New URL for NEMO forge!   http://forge.nemo-ocean.eu

Since March 2022 along with NEMO 4.2 release, the code development moved to a self-hosted GitLab.
This present forge is now archived and remained online for history.
Chap_SBC.tex in trunk/DOC/TexFiles/Chapters – NEMO

source: trunk/DOC/TexFiles/Chapters/Chap_SBC.tex @ 6320

Last change on this file since 6320 was 6320, checked in by mathiot, 8 years ago

ISF: update documentation

File size: 83.3 KB
Line 
1% ================================================================
2% Chapter —— Surface Boundary Condition (SBC, ISF, ICB)
3% ================================================================
4\chapter{Surface Boundary Condition (SBC, ISF, ICB) }
5\label{SBC}
6\minitoc
7
8\newpage
9$\ $\newline    % force a new ligne
10%---------------------------------------namsbc--------------------------------------------------
11\namdisplay{namsbc}
12%--------------------------------------------------------------------------------------------------------------
13$\ $\newline    % force a new ligne
14
15The ocean needs six fields as surface boundary condition:
16\begin{itemize}
17   \item the two components of the surface ocean stress $\left( {\tau _u \;,\;\tau _v} \right)$
18   \item the incoming solar and non solar heat fluxes $\left( {Q_{ns} \;,\;Q_{sr} } \right)$
19   \item the surface freshwater budget $\left( {\textit{emp}} \right)$
20   \item the surface salt flux associated with freezing/melting of seawater $\left( {\textit{sfx}} \right)$
21\end{itemize}
22plus an optional field:
23\begin{itemize}
24   \item the atmospheric pressure at the ocean surface $\left( p_a \right)$
25\end{itemize}
26
27Five different ways to provide the first six fields to the ocean are available which
28are controlled by namelist \ngn{namsbc} variables: an analytical formulation (\np{ln\_ana}~=~true),
29a flux formulation (\np{ln\_flx}~=~true), a bulk formulae formulation (CORE
30(\np{ln\_blk\_core}~=~true), CLIO (\np{ln\_blk\_clio}~=~true) or MFS
31\footnote { Note that MFS bulk formulae compute fluxes only for the ocean component}
32(\np{ln\_blk\_mfs}~=~true) bulk formulae) and a coupled or mixed forced/coupled formulation
33(exchanges with a atmospheric model via the OASIS coupler) (\np{ln\_cpl} or \np{ln\_mixcpl}~=~true).
34When used ($i.e.$ \np{ln\_apr\_dyn}~=~true), the atmospheric pressure forces both ocean and ice dynamics.
35
36The frequency at which the forcing fields have to be updated is given by the \np{nn\_fsbc} namelist parameter.
37When the fields are supplied from data files (flux and bulk formulations), the input fields
38need not be supplied on the model grid. Instead a file of coordinates and weights can
39be supplied which maps the data from the supplied grid to the model points
40(so called "Interpolation on the Fly", see \S\ref{SBC_iof}).
41If the Interpolation on the Fly option is used, input data belonging to land points (in the native grid),
42can be masked to avoid spurious results in proximity of the coasts  as large sea-land gradients characterize
43most of the atmospheric variables.
44
45In addition, the resulting fields can be further modified using several namelist options.
46These options control
47\begin{itemize}
48\item the rotation of vector components supplied relative to an east-north
49coordinate system onto the local grid directions in the model ;
50\item the addition of a surface restoring term to observed SST and/or SSS (\np{ln\_ssr}~=~true) ;
51\item the modification of fluxes below ice-covered areas (using observed ice-cover or a sea-ice model) (\np{nn\_ice}~=~0,1, 2 or 3) ;
52\item the addition of river runoffs as surface freshwater fluxes or lateral inflow (\np{ln\_rnf}~=~true) ;
53\item the addition of isf melting as lateral inflow (parameterisation) or as fluxes applied at the land-ice ocean interface (\np{ln\_isf}) ;
54\item the addition of a freshwater flux adjustment in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2) ;
55\item the transformation of the solar radiation (if provided as daily mean) into a diurnal cycle (\np{ln\_dm2dc}~=~true) ;
56and a neutral drag coefficient can be read from an external wave model (\np{ln\_cdgw}~=~true).
57\end{itemize}
58The latter option is possible only in case core or mfs bulk formulas are selected.
59
60In this chapter, we first discuss where the surface boundary condition appears in the
61model equations. Then we present the five ways of providing the surface boundary condition,
62followed by the description of the atmospheric pressure and the river runoff.
63Next the scheme for interpolation on the fly is described.
64Finally, the different options that further modify the fluxes applied to the ocean are discussed.
65One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water.
66Another example of modification is that due to the ice shelf melting/freezing (see \S\ref{SBC_isf}),
67which provides additional sources of fresh water.
68
69
70% ================================================================
71% Surface boundary condition for the ocean
72% ================================================================
73\section{Surface boundary condition for the ocean}
74\label{SBC_general}
75
76The surface ocean stress is the stress exerted by the wind and the sea-ice
77on the ocean. It is applied in \mdl{dynzdf} module as a surface boundary condition of the
78computation of the momentum vertical mixing trend (see \eqref{Eq_dynzdf_sbc} in \S\ref{DYN_zdf}).
79As such, it has to be provided as a 2D vector interpolated
80onto the horizontal velocity ocean mesh, $i.e.$ resolved onto the model
81(\textbf{i},\textbf{j}) direction at $u$- and $v$-points.
82
83The surface heat flux is decomposed into two parts, a non solar and a solar heat
84flux, $Q_{ns}$ and $Q_{sr}$, respectively. The former is the non penetrative part
85of the heat flux ($i.e.$ the sum of sensible, latent and long wave heat fluxes
86plus the heat content of the mass exchange with the atmosphere and sea-ice).
87It is applied in \mdl{trasbc} module as a surface boundary condition trend of
88the first level temperature time evolution equation (see \eqref{Eq_tra_sbc} 
89and \eqref{Eq_tra_sbc_lin} in \S\ref{TRA_sbc}).
90The latter is the penetrative part of the heat flux. It is applied as a 3D
91trends of the temperature equation (\mdl{traqsr} module) when \np{ln\_traqsr}=\textit{true}.
92The way the light penetrates inside the water column is generally a sum of decreasing
93exponentials (see \S\ref{TRA_qsr}).
94
95The surface freshwater budget is provided by the \textit{emp} field.
96It represents the mass flux exchanged with the atmosphere (evaporation minus precipitation)
97and possibly with the sea-ice and ice shelves (freezing minus melting of ice).
98It affects both the ocean in two different ways:
99$(i)$   it changes the volume of the ocean and therefore appears in the sea surface height
100equation as a volume flux, and
101$(ii)$  it changes the surface temperature and salinity through the heat and salt contents
102of the mass exchanged with the atmosphere, the sea-ice and the ice shelves.
103
104
105%\colorbox{yellow}{Miss: }
106%
107%A extensive description of all namsbc namelist (parameter that have to be
108%created!)
109%
110%Especially the \np{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
111%ssv) i.e. information required by flux computation or sea-ice
112%
113%\mdl{sbc\_oce} containt the definition in memory of the 7 fields (6+runoff), add
114%a word on runoff: included in surface bc or add as lateral obc{\ldots}.
115%
116%Sbcmod manage the ``providing'' (fourniture) to the ocean the 7 fields
117%
118%Fluxes update only each nf{\_}sbc time step (namsbc) explain relation
119%between nf{\_}sbc and nf{\_}ice, do we define nf{\_}blk??? ? only one
120%nf{\_}sbc
121%
122%Explain here all the namlist namsbc variable{\ldots}.
123%
124% explain : use or not of surface currents
125%
126%\colorbox{yellow}{End Miss }
127
128The ocean model provides, at each time step, to the surface module (\mdl{sbcmod})
129the surface currents, temperature and salinity. 
130These variables are averaged over \np{nf\_sbc} time-step (\ref{Tab_ssm}),
131and it is these averaged fields which are used to computes the surface fluxes
132at a frequency of \np{nf\_sbc} time-step.
133
134
135%-------------------------------------------------TABLE---------------------------------------------------
136\begin{table}[tb]   \begin{center}   \begin{tabular}{|l|l|l|l|}
137\hline
138Variable description             & Model variable  & Units  & point \\  \hline
139i-component of the surface current  & ssu\_m & $m.s^{-1}$   & U \\   \hline
140j-component of the surface current  & ssv\_m & $m.s^{-1}$   & V \\   \hline
141Sea surface temperature          & sst\_m & \r{}$K$      & T \\   \hline
142Sea surface salinty              & sss\_m & $psu$        & T \\   \hline
143\end{tabular}
144\caption{  \label{Tab_ssm}   
145Ocean variables provided by the ocean to the surface module (SBC).
146The variable are averaged over nf{\_}sbc time step, $i.e.$ the frequency of
147computation of surface fluxes.}
148\end{center}   \end{table}
149%--------------------------------------------------------------------------------------------------------------
150
151%\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
152
153
154% ================================================================
155%       Input Data
156% ================================================================
157\section{Input Data generic interface}
158\label{SBC_input}
159
160A generic interface has been introduced to manage the way input data (2D or 3D fields,
161like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by fldread.F90.
162The module was design with four main objectives in mind:
163\begin{enumerate} 
164\item optionally provide a time interpolation of the input data at model time-step,
165whatever their input frequency is, and according to the different calendars available in the model.
166\item optionally provide an on-the-fly space interpolation from the native input data grid to the model grid.
167\item make the run duration independent from the period cover by the input files.
168\item provide a simple user interface and a rather simple developer interface by limiting the
169 number of prerequisite information.
170\end{enumerate} 
171
172As a results the user have only to fill in for each variable a structure in the namelist file
173to defined the input data file and variable names, the frequency of the data (in hours or months),
174whether its is climatological data or not, the period covered by the input file (one year, month, week or day),
175and three additional parameters for on-the-fly interpolation. When adding a new input variable,
176the developer has to add the associated structure in the namelist, read this information
177by mirroring the namelist read in \rou{sbc\_blk\_init} for example, and simply call \rou{fld\_read} 
178to obtain the desired input field at the model time-step and grid points.
179
180The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature
181(see \S\ref{SBC_fldread}), the period it cover is one year, month, week or day, and, if on-the-fly
182interpolation is used, a file of weights must be supplied (see \S\ref{SBC_iof}).
183
184Note that when an input data is archived on a disc which is accessible directly
185from the workspace where the code is executed, then the use can set the \np{cn\_dir} 
186to the pathway leading to the data. By default, the data are assumed to have been
187copied so that cn\_dir='./'.
188
189% -------------------------------------------------------------------------------------------------------------
190% Input Data specification (\mdl{fldread})
191% -------------------------------------------------------------------------------------------------------------
192\subsection{Input Data specification (\mdl{fldread})}
193\label{SBC_fldread}
194
195The structure associated with an input variable contains the following information:
196\begin{alltt}  {{\tiny   
197\begin{verbatim}
198!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation ! land/sea mask !
199!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  ! filename      !
200\end{verbatim}
201}}\end{alltt} 
202where
203\begin{description} 
204\item[File name]: the stem name of the NetCDF file to be open.
205This stem will be completed automatically by the model, with the addition of a '.nc' at its end
206and by date information and possibly a prefix (when using AGRIF).
207Tab.\ref{Tab_fldread} provides the resulting file name in all possible cases according to whether
208it is a climatological file or not, and to the open/close frequency (see below for definition).
209
210%--------------------------------------------------TABLE--------------------------------------------------
211\begin{table}[htbp]
212\begin{center}
213\begin{tabular}{|l|c|c|c|}
214\hline
215                         & daily or weekLLL          & monthly                   &   yearly          \\   \hline
216clim = false   & fn\_yYYYYmMMdDD  &   fn\_yYYYYmMM   &   fn\_yYYYY  \\   \hline
217clim = true       & not possible                  &  fn\_m??.nc             &   fn                \\   \hline
218\end{tabular}
219\end{center}
220\caption{ \label{Tab_fldread}   naming nomenclature for climatological or interannual input file,
221as a function of the Open/close frequency. The stem name is assumed to be 'fn'.
222For weekly files, the 'LLL' corresponds to the first three letters of the first day of the week ($i.e.$ 'sun','sat','fri','thu','wed','tue','mon'). The 'YYYY', 'MM' and 'DD' should be replaced by the
223actual year/month/day, always coded with 4 or 2 digits. Note that (1) in mpp, if the file is split
224over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc', where 'PPPP' is the
225process number coded with 4 digits; (2) when using AGRIF, the prefix
226'\_N' is added to files,
227where 'N'  is the child grid number.}
228\end{table}
229%--------------------------------------------------------------------------------------------------------------
230 
231
232\item[Record frequency]: the frequency of the records contained in the input file.
233Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative
234(for example -1 for monthly forcing or -12 for annual forcing).
235Note that this frequency must really be an integer and not a real.
236On some computers, seting it to '24.' can be interpreted as 240!
237
238\item[Variable name]: the name of the variable to be read in the input NetCDF file.
239
240\item[Time interpolation]: a logical to activate, or not, the time interpolation. If set to 'false',
241the forcing will have a steplike shape remaining constant during each forcing period.
242For example, when using a daily forcing without time interpolation, the forcing remaining
243constant from 00h00'00'' to 23h59'59". If set to 'true', the forcing will have a broken line shape.
244Records are assumed to be dated the middle of the forcing period.
245For example, when using a daily forcing with time interpolation, linear interpolation will
246be performed between mid-day of two consecutive days.
247
248\item[Climatological forcing]: a logical to specify if a input file contains climatological forcing
249which can be cycle in time, or an interannual forcing which will requires additional files
250if the period covered by the simulation exceed the one of the file. See the above the file
251naming strategy which impacts the expected name of the file to be opened.
252
253\item[Open/close frequency]: the frequency at which forcing files must be opened/closed.
254Four cases are coded: 'daily', 'weekLLL' (with 'LLL' the first 3 letters of the first day of the week),
255'monthly' and 'yearly' which means the forcing files will contain data for one day, one week,
256one month or one year. Files are assumed to contain data from the beginning of the open/close period.
257For example, the first record of a yearly file containing daily data is Jan 1st even if the experiment
258is not starting at the beginning of the year.
259
260\item[Others]: 'weights filename', 'pairing rotation' and 'land/sea mask' are associted with on-the-fly interpolation
261which is described in \S\ref{SBC_iof}.
262
263\end{description}
264
265Additional remarks:\\
266(1) The time interpolation is a simple linear interpolation between two consecutive records of
267the input data. The only tricky point is therefore to specify the date at which we need to do
268the interpolation and the date of the records read in the input files.
269Following \citet{Leclair_Madec_OM09}, the date of a time step is set at the middle of the
270time step. For example, for an experiment starting at 0h00'00" with a one hour time-step,
271a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
272However, for forcing data related to the surface module, values are not needed at every
273time-step but at every \np{nn\_fsbc} time-step. For example with \np{nn\_fsbc}~=~3,
274the surface module will be called at time-steps 1, 4, 7, etc. The date used for the time interpolation
275is thus redefined to be at the middle of \np{nn\_fsbc} time-step period. In the previous example,
276this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
277(2) For code readablility and maintenance issues, we don't take into account the NetCDF input file
278calendar. The calendar associated with the forcing field is build according to the information
279provided by user in the record frequency, the open/close frequency and the type of temporal interpolation.
280For example, the first record of a yearly file containing daily data that will be interpolated in time
281is assumed to be start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\
282(3) If a time interpolation is requested, the code will pick up the needed data in the previous (next) file
283when interpolating data with the first (last) record of the open/close period.
284For example, if the input file specifications are ''yearly, containing daily data to be interpolated in time'',
285the values given by the code between 00h00'00" and 11h59'59" on Jan 1st will be interpolated values
286between Dec 31st 12h00'00" and Jan 1st 12h00'00". If the forcing is climatological, Dec and Jan will
287be keep-up from the same year. However, if the forcing is not climatological, at the end of the
288open/close period the code will automatically close the current file and open the next one.
289Note that, if the experiment is starting (ending) at the beginning (end) of an open/close period
290we do accept that the previous (next) file is not existing. In this case, the time interpolation
291will be performed between two identical values. For example, when starting an experiment on
292Jan 1st of year Y with yearly files and daily data to be interpolated, we do accept that the file
293related to year Y-1 is not existing. The value of Jan 1st will be used as the missing one for
294Dec 31st of year Y-1. If the file of year Y-1 exists, the code will read its last record.
295Therefore, this file can contain only one record corresponding to Dec 31st, a useful feature for
296user considering that it is too heavy to manipulate the complete file for year Y-1.
297
298
299% -------------------------------------------------------------------------------------------------------------
300% Interpolation on the Fly
301% -------------------------------------------------------------------------------------------------------------
302\subsection [Interpolation on-the-Fly] {Interpolation on-the-Fly}
303\label{SBC_iof}
304
305Interpolation on the Fly allows the user to supply input files required
306for the surface forcing on grids other than the model grid.
307To do this he or she must supply, in addition to the source data file,
308a file of weights to be used to interpolate from the data grid to the model grid.
309The original development of this code used the SCRIP package (freely available
310\href{http://climate.lanl.gov/Software/SCRIP}{here} under a copyright agreement).
311In principle, any package can be used to generate the weights, but the
312variables in the input weights file must have the same names and meanings as
313assumed by the model.
314Two methods are currently available: bilinear and bicubic interpolation.
315Prior to the interpolation, providing a land/sea mask file, the user can decide to
316 remove land points from the input file and substitute the corresponding values
317with the average of the 8 neighbouring points in the native external grid.
318 Only "sea points" are considered for the averaging. The land/sea mask file must
319be provided in the structure associated with the input variable.
320 The netcdf land/sea mask variable name must be 'LSM' it must have the same
321horizontal and vertical dimensions of the associated variable and should
322be equal to 1 over land and 0 elsewhere.
323The procedure can be recursively applied setting nn\_lsm > 1 in namsbc namelist.
324Note that nn\_lsm=0 forces the code to not apply the procedure even if a file for land/sea mask is supplied.
325
326\subsubsection{Bilinear Interpolation}
327\label{SBC_iof_bilinear}
328
329The input weights file in this case has two sets of variables: src01, src02,
330src03, src04 and wgt01, wgt02, wgt03, wgt04.
331The "src" variables correspond to the point in the input grid to which the weight
332"wgt" is to be applied. Each src value is an integer corresponding to the index of a
333point in the input grid when written as a one dimensional array.  For example, for an input grid
334of size 5x10, point (3,2) is referenced as point 8, since (2-1)*5+3=8.
335There are four of each variable because bilinear interpolation uses the four points defining
336the grid box containing the point to be interpolated.
337All of these arrays are on the model grid, so that values src01(i,j) and
338wgt01(i,j) are used to generate a value for point (i,j) in the model.
339
340Symbolically, the algorithm used is:
341
342\begin{equation}
343f_{m}(i,j) = f_{m}(i,j) + \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}
344\end{equation}
345where function idx() transforms a one dimensional index src(k) into a two dimensional index,
346and wgt(1) corresponds to variable "wgt01" for example.
347
348\subsubsection{Bicubic Interpolation}
349\label{SBC_iof_bicubic}
350
351Again there are two sets of variables: "src" and "wgt".
352But in this case there are 16 of each.
353The symbolic algorithm used to calculate values on the model grid is now:
354
355\begin{equation*} \begin{split}
356f_{m}(i,j) =  f_{m}(i,j) +& \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}     
357              +   \sum_{k=5}^{8} {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\
358              +& \sum_{k=9}^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} }   
359              +   \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} }
360\end{split}
361\end{equation*}
362The gradients here are taken with respect to the horizontal indices and not distances since the spatial dependency has been absorbed into the weights.
363
364\subsubsection{Implementation}
365\label{SBC_iof_imp}
366
367To activate this option, a non-empty string should be supplied in the weights filename column
368of the relevant namelist; if this is left as an empty string no action is taken.
369In the model, weights files are read in and stored in a structured type (WGT) in the fldread
370module, as and when they are first required.
371This initialisation procedure determines whether the input data grid should be treated
372as cyclical or not by inspecting a global attribute stored in the weights input file.
373This attribute must be called "ew\_wrap" and be of integer type.
374If it is negative, the input non-model grid is assumed not to be cyclic.
375If zero or greater, then the value represents the number of columns that overlap.
376$E.g.$ if the input grid has columns at longitudes 0, 1, 2, .... , 359, then ew\_wrap should be set to 0;
377if longitudes are 0.5, 2.5, .... , 358.5, 360.5, 362.5, ew\_wrap should be 2.
378If the model does not find attribute ew\_wrap, then a value of -999 is assumed.
379In this case the \rou{fld\_read} routine defaults ew\_wrap to value 0 and therefore the grid
380is assumed to be cyclic with no overlapping columns.
381(In fact this only matters when bicubic interpolation is required.)
382Note that no testing is done to check the validity in the model, since there is no way
383of knowing the name used for the longitude variable,
384so it is up to the user to make sure his or her data is correctly represented.
385
386Next the routine reads in the weights.
387Bicubic interpolation is assumed if it finds a variable with name "src05", otherwise
388bilinear interpolation is used. The WGT structure includes dynamic arrays both for
389the storage of the weights (on the model grid), and when required, for reading in
390the variable to be interpolated (on the input data grid).
391The size of the input data array is determined by examining the values in the "src"
392arrays to find the minimum and maximum i and j values required.
393Since bicubic interpolation requires the calculation of gradients at each point on the grid,
394the corresponding arrays are dimensioned with a halo of width one grid point all the way around.
395When the array of points from the data file is adjacent to an edge of the data grid,
396the halo is either a copy of the row/column next to it (non-cyclical case), or is a copy
397of one from the first few columns on the opposite side of the grid (cyclical case).
398
399\subsubsection{Limitations}
400\label{SBC_iof_lim}
401
402\begin{enumerate} 
403\item  The case where input data grids are not logically rectangular has not been tested.
404\item  This code is not guaranteed to produce positive definite answers from positive definite inputs
405          when a bicubic interpolation method is used.
406\item  The cyclic condition is only applied on left and right columns, and not to top and bottom rows.
407\item  The gradients across the ends of a cyclical grid assume that the grid spacing between
408          the two columns involved are consistent with the weights used.
409\item  Neither interpolation scheme is conservative. (There is a conservative scheme available
410          in SCRIP, but this has not been implemented.)
411\end{enumerate}
412
413\subsubsection{Utilities}
414\label{SBC_iof_util}
415
416% to be completed
417A set of utilities to create a weights file for a rectilinear input grid is available
418(see the directory NEMOGCM/TOOLS/WEIGHTS).
419
420% -------------------------------------------------------------------------------------------------------------
421% Standalone Surface Boundary Condition Scheme
422% -------------------------------------------------------------------------------------------------------------
423\subsection [Standalone Surface Boundary Condition Scheme] {Standalone Surface Boundary Condition Scheme}
424\label{SAS_iof}
425
426%---------------------------------------namsbc_ana--------------------------------------------------
427\namdisplay{namsbc_sas}
428%--------------------------------------------------------------------------------------------------------------
429
430In some circumstances it may be useful to avoid calculating the 3D temperature, salinity and velocity fields
431and simply read them in from a previous run or receive them from OASIS. 
432For example:
433
434\begin{itemize}
435\item  Multiple runs of the model are required in code development to see the effect of different algorithms in
436       the bulk formulae.
437\item  The effect of different parameter sets in the ice model is to be examined.
438\item  Development of sea-ice algorithms or parameterizations.
439\item  spinup of the iceberg floats
440\item  ocean/sea-ice simulation with both media running in parallel (\np{ln\_mixcpl}~=~\textit{true})
441\end{itemize}
442
443The StandAlone Surface scheme provides this utility.
444Its options are defined through the \ngn{namsbc\_sas} namelist variables.
445A new copy of the model has to be compiled with a configuration based on ORCA2\_SAS\_LIM.
446However no namelist parameters need be changed from the settings of the previous run (except perhaps nn{\_}date0)
447In this configuration, a few routines in the standard model are overriden by new versions.
448Routines replaced are:
449
450\begin{itemize}
451\item \mdl{nemogcm} : This routine initialises the rest of the model and repeatedly calls the stp time stepping routine (step.F90)
452       Since the ocean state is not calculated all associated initialisations have been removed.
453\item  \mdl{step} : The main time stepping routine now only needs to call the sbc routine (and a few utility functions).
454\item  \mdl{sbcmod} : This has been cut down and now only calculates surface forcing and the ice model required.  New surface modules
455       that can function when only the surface level of the ocean state is defined can also be added (e.g. icebergs).
456\item  \mdl{daymod} : No ocean restarts are read or written (though the ice model restarts are retained), so calls to restart functions
457       have been removed.  This also means that the calendar cannot be controlled by time in a restart file, so the user
458       must make sure that nn{\_}date0 in the model namelist is correct for his or her purposes.
459\item  \mdl{stpctl} : Since there is no free surface solver, references to it have been removed from \rou{stp\_ctl} module.
460\item  \mdl{diawri} : All 3D data have been removed from the output.  The surface temperature, salinity and velocity components (which
461       have been read in) are written along with relevant forcing and ice data.
462\end{itemize}
463
464One new routine has been added:
465
466\begin{itemize}
467\item  \mdl{sbcsas} : This module initialises the input files needed for reading temperature, salinity and velocity arrays at the surface.
468       These filenames are supplied in namelist namsbc{\_}sas.  Unfortunately because of limitations with the \mdl{iom} module,
469       the full 3D fields from the mean files have to be read in and interpolated in time, before using just the top level.
470       Since fldread is used to read in the data, Interpolation on the Fly may be used to change input data resolution.
471\end{itemize}
472
473
474% Missing the description of the 2 following variables:
475%   ln_3d_uve   = .true.    !  specify whether we are supplying a 3D u,v and e3 field
476%   ln_read_frq = .false.    !  specify whether we must read frq or not
477
478
479
480% ================================================================
481% Analytical formulation (sbcana module)
482% ================================================================
483\section  [Analytical formulation (\textit{sbcana}) ]
484      {Analytical formulation (\mdl{sbcana} module) }
485\label{SBC_ana}
486
487%---------------------------------------namsbc_ana--------------------------------------------------
488\namdisplay{namsbc_ana}
489%--------------------------------------------------------------------------------------------------------------
490
491The analytical formulation of the surface boundary condition is the default scheme.
492In this case, all the six fluxes needed by the ocean are assumed to
493be uniform in space. They take constant values given in the namelist
494\ngn{namsbc{\_}ana} by the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0},
495\np{rn\_qsr0}, and \np{rn\_emp0} ($\textit{emp}=\textit{emp}_S$). The runoff is set to zero.
496In addition, the wind is allowed to reach its nominal value within a given number
497of time steps (\np{nn\_tau000}).
498
499If a user wants to apply a different analytical forcing, the \mdl{sbcana} 
500module can be modified to use another scheme. As an example,
501the \mdl{sbc\_ana\_gyre} routine provides the analytical forcing for the
502GYRE configuration (see GYRE configuration manual, in preparation).
503
504
505% ================================================================
506% Flux formulation
507% ================================================================
508\section  [Flux formulation (\textit{sbcflx}) ]
509      {Flux formulation (\mdl{sbcflx} module) }
510\label{SBC_flx}
511%------------------------------------------namsbc_flx----------------------------------------------------
512\namdisplay{namsbc_flx} 
513%-------------------------------------------------------------------------------------------------------------
514
515In the flux formulation (\np{ln\_flx}=true), the surface boundary
516condition fields are directly read from input files. The user has to define
517in the namelist \ngn{namsbc{\_}flx} the name of the file, the name of the variable
518read in the file, the time frequency at which it is given (in hours), and a logical
519setting whether a time interpolation to the model time step is required
520for this field. See \S\ref{SBC_fldread} for a more detailed description of the parameters.
521
522Note that in general, a flux formulation is used in associated with a
523restoring term to observed SST and/or SSS. See \S\ref{SBC_ssr} for its
524specification.
525
526
527% ================================================================
528% Bulk formulation
529% ================================================================
530\section  [Bulk formulation (\textit{sbcblk\_core}, \textit{sbcblk\_clio} or \textit{sbcblk\_mfs}) ]
531      {Bulk formulation \small{(\mdl{sbcblk\_core} \mdl{sbcblk\_clio} \mdl{sbcblk\_mfs} modules)} }
532\label{SBC_blk}
533
534In the bulk formulation, the surface boundary condition fields are computed
535using bulk formulae and atmospheric fields and ocean (and ice) variables.
536
537The atmospheric fields used depend on the bulk formulae used. Three bulk formulations
538are available : the CORE, the CLIO and the MFS bulk formulea. The choice is made by setting to true
539one of the following namelist variable : \np{ln\_core} ; \np{ln\_clio} or  \np{ln\_mfs}.
540
541Note : in forced mode, when a sea-ice model is used, a bulk formulation (CLIO or CORE) have to be used.
542Therefore the two bulk (CLIO and CORE) formulea include the computation of the fluxes over both
543an ocean and an ice surface.
544
545% -------------------------------------------------------------------------------------------------------------
546%        CORE Bulk formulea
547% -------------------------------------------------------------------------------------------------------------
548\subsection    [CORE Bulk formulea (\np{ln\_core}=true)]
549            {CORE Bulk formulea (\np{ln\_core}=true, \mdl{sbcblk\_core})}
550\label{SBC_blk_core}
551%------------------------------------------namsbc_core----------------------------------------------------
552\namdisplay{namsbc_core} 
553%-------------------------------------------------------------------------------------------------------------
554
555The CORE bulk formulae have been developed by \citet{Large_Yeager_Rep04}.
556They have been designed to handle the CORE forcing, a mixture of NCEP
557reanalysis and satellite data. They use an inertial dissipative method to compute
558the turbulent transfer coefficients (momentum, sensible heat and evaporation)
559from the 10 metre wind speed, air temperature and specific humidity.
560This \citet{Large_Yeager_Rep04} dataset is available through the
561\href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
562
563Note that substituting ERA40 to NCEP reanalysis fields
564does not require changes in the bulk formulea themself.
565This is the so-called DRAKKAR Forcing Set (DFS) \citep{Brodeau_al_OM09}.
566
567Options are defined through the  \ngn{namsbc\_core} namelist variables.
568The required 8 input fields are:
569
570%--------------------------------------------------TABLE--------------------------------------------------
571\begin{table}[htbp]   \label{Tab_CORE}
572\begin{center}
573\begin{tabular}{|l|c|c|c|}
574\hline
575Variable desciption              & Model variable  & Units   & point \\    \hline
576i-component of the 10m air velocity & utau      & $m.s^{-1}$         & T  \\  \hline
577j-component of the 10m air velocity & vtau      & $m.s^{-1}$         & T  \\  \hline
57810m air temperature              & tair      & \r{}$K$            & T   \\ \hline
579Specific humidity             & humi      & \%              & T \\      \hline
580Incoming long wave radiation     & qlw    & $W.m^{-2}$         & T \\      \hline
581Incoming short wave radiation    & qsr    & $W.m^{-2}$         & T \\      \hline
582Total precipitation (liquid + solid)   & precip & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
583Solid precipitation              & snow      & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
584\end{tabular}
585\end{center}
586\end{table}
587%--------------------------------------------------------------------------------------------------------------
588
589Note that the air velocity is provided at a tracer ocean point, not at a velocity ocean
590point ($u$- and $v$-points). It is simpler and faster (less fields to be read),
591but it is not the recommended method when the ocean grid size is the same
592or larger than the one of the input atmospheric fields.
593
594% -------------------------------------------------------------------------------------------------------------
595%        CLIO Bulk formulea
596% -------------------------------------------------------------------------------------------------------------
597\subsection    [CLIO Bulk formulea (\np{ln\_clio}=true)]
598            {CLIO Bulk formulea (\np{ln\_clio}=true, \mdl{sbcblk\_clio})}
599\label{SBC_blk_clio}
600%------------------------------------------namsbc_clio----------------------------------------------------
601\namdisplay{namsbc_clio} 
602%-------------------------------------------------------------------------------------------------------------
603
604The CLIO bulk formulae were developed several years ago for the
605Louvain-la-neuve coupled ice-ocean model (CLIO, \cite{Goosse_al_JGR99}).
606They are simpler bulk formulae. They assume the stress to be known and
607compute the radiative fluxes from a climatological cloud cover.
608
609Options are defined through the  \ngn{namsbc\_clio} namelist variables.
610The required 7 input fields are:
611
612%--------------------------------------------------TABLE--------------------------------------------------
613\begin{table}[htbp]   \label{Tab_CLIO}
614\begin{center}
615\begin{tabular}{|l|l|l|l|}
616\hline
617Variable desciption           & Model variable  & Units           & point \\  \hline
618i-component of the ocean stress     & utau         & $N.m^{-2}$         & U \\   \hline
619j-component of the ocean stress     & vtau         & $N.m^{-2}$         & V \\   \hline
620Wind speed module             & vatm         & $m.s^{-1}$         & T \\   \hline
62110m air temperature              & tair         & \r{}$K$            & T \\   \hline
622Specific humidity                & humi         & \%              & T \\   \hline
623Cloud cover                   &           & \%              & T \\   \hline
624Total precipitation (liquid + solid)   & precip    & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
625Solid precipitation              & snow         & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
626\end{tabular}
627\end{center}
628\end{table}
629%--------------------------------------------------------------------------------------------------------------
630
631As for the flux formulation, information about the input data required by the
632model is provided in the namsbc\_blk\_core or namsbc\_blk\_clio
633namelist (see \S\ref{SBC_fldread}).
634
635% -------------------------------------------------------------------------------------------------------------
636%        MFS Bulk formulae
637% -------------------------------------------------------------------------------------------------------------
638\subsection    [MFS Bulk formulea (\np{ln\_mfs}=true)]
639            {MFS Bulk formulea (\np{ln\_mfs}=true, \mdl{sbcblk\_mfs})}
640\label{SBC_blk_mfs}
641%------------------------------------------namsbc_mfs----------------------------------------------------
642\namdisplay{namsbc_mfs} 
643%----------------------------------------------------------------------------------------------------------
644
645The MFS (Mediterranean Forecasting System) bulk formulae have been developed by
646 \citet{Castellari_al_JMS1998}.
647They have been designed to handle the ECMWF operational data and are currently
648in use in the MFS operational system \citep{Tonani_al_OS08}, \citep{Oddo_al_OS09}.
649The wind stress computation uses a drag coefficient computed according to \citet{Hellerman_Rosenstein_JPO83}.
650The surface boundary condition for temperature involves the balance between surface solar radiation,
651net long-wave radiation, the latent and sensible heat fluxes.
652Solar radiation is dependent on cloud cover and is computed by means of
653an astronomical formula \citep{Reed_JPO77}. Albedo monthly values are from \citet{Payne_JAS72} 
654as means of the values at $40^{o}N$ and $30^{o}N$ for the Atlantic Ocean (hence the same latitudinal
655band of the Mediterranean Sea). The net long-wave radiation flux
656\citep{Bignami_al_JGR95} is a function of
657air temperature, sea-surface temperature, cloud cover and relative humidity.
658Sensible heat and latent heat fluxes are computed by classical
659bulk formulae parameterised according to \citet{Kondo1975}.
660Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}.
661
662Options are defined through the  \ngn{namsbc\_mfs} namelist variables.
663The required 7 input fields must be provided on the model Grid-T and  are:
664\begin{itemize}
665\item          Zonal Component of the 10m wind ($ms^{-1}$)  (\np{sn\_windi})
666\item          Meridional Component of the 10m wind ($ms^{-1}$)  (\np{sn\_windj})
667\item          Total Claud Cover (\%)  (\np{sn\_clc})
668\item          2m Air Temperature ($K$) (\np{sn\_tair})
669\item          2m Dew Point Temperature ($K$)  (\np{sn\_rhm})
670\item          Total Precipitation ${Kg} m^{-2} s^{-1}$ (\np{sn\_prec})
671\item          Mean Sea Level Pressure (${Pa}$) (\np{sn\_msl})
672\end{itemize}
673% -------------------------------------------------------------------------------------------------------------
674% ================================================================
675% Coupled formulation
676% ================================================================
677\section  [Coupled formulation (\textit{sbccpl}) ]
678      {Coupled formulation (\mdl{sbccpl} module)}
679\label{SBC_cpl}
680%------------------------------------------namsbc_cpl----------------------------------------------------
681\namdisplay{namsbc_cpl} 
682%-------------------------------------------------------------------------------------------------------------
683
684In the coupled formulation of the surface boundary condition, the fluxes are
685provided by the OASIS coupler at a frequency which is defined in the OASIS coupler,
686while sea and ice surface temperature, ocean and ice albedo, and ocean currents
687are sent to the atmospheric component.
688
689A generalised coupled interface has been developed.
690It is currently interfaced with OASIS-3-MCT (\key{oasis3}).
691It has been successfully used to interface \NEMO to most of the European atmospheric
692GCM (ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz),
693as well as to \href{http://wrf-model.org/}{WRF} (Weather Research and Forecasting Model).
694
695Note that in addition to the setting of \np{ln\_cpl} to true, the \key{coupled} have to be defined.
696The CPP key is mainly used in sea-ice to ensure that the atmospheric fluxes are
697actually recieved by the ice-ocean system (no calculation of ice sublimation in coupled mode).
698When PISCES biogeochemical model (\key{top} and \key{pisces}) is also used in the coupled system,
699the whole carbon cycle is computed by defining \key{cpl\_carbon\_cycle}. In this case,
700CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system (and need to be activated in \ngn{namsbc{\_}cpl} ).
701
702The namelist above allows control of various aspects of the coupling fields (particularly for
703vectors) and now allows for any coupling fields to have multiple sea ice categories (as required by LIM3
704and CICE).  When indicating a multi-category coupling field in namsbc{\_}cpl the number of categories will be
705determined by the number used in the sea ice model.  In some limited cases it may be possible to specify
706single category coupling fields even when the sea ice model is running with multiple categories - in this
707case the user should examine the code to be sure the assumptions made are satisfactory.  In cases where
708this is definitely not possible the model should abort with an error message.  The new code has been tested using
709ECHAM with LIM2, and HadGAM3 with CICE but although it will compile with \key{lim3} additional minor code changes
710may be required to run using LIM3.
711
712
713% ================================================================
714%        Atmospheric pressure
715% ================================================================
716\section   [Atmospheric pressure (\textit{sbcapr})]
717         {Atmospheric pressure (\mdl{sbcapr})}
718\label{SBC_apr}
719%------------------------------------------namsbc_apr----------------------------------------------------
720\namdisplay{namsbc_apr} 
721%-------------------------------------------------------------------------------------------------------------
722
723The optional atmospheric pressure can be used to force ocean and ice dynamics
724(\np{ln\_apr\_dyn}~=~true, \textit{\ngn{namsbc}} namelist ).
725The input atmospheric forcing defined via \np{sn\_apr} structure (\textit{namsbc\_apr} namelist)
726can be interpolated in time to the model time step, and even in space when the
727interpolation on-the-fly is used. When used to force the dynamics, the atmospheric
728pressure is further transformed into an equivalent inverse barometer sea surface height,
729$\eta_{ib}$, using:
730\begin{equation} \label{SBC_ssh_ib}
731   \eta_{ib} = -  \frac{1}{g\,\rho_o}  \left( P_{atm} - P_o \right)
732\end{equation}
733where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure.
734A value of $101,000~N/m^2$ is used unless \np{ln\_ref\_apr} is set to true. In this case $P_o$ 
735is set to the value of $P_{atm}$ averaged over the ocean domain, $i.e.$ the mean value of
736$\eta_{ib}$ is kept to zero at all time step.
737
738The gradient of $\eta_{ib}$ is added to the RHS of the ocean momentum equation
739(see \mdl{dynspg} for the ocean). For sea-ice, the sea surface height, $\eta_m$,
740which is provided to the sea ice model is set to $\eta - \eta_{ib}$ (see \mdl{sbcssr} module).
741$\eta_{ib}$ can be set in the output. This can simplify altimetry data and model comparison
742as inverse barometer sea surface height is usually removed from these date prior to their distribution.
743
744When using time-splitting and BDY package for open boundaries conditions, the equivalent
745inverse barometer sea surface height $\eta_{ib}$ can be added to BDY ssh data:
746\np{ln\_apr\_obc}  might be set to true.
747
748% ================================================================
749%        Tidal Potential
750% ================================================================
751\section   [Tidal Potential (\textit{sbctide})]
752                        {Tidal Potential (\mdl{sbctide})}
753\label{SBC_tide}
754
755%------------------------------------------nam_tide---------------------------------------
756\namdisplay{nam_tide}
757%-----------------------------------------------------------------------------------------
758
759A module is available to compute the tidal potential and use it in the momentum equation.
760This option is activated when \key{tide} is defined.
761
762Some parameters are available in namelist \ngn{nam\_tide}:
763
764- \np{ln\_tide\_pot} activate the tidal potential forcing
765
766- \np{nb\_harmo} is the number of constituent used
767
768- \np{clname} is the name of constituent
769
770The tide is generated by the forces of gravity ot the Earth-Moon and Earth-Sun sytem;
771they are expressed as the gradient of the astronomical potential ($\vec{\nabla}\Pi_{a}$). \\
772
773The potential astronomical expressed, for the three types of tidal frequencies
774following, by : \\
775Tide long period :
776\begin{equation}
777\Pi_{a}=gA_{k}(\frac{1}{2}-\frac{3}{2}sin^{2}\phi)cos(\omega_{k}t+V_{0k})
778\end{equation}
779diurnal Tide :
780\begin{equation}
781\Pi_{a}=gA_{k}(sin 2\phi)cos(\omega_{k}t+\lambda+V_{0k})
782\end{equation}
783Semi-diurnal tide:
784\begin{equation}
785\Pi_{a}=gA_{k}(cos^{2}\phi)cos(\omega_{k}t+2\lambda+V_{0k})
786\end{equation}
787
788
789$A_{k}$ is the amplitude of the wave k, $\omega_{k}$ the pulsation of the wave k, $V_{0k}$ the astronomical phase of the wave
790$k$ to Greenwich.
791
792We make corrections to the astronomical potential.
793We obtain :
794\begin{equation}
795\Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi)
796\end{equation}
797with $k$ a number of Love estimated to 0.6 which parameterised the astronomical tidal land,
798and $h$ a number of Love to 0.3 which parameterised the parameterisation due to the astronomical tidal land.
799
800% ================================================================
801%        River runoffs
802% ================================================================
803\section   [River runoffs (\textit{sbcrnf})]
804         {River runoffs (\mdl{sbcrnf})}
805\label{SBC_rnf}
806%------------------------------------------namsbc_rnf----------------------------------------------------
807\namdisplay{namsbc_rnf} 
808%-------------------------------------------------------------------------------------------------------------
809
810%River runoff generally enters the ocean at a nonzero depth rather than through the surface.
811%Many models, however, have traditionally inserted river runoff to the top model cell.
812%This was the case in \NEMO prior to the version 3.3. The switch toward a input of runoff
813%throughout a nonzero depth has been motivated by the numerical and physical problems
814%that arise when the top grid cells are of the order of one meter. This situation is common in
815%coastal modelling and becomes more and more often open ocean and climate modelling
816%\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
817%required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \S\ref{SBC_dcy}.}.
818
819
820%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the
821%\mdl{tra\_sbc} module.  We decided to separate them throughout the code, so that the variable
822%\textit{emp} represented solely evaporation minus precipitation fluxes, and a new 2d variable
823%rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with
824%emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use
825%emp or emps and the changes made are below:
826
827
828%Rachel:
829River runoff generally enters the ocean at a nonzero depth rather than through the surface.
830Many models, however, have traditionally inserted river runoff to the top model cell.
831This was the case in \NEMO prior to the version 3.3, and was combined with an option
832to increase vertical mixing near the river mouth.
833
834However, with this method numerical and physical problems arise when the top grid cells are
835of the order of one meter. This situation is common in coastal modelling and is becoming
836more common in open ocean and climate modelling
837\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
838required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \S\ref{SBC_dcy}.}.
839
840As such from V~3.3 onwards it is possible to add river runoff through a non-zero depth, and for the
841temperature and salinity of the river to effect the surrounding ocean.
842The user is able to specify, in a NetCDF input file, the temperature and salinity of the river, along with the   
843depth (in metres) which the river should be added to.
844
845Namelist variables in \ngn{namsbc\_rnf}, \np{ln\_rnf\_depth}, \np{ln\_rnf\_sal} and \np{ln\_rnf\_temp} control whether
846the river attributes (depth, salinity and temperature) are read in and used.  If these are set
847as false the river is added to the surface box only, assumed to be fresh (0~psu), and/or
848taken as surface temperature respectively.
849
850The runoff value and attributes are read in in sbcrnf. 
851For temperature -999 is taken as missing data and the river temperature is taken to be the
852surface temperatue at the river point.
853For the depth parameter a value of -1 means the river is added to the surface box only,
854and a value of -999 means the river is added through the entire water column.
855After being read in the temperature and salinity variables are multiplied by the amount of runoff (converted into m/s)
856to give the heat and salt content of the river runoff.
857After the user specified depth is read ini, the number of grid boxes this corresponds to is
858calculated and stored in the variable \np{nz\_rnf}.
859The variable \textit{h\_dep} is then calculated to be the depth (in metres) of the bottom of the
860lowest box the river water is being added to (i.e. the total depth that river water is being added to in the model).
861
862The mass/volume addition due to the river runoff is, at each relevant depth level, added to the horizontal divergence
863(\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divcur}).
864This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux.
865The sea surface height is calculated using the sum of the horizontal divergence terms, and so the
866river runoff indirectly forces an increase in sea surface height.
867
868The \textit{hdivn} terms are used in the tracer advection modules to force vertical velocities.
869This causes a mass of water, equal to the amount of runoff, to be moved into the box above.
870The heat and salt content of the river runoff is not included in this step, and so the tracer
871concentrations are diluted as water of ocean temperature and salinity is moved upward out of the box
872and replaced by the same volume of river water with no corresponding heat and salt addition.
873
874For the linear free surface case, at the surface box the tracer advection causes a flux of water
875(of equal volume to the runoff) through the sea surface out of the domain, which causes a salt and heat flux out of the model.
876As such the volume of water does not change, but the water is diluted.
877
878For the non-linear free surface case (\key{vvl}), no flux is allowed through the surface.
879Instead in the surface box (as well as water moving up from the boxes below) a volume of runoff water
880is added with no corresponding heat and salt addition and so as happens in the lower boxes there is a dilution effect.
881(The runoff addition to the top box along with the water being moved up through boxes below means the surface box has a large
882increase in volume, whilst all other boxes remain the same size)
883
884In trasbc the addition of heat and salt due to the river runoff is added.
885This is done in the same way for both vvl and non-vvl.
886The temperature and salinity are increased through the specified depth according to the heat and salt content of the river.
887
888In the non-linear free surface case (vvl), near the end of the time step the change in sea surface height is redistrubuted
889through the grid boxes, so that the original ratios of grid box heights are restored.
890In doing this water is moved into boxes below, throughout the water column, so the large volume addition to the surface box is spread between all the grid boxes.
891
892It is also possible for runnoff to be specified as a negative value for modelling flow through straits, i.e. modelling the Baltic flow in and out of the North Sea.
893When the flow is out of the domain there is no change in temperature and salinity, regardless of the namelist options used, as the ocean water leaving the domain removes heat and salt (at the same concentration) with it.
894
895
896%\colorbox{yellow}{Nevertheless, Pb of vertical resolution and 3D input : increase vertical mixing near river mouths to mimic a 3D river
897
898%All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.}
899
900%\colorbox{yellow}{river mouths{\ldots}}
901
902%IF( ln_rnf ) THEN                                     ! increase diffusivity at rivers mouths
903%        DO jk = 2, nkrnf   ;   avt(:,:,jk) = avt(:,:,jk) + rn_avt_rnf * rnfmsk(:,:)   ;   END DO
904%ENDIF
905
906%\gmcomment{  word doc of runoffs:
907%
908%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.
909%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. 
910
911%The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between.
912
913%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:
914
915%}
916% ================================================================
917%        Ice shelf melting
918% ================================================================
919\section   [Ice shelf melting (\textit{sbcisf})]
920                        {Ice shelf melting (\mdl{sbcisf})}
921\label{SBC_isf}
922%------------------------------------------namsbc_isf----------------------------------------------------
923\namdisplay{namsbc_isf}
924%--------------------------------------------------------------------------------------------------------
925Namelist variable in \ngn{namsbc}, \np{nn\_isf}, controls the ice shelf representation used.
926\begin{description}
927\item[\np{nn\_isf}~=~1]
928The ice shelf cavity is represented (\np{ln\_isfcav}~=~true needed). The fwf and heat flux are computed. Two different bulk formula are available:
929   \begin{description}
930   \item[\np{nn\_isfblk}~=~1]
931   The bulk formula used to compute the melt is based the one described in \citet{Hunter2006}.
932        This formulation is based on a balance between the upward ocean heat flux and the latent heat flux at the ice shelf base.
933
934   \item[\np{nn\_isfblk}~=~2] 
935   The bulk formula used to compute the melt is based the one described in \citet{Jenkins1991}.
936        This formulation is based on a 3 equations formulation (a heat flux budget, a salt flux budget
937         and a linearised freezing point temperature equation).
938   \end{description}
939
940For this 2 bulk formulations, there are 3 different ways to compute the exchange coeficient:
941   \begin{description}
942        \item[\np{nn\_gammablk~=~0~}]
943   The salt and heat exchange coefficients are constant and defined by \np{rn\_gammas0} and \np{rn\_gammat0}
944
945   \item[\np{nn\_gammablk~=~1~}]
946   The salt and heat exchange coefficients are velocity dependent and defined as $\np{rn\_gammas0} \times u_{*}$ and $\np{rn\_gammat0} \times u_{*}$
947        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters).
948        See \citet{Jenkins2010} for all the details on this formulation.
949   
950   \item[\np{nn\_gammablk~=~2~}]
951   The salt and heat exchange coefficients are velocity and stability dependent and defined as
952        $\gamma_{T,S} = \frac{u_{*}}{\Gamma_{Turb} + \Gamma^{T,S}_{Mole}}$
953        where $u_{*}$ is the friction velocity in the top boundary layer (ie first \np{rn\_hisf\_tbl} meters),
954        $\Gamma_{Turb}$ the contribution of the ocean stability and
955        $\Gamma^{T,S}_{Mole}$ the contribution of the molecular diffusion.
956        See \citet{Holland1999} for all the details on this formulation.
957        \end{description}
958
959\item[\np{nn\_isf}~=~2]
960A parameterisation of isf is used. The ice shelf cavity is not represented.
961The fwf is distributed along the ice shelf edge between the depth of the average grounding line (GL)
962(\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}) as in (\np{nn\_isf}~=~3).
963Furthermore the fwf and heat flux are computed using the \citet{Beckmann2003} parameterisation of isf melting.
964The effective melting length (\np{sn\_Leff\_isf}) is read from a file.
965
966\item[\np{nn\_isf}~=~3]
967A simple parameterisation of isf is used. The ice shelf cavity is not represented.
968The fwf (\np{sn\_rnfisf}) is prescribed and distributed along the ice shelf edge between the depth of the average grounding line (GL)
969(\np{sn\_depmax\_isf}) and the base of the ice shelf along the calving front (\np{sn\_depmin\_isf}).
970The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.
971
972\item[\np{nn\_isf}~=~4]
973The ice shelf cavity is opened (\np{ln\_isfcav}~=~true needed). However, the fwf is not computed but specified from file \np{sn\_fwfisf}).
974The heat flux ($Q_h$) is computed as $Q_h = fwf \times L_f$.\\
975\end{description}
976
977
978$\bullet$ \np{nn\_isf}~=~1 and \np{nn\_isf}~=~2 compute a melt rate based on the water mass properties, ocean velocities and depth.
979 This flux is thus highly dependent of the model resolution (horizontal and vertical), realism of the water masses onto the shelf ...\\
980
981
982$\bullet$ \np{nn\_isf}~=~3 and \np{nn\_isf}~=~4 read the melt rate from a file. You have total control of the fwf forcing.
983This can be usefull if the water masses on the shelf are not realistic or the resolution (horizontal/vertical) are too
984coarse to have realistic melting or for studies where you need to control your heat and fw input.\\ 
985
986A namelist parameters control over how many meters the heat and fw fluxes are spread.
987\np{rn\_hisf\_tbl}] is the top boundary layer thickness as defined in \citet{Losch2008}.
988This parameter is only used if \np{nn\_isf}~=~1 or \np{nn\_isf}~=~4
989
990If \np{rn\_hisf\_tbl} = 0.0, the fluxes are put in the top level whatever is its tickness.
991
992If \np{rn\_hisf\_tbl} $>$ 0.0, the fluxes are spread over the first \np{rn\_hisf\_tbl} m (ie over one or several cells).\\
993
994The ice shelf melt is implemented as a volume flux with in the same way as for the runoff.
995The fw addition due to the ice shelf melting is, at each relevant depth level, added to the horizontal divergence
996(\textit{hdivn}) in the subroutine \rou{sbc\_isf\_div}, called from \mdl{divcur}.
997See the runoff section \ref{SBC_rnf} for all the details about the divergence correction.
998
999
1000\section{ Ice sheet coupling}
1001\label{SBC_iscpl}
1002%------------------------------------------namsbc_iscpl----------------------------------------------------
1003\namdisplay{namsbc_iscpl}
1004%--------------------------------------------------------------------------------------------------------
1005Ice sheet/ocean coupling is done through file exchange at the restart step. NEMO, at each restart step,
1006read the bathymetry and ice shelf draft variable in a netcdf file.
1007If \np{ln\_iscpl = ~true}, the isf draft is assume to be different at each restart step
1008with potentially some new wet/dry cells due to the ice sheet dynamics/thermodynamics.
1009The wetting and drying scheme applied on the restart is very simple and described below for the 6 different cases:
1010\begin{description}
1011\item[Thin a cell down:]
1012   T/S/ssh are unchanged and U/V in the top cell are corrected to keep the barotropic transport (bt) constant ($bt_b=bt_n$).
1013\item[Enlarge  a cell:]
1014   See case "Thin a cell down"
1015\item[Dry a cell:]
1016   mask, T/S, U/V and ssh are set to 0. Furthermore, U/V into the water column are modified to satisfy ($bt_b=bt_n$).
1017\item[Wet a cell:] 
1018   mask is set to 1, T/S is extrapolated from neighbours, $ssh_n = ssh_b$ and U/V set to 0. If no neighbours along i,j and k, T/S/U/V and mask are set to 0.
1019\item[Dry a column:]
1020   mask, T/S, U/V are set to 0 everywhere in the column and ssh set to 0.
1021\item[Wet a column:]
1022   set mask to 1, T/S is extrapolated from neighbours, ssh is extrapolated from neighbours and U/V set to 0. If no neighbour, T/S/U/V and mask set to 0.
1023\end{description}
1024The extrapolation is call \np{nn\_drown} times. It means that if the grounding line retreat by more than \np{nn\_drown} cells between 2 coupling steps,
1025 the code will be unable to fill all the new wet cells properly. The default number is set up for the MISOMIP idealised experiments.\\
1026This coupling procedure is able to take into account grounding line and calving front migration. However, it is a non-conservative processe.
1027This could lead to a trend in heat/salt content and volume. In order to remove the trend and keep the conservation level as close to 0 as possible,
1028 a simple conservation scheme is available with \np{ln\_hsb = ~true}. The heat/salt/vol. gain/loss is diagnose, as well as the location.
1029Based on what is done on sbcrnf to prescribed a source of heat/salt/vol., the heat/salt/vol. gain/loss is removed/added,
1030 over a period of \np{rn\_fiscpl} time step, into the system.
1031So after \np{rn\_fiscpl} time step, all the heat/salt/vol. gain/loss due to extrapolation process is canceled.\\
1032
1033As the before and now fields are not compatible (modification of the geometry), the restart time step is prescribed to be an euler time step instead of a leap frog and $fields_b = fields_n$.
1034%
1035% ================================================================
1036%        Handling of icebergs
1037% ================================================================
1038\section{Handling of icebergs (ICB)}
1039\label{ICB_icebergs}
1040%------------------------------------------namberg----------------------------------------------------
1041\namdisplay{namberg}
1042%-------------------------------------------------------------------------------------------------------------
1043
1044Icebergs are modelled as lagrangian particles in NEMO \citep{Marsh_GMD2015}.
1045Their physical behaviour is controlled by equations as described in \citet{Martin_Adcroft_OM10} ).
1046(Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO).
1047Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described
1048in the \ngn{namberg} namelist:
1049\np{rn\_initial\_mass} and \np{rn\_initial\_thickness}.
1050Each class has an associated scaling (\np{rn\_mass\_scaling}), which is an integer representing how many icebergs
1051of this class are being described as one lagrangian point (this reduces the numerical problem of tracking every single iceberg).
1052They are enabled by setting \np{ln\_icebergs}~=~true.
1053
1054Two initialisation schemes are possible.
1055\begin{description}
1056\item[\np{nn\_test\_icebergs}~$>$~0]
1057In this scheme, the value of \np{nn\_test\_icebergs} represents the class of iceberg to generate
1058(so between 1 and 10), and \np{nn\_test\_icebergs} provides a lon/lat box in the domain at each
1059grid point of which an iceberg is generated at the beginning of the run.
1060(Note that this happens each time the timestep equals \np{nn\_nit000}.)
1061\np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners
1062of the geographical box: lonmin,lonmax,latmin,latmax
1063\item[\np{nn\_test\_icebergs}~=~-1]
1064In this scheme the model reads a calving file supplied in the \np{sn\_icb} parameter.
1065This should be a file with a field on the configuration grid (typically ORCA) representing ice accumulation rate at each model point.
1066These should be ocean points adjacent to land where icebergs are known to calve.
1067Most points in this input grid are going to have value zero.
1068When the model runs, ice is accumulated at each grid point which has a non-zero source term.
1069At each time step, a test is performed to see if there is enough ice mass to calve an iceberg of each class in order (1 to 10).
1070Note that this is the initial mass multiplied by the number each particle represents ($i.e.$ the scaling).
1071If there is enough ice, a new iceberg is spawned and the total available ice reduced accordingly.
1072\end{description}
1073
1074Icebergs are influenced by wind, waves and currents, bottom melt and erosion.
1075The latter act to disintegrate the iceberg. This is either all melted freshwater, or
1076(if \np{rn\_bits\_erosion\_fraction}~$>$~0) into melt and additionally small ice bits
1077which are assumed to propagate with their larger parent and thus delay fluxing into the ocean.
1078Melt water (and other variables on the configuration grid) are written into the main NEMO model output files.
1079
1080Extensive diagnostics can be produced.
1081Separate output files are maintained for human-readable iceberg information.
1082A separate file is produced for each processor (independent of \np{ln\_ctl}).
1083The amount of information is controlled by two integer parameters:
1084\begin{description}
1085\item[\np{nn\_verbose\_level}]  takes a value between one and four and represents
1086an increasing number of points in the code at which variables are written, and an
1087increasing level of obscurity.
1088\item[\np{nn\_verbose\_write}] is the number of timesteps between writes
1089\end{description}
1090
1091Iceberg trajectories can also be written out and this is enabled by setting \np{nn\_sample\_rate}~$>$~0.
1092A non-zero value represents how many timesteps between writes of information into the output file.
1093These output files are in NETCDF format.
1094When \key{mpp\_mpi} is defined, each output file contains only those icebergs in the corresponding processor.
1095Trajectory points are written out in the order of their parent iceberg in the model's "linked list" of icebergs.
1096So care is needed to recreate data for individual icebergs, since its trajectory data may be spread across
1097multiple files.
1098
1099
1100% ================================================================
1101% Miscellanea options
1102% ================================================================
1103\section{Miscellaneous options}
1104\label{SBC_misc}
1105
1106% -------------------------------------------------------------------------------------------------------------
1107%        Diurnal cycle
1108% -------------------------------------------------------------------------------------------------------------
1109\subsection   [Diurnal  cycle (\textit{sbcdcy})]
1110         {Diurnal cycle (\mdl{sbcdcy})}
1111\label{SBC_dcy}
1112%------------------------------------------namsbc_rnf----------------------------------------------------
1113%\namdisplay{namsbc}
1114%-------------------------------------------------------------------------------------------------------------
1115
1116%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1117\begin{figure}[!t]    \begin{center}
1118\includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf}
1119\caption{ \label{Fig_SBC_diurnal}   
1120Example of recontruction of the diurnal cycle variation of short wave flux 
1121from daily mean values. The reconstructed diurnal cycle (black line) is chosen
1122as the mean value of the analytical cycle (blue line) over a time step, not
1123as the mid time step value of the analytically cycle (red square). From \citet{Bernie_al_CD07}.}
1124\end{center}   \end{figure}
1125%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1126
1127\cite{Bernie_al_JC05} have shown that to capture 90$\%$ of the diurnal variability of
1128SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution
1129of the surface fluxes of 3~h or less. Unfortunately high frequency forcing fields are rare,
1130not to say inexistent. Nevertheless, it is possible to obtain a reasonable diurnal cycle
1131of the SST knowning only short wave flux (SWF) at high frequency \citep{Bernie_al_CD07}.
1132Furthermore, only the knowledge of daily mean value of SWF is needed,
1133as higher frequency variations can be reconstructed from them, assuming that
1134the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle
1135of incident SWF. The \cite{Bernie_al_CD07} reconstruction algorithm is available
1136in \NEMO by setting \np{ln\_dm2dc}~=~true (a \textit{\ngn{namsbc}} namelist variable) when using
1137CORE bulk formulea (\np{ln\_blk\_core}~=~true) or the flux formulation (\np{ln\_flx}~=~true).
1138The reconstruction is performed in the \mdl{sbcdcy} module. The detail of the algoritm used
1139can be found in the appendix~A of \cite{Bernie_al_CD07}. The algorithm preserve the daily
1140mean incomming SWF as the reconstructed SWF at a given time step is the mean value
1141of the analytical cycle over this time step (Fig.\ref{Fig_SBC_diurnal}).
1142The use of diurnal cycle reconstruction requires the input SWF to be daily
1143($i.e.$ a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
1144Furthermore, it is recommended to have a least 8 surface module time step per day,
1145that is  $\rdt \ \np{nn\_fsbc} < 10,800~s = 3~h$. An example of recontructed SWF
1146is given in Fig.\ref{Fig_SBC_dcy} for a 12 reconstructed diurnal cycle, one every 2~hours
1147(from 1am to 11pm).
1148
1149%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1150\begin{figure}[!t]  \begin{center}
1151\includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf}
1152\caption{ \label{Fig_SBC_dcy}   
1153Example of recontruction of the diurnal cycle variation of short wave flux 
1154from daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm).
1155The display is on (i,j) plane. }
1156\end{center}   \end{figure}
1157%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
1158
1159Note also that the setting a diurnal cycle in SWF is highly recommended  when
1160the top layer thickness approach 1~m or less, otherwise large error in SST can
1161appear due to an inconsistency between the scale of the vertical resolution
1162and the forcing acting on that scale.
1163
1164% -------------------------------------------------------------------------------------------------------------
1165%        Rotation of vector pairs onto the model grid directions
1166% -------------------------------------------------------------------------------------------------------------
1167\subsection{Rotation of vector pairs onto the model grid directions}
1168\label{SBC_rotation}
1169
1170When using a flux (\np{ln\_flx}=true) or bulk (\np{ln\_clio}=true or \np{ln\_core}=true) formulation,
1171pairs of vector components can be rotated from east-north directions onto the local grid directions. 
1172This is particularly useful when interpolation on the fly is used since here any vectors are likely to be defined
1173relative to a rectilinear grid.
1174To activate this option a non-empty string is supplied in the rotation pair column of the relevant namelist.
1175The eastward component must start with "U" and the northward component with "V". 
1176The remaining characters in the strings are used to identify which pair of components go together.
1177So for example, strings "U1" and "V1" next to "utau" and "vtau" would pair the wind stress components together
1178and rotate them on to the model grid directions; "U2" and "V2" could be used against a second pair of components,
1179and so on.
1180The extra characters used in the strings are arbitrary.
1181The rot\_rep routine from the \mdl{geo2ocean} module is used to perform the rotation.
1182
1183% -------------------------------------------------------------------------------------------------------------
1184%        Surface restoring to observed SST and/or SSS
1185% -------------------------------------------------------------------------------------------------------------
1186\subsection    [Surface restoring to observed SST and/or SSS (\textit{sbcssr})]
1187         {Surface restoring to observed SST and/or SSS (\mdl{sbcssr})}
1188\label{SBC_ssr}
1189%------------------------------------------namsbc_ssr----------------------------------------------------
1190\namdisplay{namsbc_ssr} 
1191%-------------------------------------------------------------------------------------------------------------
1192
1193IOptions are defined through the  \ngn{namsbc\_ssr} namelist variables.
1194n forced mode using a flux formulation (\np{ln\_flx}~=~true), a
1195feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
1196\begin{equation} \label{Eq_sbc_dmp_q}
1197Q_{ns} = Q_{ns}^o + \frac{dQ}{dT} \left( \left. T \right|_{k=1} - SST_{Obs} \right)
1198\end{equation}
1199where SST is a sea surface temperature field (observed or climatological), $T$ is
1200the model surface layer temperature and $\frac{dQ}{dT}$ is a negative feedback
1201coefficient usually taken equal to $-40~W/m^2/K$. For a $50~m$ 
1202mixed-layer depth, this value corresponds to a relaxation time scale of two months.
1203This term ensures that if $T$ perfectly matches the supplied SST, then $Q$ is
1204equal to $Q_o$.
1205
1206In the fresh water budget, a feedback term can also be added. Converted into an
1207equivalent freshwater flux, it takes the following expression :
1208
1209\begin{equation} \label{Eq_sbc_dmp_emp}
1210\textit{emp} = \textit{emp}_o + \gamma_s^{-1} e_{3t}  \frac{  \left(\left.S\right|_{k=1}-SSS_{Obs}\right)}
1211                                             {\left.S\right|_{k=1}}
1212\end{equation}
1213
1214where $\textit{emp}_{o }$ is a net surface fresh water flux (observed, climatological or an
1215atmospheric model product), \textit{SSS}$_{Obs}$ is a sea surface salinity (usually a time
1216interpolation of the monthly mean Polar Hydrographic Climatology \citep{Steele2001}),
1217$\left.S\right|_{k=1}$ is the model surface layer salinity and $\gamma_s$ is a negative
1218feedback coefficient which is provided as a namelist parameter. Unlike heat flux, there is no
1219physical justification for the feedback term in \ref{Eq_sbc_dmp_emp} as the atmosphere
1220does not care about ocean surface salinity \citep{Madec1997}. The SSS restoring
1221term should be viewed as a flux correction on freshwater fluxes to reduce the
1222uncertainties we have on the observed freshwater budget.
1223
1224% -------------------------------------------------------------------------------------------------------------
1225%        Handling of ice-covered area
1226% -------------------------------------------------------------------------------------------------------------
1227\subsection{Handling of ice-covered area  (\textit{sbcice\_...})}
1228\label{SBC_ice-cover}
1229
1230The presence at the sea surface of an ice covered area modifies all the fluxes
1231transmitted to the ocean. There are several way to handle sea-ice in the system
1232depending on the value of the \np{nn\_ice} namelist parameter found in \ngn{namsbc} namelist. 
1233\begin{description}
1234\item[nn{\_}ice = 0]  there will never be sea-ice in the computational domain.
1235This is a typical namelist value used for tropical ocean domain. The surface fluxes
1236are simply specified for an ice-free ocean. No specific things is done for sea-ice.
1237\item[nn{\_}ice = 1]  sea-ice can exist in the computational domain, but no sea-ice model
1238is used. An observed ice covered area is read in a file. Below this area, the SST is
1239restored to the freezing point and the heat fluxes are set to $-4~W/m^2$ ($-2~W/m^2$)
1240in the northern (southern) hemisphere. The associated modification of the freshwater
1241fluxes are done in such a way that the change in buoyancy fluxes remains zero.
1242This prevents deep convection to occur when trying to reach the freezing point
1243(and so ice covered area condition) while the SSS is too large. This manner of
1244managing sea-ice area, just by using si IF case, is usually referred as the \textit{ice-if} 
1245model. It can be found in the \mdl{sbcice{\_}if} module.
1246\item[nn{\_}ice = 2 or more]  A full sea ice model is used. This model computes the
1247ice-ocean fluxes, that are combined with the air-sea fluxes using the ice fraction of
1248each model cell to provide the surface ocean fluxes. Note that the activation of a
1249sea-ice model is is done by defining a CPP key (\key{lim2}, \key{lim3} or \key{cice}).
1250The activation automatically overwrites the read value of nn{\_}ice to its appropriate
1251value ($i.e.$ $2$ for LIM-2, $3$ for LIM-3 or $4$ for CICE).
1252\end{description}
1253
1254% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
1255
1256\subsection   [Interface to CICE (\textit{sbcice\_cice})]
1257         {Interface to CICE (\mdl{sbcice\_cice})}
1258\label{SBC_cice}
1259
1260It is now possible to couple a regional or global NEMO configuration (without AGRIF) to the CICE sea-ice
1261model by using \key{cice}.  The CICE code can be obtained from
1262\href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and the additional 'hadgem3' drivers will be required,
1263even with the latest code release.  Input grid files consistent with those used in NEMO will also be needed,
1264and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used (seek advice from UKMO
1265if necessary).  Currently the code is only designed to work when using the CORE forcing option for NEMO (with
1266\textit{calc\_strair~=~true} and \textit{calc\_Tsfc~=~true} in the CICE name-list), or alternatively when NEMO
1267is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair~=~false} and \textit{calc\_Tsfc~=~false}).
1268The code is intended to be used with \np{nn\_fsbc} set to 1 (although coupling ocean and ice less frequently
1269should work, it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - the
1270user should check that results are not significantly different to the standard case).
1271
1272There are two options for the technical coupling between NEMO and CICE.  The standard version allows
1273complete flexibility for the domain decompositions in the individual models, but this is at the expense of global
1274gather and scatter operations in the coupling which become very expensive on larger numbers of processors. The
1275alternative option (using \key{nemocice\_decomp} for both NEMO and CICE) ensures that the domain decomposition is
1276identical in both models (provided domain parameters are set appropriately, and
1277\textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and allows
1278much more efficient direct coupling on individual processors.  This solution scales much better although it is at
1279the expense of having more idle CICE processors in areas where there is no sea ice.
1280
1281% -------------------------------------------------------------------------------------------------------------
1282%        Freshwater budget control
1283% -------------------------------------------------------------------------------------------------------------
1284\subsection   [Freshwater budget control (\textit{sbcfwb})]
1285         {Freshwater budget control (\mdl{sbcfwb})}
1286\label{SBC_fwb}
1287
1288For global ocean simulation it can be useful to introduce a control of the mean sea
1289level in order to prevent unrealistic drift of the sea surface height due to inaccuracy
1290in the freshwater fluxes. In \NEMO, two way of controlling the the freshwater budget.
1291\begin{description}
1292\item[\np{nn\_fwb}=0]  no control at all. The mean sea level is free to drift, and will
1293certainly do so.
1294\item[\np{nn\_fwb}=1]  global mean \textit{emp} set to zero at each model time step.
1295%Note that with a sea-ice model, this technique only control the mean sea level with linear free surface (\key{vvl} not defined) and no mass flux between ocean and ice (as it is implemented in the current ice-ocean coupling).
1296\item[\np{nn\_fwb}=2]  freshwater budget is adjusted from the previous year annual
1297mean budget which is read in the \textit{EMPave\_old.dat} file. As the model uses the
1298Boussinesq approximation, the annual mean fresh water budget is simply evaluated
1299from the change in the mean sea level at January the first and saved in the
1300\textit{EMPav.dat} file.
1301\end{description}
1302
1303% -------------------------------------------------------------------------------------------------------------
1304%        Neutral Drag Coefficient from external wave model
1305% -------------------------------------------------------------------------------------------------------------
1306\subsection   [Neutral drag coefficient from external wave model (\textit{sbcwave})]
1307              {Neutral drag coefficient from external wave model (\mdl{sbcwave})}
1308\label{SBC_wave}
1309%------------------------------------------namwave----------------------------------------------------
1310\namdisplay{namsbc_wave}
1311%-------------------------------------------------------------------------------------------------------------
1312
1313In order to read a neutral drag coeff, from an external data source ($i.e.$ a wave model), the
1314logical variable \np{ln\_cdgw} in \ngn{namsbc} namelist must be set to \textit{true}.
1315The \mdl{sbcwave} module containing the routine \np{sbc\_wave} reads the
1316namelist \ngn{namsbc\_wave} (for external data names, locations, frequency, interpolation and all
1317the miscellanous options allowed by Input Data generic Interface see \S\ref{SBC_input})
1318and a 2D field of neutral drag coefficient.
1319Then using the routine TURB\_CORE\_1Z or TURB\_CORE\_2Z, and starting from the neutral drag coefficent provided,
1320the drag coefficient is computed according to stable/unstable conditions of the air-sea interface following \citet{Large_Yeager_Rep04}.
1321
1322
1323% Griffies doc:
1324% When running ocean-ice simulations, we are not explicitly representing land processes,
1325% such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift,
1326% it is important to balance the hydrological cycle in ocean-ice models.
1327% We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff.
1328% The result of the normalization should be a global integrated zero net water input to the ocean-ice system over
1329% a chosen time scale.
1330%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step,
1331% so that there is always a zero net input of water to the ocean-ice system.
1332% Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used
1333% to alter the subsequent year�s water budget in an attempt to damp the annual water imbalance.
1334% Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
1335% When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean
1336% and ice models when aiming to balance the hydrological cycle.
1337% 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,
1338% not the water in any one sub-component. As an extreme example to illustrate the issue,
1339% consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up,
1340% there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean.
1341% The total water contained in the ocean plus ice system is constant, but there is an exchange of water between
1342% the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle
1343% in ocean-ice models.
1344
1345
Note: See TracBrowser for help on using the repository browser.