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Chap_SBC.tex in branches/2012/dev_r3337_NOCS10_ICB/DOC/TexFiles/Chapters – NEMO

source: branches/2012/dev_r3337_NOCS10_ICB/DOC/TexFiles/Chapters/Chap_SBC.tex @ 3342

Last change on this file since 3342 was 3342, checked in by sga, 12 years ago

NEMO branch dev_r3337_NOCS10_ICB: add documentation for iceberg code

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1% ================================================================
2% Chapter Ñ Surface Boundary Condition (SBC, ICB)
3% ================================================================
4\chapter{Surface Boundary Condition (SBC, 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 $\left( {\textit{emp},\;\textit{emp}_S } \right)$
20\end{itemize}
21plus an optional field:
22\begin{itemize}
23   \item the atmospheric pressure at the ocean surface $\left( p_a \right)$
24\end{itemize}
25
26Five different ways to provide the first six fields to the ocean are available which
27are controlled by namelist variables: an analytical formulation (\np{ln\_ana}~=~true),
28a flux formulation (\np{ln\_flx}~=~true), a bulk formulae formulation (CORE
29(\np{ln\_core}~=~true), CLIO (\np{ln\_clio}~=~true) or MFS
30\footnote { Note that MFS bulk formulae compute fluxes only for the ocean component}
31(\np{ln\_mfs}~=~true) bulk formulae) and a coupled
32formulation (exchanges with a atmospheric model via the OASIS coupler)
33(\np{ln\_cpl}~=~true). When used, the atmospheric pressure forces both
34ocean and ice dynamics (\np{ln\_apr\_dyn}~=~true).
35The frequency at which the six or seven fields have to be updated is the \np{nn\_fsbc} 
36namelist 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}).
41In addition, the resulting fields can be further modified using several namelist options.
42These options control  the rotation of vector components supplied relative to an east-north
43coordinate system onto the local grid directions in the model; the addition of a surface
44restoring term to observed SST and/or SSS (\np{ln\_ssr}~=~true); the modification of fluxes
45below ice-covered areas (using observed ice-cover or a sea-ice model)
46(\np{nn\_ice}~=~0,1, 2 or 3); the addition of river runoffs as surface freshwater
47fluxes or lateral inflow (\np{ln\_rnf}~=~true); the addition of a freshwater flux adjustment
48in order to avoid a mean sea-level drift (\np{nn\_fwb}~=~0,~1~or~2); the
49transformation of the solar radiation (if provided as daily mean) into a diurnal
50cycle (\np{ln\_dm2dc}~=~true); and a neutral drag coefficient can be read from an external wave
51model (\np{ln\_cdgw}~=~true). The latter option is possible only in case core or mfs bulk formulas are selected.
52
53In this chapter, we first discuss where the surface boundary condition appears in the
54model equations. Then we present the five ways of providing the surface boundary condition,
55followed by the description of the atmospheric pressure and the river runoff.
56Next the scheme for interpolation on the fly is described.
57Finally, the different options that further modify the fluxes applied to the ocean are discussed.
58One of these is modification by icebergs (see \S\ref{ICB_icebergs}), which act as drifting sources of fresh water.
59
60
61% ================================================================
62% Surface boundary condition for the ocean
63% ================================================================
64\section{Surface boundary condition for the ocean}
65\label{SBC_general}
66
67The surface ocean stress is the stress exerted by the wind and the sea-ice
68on the ocean. The two components of stress are assumed to be interpolated
69onto the ocean mesh, $i.e.$ resolved onto the model (\textbf{i},\textbf{j}) direction
70at $u$- and $v$-points They are applied as a surface boundary condition of the
71computation of the momentum vertical mixing trend (\mdl{dynzdf} module) :
72\begin{equation} \label{Eq_sbc_dynzdf}
73\left.{\left( {\frac{A^{vm} }{e_3 }\ \frac{\partial \textbf{U}_h}{\partial k}} \right)} \right|_{z=1}
74    = \frac{1}{\rho _o} \binom{\tau _u}{\tau _v }
75\end{equation}
76where $(\tau _u ,\;\tau _v )=(utau,vtau)$ are the two components of the wind
77stress vector in the $(\textbf{i},\textbf{j})$ coordinate system.
78
79The surface heat flux is decomposed into two parts, a non solar and a solar heat
80flux, $Q_{ns}$ and $Q_{sr}$, respectively. The former is the non penetrative part
81of the heat flux ($i.e.$ the sum of sensible, latent and long wave heat fluxes).
82It is applied as a surface boundary condition trend of the first level temperature
83time evolution equation (\mdl{trasbc} module).
84\begin{equation} \label{Eq_sbc_trasbc_q}
85\frac{\partial T}{\partial t}\equiv \cdots \;+\;\left. {\frac{Q_{ns} }{\rho 
86_o \;C_p \;e_{3t} }} \right|_{k=1} \quad
87\end{equation}
88$Q_{sr}$ is the penetrative part of the heat flux. It is applied as a 3D
89trends of the temperature equation (\mdl{traqsr} module) when \np{ln\_traqsr}=True.
90
91\begin{equation} \label{Eq_sbc_traqsr}
92\frac{\partial T}{\partial t}\equiv \cdots \;+\frac{Q_{sr} }{\rho_o C_p \,e_{3t} }\delta _k \left[ {I_w } \right]
93\end{equation}
94where $I_w$ is a non-dimensional function that describes the way the light
95penetrates inside the water column. It is generally a sum of decreasing
96exponentials (see \S\ref{TRA_qsr}).
97
98The surface freshwater budget is provided by fields: \textit{emp} and $\textit{emp}_S$ which
99may or may not be identical. Indeed, a surface freshwater flux has two effects:
100it changes the volume of the ocean and it changes the surface concentration of
101salt (and other tracers). Therefore it appears in the sea surface height as a volume
102flux, \textit{emp} (\textit{dynspg\_xxx} modules), and in the salinity time evolution equations
103as a concentration/dilution effect,
104$\textit{emp}_{S}$ (\mdl{trasbc} module).
105\begin{equation} \label{Eq_trasbc_emp}
106\begin{aligned}
107&\frac{\partial \eta }{\partial t}\equiv \cdots \;+\;\textit{emp}\quad  \\ 
108\\
109 &\frac{\partial S}{\partial t}\equiv \cdots \;+\left. {\frac{\textit{emp}_S \;S}{e_{3t} }} \right|_{k=1} \\ 
110 \end{aligned}
111\end{equation} 
112
113In the real ocean, $\textit{emp}=\textit{emp}_S$ and the ocean salt content is conserved,
114but it exist several numerical reasons why this equality should be broken.
115For example, when the ocean is coupled to a sea-ice model, the water exchanged between
116ice and ocean is slightly salty (mean sea-ice salinity is $\sim $\textit{4 psu}). In this case,
117$\textit{emp}_{S}$ take into account both concentration/dilution effect associated with
118freezing/melting and the salt flux between ice and ocean, while \textit{emp} is
119only the volume flux. In addition, in the current version of \NEMO, the sea-ice is
120assumed to be above the ocean (the so-called levitating sea-ice). Freezing/melting does
121not change the ocean volume (no impact on \textit{emp}) but it modifies the SSS.
122%gm  \colorbox{yellow}{(see {\S} on LIM sea-ice model)}.
123
124Note that SST can also be modified by a freshwater flux. Precipitation (in
125particular solid precipitation) may have a temperature significantly different from
126the SST. Due to the lack of information about the temperature of
127precipitation, we assume it is equal to the SST. Therefore, no
128concentration/dilution term appears in the temperature equation. It has to
129be emphasised that this absence does not mean that there is no heat flux
130associated with precipitation! Precipitation can change the ocean volume and thus the
131ocean heat content. It is therefore associated with a heat flux (not yet 
132diagnosed in the model) \citep{Roullet_Madec_JGR00}).
133
134%\colorbox{yellow}{Miss: }
135%
136%A extensive description of all namsbc namelist (parameter that have to be
137%created!)
138%
139%Especially the \np{nn\_fsbc}, the \mdl{sbc\_oce} module (fluxes + mean sst sss ssu
140%ssv) i.e. information required by flux computation or sea-ice
141%
142%\mdl{sbc\_oce} containt the definition in memory of the 7 fields (6+runoff), add
143%a word on runoff: included in surface bc or add as lateral obc{\ldots}.
144%
145%Sbcmod manage the ``providing'' (fourniture) to the ocean the 7 fields
146%
147%Fluxes update only each nf{\_}sbc time step (namsbc) explain relation
148%between nf{\_}sbc and nf{\_}ice, do we define nf{\_}blk??? ? only one
149%nf{\_}sbc
150%
151%Explain here all the namlist namsbc variable{\ldots}.
152%
153%\colorbox{yellow}{End Miss }
154
155The ocean model provides the surface currents, temperature and salinity
156averaged over \np{nf\_sbc} time-step (\ref{Tab_ssm}).The computation of the
157mean is done in \mdl{sbcmod} module.
158
159%-------------------------------------------------TABLE---------------------------------------------------
160\begin{table}[tb]   \begin{center}   \begin{tabular}{|l|l|l|l|}
161\hline
162Variable description             & Model variable  & Units  & point \\  \hline
163i-component of the surface current  & ssu\_m & $m.s^{-1}$   & U \\   \hline
164j-component of the surface current  & ssv\_m & $m.s^{-1}$   & V \\   \hline
165Sea surface temperature          & sst\_m & \r{}$K$      & T \\   \hline
166Sea surface salinty              & sss\_m & $psu$        & T \\   \hline
167\end{tabular}
168\caption{  \label{Tab_ssm}   
169Ocean variables provided by the ocean to the surface module (SBC).
170The variable are averaged over nf{\_}sbc time step, $i.e.$ the frequency of
171computation of surface fluxes.}
172\end{center}   \end{table}
173%--------------------------------------------------------------------------------------------------------------
174
175%\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
176
177
178% ================================================================
179%       Input Data
180% ================================================================
181\section{Input Data generic interface}
182\label{SBC_input}
183
184A generic interface has been introduced to manage the way input data (2D or 3D fields,
185like surface forcing or ocean T and S) are specify in \NEMO. This task is archieved by fldread.F90.
186The module was design with four main objectives in mind:
187\begin{enumerate} 
188\item optionally provide a time interpolation of the input data at model time-step,
189whatever their input frequency is, and according to the different calendars available in the model.
190\item optionally provide an on-the-fly space interpolation from the native input data grid to the model grid.
191\item make the run duration independent from the period cover by the input files.
192\item provide a simple user interface and a rather simple developer interface by limiting the
193 number of prerequisite information.
194\end{enumerate} 
195
196As a results the user have only to fill in for each variable a structure in the namelist file
197to defined the input data file and variable names, the frequency of the data (in hours or months),
198whether its is climatological data or not, the period covered by the input file (one year, month, week or day),
199and two additional parameters for on-the-fly interpolation. When adding a new input variable,
200the developer has to add the associated structure in the namelist, read this information
201by mirroring the namelist read in \rou{sbc\_blk\_init} for example, and simply call \rou{fld\_read} 
202to obtain the desired input field at the model time-step and grid points.
203
204The only constraints are that the input file is a NetCDF file, the file name follows a nomenclature
205(see \S\ref{SBC_fldread}), the period it cover is one year, month, week or day, and, if on-the-fly
206interpolation is used, a file of weights must be supplied (see \S\ref{SBC_iof}).
207
208Note that when an input data is archived on a disc which is accessible directly
209from the workspace where the code is executed, then the use can set the \np{cn\_dir} 
210to the pathway leading to the data. By default, the data are assumed to have been
211copied so that cn\_dir='./'.
212
213% -------------------------------------------------------------------------------------------------------------
214% Input Data specification (\mdl{fldread})
215% -------------------------------------------------------------------------------------------------------------
216\subsection{Input Data specification (\mdl{fldread})}
217\label{SBC_fldread}
218
219The structure associated with an input variable contains the following information:
220\begin{alltt}  {{\tiny   
221\begin{verbatim}
222!  file name  ! frequency (hours) ! variable  ! time interp. !  clim  ! 'yearly'/ ! weights  ! rotation !
223!             !  (if <0  months)  !   name    !   (logical)  !  (T/F) ! 'monthly' ! filename ! pairing  !
224\end{verbatim}
225}}\end{alltt} 
226where
227\begin{description} 
228\item[File name]: the stem name of the NetCDF file to be open.
229This stem will be completed automatically by the model, with the addition of a '.nc' at its end
230and by date information and possibly a prefix (when using AGRIF).
231Tab.\ref{Tab_fldread} provides the resulting file name in all possible cases according to whether
232it is a climatological file or not, and to the open/close frequency (see below for definition).
233
234%--------------------------------------------------TABLE--------------------------------------------------
235\begin{table}[htbp]
236\begin{center}
237\begin{tabular}{|l|c|c|c|}
238\hline
239                         & daily or weekLLL          & monthly                   &   yearly          \\   \hline
240clim = false   & fn\_yYYYYmMMdDD  &   fn\_yYYYYmMM   &   fn\_yYYYY  \\   \hline
241clim = true       & not possible                  &  fn\_m??.nc             &   fn                \\   \hline
242\end{tabular}
243\end{center}
244\caption{ \label{Tab_fldread}   naming nomenclature for climatological or interannual input file,
245as a function of the Open/close frequency. The stem name is assumed to be 'fn'.
246For 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
247actual year/month/day, always coded with 4 or 2 digits. Note that (1) in mpp, if the file is split
248over each subdomain, the suffix '.nc' is replaced by '\_PPPP.nc', where 'PPPP' is the
249process number coded with 4 digits; (2) when using AGRIF, the prefix
250'\_N' is added to files,
251where 'N'  is the child grid number.}
252\end{table}
253%--------------------------------------------------------------------------------------------------------------
254 
255
256\item[Record frequency]: the frequency of the records contained in the input file.
257Its unit is in hours if it is positive (for example 24 for daily forcing) or in months if negative
258(for example -1 for monthly forcing or -12 for annual forcing).
259Note that this frequency must really be an integer and not a real.
260On some computers, seting it to '24.' can be interpreted as 240!
261
262\item[Variable name]: the name of the variable to be read in the input NetCDF file.
263
264\item[Time interpolation]: a logical to activate, or not, the time interpolation. If set to 'false',
265the forcing will have a steplike shape remaining constant during each forcing period.
266For example, when using a daily forcing without time interpolation, the forcing remaining
267constant from 00h00'00'' to 23h59'59". If set to 'true', the forcing will have a broken line shape.
268Records are assumed to be dated the middle of the forcing period.
269For example, when using a daily forcing with time interpolation, linear interpolation will
270be performed between mid-day of two consecutive days.
271
272\item[Climatological forcing]: a logical to specify if a input file contains climatological forcing
273which can be cycle in time, or an interannual forcing which will requires additional files
274if the period covered by the simulation exceed the one of the file. See the above the file
275naming strategy which impacts the expected name of the file to be opened.
276
277\item[Open/close frequency]: the frequency at which forcing files must be opened/closed.
278Four cases are coded: 'daily', 'weekLLL' (with 'LLL' the first 3 letters of the first day of the week),
279'monthly' and 'yearly' which means the forcing files will contain data for one day, one week,
280one month or one year. Files are assumed to contain data from the beginning of the open/close period.
281For example, the first record of a yearly file containing daily data is Jan 1st even if the experiment
282is not starting at the beginning of the year.
283
284\item[Others]: 'weights filename' and 'pairing rotation' are associted with on-the-fly interpolation
285which is described in \S\ref{SBC_iof}.
286
287\end{description}
288
289Additional remarks:\\
290(1) The time interpolation is a simple linear interpolation between two consecutive records of
291the input data. The only tricky point is therefore to specify the date at which we need to do
292the interpolation and the date of the records read in the input files.
293Following \citet{Leclair_Madec_OM09}, the date of a time step is set at the middle of the
294time step. For example, for an experiment starting at 0h00'00" with a one hour time-step,
295a time interpolation will be performed at the following time: 0h30'00", 1h30'00", 2h30'00", etc.
296However, for forcing data related to the surface module, values are not needed at every
297time-step but at every \np{nn\_fsbc} time-step. For example with \np{nn\_fsbc}~=~3,
298the surface module will be called at time-steps 1, 4, 7, etc. The date used for the time interpolation
299is thus redefined to be at the middle of \np{nn\_fsbc} time-step period. In the previous example,
300this leads to: 1h30'00", 4h30'00", 7h30'00", etc. \\ 
301(2) For code readablility and maintenance issues, we don't take into account the NetCDF input file
302calendar. The calendar associated with the forcing field is build according to the information
303provided by user in the record frequency, the open/close frequency and the type of temporal interpolation.
304For example, the first record of a yearly file containing daily data that will be interpolated in time
305is assumed to be start Jan 1st at 12h00'00" and end Dec 31st at 12h00'00". \\
306(3) If a time interpolation is requested, the code will pick up the needed data in the previous (next) file
307when interpolating data with the first (last) record of the open/close period.
308For example, if the input file specifications are ''yearly, containing daily data to be interpolated in time'',
309the values given by the code between 00h00'00" and 11h59'59" on Jan 1st will be interpolated values
310between Dec 31st 12h00'00" and Jan 1st 12h00'00". If the forcing is climatological, Dec and Jan will
311be keep-up from the same year. However, if the forcing is not climatological, at the end of the
312open/close period the code will automatically close the current file and open the next one.
313Note that, if the experiment is starting (ending) at the beginning (end) of an open/close period
314we do accept that the previous (next) file is not existing. In this case, the time interpolation
315will be performed between two identical values. For example, when starting an experiment on
316Jan 1st of year Y with yearly files and daily data to be interpolated, we do accept that the file
317related to year Y-1 is not existing. The value of Jan 1st will be used as the missing one for
318Dec 31st of year Y-1. If the file of year Y-1 exists, the code will read its last record.
319Therefore, this file can contain only one record corresponding to Dec 31st, a useful feature for
320user considering that it is too heavy to manipulate the complete file for year Y-1.
321
322
323% -------------------------------------------------------------------------------------------------------------
324% Interpolation on the Fly
325% -------------------------------------------------------------------------------------------------------------
326\subsection [Interpolation on-the-Fly] {Interpolation on-the-Fly}
327\label{SBC_iof}
328
329Interpolation on the Fly allows the user to supply input files required
330for the surface forcing on grids other than the model grid.
331To do this he or she must supply, in addition to the source data file,
332a file of weights to be used to interpolate from the data grid to the model grid.
333The original development of this code used the SCRIP package (freely available
334\href{http://climate.lanl.gov/Software/SCRIP}{here} under a copyright agreement).
335In principle, any package can be used to generate the weights, but the
336variables in the input weights file must have the same names and meanings as
337assumed by the model.
338Two methods are currently available: bilinear and bicubic interpolation.
339
340\subsubsection{Bilinear Interpolation}
341\label{SBC_iof_bilinear}
342
343The input weights file in this case has two sets of variables: src01, src02,
344src03, src04 and wgt01, wgt02, wgt03, wgt04.
345The "src" variables correspond to the point in the input grid to which the weight
346"wgt" is to be applied. Each src value is an integer corresponding to the index of a
347point in the input grid when written as a one dimensional array.  For example, for an input grid
348of size 5x10, point (3,2) is referenced as point 8, since (2-1)*5+3=8.
349There are four of each variable because bilinear interpolation uses the four points defining
350the grid box containing the point to be interpolated.
351All of these arrays are on the model grid, so that values src01(i,j) and
352wgt01(i,j) are used to generate a value for point (i,j) in the model.
353
354Symbolically, the algorithm used is:
355
356\begin{equation}
357f_{m}(i,j) = f_{m}(i,j) + \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}
358\end{equation}
359where function idx() transforms a one dimensional index src(k) into a two dimensional index,
360and wgt(1) corresponds to variable "wgt01" for example.
361
362\subsubsection{Bicubic Interpolation}
363\label{SBC_iof_bicubic}
364
365Again there are two sets of variables: "src" and "wgt".
366But in this case there are 16 of each.
367The symbolic algorithm used to calculate values on the model grid is now:
368
369\begin{equation*} \begin{split}
370f_{m}(i,j) =  f_{m}(i,j) +& \sum_{k=1}^{4} {wgt(k)f(idx(src(k)))}     
371              +   \sum_{k=5}^{8} {wgt(k)\left.\frac{\partial f}{\partial i}\right| _{idx(src(k))} }    \\
372              +& \sum_{k=9}^{12} {wgt(k)\left.\frac{\partial f}{\partial j}\right| _{idx(src(k))} }   
373              +   \sum_{k=13}^{16} {wgt(k)\left.\frac{\partial ^2 f}{\partial i \partial j}\right| _{idx(src(k))} }
374\end{split}
375\end{equation*}
376The gradients here are taken with respect to the horizontal indices and not distances since the spatial dependency has been absorbed into the weights.
377
378\subsubsection{Implementation}
379\label{SBC_iof_imp}
380
381To activate this option, a non-empty string should be supplied in the weights filename column
382of the relevant namelist; if this is left as an empty string no action is taken.
383In the model, weights files are read in and stored in a structured type (WGT) in the fldread
384module, as and when they are first required.
385This initialisation procedure determines whether the input data grid should be treated
386as cyclical or not by inspecting a global attribute stored in the weights input file.
387This attribute must be called "ew\_wrap" and be of integer type.
388If it is negative, the input non-model grid is assumed not to be cyclic.
389If zero or greater, then the value represents the number of columns that overlap.
390$E.g.$ if the input grid has columns at longitudes 0, 1, 2, .... , 359, then ew\_wrap should be set to 0;
391if longitudes are 0.5, 2.5, .... , 358.5, 360.5, 362.5, ew\_wrap should be 2.
392If the model does not find attribute ew\_wrap, then a value of -999 is assumed.
393In this case the \rou{fld\_read} routine defaults ew\_wrap to value 0 and therefore the grid
394is assumed to be cyclic with no overlapping columns.
395(In fact this only matters when bicubic interpolation is required.)
396Note that no testing is done to check the validity in the model, since there is no way
397of knowing the name used for the longitude variable,
398so it is up to the user to make sure his or her data is correctly represented.
399
400Next the routine reads in the weights.
401Bicubic interpolation is assumed if it finds a variable with name "src05", otherwise
402bilinear interpolation is used. The WGT structure includes dynamic arrays both for
403the storage of the weights (on the model grid), and when required, for reading in
404the variable to be interpolated (on the input data grid).
405The size of the input data array is determined by examining the values in the "src"
406arrays to find the minimum and maximum i and j values required.
407Since bicubic interpolation requires the calculation of gradients at each point on the grid,
408the corresponding arrays are dimensioned with a halo of width one grid point all the way around.
409When the array of points from the data file is adjacent to an edge of the data grid,
410the halo is either a copy of the row/column next to it (non-cyclical case), or is a copy
411of one from the first few columns on the opposite side of the grid (cyclical case).
412
413\subsubsection{Limitations}
414\label{SBC_iof_lim}
415
416\begin{enumerate} 
417\item  The case where input data grids are not logically rectangular has not been tested.
418\item  This code is not guaranteed to produce positive definite answers from positive definite inputs
419          when a bicubic interpolation method is used.
420\item  The cyclic condition is only applied on left and right columns, and not to top and bottom rows.
421\item  The gradients across the ends of a cyclical grid assume that the grid spacing between
422          the two columns involved are consistent with the weights used.
423\item  Neither interpolation scheme is conservative. (There is a conservative scheme available
424          in SCRIP, but this has not been implemented.)
425\end{enumerate}
426
427\subsubsection{Utilities}
428\label{SBC_iof_util}
429
430% to be completed
431A set of utilities to create a weights file for a rectilinear input grid is available
432(see the directory NEMOGCM/TOOLS/WEIGHTS).
433
434
435% ================================================================
436% Analytical formulation (sbcana module)
437% ================================================================
438\section  [Analytical formulation (\textit{sbcana}) ]
439      {Analytical formulation (\mdl{sbcana} module) }
440\label{SBC_ana}
441
442%---------------------------------------namsbc_ana--------------------------------------------------
443\namdisplay{namsbc_ana}
444%--------------------------------------------------------------------------------------------------------------
445
446The analytical formulation of the surface boundary condition is the default scheme.
447In this case, all the six fluxes needed by the ocean are assumed to
448be uniform in space. They take constant values given in the namelist
449namsbc{\_}ana by the variables \np{rn\_utau0}, \np{rn\_vtau0}, \np{rn\_qns0},
450\np{rn\_qsr0}, and \np{rn\_emp0} ($\textit{emp}=\textit{emp}_S$). The runoff is set to zero.
451In addition, the wind is allowed to reach its nominal value within a given number
452of time steps (\np{nn\_tau000}).
453
454If a user wants to apply a different analytical forcing, the \mdl{sbcana} 
455module can be modified to use another scheme. As an example,
456the \mdl{sbc\_ana\_gyre} routine provides the analytical forcing for the
457GYRE configuration (see GYRE configuration manual, in preparation).
458
459
460% ================================================================
461% Flux formulation
462% ================================================================
463\section  [Flux formulation (\textit{sbcflx}) ]
464      {Flux formulation (\mdl{sbcflx} module) }
465\label{SBC_flx}
466%------------------------------------------namsbc_flx----------------------------------------------------
467\namdisplay{namsbc_flx} 
468%-------------------------------------------------------------------------------------------------------------
469
470In the flux formulation (\np{ln\_flx}=true), the surface boundary
471condition fields are directly read from input files. The user has to define
472in the namelist namsbc{\_}flx the name of the file, the name of the variable
473read in the file, the time frequency at which it is given (in hours), and a logical
474setting whether a time interpolation to the model time step is required
475for this field. See \S\ref{SBC_fldread} for a more detailed description of the parameters.
476
477Note that in general, a flux formulation is used in associated with a
478restoring term to observed SST and/or SSS. See \S\ref{SBC_ssr} for its
479specification.
480
481
482% ================================================================
483% Bulk formulation
484% ================================================================
485\section  [Bulk formulation (\textit{sbcblk\_core}, \textit{sbcblk\_clio} or \textit{sbcblk\_mfs}) ]
486      {Bulk formulation \small{(\mdl{sbcblk\_core} \mdl{sbcblk\_clio} \mdl{sbcblk\_mfs} modules)} }
487\label{SBC_blk}
488
489In the bulk formulation, the surface boundary condition fields are computed
490using bulk formulae and atmospheric fields and ocean (and ice) variables.
491
492The atmospheric fields used depend on the bulk formulae used. Three bulk formulations
493are available : the CORE, the CLIO and the MFS bulk formulea. The choice is made by setting to true
494one of the following namelist variable : \np{ln\_core} ; \np{ln\_clio} or  \np{ln\_mfs}.
495
496Note : in forced mode, when a sea-ice model is used, a bulk formulation (CLIO or CORE) have to be used.
497Therefore the two bulk (CLIO and CORE) formulea include the computation of the fluxes over both
498an ocean and an ice surface.
499
500% -------------------------------------------------------------------------------------------------------------
501%        CORE Bulk formulea
502% -------------------------------------------------------------------------------------------------------------
503\subsection    [CORE Bulk formulea (\np{ln\_core}=true)]
504            {CORE Bulk formulea (\np{ln\_core}=true, \mdl{sbcblk\_core})}
505\label{SBC_blk_core}
506%------------------------------------------namsbc_core----------------------------------------------------
507\namdisplay{namsbc_core} 
508%-------------------------------------------------------------------------------------------------------------
509
510The CORE bulk formulae have been developed by \citet{Large_Yeager_Rep04}.
511They have been designed to handle the CORE forcing, a mixture of NCEP
512reanalysis and satellite data. They use an inertial dissipative method to compute
513the turbulent transfer coefficients (momentum, sensible heat and evaporation)
514from the 10 metre wind speed, air temperature and specific humidity.
515This \citet{Large_Yeager_Rep04} dataset is available through the
516\href{http://nomads.gfdl.noaa.gov/nomads/forms/mom4/CORE.html}{GFDL web site}.
517
518Note that substituting ERA40 to NCEP reanalysis fields
519does not require changes in the bulk formulea themself.
520This is the so-called DRAKKAR Forcing Set (DFS) \citep{Brodeau_al_OM09}.
521
522The required 8 input fields are:
523
524%--------------------------------------------------TABLE--------------------------------------------------
525\begin{table}[htbp]   \label{Tab_CORE}
526\begin{center}
527\begin{tabular}{|l|c|c|c|}
528\hline
529Variable desciption              & Model variable  & Units   & point \\    \hline
530i-component of the 10m air velocity & utau      & $m.s^{-1}$         & T  \\  \hline
531j-component of the 10m air velocity & vtau      & $m.s^{-1}$         & T  \\  \hline
53210m air temperature              & tair      & \r{}$K$            & T   \\ \hline
533Specific humidity             & humi      & \%              & T \\      \hline
534Incoming long wave radiation     & qlw    & $W.m^{-2}$         & T \\      \hline
535Incoming short wave radiation    & qsr    & $W.m^{-2}$         & T \\      \hline
536Total precipitation (liquid + solid)   & precip & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
537Solid precipitation              & snow      & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
538\end{tabular}
539\end{center}
540\end{table}
541%--------------------------------------------------------------------------------------------------------------
542
543Note that the air velocity is provided at a tracer ocean point, not at a velocity ocean
544point ($u$- and $v$-points). It is simpler and faster (less fields to be read),
545but it is not the recommended method when the ocean grid size is the same
546or larger than the one of the input atmospheric fields.
547
548% -------------------------------------------------------------------------------------------------------------
549%        CLIO Bulk formulea
550% -------------------------------------------------------------------------------------------------------------
551\subsection    [CLIO Bulk formulea (\np{ln\_clio}=true)]
552            {CLIO Bulk formulea (\np{ln\_clio}=true, \mdl{sbcblk\_clio})}
553\label{SBC_blk_clio}
554%------------------------------------------namsbc_clio----------------------------------------------------
555\namdisplay{namsbc_clio} 
556%-------------------------------------------------------------------------------------------------------------
557
558The CLIO bulk formulae were developed several years ago for the
559Louvain-la-neuve coupled ice-ocean model (CLIO, \cite{Goosse_al_JGR99}).
560They are simpler bulk formulae. They assume the stress to be known and
561compute the radiative fluxes from a climatological cloud cover.
562
563The required 7 input fields are:
564
565%--------------------------------------------------TABLE--------------------------------------------------
566\begin{table}[htbp]   \label{Tab_CLIO}
567\begin{center}
568\begin{tabular}{|l|l|l|l|}
569\hline
570Variable desciption           & Model variable  & Units           & point \\  \hline
571i-component of the ocean stress     & utau         & $N.m^{-2}$         & U \\   \hline
572j-component of the ocean stress     & vtau         & $N.m^{-2}$         & V \\   \hline
573Wind speed module             & vatm         & $m.s^{-1}$         & T \\   \hline
57410m air temperature              & tair         & \r{}$K$            & T \\   \hline
575Specific humidity                & humi         & \%              & T \\   \hline
576Cloud cover                   &           & \%              & T \\   \hline
577Total precipitation (liquid + solid)   & precip    & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
578Solid precipitation              & snow         & $Kg.m^{-2}.s^{-1}$ & T \\   \hline
579\end{tabular}
580\end{center}
581\end{table}
582%--------------------------------------------------------------------------------------------------------------
583
584As for the flux formulation, information about the input data required by the
585model is provided in the namsbc\_blk\_core or namsbc\_blk\_clio
586namelist (see \S\ref{SBC_fldread}).
587
588% -------------------------------------------------------------------------------------------------------------
589%        MFS Bulk formulae
590% -------------------------------------------------------------------------------------------------------------
591\subsection    [MFS Bulk formulea (\np{ln\_mfs}=true)]
592            {MFS Bulk formulea (\np{ln\_mfs}=true, \mdl{sbcblk\_mfs})}
593\label{SBC_blk_mfs}
594%------------------------------------------namsbc_mfs----------------------------------------------------
595\namdisplay{namsbc_mfs} 
596%----------------------------------------------------------------------------------------------------------
597
598The MFS (Mediterranean Forecasting System) bulk formulae have been developed by
599 \citet{Castellari_al_JMS1998}.
600They have been designed to handle the ECMWF operational data and are currently
601in use in the MFS operational system \citep{Tonani_al_OS08}, \citep{Oddo_al_OS09}.
602The wind stress computation uses a drag coefficient computed according to \citet{Hellerman_Rosenstein_JPO83}.
603The surface boundary condition for temperature involves the balance between surface solar radiation,
604net long-wave radiation, the latent and sensible heat fluxes.
605Solar radiation is dependent on cloud cover and is computed by means of
606an astronomical formula \citep{Reed_JPO77}. Albedo monthly values are from \citet{Payne_JAS72} 
607as means of the values at $40^{o}N$ and $30^{o}N$ for the Atlantic Ocean (hence the same latitudinal
608band of the Mediterranean Sea). The net long-wave radiation flux
609\citep{Bignami_al_JGR95} is a function of
610air temperature, sea-surface temperature, cloud cover and relative humidity.
611Sensible heat and latent heat fluxes are computed by classical
612bulk formulae parameterized according to \citet{Kondo1975}.
613Details on the bulk formulae used can be found in \citet{Maggiore_al_PCE98} and \citet{Castellari_al_JMS1998}.
614
615The required 7 input fields must be provided on the model Grid-T and  are:
616\begin{itemize}
617\item          Zonal Component of the 10m wind ($ms^{-1}$)  (\np{sn\_windi})
618\item          Meridional Component of the 10m wind ($ms^{-1}$)  (\np{sn\_windj})
619\item          Total Claud Cover (\%)  (\np{sn\_clc})
620\item          2m Air Temperature ($K$) (\np{sn\_tair})
621\item          2m Dew Point Temperature ($K$)  (\np{sn\_rhm})
622\item          Total Precipitation ${Kg} m^{-2} s^{-1}$ (\np{sn\_prec})
623\item          Mean Sea Level Pressure (${Pa}$) (\np{sn\_msl})
624\end{itemize}
625% -------------------------------------------------------------------------------------------------------------
626% ================================================================
627% Coupled formulation
628% ================================================================
629\section  [Coupled formulation (\textit{sbccpl}) ]
630      {Coupled formulation (\mdl{sbccpl} module)}
631\label{SBC_cpl}
632%------------------------------------------namsbc_cpl----------------------------------------------------
633\namdisplay{namsbc_cpl} 
634%-------------------------------------------------------------------------------------------------------------
635
636In the coupled formulation of the surface boundary condition, the fluxes are
637provided by the OASIS coupler at a frequency which is defined in the OASIS coupler,
638while sea and ice surface temperature, ocean and ice albedo, and ocean currents
639are sent to the atmospheric component.
640
641A generalised coupled interface has been developed. It is currently interfaced with OASIS 3
642(\key{oasis3}) and does not support OASIS 4
643\footnote{The \key{oasis4} exist. It activates portion of the code that are still under development.}.
644It has been successfully used to interface \NEMO to most of the European atmospheric
645GCM (ARPEGE, ECHAM, ECMWF, HadAM, HadGAM, LMDz),
646as well as to \href{http://wrf-model.org/}{WRF} (Weather Research and Forecasting Model).
647
648Note that in addition to the setting of \np{ln\_cpl} to true, the \key{coupled} have to be defined.
649The CPP key is mainly used in sea-ice to ensure that the atmospheric fluxes are
650actually recieved by the ice-ocean system (no calculation of ice sublimation in coupled mode).
651When PISCES biogeochemical model (\key{top} and \key{pisces}) is also used in the coupled system,
652the whole carbon cycle is computed by defining \key{cpl\_carbon\_cycle}. In this case,
653CO$_2$ fluxes will be exchanged between the atmosphere and the ice-ocean system (and need to be activated
654in namsbc{\_}cpl).
655
656The new namelist above allows control of various aspects of the coupling fields (particularly for
657vectors) and now allows for any coupling fields to have multiple sea ice categories (as required by LIM3
658and CICE).  When indicating a multi-category coupling field in namsbc{\_}cpl the number of categories will be
659determined by the number used in the sea ice model.  In some limited cases it may be possible to specify
660single category coupling fields even when the sea ice model is running with multiple categories - in this
661case the user should examine the code to be sure the assumptions made are satisfactory.  In cases where
662this is definitely not possible the model should abort with an error message.  The new code has been tested using
663ECHAM with LIM2, and HadGAM3 with CICE but although it will compile with \key{lim3} additional minor code changes
664may be required to run using LIM3.
665
666
667% ================================================================
668%        Atmospheric pressure
669% ================================================================
670\section   [Atmospheric pressure (\textit{sbcapr})]
671         {Atmospheric pressure (\mdl{sbcapr})}
672\label{SBC_apr}
673%------------------------------------------namsbc_apr----------------------------------------------------
674\namdisplay{namsbc_apr} 
675%-------------------------------------------------------------------------------------------------------------
676
677The optional atmospheric pressure can be used to force ocean and ice dynamics
678(\np{ln\_apr\_dyn}~=~true, \textit{namsbc} namelist ).
679The input atmospheric forcing defined via \np{sn\_apr} structure (\textit{namsbc\_apr} namelist)
680can be interpolated in time to the model time step, and even in space when the
681interpolation on-the-fly is used. When used to force the dynamics, the atmospheric
682pressure is further transformed into an equivalent inverse barometer sea surface height,
683$\eta_{ib}$, using:
684\begin{equation} \label{SBC_ssh_ib}
685   \eta_{ib} = -  \frac{1}{g\,\rho_o}  \left( P_{atm} - P_o \right)
686\end{equation}
687where $P_{atm}$ is the atmospheric pressure and $P_o$ a reference atmospheric pressure.
688A value of $101,000~N/m^2$ is used unless \np{ln\_ref\_apr} is set to true. In this case $P_o$ 
689is set to the value of $P_{atm}$ averaged over the ocean domain, $i.e.$ the mean value of
690$\eta_{ib}$ is kept to zero at all time step.
691
692The gradient of $\eta_{ib}$ is added to the RHS of the ocean momentum equation
693(see \mdl{dynspg} for the ocean). For sea-ice, the sea surface height, $\eta_m$,
694which is provided to the sea ice model is set to $\eta - \eta_{ib}$ (see \mdl{sbcssr} module).
695$\eta_{ib}$ can be set in the output. This can simplify altimetry data and model comparison
696as inverse barometer sea surface height is usually removed from these date prior to their distribution.
697
698% ================================================================
699%        Tidal Potential
700% ================================================================
701\section   [Tidal Potential (\textit{sbctide})]
702                        {Tidal Potential (\mdl{sbctide})}
703\label{SBC_tide}
704
705A module is available to use the tidal potential forcing and is activated with with \key{tide}.
706
707
708%------------------------------------------nam_tide----------------------------------------------------
709\namdisplay{nam_tide}
710%-------------------------------------------------------------------------------------------------------------
711
712Concerning the tidal potential, some parameters are available in namelist:
713
714- \texttt{ln\_tide\_pot} activate the tidal potential forcing
715
716- \texttt{nb\_harmo} is the number of constituent used
717
718- \texttt{clname} is the name of constituent
719
720
721The tide is generated by the forces of gravity ot the Earth-Moon and Earth-Sun sytem;
722they are expressed as the gradient of the astronomical potential ($\vec{\nabla}\Pi_{a}$). \\
723
724The potential astronomical expressed, for the three types of tidal frequencies
725following, by : \\
726Tide long period :
727\begin{equation}
728\Pi_{a}=gA_{k}(\frac{1}{2}-\frac{3}{2}sin^{2}\phi)cos(\omega_{k}t+V_{0k})
729\end{equation}
730diurnal Tide :
731\begin{equation}
732\Pi_{a}=gA_{k}(sin 2\phi)cos(\omega_{k}t+\lambda+V_{0k})
733\end{equation}
734Semi-diurnal tide:
735\begin{equation}
736\Pi_{a}=gA_{k}(cos^{2}\phi)cos(\omega_{k}t+2\lambda+V_{0k})
737\end{equation}
738
739
740$A_{k}$ is the amplitude of the wave k, $\omega_{k}$ the pulsation of the wave k, $V_{0k}$ the astronomical phase of the wave
741$k$ to Greenwich.
742
743We make corrections to the astronomical potential.
744We obtain :
745\begin{equation}
746\Pi-g\delta = (1+k-h) \Pi_{A}(\lambda,\phi)
747\end{equation}
748with $k$ a number of Love estimated to 0.6 which parametrized the astronomical tidal land,
749and $h$ a number of Love to 0.3 which parametrized the parametrization due to the astronomical tidal land.
750
751% ================================================================
752%        River runoffs
753% ================================================================
754\section   [River runoffs (\textit{sbcrnf})]
755         {River runoffs (\mdl{sbcrnf})}
756\label{SBC_rnf}
757%------------------------------------------namsbc_rnf----------------------------------------------------
758\namdisplay{namsbc_rnf} 
759%-------------------------------------------------------------------------------------------------------------
760
761%River runoff generally enters the ocean at a nonzero depth rather than through the surface.
762%Many models, however, have traditionally inserted river runoff to the top model cell.
763%This was the case in \NEMO prior to the version 3.3. The switch toward a input of runoff
764%throughout a nonzero depth has been motivated by the numerical and physical problems
765%that arise when the top grid cells are of the order of one meter. This situation is common in
766%coastal modelling and becomes more and more often open ocean and climate modelling
767%\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
768%required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \S\ref{SBC_dcy}.}.
769
770
771%To do this we need to treat evaporation/precipitation fluxes and river runoff differently in the
772%\mdl{tra\_sbc} module.  We decided to separate them throughout the code, so that the variable
773%\textit{emp} represented solely evaporation minus precipitation fluxes, and a new 2d variable
774%rnf was added which represents the volume flux of river runoff (in kg/m2s to remain consistent with
775%emp).  This meant many uses of emp and emps needed to be changed, a list of all modules which use
776%emp or emps and the changes made are below:
777
778
779%Rachel:
780River runoff generally enters the ocean at a nonzero depth rather than through the surface.
781Many models, however, have traditionally inserted river runoff to the top model cell.
782This was the case in \NEMO prior to the version 3.3, and was combined with an option
783to increase vertical mixing near the river mouth.
784
785However, with this method numerical and physical problems arise when the top grid cells are
786of the order of one meter. This situation is common in coastal modelling and is becoming
787more common in open ocean and climate modelling
788\footnote{At least a top cells thickness of 1~meter and a 3 hours forcing frequency are
789required to properly represent the diurnal cycle \citep{Bernie_al_JC05}. see also \S\ref{SBC_dcy}.}.
790
791As such from V~3.3 onwards it is possible to add river runoff through a non-zero depth, and for the
792temperature and salinity of the river to effect the surrounding ocean.
793The user is able to specify, in a NetCDF input file, the temperature and salinity of the river, along with the   
794depth (in metres) which the river should be added to.
795
796Namelist options, \np{ln\_rnf\_depth}, \np{ln\_rnf\_sal} and \np{ln\_rnf\_temp} control whether
797the river attributes (depth, salinity and temperature) are read in and used.  If these are set
798as false the river is added to the surface box only, assumed to be fresh (0~psu), and/or
799taken as surface temperature respectively.
800
801The runoff value and attributes are read in in sbcrnf. 
802For temperature -999 is taken as missing data and the river temperature is taken to be the
803surface temperatue at the river point.
804For the depth parameter a value of -1 means the river is added to the surface box only,
805and a value of -999 means the river is added through the entire water column.
806After being read in the temperature and salinity variables are multiplied by the amount of runoff (converted into m/s)
807to give the heat and salt content of the river runoff.
808After the user specified depth is read ini, the number of grid boxes this corresponds to is
809calculated and stored in the variable \np{nz\_rnf}.
810The variable \textit{h\_dep} is then calculated to be the depth (in metres) of the bottom of the
811lowest box the river water is being added to (i.e. the total depth that river water is being added to in the model).
812
813The mass/volume addition due to the river runoff is, at each relevant depth level, added to the horizontal divergence
814(\textit{hdivn}) in the subroutine \rou{sbc\_rnf\_div} (called from \mdl{divcur}).
815This increases the diffusion term in the vicinity of the river, thereby simulating a momentum flux.
816The sea surface height is calculated using the sum of the horizontal divergence terms, and so the
817river runoff indirectly forces an increase in sea surface height.
818
819The \textit{hdivn} terms are used in the tracer advection modules to force vertical velocities.
820This causes a mass of water, equal to the amount of runoff, to be moved into the box above.
821The heat and salt content of the river runoff is not included in this step, and so the tracer
822concentrations are diluted as water of ocean temperature and salinity is moved upward out of the box
823and replaced by the same volume of river water with no corresponding heat and salt addition.
824
825For the linear free surface case, at the surface box the tracer advection causes a flux of water
826(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.
827As such the volume of water does not change, but the water is diluted.
828
829For the non-linear free surface case (\key{vvl}), no flux is allowed through the surface.
830Instead in the surface box (as well as water moving up from the boxes below) a volume of runoff water
831is added with no corresponding heat and salt addition and so as happens in the lower boxes there is a dilution effect.
832(The runoff addition to the top box along with the water being moved up through boxes below means the surface box has a large
833increase in volume, whilst all other boxes remain the same size)
834
835In trasbc the addition of heat and salt due to the river runoff is added.
836This is done in the same way for both vvl and non-vvl.
837The temperature and salinity are increased through the specified depth according to the heat and salt content of the river.
838
839In the non-linear free surface case (vvl), near the end of the time step the change in sea surface height is redistrubuted
840through the grid boxes, so that the original ratios of grid box heights are restored.
841In 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.
842
843It 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.
844When 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.
845
846
847%\colorbox{yellow}{Nevertheless, Pb of vertical resolution and 3D input : increase vertical mixing near river mouths to mimic a 3D river
848
849%All river runoff and emp fluxes are assumed to be fresh water (zero salinity) and at the same temperature as the sea surface.}
850
851%\colorbox{yellow}{river mouths{\ldots}}
852
853%IF( ln_rnf ) THEN                                     ! increase diffusivity at rivers mouths
854%        DO jk = 2, nkrnf   ;   avt(:,:,jk) = avt(:,:,jk) + rn_avt_rnf * rnfmsk(:,:)   ;   END DO
855%ENDIF
856
857%\gmcomment{  word doc of runoffs:
858%
859%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.
860%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. 
861
862%The depth option makes it possible to have the river water affecting just the surface layer, throughout depth, or some specified point in between.
863
864%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:
865
866%}
867
868% ================================================================
869% Miscellanea options
870% ================================================================
871\section{Miscellaneous options}
872\label{SBC_misc}
873
874% -------------------------------------------------------------------------------------------------------------
875%        Diurnal cycle
876% -------------------------------------------------------------------------------------------------------------
877\subsection   [Diurnal  cycle (\textit{sbcdcy})]
878         {Diurnal cycle (\mdl{sbcdcy})}
879\label{SBC_dcy}
880%------------------------------------------namsbc_rnf----------------------------------------------------
881%\namdisplay{namsbc}
882%-------------------------------------------------------------------------------------------------------------
883
884%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
885\begin{figure}[!t]    \begin{center}
886\includegraphics[width=0.8\textwidth]{./TexFiles/Figures/Fig_SBC_diurnal.pdf}
887\caption{ \label{Fig_SBC_diurnal}   
888Example of recontruction of the diurnal cycle variation of short wave flux 
889from daily mean values. The reconstructed diurnal cycle (black line) is chosen
890as the mean value of the analytical cycle (blue line) over a time step, not
891as the mid time step value of the analytically cycle (red square). From \citet{Bernie_al_CD07}.}
892\end{center}   \end{figure}
893%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
894
895\cite{Bernie_al_JC05} have shown that to capture 90$\%$ of the diurnal variability of
896SST requires a vertical resolution in upper ocean of 1~m or better and a temporal resolution
897of the surface fluxes of 3~h or less. Unfortunately high frequency forcing fields are rare,
898not to say inexistent. Nevertheless, it is possible to obtain a reasonable diurnal cycle
899of the SST knowning only short wave flux (SWF) at high frequency \citep{Bernie_al_CD07}.
900Furthermore, only the knowledge of daily mean value of SWF is needed,
901as higher frequency variations can be reconstructed from them, assuming that
902the diurnal cycle of SWF is a scaling of the top of the atmosphere diurnal cycle
903of incident SWF. The \cite{Bernie_al_CD07} reconstruction algorithm is available
904in \NEMO by setting \np{ln\_dm2dc}~=~true (a \textit{namsbc} namelist parameter) when using
905CORE bulk formulea (\np{ln\_blk\_core}~=~true) or the flux formulation (\np{ln\_flx}~=~true).
906The reconstruction is performed in the \mdl{sbcdcy} module. The detail of the algoritm used
907can be found in the appendix~A of \cite{Bernie_al_CD07}. The algorithm preserve the daily
908mean incomming SWF as the reconstructed SWF at a given time step is the mean value
909of the analytical cycle over this time step (Fig.\ref{Fig_SBC_diurnal}).
910The use of diurnal cycle reconstruction requires the input SWF to be daily
911($i.e.$ a frequency of 24 and a time interpolation set to true in \np{sn\_qsr} namelist parameter).
912Furthermore, it is recommended to have a least 8 surface module time step per day,
913that is  $\rdt \ \np{nn\_fsbc} < 10,800~s = 3~h$. An example of recontructed SWF
914is given in Fig.\ref{Fig_SBC_dcy} for a 12 reconstructed diurnal cycle, one every 2~hours
915(from 1am to 11pm).
916
917%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
918\begin{figure}[!t]  \begin{center}
919\includegraphics[width=0.7\textwidth]{./TexFiles/Figures/Fig_SBC_dcy.pdf}
920\caption{ \label{Fig_SBC_dcy}   
921Example of recontruction of the diurnal cycle variation of short wave flux 
922from daily mean values on an ORCA2 grid with a time sampling of 2~hours (from 1am to 11pm).
923The display is on (i,j) plane. }
924\end{center}   \end{figure}
925%>>>>>>>>>>>>>>>>>>>>>>>>>>>>
926
927Note also that the setting a diurnal cycle in SWF is highly recommended  when
928the top layer thickness approach 1~m or less, otherwise large error in SST can
929appear due to an inconsistency between the scale of the vertical resolution
930and the forcing acting on that scale.
931
932% -------------------------------------------------------------------------------------------------------------
933%        Rotation of vector pairs onto the model grid directions
934% -------------------------------------------------------------------------------------------------------------
935\subsection{Rotation of vector pairs onto the model grid directions}
936\label{SBC_rotation}
937
938When using a flux (\np{ln\_flx}=true) or bulk (\np{ln\_clio}=true or \np{ln\_core}=true) formulation,
939pairs of vector components can be rotated from east-north directions onto the local grid directions. 
940This is particularly useful when interpolation on the fly is used since here any vectors are likely to be defined
941relative to a rectilinear grid.
942To activate this option a non-empty string is supplied in the rotation pair column of the relevant namelist.
943The eastward component must start with "U" and the northward component with "V". 
944The remaining characters in the strings are used to identify which pair of components go together.
945So for example, strings "U1" and "V1" next to "utau" and "vtau" would pair the wind stress components together
946and rotate them on to the model grid directions; "U2" and "V2" could be used against a second pair of components,
947and so on.
948The extra characters used in the strings are arbitrary.
949The rot\_rep routine from the \mdl{geo2ocean} module is used to perform the rotation.
950
951% -------------------------------------------------------------------------------------------------------------
952%        Surface restoring to observed SST and/or SSS
953% -------------------------------------------------------------------------------------------------------------
954\subsection    [Surface restoring to observed SST and/or SSS (\textit{sbcssr})]
955         {Surface restoring to observed SST and/or SSS (\mdl{sbcssr})}
956\label{SBC_ssr}
957%------------------------------------------namsbc_ssr----------------------------------------------------
958\namdisplay{namsbc_ssr} 
959%-------------------------------------------------------------------------------------------------------------
960
961In forced mode using a flux formulation (\np{ln\_flx}~=~true), a
962feedback term \emph{must} be added to the surface heat flux $Q_{ns}^o$:
963\begin{equation} \label{Eq_sbc_dmp_q}
964Q_{ns} = Q_{ns}^o + \frac{dQ}{dT} \left( \left. T \right|_{k=1} - SST_{Obs} \right)
965\end{equation}
966where SST is a sea surface temperature field (observed or climatological), $T$ is
967the model surface layer temperature and $\frac{dQ}{dT}$ is a negative feedback
968coefficient usually taken equal to $-40~W/m^2/K$. For a $50~m$ 
969mixed-layer depth, this value corresponds to a relaxation time scale of two months.
970This term ensures that if $T$ perfectly matches the supplied SST, then $Q$ is
971equal to $Q_o$.
972
973In the fresh water budget, a feedback term can also be added. Converted into an
974equivalent freshwater flux, it takes the following expression :
975
976\begin{equation} \label{Eq_sbc_dmp_emp}
977\textit{emp} = \textit{emp}_o + \gamma_s^{-1} e_{3t}  \frac{  \left(\left.S\right|_{k=1}-SSS_{Obs}\right)}
978                                             {\left.S\right|_{k=1}}
979\end{equation}
980
981where $\textit{emp}_{o }$ is a net surface fresh water flux (observed, climatological or an
982atmospheric model product), \textit{SSS}$_{Obs}$ is a sea surface salinity (usually a time
983interpolation of the monthly mean Polar Hydrographic Climatology \citep{Steele2001}),
984$\left.S\right|_{k=1}$ is the model surface layer salinity and $\gamma_s$ is a negative
985feedback coefficient which is provided as a namelist parameter. Unlike heat flux, there is no
986physical justification for the feedback term in \ref{Eq_sbc_dmp_emp} as the atmosphere
987does not care about ocean surface salinity \citep{Madec1997}. The SSS restoring
988term should be viewed as a flux correction on freshwater fluxes to reduce the
989uncertainties we have on the observed freshwater budget.
990
991% -------------------------------------------------------------------------------------------------------------
992%        Handling of ice-covered area
993% -------------------------------------------------------------------------------------------------------------
994\subsection{Handling of ice-covered area  (\textit{sbcice\_...})}
995\label{SBC_ice-cover}
996
997The presence at the sea surface of an ice covered area modifies all the fluxes
998transmitted to the ocean. There are several way to handle sea-ice in the system
999depending on the value of the \np{nn{\_}ice} namelist parameter. 
1000\begin{description}
1001\item[nn{\_}ice = 0]  there will never be sea-ice in the computational domain.
1002This is a typical namelist value used for tropical ocean domain. The surface fluxes
1003are simply specified for an ice-free ocean. No specific things is done for sea-ice.
1004\item[nn{\_}ice = 1]  sea-ice can exist in the computational domain, but no sea-ice model
1005is used. An observed ice covered area is read in a file. Below this area, the SST is
1006restored to the freezing point and the heat fluxes are set to $-4~W/m^2$ ($-2~W/m^2$)
1007in the northern (southern) hemisphere. The associated modification of the freshwater
1008fluxes are done in such a way that the change in buoyancy fluxes remains zero.
1009This prevents deep convection to occur when trying to reach the freezing point
1010(and so ice covered area condition) while the SSS is too large. This manner of
1011managing sea-ice area, just by using si IF case, is usually referred as the \textit{ice-if} 
1012model. It can be found in the \mdl{sbcice{\_}if} module.
1013\item[nn{\_}ice = 2 or more]  A full sea ice model is used. This model computes the
1014ice-ocean fluxes, that are combined with the air-sea fluxes using the ice fraction of
1015each model cell to provide the surface ocean fluxes. Note that the activation of a
1016sea-ice model is is done by defining a CPP key (\key{lim2}, \key{lim3} or \key{cice}).
1017The activation automatically overwrites the read value of nn{\_}ice to its appropriate
1018value ($i.e.$ $2$ for LIM-2, $3$ for LIM-3 or $4$ for CICE).
1019\end{description}
1020
1021% {Description of Ice-ocean interface to be added here or in LIM 2 and 3 doc ?}
1022
1023\subsection   [Interface to CICE (\textit{sbcice\_cice})]
1024         {Interface to CICE (\mdl{sbcice\_cice})}
1025\label{SBC_cice}
1026
1027It is now possible to couple a global NEMO configuration (without AGRIF) to the CICE sea-ice
1028model by using \key{cice}.  The CICE code can be obtained from
1029\href{http://oceans11.lanl.gov/trac/CICE/}{LANL} and the additional 'hadgem3' drivers will be required,
1030even with the latest code release.  Input grid files consistent with those used in NEMO will also be needed,
1031and CICE CPP keys \textbf{ORCA\_GRID}, \textbf{CICE\_IN\_NEMO} and \textbf{coupled} should be used (seek advice from UKMO
1032if necessary).  Currently the code is only designed to work when using the CORE forcing option for NEMO (with
1033\textit{calc\_strair~=~true} and \textit{calc\_Tsfc~=~true} in the CICE name-list), or alternatively when NEMO
1034is coupled to the HadGAM3 atmosphere model (with \textit{calc\_strair~=~false} and \textit{calc\_Tsfc~=~false}).
1035The code is intended to be used with \np{nn\_fsbc} set to 1 (although coupling ocean and ice less frequently
1036should work, it is possible the calculation of some of the ocean-ice fluxes needs to be modified slightly - the
1037user should check that results are not significantly different to the standard case).
1038
1039There are two options for the technical coupling between NEMO and CICE.  The standard version allows
1040complete flexibility for the domain decompositions in the individual models, but this is at the expense of global
1041gather and scatter operations in the coupling which become very expensive on larger numbers of processors. The
1042alternative option (using \key{nemocice\_decomp} for both NEMO and CICE) ensures that the domain decomposition is
1043identical in both models (provided domain parameters are set appropriately, and
1044\textit{processor\_shape~=~square-ice} and \textit{distribution\_wght~=~block} in the CICE name-list) and allows
1045much more efficient direct coupling on individual processors.  This solution scales much better although it is at
1046the expense of having more idle CICE processors in areas where there is no sea ice.
1047
1048% -------------------------------------------------------------------------------------------------------------
1049%        Handling of icebergs
1050% -------------------------------------------------------------------------------------------------------------
1051\subsection{ Handling of icebergs (ICB) }
1052\label{ICB_icebergs}
1053%------------------------------------------namberg----------------------------------------------------
1054\namdisplay{namberg}
1055%-------------------------------------------------------------------------------------------------------------
1056
1057Icebergs are modelled as lagrangian particles in NEMO.
1058Their physical behaviour is controlled by equations as described in Martin and Adcroft (2010).
1059(Note that the authors kindly provided a copy of their code to act as a basis for implementation in NEMO.)
1060Icebergs are initially spawned into one of ten classes which have specific mass and thickness as described by
1061\np{rn\_initial\_mass} and \np{rn\_initial\_thickness}.
1062Each class has an associated scaling (\np{rn\_mass\_scaling}), which is an integer representing how many icebergs
1063of this class are being described as one lagrangian point (this reduces the numerical problem of tracking every single iceberg).
1064They are enabled by setting \np{ln\_icebergs}~=~true.
1065
1066Two initialisation schemes are possible.
1067\begin{description}
1068\item[\np{nn\_test\_icebergs}~>~0]
1069In this scheme, the value of \np{nn\_test\_icebergs} represents the class of iceberg to generate (so between 1 and 10), and
1070\np{nn\_test\_icebergs} provides a lon/lat box in the domain at each grid point of which an iceberg is generated at the
1071beginning of the run. (Note that this happens each time the timestep equals \np{nn\_nit000}.)
1072\np{nn\_test\_icebergs} is defined by four numbers in \np{nn\_test\_box} representing the corners of the geographical
1073box: lonmin,lonmax,latmin,latmax
1074\item[\np{nn\_test\_icebergs}~=~-1]
1075In this scheme the model reads a calving file supplied in the \np{sn\_icb} parameter.
1076This should be a file with a field on the configuration grid (typically ORCA) representing ice accumulation rate at each model point.
1077These should be ocean points adjacent to land where icebergs are known to calve.
1078Most points in this input grid are going to have value zero.
1079When the model runs, ice is accumulated at each grid point which has a non-zero source term.
1080At 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).
1081Note that this is the initial mass multiplied by the number each particle represents (i.e. the scaling).
1082If there is enough ice, a new iceberg is spawned and the total available ice reduced accordingly.
1083\end{description}
1084
1085Icebergs are influenced by wind, waves and currents, bottom melt and erosion.
1086The latter act to disintegrate the iceberg.
1087This is either all melted freshwater, or (if \np{rn\_bits\_erosion\_fraction}~>~0) into melt and additionally small ice bits
1088which are assumed to propagate with their larger parent and thus delay fluxing into the ocean.
1089Melt water (and other variables on the configuration grid) are written into the main NEMO model output files.
1090
1091Extensive diagnostics can be produced.
1092Separate output files are maintained for human-readable iceberg information.
1093A separate file is produced for each processor (independent of \np{ln\_ctl}).
1094The amount of information is controlled by two integer parameters:
1095\begin{description}
1096\item[\np{nn\_verbose\_level}]  takes a value between one and four and represents an increasing number of points in the code
1097at which variables are written, and an increasing level of obscurity.
1098\item[\np{nn\_verbose\_level}] is the number of timesteps between writes
1099\end{description}
1100
1101Iceberg trajectories can also be written out and this is enabled by setting \np{nn\_sample\_rate}~>~0.
1102A non-zero value represents how many timesteps between writes of information into the output file.
1103These output files are in NETCDF format.
1104When \key{mpp\_mpi} is defined, each output file contains only those icebergs in the corresponding processor,
1105so care is needed to recreate data for individual icebergs.
1106
1107% -------------------------------------------------------------------------------------------------------------
1108%        Freshwater budget control
1109% -------------------------------------------------------------------------------------------------------------
1110\subsection   [Freshwater budget control (\textit{sbcfwb})]
1111         {Freshwater budget control (\mdl{sbcfwb})}
1112\label{SBC_fwb}
1113
1114For global ocean simulation it can be useful to introduce a control of the mean sea
1115level in order to prevent unrealistic drift of the sea surface height due to inaccuracy
1116in the freshwater fluxes. In \NEMO, two way of controlling the the freshwater budget.
1117\begin{description}
1118\item[\np{nn\_fwb}=0]  no control at all. The mean sea level is free to drift, and will
1119certainly do so.
1120\item[\np{nn\_fwb}=1]  global mean \textit{emp} set to zero at each model time step.
1121%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).
1122\item[\np{nn\_fwb}=2]  freshwater budget is adjusted from the previous year annual
1123mean budget which is read in the \textit{EMPave\_old.dat} file. As the model uses the
1124Boussinesq approximation, the annual mean fresh water budget is simply evaluated
1125from the change in the mean sea level at January the first and saved in the
1126\textit{EMPav.dat} file.
1127\end{description}
1128
1129% -------------------------------------------------------------------------------------------------------------
1130%        Neutral Drag Coefficient from external wave model
1131% -------------------------------------------------------------------------------------------------------------
1132\subsection   [Neutral drag coefficient from external wave model (\textit{sbcwave})]
1133                        {Neutral drag coefficient from external wave model (\mdl{sbcwave})}
1134\label{SBC_wave}
1135%------------------------------------------namwave----------------------------------------------------
1136\namdisplay{namsbc_wave}
1137%-------------------------------------------------------------------------------------------------------------
1138\begin{description}
1139
1140\item [??] In order to read a neutral drag coeff, from an external data source (i.e. a wave model), the
1141logical variable \np{ln\_cdgw}
1142 in $namsbc$ namelist must be defined ${.true.}$.
1143The \mdl{sbcwave} module containing the routine \np{sbc\_wave} reads the
1144namelist ${namsbc\_wave}$ (for external data names, locations, frequency, interpolation and all
1145the miscellanous options allowed by Input Data generic Interface see \S\ref{SBC_input})
1146and a 2D field of neutral drag coefficient. Then using the routine
1147TURB\_CORE\_1Z or TURB\_CORE\_2Z, and starting from the neutral drag coefficent provided, the drag coefficient is computed according
1148to stable/unstable conditions of the air-sea interface following \citet{Large_Yeager_Rep04}.
1149
1150\end{description}
1151
1152% Griffies doc:
1153% When running ocean-ice simulations, we are not explicitly representing land processes, such as rivers, catchment areas, snow accumulation, etc. However, to reduce model drift, it is important to balance the hydrological cycle in ocean-ice models. We thus need to prescribe some form of global normalization to the precipitation minus evaporation plus river runoff. The result of the normalization should be a global integrated zero net water input to the ocean-ice system over a chosen time scale.
1154%How often the normalization is done is a matter of choice. In mom4p1, we choose to do so at each model time step, so that there is always a zero net input of water to the ocean-ice system. Others choose to normalize over an annual cycle, in which case the net imbalance over an annual cycle is used to alter the subsequent yearÕs water budget in an attempt to damp the annual water imbalance. Note that the annual budget approach may be inappropriate with interannually varying precipitation forcing.
1155%When running ocean-ice coupled models, it is incorrect to include the water transport between the ocean and ice models when aiming to balance the hydrological cycle. 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, not the water in any one sub-component. As an extreme example to illustrate the issue, consider an ocean-ice model with zero initial sea ice. As the ocean-ice model spins up, there should be a net accumulation of water in the growing sea ice, and thus a net loss of water from the ocean. The total water contained in the ocean plus ice system is constant, but there is an exchange of water between the subcomponents. This exchange should not be part of the normalization used to balance the hydrological cycle in ocean-ice models.
1156
1157
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