1494So the atmospheric stress felt by the ocean circulation $\tau_{oc,a}$ can be expressed as:
1497  % \label{eq:SBC_wave_tauoc}
1498  \tau_{oc,a} = \tau_a - \tau_w
1501where $\tau_a$ is the atmospheric surface stress;
1502$\tau_w$ is the atmospheric stress going into the waves defined as:
1505  % \label{eq:SBC_wave_tauw}
1506  \tau_w = \rho g \int {\frac{dk}{c_p} (S_{in}+S_{nl}+S_{diss})}
1509where: $c_p$ is the phase speed of the gravity waves,
1510$S_{in}$, $S_{nl}$ and $S_{diss}$ are three source terms that represent
1511the physics of ocean waves. The first one, $S_{in}$, describes the generation
1512of ocean waves by wind and therefore represents the momentum and energy transfer
1513from air to ocean waves; the second term $S_{nl}$ denotes
1514the nonlinear transfer by resonant four-wave interactions; while the third term $S_{diss}$
1515describes the dissipation of waves by processes such as white-capping, large scale breaking
1516eddy-induced damping.
1518The wave stress derived from an external wave model can be provided either through the normalized
1519wave stress into the ocean by setting \np{ln_tauwoc}{ln\_tauwoc}\forcode{=.true.}, or through the zonal and
1520meridional stress components by setting \np{ln_tauw}{ln\_tauw}\forcode{=.true.}.
1524% ================================================================
1525% Miscellanea options
1526% ================================================================
1527\section{Miscellaneous options}
1531% -------------------------------------------------------------------------------------------------------------
1532%        Diurnal cycle
1533% -------------------------------------------------------------------------------------------------------------
1534\subsection[Diurnal cycle (\textit{sbcdcy.F90})]{Diurnal cycle (\protect\mdl{sbcdcy})}
1543  \centering
1544  \includegraphics[width=0.66\textwidth]{Fig_SBC_diurnal}
1545  \caption[Reconstruction of the diurnal cycle variation of short wave flux]{
1546    Example of reconstruction of the diurnal cycle variation of short wave flux from
1547    daily mean values.
1548    The reconstructed diurnal cycle (black line) is chosen as
1549    the mean value of the analytical cycle (blue line) over a time step,
1550    not as the mid time step value of the analytically cycle (red square).
1551    From \citet{bernie.guilyardi.ea_CD07}.}
1552  \label{fig:SBC_diurnal}
1556\cite{bernie.woolnough.ea_JC05} have shown that to capture 90$\%$ of the diurnal variability of SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution of the surface fluxes of 3~h or less.
1557%Unfortunately high frequency forcing fields are rare, not to say inexistent. GS: not true anymore !
1558Nevertheless, it is possible to obtain a reasonable diurnal cycle of the SST knowning only short wave flux (SWF) at high frequency \citep{bernie.guilyardi.ea_CD07}.
1559Furthermore, only the knowledge of daily mean value of SWF is needed,
1560as higher frequency variations can be reconstructed from them,
1561assuming that the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle of incident SWF.
1562The \cite{bernie.guilyardi.ea_CD07} reconstruction algorithm is available in \NEMO\ by
1563setting \np{ln_dm2dc}{ln\_dm2dc}\forcode{=.true.} (a \textit{\nam{sbc}} namelist variable) when
1564using a bulk formulation (\np{ln_blk}{ln\_blk}\forcode{=.true.}) or
1565the flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}).
1566The reconstruction is performed in the \mdl{sbcdcy} module.
1567The detail of the algoritm used can be found in the appendix~A of \cite{bernie.guilyardi.ea_CD07}.
1568The algorithm preserves the daily mean incoming SWF as the reconstructed SWF at
1569a given time step is the mean value of the analytical cycle over this time step (\autoref{fig:SBC_diurnal}).
1570The use of diurnal cycle reconstruction requires the input SWF to be daily
1571(\ie\ a frequency of 24 hours and a time interpolation set to true in \np{sn_qsr}{sn\_qsr} namelist parameter).
1572Furthermore, it is recommended to have a least 8 surface module time steps per day,
1573that is  $\rdt \ nn\_fsbc < 10,800~s = 3~h$.
1574An example of recontructed SWF is given in \autoref{fig:SBC_dcy} for a 12 reconstructed diurnal cycle,
1575one every 2~hours (from 1am to 11pm).
1579  \centering
1580  \includegraphics[width=0.66\textwidth]{Fig_SBC_dcy}
1581  \caption[Reconstruction of the diurnal cycle variation of short wave flux on an ORCA2 grid]{
1582    Example of reconstruction of the diurnal cycle variation of short wave flux from
1583    daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm).
1584    The display is on (i,j) plane.}
1585  \label{fig:SBC_dcy}
1589Note also that the setting a diurnal cycle in SWF is highly recommended when
1590the top layer thickness approach 1~m or less, otherwise large error in SST can appear due to
1591an inconsistency between the scale of the vertical resolution and the forcing acting on that scale.
1594% -------------------------------------------------------------------------------------------------------------
1595%        Rotation of vector pairs onto the model grid directions
1596% -------------------------------------------------------------------------------------------------------------
1597\subsection{Rotation of vector pairs onto the model grid directions}
1600When using a flux (\np{ln_flx}{ln\_flx}\forcode{=.true.}) or bulk (\np{ln_blk}{ln\_blk}\forcode{=.true.}) formulation,
1601pairs of vector components can be rotated from east-north directions onto the local grid directions.
1602This is particularly useful when interpolation on the fly is used since here any vectors are likely to
1603be defined relative to a rectilinear grid.
1604To activate this option, a non-empty string is supplied in the rotation pair column of the relevant namelist.
1605The eastward component must start with "U" and the northward component with "V".
1606The remaining characters in the strings are used to identify which pair of components go together.
1607So for example, strings "U1" and "V1" next to "utau" and "vtau" would pair the wind stress components together and
1608rotate them on to the model grid directions;
1609"U2" and "V2" could be used against a second pair of components, and so on.
1610The extra characters used in the strings are arbitrary.
1611The rot\_rep routine from the \mdl{geo2ocean} module is used to perform the rotation.
1614% -------------------------------------------------------------------------------------------------------------
1615%        Surface restoring to observed SST and/or SSS
1616% -------------------------------------------------------------------------------------------------------------
1617\subsection[Surface restoring to observed SST and/or SSS (\textit{sbcssr.F90})]{Surface restoring to observed SST and/or SSS (\protect\mdl{sbcssr})}
1622  \nlst{namsbc_ssr}
1623  \caption{\forcode{&namsbc_ssr}}
1624  \label{lst:namsbc_ssr}
1628Options are defined through the \nam{sbc_ssr}{sbc\_ssr} namelist variables.
1629On forced mode using a flux formulation (\np{ln_flx}{ln\_flx}\forcode{=.true.}),
1630a feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
1632  % \label{eq:SBC_dmp_q}
1633  Q_{ns} = Q_{ns}^o + \frac{dQ}{dT} \left( \left. T \right|_{k=1} - SST_{Obs} \right)
1635where SST is a sea surface temperature field (observed or climatological),
1636$T$ is the model surface layer temperature and
1637$\frac{dQ}{dT}$ is a negative feedback coefficient usually taken equal to $-40~W/m^2/K$.
1638For a $50~m$ mixed-layer depth, this value corresponds to a relaxation time scale of two months.
1639This term ensures that if $T$ perfectly matches the supplied SST, then $Q$ is equal to $Q_o$.
1641In the fresh water budget, a feedback term can also be added.
1642Converted into an equivalent freshwater flux, it takes the following expression :
1645  \label{eq:SBC_dmp_emp}
1646  \textit{emp} = \textit{emp}_o + \gamma_s^{-1} e_{3t}  \frac{  \left(\left.S\right|_{k=1}-SSS_{Obs}\right)}
1647  {\left.S\right|_{k=1}}
1650where $\textit{emp}_{o }$ is a net surface fresh water flux
1651(observed, climatological or an atmospheric model product),
1652\textit{SSS}$_{Obs}$ is a sea surface salinity
1653(usually a time interpolation of the monthly mean Polar Hydrographic Climatology \citep{steele.morley.ea_JC01}),
1654$\left.S\right|_{k=1}$ is the model surface layer salinity and
1655$\gamma_s$ is a negative feedback coefficient which is provided as a namelist parameter.
1656Unlike heat flux, there is no physical justification for the feedback term in \autoref{eq:SBC_dmp_emp} as
1657the atmosphere does not care about ocean surface salinity \citep{madec.delecluse_IWN97}.
1658The SSS restoring term should be viewed as a flux correction on freshwater fluxes to
1659reduce the uncertainties we have on the observed freshwater budget.
1662% -------------------------------------------------------------------------------------------------------------
1663%        Handling of ice-covered area
1664% -------------------------------------------------------------------------------------------------------------
1665\subsection{Handling of ice-covered area  (\textit{sbcice\_...})}
1668The presence at the sea surface of an ice covered area modifies all the fluxes transmitted to the ocean.
1669There are several way to handle sea-ice in the system depending on
1670the value of the \np{nn_ice}{nn\_ice} namelist parameter found in \nam{sbc} namelist.
1672\item[nn\_ice = 0]
1673  there will never be sea-ice in the computational domain.
1674  This is a typical namelist value used for tropical ocean domain.
1675  The surface fluxes are simply specified for an ice-free ocean.
1676  No specific things is done for sea-ice.
1677\item[nn\_ice = 1]
1678  sea-ice can exist in the computational domain, but no sea-ice model is used.
1679  An observed ice covered area is read in a file.
1680  Below this area, the SST is restored to the freezing point and
1681  the heat fluxes are set to $-4~W/m^2$ ($-2~W/m^2$) in the northern (southern) hemisphere.
1682  The associated modification of the freshwater fluxes are done in such a way that
1683  the change in buoyancy fluxes remains zero.
1684  This prevents deep convection to occur when trying to reach the freezing point
1685  (and so ice covered area condition) while the SSS is too large.
1686  This manner of managing sea-ice area, just by using a IF case,
1687  is usually referred as the \textit{ice-if} model.
1688  It can be found in the \mdl{sbcice\_if} module.
1689\item[nn\_ice = 2 or more]
1690  A full sea ice model is used.
1691  This model computes the ice-ocean fluxes,
1692  that are combined with the air-sea fluxes using the ice fraction of each model cell to
1693  provide the surface averaged ocean fluxes.
1694  Note that the activation of a sea-ice model is done by defining a CPP key (\key{si3} or \key{cice}).
1695  The activation automatically overwrites the read value of nn\_ice to its appropriate value
1696  (\ie\ $2$ for SI3 or $3$ for CICE).
1699% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
1700%GS: ocean-ice (SI3) interface is not located in SBC directory anymore, so it should be included in SI3 doc
1703% -------------------------------------------------------------------------------------------------------------
1704%        CICE-ocean Interface
1705% -------------------------------------------------------------------------------------------------------------
1706\subsection[Interface to CICE (\textit{sbcice\_cice.F90})]{Interface to CICE (\protect\mdl{sbcice\_cice})}
1709It is possible to couple a regional or global \NEMO\ configuration (without AGRIF)
1710to the CICE sea-ice model by using \key{cice}.
1711The CICE code can be obtained from \href{}{LANL} and
1712the additional 'hadgem3' drivers will be required, even with the latest code release.
1713Input grid files consistent with those used in \NEMO\ will also be needed,
1714and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used
1715(seek advice from UKMO if necessary).
1716Currently, the code is only designed to work when using the NCAR forcing option for \NEMO\ %GS: still true ?
1717(with \textit{calc\_strair}\forcode{=.true.} and \textit{calc\_Tsfc}\forcode{=.true.} in the CICE name-list),
1718or alternatively when \NEMO\ is coupled to the HadGAM3 atmosphere model
1719(with \textit{calc\_strair}\forcode{=.false.} and \textit{calc\_Tsfc}\forcode{=false}).
1720The code is intended to be used with \np{nn_fsbc}{nn\_fsbc} set to 1
1721(although coupling ocean and ice less frequently should work,
1722it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly -
1723the user should check that results are not significantly different to the standard case).
1725There are two options for the technical coupling between \NEMO\ and CICE.
1726The standard version allows complete flexibility for the domain decompositions in the individual models,
1727but this is at the expense of global gather and scatter operations in the coupling which
1728become very expensive on larger numbers of processors.
1729The alternative option (using \key{nemocice\_decomp} for both \NEMO\ and CICE) ensures that
1730the domain decomposition is identical in both models (provided domain parameters are set appropriately,
1731and \textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and
1732allows much more efficient direct coupling on individual processors.
1733This solution scales much better although it is at the expense of having more idle CICE processors in areas where
1734there is no sea ice.
1737% -------------------------------------------------------------------------------------------------------------
1738%        Freshwater budget control
1739% -------------------------------------------------------------------------------------------------------------
1740\subsection[Freshwater budget control (\textit{sbcfwb.F90})]{Freshwater budget control (\protect\mdl{sbcfwb})}
1743For global ocean simulation, it can be useful to introduce a control of the mean sea level in order to
1744prevent unrealistic drift of the sea surface height due to inaccuracy in the freshwater fluxes.
1745In \NEMO, two way of controlling the freshwater budget are proposed:
1749  no control at all.
1750  The mean sea level is free to drift, and will certainly do so.
1752  global mean \textit{emp} set to zero at each model time step.
1753  %GS: comment below still relevant ?
1754  %Note that with a sea-ice model, this technique only controls the mean sea level with linear free surface and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling).
1756  freshwater budget is adjusted from the previous year annual mean budget which
1757  is read in the \textit{EMPave\_old.dat} file.
1758  As the model uses the Boussinesq approximation, the annual mean fresh water budget is simply evaluated from
1759  the change in the mean sea level at January the first and saved in the \textit{EMPav.dat} file.
1762% Griffies doc:
1763% When running ocean-ice simulations, we are not explicitly representing land processes,
1764% such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift,
1765% it is important to balance the hydrological cycle in ocean-ice models.
1766% We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff.
1767% The result of the normalization should be a global integrated zero net water input to the ocean-ice system over
1768% a chosen time scale.
1769% How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step,
1770% so that there is always a zero net input of water to the ocean-ice system.
1771% Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used
1772% to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance.
1773% Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
1774% When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean
1775% and ice models when aiming to balance the hydrological cycle.
1776% The reason is that it is the sum of the water in the ocean plus ice that should be balanced when running ocean-ice models,
1777% not the water in any one sub-component. As an extreme example to illustrate the issue,
1778% consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up,
1779% there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean.
1780% The total water contained in the ocean plus ice system is constant, but there is an exchange of water between
1781% the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle
1782% in ocean-ice models.
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